From c7b2bbc3dee45d75a5cc07a6f0e13ca938d18149 Mon Sep 17 00:00:00 2001 From: Charles Date: Sat, 19 Jun 2021 11:21:13 -0500 Subject: [PATCH 001/144] gnu: Add new variable font-borg-sans-mono. * gnu/packages/fonts.scm (font-borg-sans-mono): Add new variable. Signed-off-by: Leo Prikler --- gnu/packages/fonts.scm | 21 +++++++++++++++++++++ 1 file changed, 21 insertions(+) diff --git a/gnu/packages/fonts.scm b/gnu/packages/fonts.scm index 618686a0ea..4d57bbd514 100644 --- a/gnu/packages/fonts.scm +++ b/gnu/packages/fonts.scm @@ -809,6 +809,27 @@ and Chrome OS, and the recommended font for the visual language \"Material Design\".") (license license:asl2.0))) +(define-public font-borg-sans-mono + (package + (name "font-borg-sans-mono") + (version "0.3.1") + (source + (origin + (method url-fetch) + (uri (string-append + "https://github.com/charje/borg-sans-mono" + "/releases/download/v" version "/borg-sans-mono.zip")) + (sha256 + (base32 + "1xxakd9nfb8wz76rh0gbd69gh0mlqs2453g0j516xgxn8bxip2yj")))) + (build-system font-build-system) + (home-page "https://github.com/charje/borg-sans-mono") + (synopsis "The Borg Sans Mono font") + (description "Borg Sans Mono is a monospaced font derived from Droid Sans +Mono. It includes additions commonly found in programming fonts such as a +slashed zero and ligatures for operators.") + (license license:asl2.0))) + (define-public font-un (package (name "font-un") From b04cba9ee533945f90ffd72637f064c60188f945 Mon Sep 17 00:00:00 2001 From: Stefan Date: Sat, 19 Jun 2021 20:03:11 +0200 Subject: [PATCH 002/144] gnu: linux-libre: Correct name of EXTRAVERSION, and prepend "-" to content. * gnu/packages/linux.scm (make-linux-libre): Move the comment for the configuration-file argument to the correct position. (make-linux-libre*): Move the comment for the configuration-file argument to the correct position. Fix name of environment variable EXTRAVERSION. Prepend a hyphen to the content of EXTRAVERSION. Signed-off-by: Danny Milosavljevic --- gnu/packages/linux.scm | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/gnu/packages/linux.scm b/gnu/packages/linux.scm index 699a01ee41..904338da73 100644 --- a/gnu/packages/linux.scm +++ b/gnu/packages/linux.scm @@ -727,9 +727,9 @@ for ARCH and optionally VARIANT, or #f if there is no such configuration." (define* (make-linux-libre version hash-string supported-systems #:key + (extra-version #f) ;; A function that takes an arch and a variant. ;; See kernel-config for an example. - (extra-version #f) (configuration-file #f) (defconfig "defconfig") (extra-options %default-extra-linux-options) @@ -748,9 +748,9 @@ for ARCH and optionally VARIANT, or #f if there is no such configuration." (define* (make-linux-libre* version source supported-systems #:key + (extra-version #f) ;; A function that takes an arch and a variant. ;; See kernel-config for an example. - (extra-version #f) (configuration-file #f) (defconfig "defconfig") (extra-options %default-extra-linux-options)) @@ -816,7 +816,8 @@ for ARCH and optionally VARIANT, or #f if there is no such configuration." (format #t "`CROSS_COMPILE' set to `~a'~%" (getenv "CROSS_COMPILE")))) - (setenv "EXTRA_VERSION" ,extra-version) + (setenv "EXTRAVERSION" ,(and extra-version + (string-append "-" extra-version))) (let ((build (assoc-ref %standard-phases 'build)) (config (assoc-ref (or native-inputs inputs) "kconfig"))) From 0a90bea34d76ea4cd51aea61876218d059830045 Mon Sep 17 00:00:00 2001 From: Arun Isaac Date: Fri, 18 Jun 2021 17:16:18 +0530 Subject: [PATCH 003/144] gnu: linkchecker: Update to 10.0.1. * gnu/packages/web.scm (linkchecker): Update to 10.0.1. [source]: Remove patches. [inputs]: Add python-beautifulsoup4. Replace python2-dnspython-1.16, python2-pyxdg and python2-requests with python-dnspython, python-pyxdg and python-requests respectively. [native-inputs]: Replace python2-pytest, python2-miniboa and python2-parameterized with python-pytest, python-miniboa and python-parameterized respectively. [arguments]: Use python 3. Replace check phase instead of deleting the standard phase and adding a custom one. Use add-installed-pythonpath instead of setting PYTHONPATH directly. Support disabling of tests with tests?. [home-page]: Update URI. * gnu/packages/patches/linkchecker-tests-require-network.patch: Delete file. * gnu/local.mk (dist_patch_DATA): Unregister it. --- gnu/local.mk | 1 - .../linkchecker-tests-require-network.patch | 182 ------------------ gnu/packages/web.scm | 48 ++--- 3 files changed, 17 insertions(+), 214 deletions(-) delete mode 100644 gnu/packages/patches/linkchecker-tests-require-network.patch diff --git a/gnu/local.mk b/gnu/local.mk index da86c66cda..375883de03 100644 --- a/gnu/local.mk +++ b/gnu/local.mk @@ -1387,7 +1387,6 @@ dist_patch_DATA = \ %D%/packages/patches/lierolibre-remove-arch-warning.patch \ %D%/packages/patches/lierolibre-try-building-other-arch.patch \ %D%/packages/patches/linbox-fix-pkgconfig.patch \ - %D%/packages/patches/linkchecker-tests-require-network.patch \ %D%/packages/patches/linphone-desktop-without-sdk.patch \ %D%/packages/patches/linux-libre-support-for-Pinebook-Pro.patch \ %D%/packages/patches/linux-libre-arm64-generic-pinebook-lcd.patch \ diff --git a/gnu/packages/patches/linkchecker-tests-require-network.patch b/gnu/packages/patches/linkchecker-tests-require-network.patch deleted file mode 100644 index f3e488cec2..0000000000 --- a/gnu/packages/patches/linkchecker-tests-require-network.patch +++ /dev/null @@ -1,182 +0,0 @@ -From f24c88a0732024028fffe0372039a847e91722ea Mon Sep 17 00:00:00 2001 -From: Christopher Baines -Date: Tue, 1 Jan 2019 22:36:29 +0000 -Subject: [PATCH] Mark more tests that require the network - -I believe all these tests require the network, at least they seem to -fail if it's I run them without connecting my computer to the web. - -I'm looking at this as part of packaging linkchecker for GNU Guix, -where the package is build and the tests are run in a isolated -environment, intentionally without network access, to avoid issues -with non-reproducible package builds. ---- - tests/checker/test_http.py | 2 ++ - tests/checker/test_http_misc.py | 2 ++ - tests/checker/test_http_redirect.py | 2 ++ - tests/checker/test_httpbin.py | 5 +++++ - tests/checker/test_misc.py | 4 ++++ - tests/checker/test_whitespace.py | 3 +++ - 6 files changed, 18 insertions(+) - -diff --git a/tests/checker/test_http.py b/tests/checker/test_http.py -index e4c1e097..8a8af567 100644 ---- a/tests/checker/test_http.py -+++ b/tests/checker/test_http.py -@@ -20,6 +20,7 @@ - - import pytest - -+from tests import need_network - from .httpserver import HttpServerTest, CookieRedirectHttpRequestHandler - - class TestHttp (HttpServerTest): -@@ -29,6 +30,7 @@ def __init__(self, methodName='runTest'): - super(TestHttp, self).__init__(methodName=methodName) - self.handler = CookieRedirectHttpRequestHandler - -+ @need_network - def test_html (self): - confargs = dict(recursionlevel=1) - self.file_test("http.html", confargs=confargs) -diff --git a/tests/checker/test_http_misc.py b/tests/checker/test_http_misc.py -index 9922d85f..c6b6afdb 100644 ---- a/tests/checker/test_http_misc.py -+++ b/tests/checker/test_http_misc.py -@@ -20,11 +20,13 @@ - import os - import sys - from .httpserver import HttpServerTest -+from tests import need_network - from linkcheck.network import iputil - - class TestHttpMisc (HttpServerTest): - """Test http:// misc link checking.""" - -+ @need_network - def test_html (self): - self.swf_test() - self.obfuscate_test() -diff --git a/tests/checker/test_http_redirect.py b/tests/checker/test_http_redirect.py -index f212d98e..2253a70d 100644 ---- a/tests/checker/test_http_redirect.py -+++ b/tests/checker/test_http_redirect.py -@@ -17,6 +17,7 @@ - """ - Test http checking. - """ -+from tests import need_network - from .httpserver import HttpServerTest, CookieRedirectHttpRequestHandler - - class TestHttpRedirect (HttpServerTest): -@@ -26,6 +27,7 @@ def __init__(self, methodName='runTest'): - super(TestHttpRedirect, self).__init__(methodName=methodName) - self.handler = CookieRedirectHttpRequestHandler - -+ @need_network - def test_redirect (self): - self.redirect1() - self.redirect2() -diff --git a/tests/checker/test_httpbin.py b/tests/checker/test_httpbin.py -index 0319c2f6..4c8fa846 100644 ---- a/tests/checker/test_httpbin.py -+++ b/tests/checker/test_httpbin.py -@@ -18,6 +18,7 @@ - Test http stuff with httpbin.org. - """ - import re -+from tests import need_network - from . import LinkCheckTest - - -@@ -30,6 +31,7 @@ def get_httpbin_url(path): - class TestHttpbin(LinkCheckTest): - """Test http:// link redirection checking.""" - -+ @need_network - def test_http_link(self): - linkurl = u"http://www.example.com" - nlinkurl = self.norm(linkurl) -@@ -48,6 +50,7 @@ def test_http_link(self): - ] - self.direct(url, resultlines, recursionlevel=1) - -+ @need_network - def test_basic_auth(self): - user = u"testuser" - password = u"testpassword" -@@ -67,6 +70,7 @@ def test_basic_auth(self): - ] - self.direct(url, resultlines, confargs=confargs) - -+ @need_network - def test_http_refresh_header(self): - linkurl = u"http://www.example.com" - nlinkurl = self.norm(linkurl) -@@ -85,6 +89,7 @@ def test_http_refresh_header(self): - ] - self.direct(url, resultlines, recursionlevel=1) - -+ @need_network - def test_http_content_location_header(self): - linkurl = u"http://www.example.com" - nlinkurl = self.norm(linkurl) -diff --git a/tests/checker/test_misc.py b/tests/checker/test_misc.py -index 2e4cfd07..f9591f9d 100644 ---- a/tests/checker/test_misc.py -+++ b/tests/checker/test_misc.py -@@ -17,6 +17,7 @@ - """ - Test miscellaneous html tag parsing and URL types - """ -+from tests import need_network - from . import LinkCheckTest - - -@@ -25,15 +26,18 @@ class TestMisc (LinkCheckTest): - Test misc link types. - """ - -+ @need_network - def test_misc (self): - self.file_test("misc.html") - - def test_html5 (self): - self.file_test("html5.html") - -+ @need_network - def test_archive (self): - self.file_test("archive.html") - -+ @need_network - def test_itms_services(self): - url = u"itms-services:?action=download-manifest&url=http://www.example.com/" - resultlines = [ -diff --git a/tests/checker/test_whitespace.py b/tests/checker/test_whitespace.py -index 609c108a..fc2727d6 100644 ---- a/tests/checker/test_whitespace.py -+++ b/tests/checker/test_whitespace.py -@@ -17,6 +17,7 @@ - """ - Test whitespace handling. - """ -+from tests import need_network - from . import LinkCheckTest - - -@@ -25,6 +26,7 @@ class TestWhitespace (LinkCheckTest): - Test whitespace in URLs. - """ - -+ @need_network - def test_leading_whitespace (self): - # Leading whitespace - url = u" http://www.example.org/" -@@ -50,6 +52,7 @@ def test_leading_whitespace (self): - ] - self.direct(url, resultlines) - -+ @need_network - def test_trailing_whitespace (self): - # Trailing whitespace - url = u"http://www.example.org/ " diff --git a/gnu/packages/web.scm b/gnu/packages/web.scm index d1f1d0f755..412308b417 100644 --- a/gnu/packages/web.scm +++ b/gnu/packages/web.scm @@ -15,7 +15,7 @@ ;;; Copyright © 2016 Ben Woodcroft ;;; Copyright © 2016 Clément Lassieur ;;; Copyright © 2016, 2017 Nikita -;;; Copyright © 2016, 2017, 2018, 2019 Arun Isaac +;;; Copyright © 2016, 2017, 2018, 2019, 2021 Arun Isaac ;;; Copyright © 2016–2021 Tobias Geerinckx-Rice ;;; Copyright © 2016 Bake Timmons ;;; Copyright © 2017 Thomas Danckaert @@ -6578,51 +6578,37 @@ Instagram and YouTube.") (define-public linkchecker (package (name "linkchecker") - (version "9.4.0") + (version "10.0.1") (source (origin (method git-fetch) (uri (git-reference (url "https://github.com/linkchecker/linkchecker") (commit (string-append "v" version)))) - (patches - (search-patches "linkchecker-tests-require-network.patch")) (file-name (git-file-name name version)) (sha256 (base32 - "03ihjmc4bqxxqv71bb43r2f23sx0xnbq1k2fsg9fw05qa5s9x187")))) + "1j97dc9a4yhpscwadhv5dxp7036pnrxiaky18l8ddr3pvxdjvkxs")))) (build-system python-build-system) (inputs - `(("python2-dnspython" ,python2-dnspython-1.16) - ("python2-pyxdg" ,python2-pyxdg) - ("python2-requests" ,python2-requests))) + `(("python-beautifulsoup4" ,python-beautifulsoup4) + ("python-dnspython" ,python-dnspython) + ("python-pyxdg" ,python-pyxdg) + ("python-requests" ,python-requests))) (native-inputs `(("gettext" ,gettext-minimal) - ("python2-pytest" ,python2-pytest) - ("python2-miniboa" ,python2-miniboa) - ("python2-parameterized" ,python2-parameterized))) + ("python-pytest" ,python-pytest) + ("python-miniboa" ,python-miniboa) + ("python-parameterized" ,python-parameterized))) (arguments - `(#:python ,python-2 - #:phases + `(#:phases (modify-phases %standard-phases - ;; Move the 'check phase to after 'install, so that the installed - ;; library can be used - (delete 'check) - (add-after 'install 'check - (lambda* (#:key outputs #:allow-other-keys) - (let ((out (assoc-ref outputs "out"))) - ;; Set PYTHONPATH so that the installed linkchecker is used - (setenv "PYTHONPATH" - (string-append out "/lib/python2.7/site-packages" - ":" - (getenv "PYTHONPATH"))) - ;; Remove this directory to avoid it being used when running - ;; the tests - (delete-file-recursively "linkcheck") - - (invoke "py.test" "tests")) - #t))))) - (home-page "https://linkcheck.github.io/linkchecker") + (replace 'check + (lambda* (#:key inputs outputs tests? #:allow-other-keys) + (when tests? + (add-installed-pythonpath inputs outputs) + (invoke "py.test" "tests"))))))) + (home-page "https://linkchecker.github.io/linkchecker/") (synopsis "Check websites for broken links") (description "LinkChecker is a website validator. It checks for broken links in websites. It is recursive and multithreaded providing output in From 9fd9364492b95baf48baf054a326145fde5bc21b Mon Sep 17 00:00:00 2001 From: Brice Waegeneire Date: Sun, 13 Jun 2021 09:37:31 +0200 Subject: [PATCH 004/144] gnu: Add duc. * gnu/packages/disk.scm (duc): New variable. --- gnu/packages/disk.scm | 52 +++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 52 insertions(+) diff --git a/gnu/packages/disk.scm b/gnu/packages/disk.scm index ccda71b268..2a4dbee748 100644 --- a/gnu/packages/disk.scm +++ b/gnu/packages/disk.scm @@ -20,6 +20,7 @@ ;;; Copyright © 2020 Raghav Gururajan ;;; Copyright © 2021 Michael Rohleder ;;; Copyright © 2021 Mathieu Othacehe +;;; Copyright © 2021 Brice Waegeneire ;;; ;;; This file is part of GNU Guix. ;;; @@ -46,6 +47,7 @@ #:use-module (gnu packages compression) #:use-module (gnu packages crypto) #:use-module (gnu packages cryptsetup) + #:use-module (gnu packages databases) #:use-module (gnu packages docbook) #:use-module (gnu packages documentation) #:use-module (gnu packages elf) @@ -1303,3 +1305,53 @@ like raw system image files, can be copied or flashed a lot faster and more reliably with @code{bmaptool} than with traditional tools, like @code{dd} or @code{cp}.") (license license:gpl2))) + +(define-public duc + (package + (name "duc") + (version "1.4.4") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/zevv/duc") + (commit version))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "1i7ry25xzy027g6ysv6qlf09ax04q4vy0kikl8h0aq5jbxsl9q52")))) + (build-system gnu-build-system) + (arguments + `(#:phases + (modify-phases %standard-phases + (add-after 'unpack 'patch + (lambda* (#:key outputs #:allow-other-keys) + (let* ((out (assoc-ref outputs "out"))) + (substitute* "src/duc/cmd-ui.c" + (("ncursesw/ncurses.h") "ncurses.h")) + (substitute* "examples/index.cgi" + (("/usr/local/bin/duc") + (string-append out "/bin/duc")))))) + (add-after 'install 'install-examples + (lambda* (#:key outputs #:allow-other-keys) + (let* ((out (assoc-ref outputs "out")) + (doc (string-append out "/share/doc/" ,name "-" ,version))) + (copy-recursively "examples" (string-append doc "/examples")))))))) + (native-inputs + `(("autoconf" ,autoconf) + ("automake" ,automake) + ("libtool" ,libtool) + ("pkg-config" ,pkg-config))) + (inputs + `(("cairo" ,cairo) + ("pango" ,pango) + ("tokyocabinet" ,tokyocabinet) + ("ncurses" ,ncurses))) + (home-page "http://duc.zevv.nl") + (synopsis "Library and suite of tools for inspecting disk usage") + (description "Duc maintains a database of accumulated sizes of +directories of the file system, and allows you to query this database with +some tools, or create fancy graphs showing you where your bytes are. + +Duc comes with console utilities, ncurses and X11 user interfaces and a CGI +wrapper for disk usage querying and visualisation.") + (license license:lgpl3+))) From 9171079e515289120405c70c143445df2a35db1c Mon Sep 17 00:00:00 2001 From: Matthew James Kraai Date: Sat, 19 Jun 2021 03:07:39 -0700 Subject: [PATCH 005/144] import: launchpad: Use repository to retrieve releases. * guix/import/launchpad.scm (latest-released-version): Use repository instead of package name. (latest-release): Pass repository to latest-released-version. Signed-off-by: Brice Waegeneire --- guix/import/launchpad.scm | 10 ++++++---- 1 file changed, 6 insertions(+), 4 deletions(-) diff --git a/guix/import/launchpad.scm b/guix/import/launchpad.scm index a52b39a085..ecd6f88738 100644 --- a/guix/import/launchpad.scm +++ b/guix/import/launchpad.scm @@ -1,5 +1,6 @@ ;;; GNU Guix --- Functional package management for GNU ;;; Copyright © 2019, 2020 Arun Isaac +;;; Copyright © 2021 Matthew James Kraai ;;; ;;; This file is part of GNU Guix. ;;; @@ -100,8 +101,8 @@ URL of the form (match (string-split (uri-path (string->uri url)) #\/) ((_ repo . rest) repo))) -(define (latest-released-version package-name) - "Return a string of the newest released version name given the PACKAGE-NAME, +(define (latest-released-version repository) + "Return a string of the newest released version name given the REPOSITORY, for example, 'linuxdcpp'. Return #f if there is no releases." (define (pre-release? x) ;; Versions containing anything other than digit characters and "." (for @@ -112,7 +113,7 @@ for example, 'linuxdcpp'. Return #f if there is no releases." (match (json-fetch (string-append "https://api.launchpad.net/1.0/" - package-name "/releases")) + repository "/releases")) (#f #f) ;404 or similar (json (assoc-ref @@ -129,7 +130,8 @@ for example, 'linuxdcpp'. Return #f if there is no releases." (let* ((source-uri (origin-github-uri (package-source pkg))) (name (package-name pkg)) - (newest-version (latest-released-version name))) + (repository (launchpad-repository source-uri)) + (newest-version (latest-released-version repository))) (if newest-version (upstream-source (package name) From 3aabe51e8c09b9a2a87c03c40e3cc0f90d531bfd Mon Sep 17 00:00:00 2001 From: Brice Waegeneire Date: Sat, 19 Jun 2021 22:21:47 +0200 Subject: [PATCH 006/144] import: launchpad: Fix typo. * guix/import/launchpad.scm (latest-release): Rename 'origin-github-uri' to 'origin-launchpad-uri'. --- guix/import/launchpad.scm | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/guix/import/launchpad.scm b/guix/import/launchpad.scm index ecd6f88738..aeb447b0a5 100644 --- a/guix/import/launchpad.scm +++ b/guix/import/launchpad.scm @@ -1,6 +1,7 @@ ;;; GNU Guix --- Functional package management for GNU ;;; Copyright © 2019, 2020 Arun Isaac ;;; Copyright © 2021 Matthew James Kraai +;;; Copyright © 2020 Brice Waegeneire ;;; ;;; This file is part of GNU Guix. ;;; @@ -122,13 +123,13 @@ for example, 'linuxdcpp'. Return #f if there is no releases." (define (latest-release pkg) "Return an for the latest release of PKG." - (define (origin-github-uri origin) + (define (origin-launchpad-uri origin) (match (origin-uri origin) ((? string? url) url) ; surely a Launchpad URL ((urls ...) (find (cut string-contains <> "launchpad.net") urls)))) - (let* ((source-uri (origin-github-uri (package-source pkg))) + (let* ((source-uri (origin-launchpad-uri (package-source pkg))) (name (package-name pkg)) (repository (launchpad-repository source-uri)) (newest-version (latest-released-version repository))) From cae5f6e54bea5a43762985f3b37818079aee326b Mon Sep 17 00:00:00 2001 From: Ryan Prior Date: Sat, 19 Jun 2021 01:45:00 +0000 Subject: [PATCH 007/144] gnu: esbuild: Update to 0.12.9. * gnu/packages/web.scm (esbuild): Update to 0.12.9. Signed-off-by: Brice Waegeneire --- gnu/packages/web.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/web.scm b/gnu/packages/web.scm index 412308b417..896125aab2 100644 --- a/gnu/packages/web.scm +++ b/gnu/packages/web.scm @@ -1596,7 +1596,7 @@ used to validate and fix HTML data.") (define-public esbuild (package (name "esbuild") - (version "0.11.14") + (version "0.12.9") (source (origin (method git-fetch) @@ -1605,7 +1605,7 @@ used to validate and fix HTML data.") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 - (base32 "0qxylzc7lzpsp5hm3dl5jvy9aca8azn8dmbjz9z5n5rkdmm8vd9p")) + (base32 "10bz1xq2frdja7mbx04m009svg8b5rj7vfq3sc2gc88n31v21b1j")) (modules '((guix build utils))) (snippet '(begin From eb939109b9c06a09e1534a403745bd362b653d95 Mon Sep 17 00:00:00 2001 From: Brice Waegeneire Date: Sat, 12 Jun 2021 15:02:12 +0200 Subject: [PATCH 008/144] gnu: opendoas: Fix restricted path "safepath". * gnu/packages/admin.scm (opendoas)[phases]: Rename 'fix-install' phase to 'pre-configure', run it before 'configure' and add a substitution for safepath. --- gnu/packages/admin.scm | 22 ++++++++++++++++------ 1 file changed, 16 insertions(+), 6 deletions(-) diff --git a/gnu/packages/admin.scm b/gnu/packages/admin.scm index f97be3c735..ea5cd91e38 100644 --- a/gnu/packages/admin.scm +++ b/gnu/packages/admin.scm @@ -41,6 +41,7 @@ ;;; Copyright © 2021 Hyunseok Kim ;;; Copyright © 2021 David Larsson ;;; Copyright © 2021 WinterHound +;;; Copyright © 2021 Brice Waegeneire ;;; ;;; This file is part of GNU Guix. ;;; @@ -1700,18 +1701,27 @@ commands and their arguments.") (arguments `(#:phases (modify-phases %standard-phases + (add-before 'configure 'pre-configure + (lambda* (#:key outputs #:allow-other-keys) + (substitute* "GNUmakefile" + (("^\tchown.*$") "")) + ;; OpenDoas look for binaries in safepath when a rule specify a + ;; relative command, such as “permit keepenv :wheel cmd guix”. + (substitute* "doas.c" + (("safepath =" match) + (string-append match " \"" + "/run/setuid-programs:" + "/run/current-system/profile/bin:" + "/run/current-system/profile/sbin:" + "\" "))) + #t)) (replace 'configure ;; The configure script doesn't accept most of the default flags. (lambda* (#:key configure-flags #:allow-other-keys) ;; The configure script can be told which compiler to use only ;; through environment variables. (setenv "CC" ,(cc-for-target)) - (apply invoke "./configure" configure-flags))) - (add-before 'install 'fix-makefile - (lambda* (#:key outputs #:allow-other-keys) - (substitute* "GNUmakefile" - (("^\tchown.*$") "")) - #t))) + (apply invoke "./configure" configure-flags)))) #:configure-flags (list (string-append "--prefix=" (assoc-ref %outputs "out")) "--with-timestamp") From 4bed8486d4c0a4ff142903b8bc1584ce84767355 Mon Sep 17 00:00:00 2001 From: Brice Waegeneire Date: Sat, 12 Jun 2021 16:46:00 +0200 Subject: [PATCH 009/144] services: pcscd: Cleanup socket when started. Otherwise when pcscd doesn't terminate properly (ie. receive a SIGKILL), it won't start again because of it's socket already existing. * gnu/services/security-token.scm (pcscd-shepherd-service)[start]: Remove existing socket file. --- gnu/services/security-token.scm | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/gnu/services/security-token.scm b/gnu/services/security-token.scm index ec26006538..0cbb591e10 100644 --- a/gnu/services/security-token.scm +++ b/gnu/services/security-token.scm @@ -1,6 +1,7 @@ ;;; GNU Guix --- Functional package management for GNU ;;; Copyright © 2018 Arun Isaac ;;; Copyright © 2020 Tobias Geerinckx-Rice +;;; Copyright © 2021 Brice Waegeneire ;;; ;;; This file is part of GNU Guix. ;;; @@ -57,6 +58,9 @@ (requirement '(syslogd)) (modules '((gnu build shepherd))) (start #~(lambda _ + (let ((socket "/run/pcscd/pcscd.comm")) + (when (file-exists? socket) + (delete-file socket))) (invoke #$(file-append pcsc-lite "/sbin/pcscd")) (call-with-input-file "/run/pcscd/pcscd.pid" read))) (stop #~(make-kill-destructor))))))) From ffe50737b2c178eba3e810ba1c8dbf90064c9503 Mon Sep 17 00:00:00 2001 From: Nicolas Goaziou Date: Sat, 19 Jun 2021 23:51:25 +0200 Subject: [PATCH 010/144] doc: Fix a typo. * doc/guix.texi (Substitute Server Authorization): Fix typo. --- doc/guix.texi | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/doc/guix.texi b/doc/guix.texi index 094d1acd2c..efeb176e3d 100644 --- a/doc/guix.texi +++ b/doc/guix.texi @@ -3736,7 +3736,7 @@ other substitute server. @cindex access control list (ACL), for substitutes @cindex ACL (access control list), for substitutes To allow Guix to download substitutes from @code{@value{SUBSTITUTE-SERVER-1}}, @code{@value{SUBSTITUTE-SERVER-2}} or a mirror, you -must add the releavnt public key to the access control list (ACL) of archive +must add the relevant public key to the access control list (ACL) of archive imports, using the @command{guix archive} command (@pxref{Invoking guix archive}). Doing so implies that you trust the substitute server to not be compromised and to serve genuine substitutes. From acb34cda237b462c6872cb698f5fc4123550d77c Mon Sep 17 00:00:00 2001 From: Nicolas Goaziou Date: Sun, 20 Jun 2021 00:05:32 +0200 Subject: [PATCH 011/144] gnu: emacs-emms: Update to 7.5. * gnu/packages/emacs-xyz.scm (emacs-emms): Update to 7.5. --- gnu/packages/emacs-xyz.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index ca87a2ed46..2a319ef2aa 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -2052,14 +2052,14 @@ incrementally confined in Isearch manner.") (define emacs-emms-print-metadata (package (name "emacs-emms-print-metadata") - (version "7.4") + (version "7.5") (source (origin (method url-fetch) (uri (string-append "https://elpa.gnu.org/packages/" "emms-" version ".tar")) (sha256 - (base32 "153j76jfnh01b4pkkpyxfh83rl975rx0mh7mx4nnf83qd4dzkkd4")))) + (base32 "0d7nsx2idzbp6d5im5rrsnwppbr2cimvxgx31bhwsm2aq3ya5v2j")))) (build-system gnu-build-system) (arguments `(#:make-flags '("emms-print-metadata") From 376b16e9a180ddef1aca795a3acf2512561976ef Mon Sep 17 00:00:00 2001 From: Xinglu Chen Date: Sat, 19 Jun 2021 17:50:32 +0200 Subject: [PATCH 012/144] gnu: Add ocaml-pcre. * gnu/packages/ocaml.scm (ocaml-pcre): New variable. Signed-off-by: Julien Lepiller --- gnu/packages/ocaml.scm | 32 ++++++++++++++++++++++++++++++++ 1 file changed, 32 insertions(+) diff --git a/gnu/packages/ocaml.scm b/gnu/packages/ocaml.scm index 4510affe0f..a6637c83ff 100644 --- a/gnu/packages/ocaml.scm +++ b/gnu/packages/ocaml.scm @@ -3086,6 +3086,38 @@ every compliant installation of OCaml and organize these libraries into a hierarchy of modules.") (license license:lgpl2.1+))) +(define-public ocaml-pcre + (package + (name "ocaml-pcre") + (version "7.4.6") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/mmottl/pcre-ocaml") + (commit version))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "11mck879p5zvkghps4ky8yslm0isgz52d84adl0dmcfxv2ibvcym")))) + (build-system dune-build-system) + (arguments + ;; No tests. + '(#:tests? #f)) + (propagated-inputs + `(("dune-configurator" ,dune-configurator) + ("pcre" ,pcre))) + (native-inputs + `(("pcre:bin" ,pcre "bin"))) + (home-page "https://mmottl.github.io/pcre-ocaml") + (synopsis + "Bindings to the Perl Compatibility Regular Expressions library") + (description "Pcre-ocaml offers library functions for string +pattern matching and substitution, similar to the functionality +offered by the Perl language.") + ;; With static linking exception + (license license:lgpl2.1+))) + (define-public ocaml4.07-pcre (package (name "ocaml4.07-pcre") From 97d3a9f781ac4e436cad4a7c1a59de8f48baec0c Mon Sep 17 00:00:00 2001 From: Xinglu Chen Date: Sat, 19 Jun 2021 17:50:35 +0200 Subject: [PATCH 013/144] gnu: ocaml4.07-expect: Switch to default OCaml compiler. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/ocaml.scm (ocaml4.07-expect): Rename to ‘ocaml-expect’. [arguments]: Use default OCaml compiler. [native-inputs]: Use ‘ocaml-*’ packages instead of ‘ocaml4.07-*’. [propagated-inputs]: Likewise. [description]: Make it a full sentence. Signed-off-by: Julien Lepiller --- gnu/packages/ocaml.scm | 23 +++++++++++------------ 1 file changed, 11 insertions(+), 12 deletions(-) diff --git a/gnu/packages/ocaml.scm b/gnu/packages/ocaml.scm index a6637c83ff..549009eb09 100644 --- a/gnu/packages/ocaml.scm +++ b/gnu/packages/ocaml.scm @@ -3148,9 +3148,9 @@ matching and substitution, similar to the functionality offered by the Perl language.") (license license:lgpl2.1+))); with the OCaml link exception -(define-public ocaml4.07-expect +(define-public ocaml-expect (package - (name "ocaml4.07-expect") + (name "ocaml-expect") (version "0.0.6") (source (origin (method url-fetch) @@ -3159,21 +3159,20 @@ language.") (base32 "098qvg9d4yrqzr5ax291y3whrpax0m3sx4gi6is0mblc96r9yqk0")))) (arguments - `(#:tests? #f - #:ocaml ,ocaml-4.07 - #:findlib ,ocaml4.07-findlib)) + `(#:tests? #f)) (build-system ocaml-build-system) (native-inputs - `(("ocamlbuild" ,(package-with-ocaml4.07 ocamlbuild)) - ("ocaml-num" ,(package-with-ocaml4.07 ocaml-num)) - ("ocaml-pcre" ,ocaml4.07-pcre) - ("ounit" ,(package-with-ocaml4.07 ocaml-ounit)))) + `(("ocamlbuild" ,ocamlbuild) + ("ocaml-num" ,ocaml-num) + ("ocaml-pcre" ,ocaml-pcre) + ("ounit" ,ocaml-ounit))) (propagated-inputs - `(("batteries" ,(package-with-ocaml4.07 ocaml-batteries)))) + `(("batteries" ,ocaml-batteries))) (home-page "https://forge.ocamlcore.org/projects/ocaml-expect/") (synopsis "Simple implementation of expect") - (description "Help building unitary testing of interactive program. You -can match the question using a regular expression or a timeout.") + (description "This package provides utilities for building unitary testing +of interactive program. You can match the question using a regular expression +or a timeout.") (license license:lgpl2.1+))) ; with the OCaml static compilation exception (define-public ocaml-stdlib-shims From 96dce8c7fe0d86a7997a771e60b735789f97bc19 Mon Sep 17 00:00:00 2001 From: Xinglu Chen Date: Sat, 19 Jun 2021 17:50:37 +0200 Subject: [PATCH 014/144] gnu: ocaml4.07-pcre: Remove package. MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/ocaml.scm (ocaml4.07-pcre): Remove package. It has been superseded by ‘ocaml-pcre’. Signed-off-by: Julien Lepiller --- gnu/packages/ocaml.scm | 30 ------------------------------ 1 file changed, 30 deletions(-) diff --git a/gnu/packages/ocaml.scm b/gnu/packages/ocaml.scm index 549009eb09..22767ee2a2 100644 --- a/gnu/packages/ocaml.scm +++ b/gnu/packages/ocaml.scm @@ -3118,36 +3118,6 @@ offered by the Perl language.") ;; With static linking exception (license license:lgpl2.1+))) -(define-public ocaml4.07-pcre - (package - (name "ocaml4.07-pcre") - (version "7.4.1") - (source (origin - (method git-fetch) - (uri (git-reference - (url "https://github.com/mmottl/pcre-ocaml") - (commit version))) - (file-name (git-file-name name version)) - (sha256 - (base32 - "11sd8g668h48790lamz0riw9jgnfkaif5qdfa0akcndwa6aj07jf")))) - (build-system dune-build-system) - (arguments - `(#:test-target "." - #:ocaml ,ocaml-4.07 - #:findlib ,ocaml4.07-findlib - #:dune ,ocaml4.07-dune)) - (native-inputs - `(("ocaml-base" ,(package-with-ocaml4.07 ocaml-base)) - ("pcre:bin" ,pcre "bin"))) - (propagated-inputs `(("pcre" ,pcre))) - (home-page "https://mmottl.github.io/pcre-ocaml") - (synopsis "Bindings to the Perl Compatibility Regular Expressions library") - (description "Pcre-ocaml offers library functions for string pattern -matching and substitution, similar to the functionality offered by the Perl -language.") - (license license:lgpl2.1+))); with the OCaml link exception - (define-public ocaml-expect (package (name "ocaml-expect") From fe6fd923a8b5a8307ae47c1f218dc9b9b41a722d Mon Sep 17 00:00:00 2001 From: Xinglu Chen Date: Sat, 19 Jun 2021 17:50:38 +0200 Subject: [PATCH 015/144] gnu: Add ocaml-mparser. * gnu/packages/ocaml.scm (ocaml-mparser): New variable. Signed-off-by: Julien Lepiller --- gnu/packages/ocaml.scm | 28 ++++++++++++++++++++++++++++ 1 file changed, 28 insertions(+) diff --git a/gnu/packages/ocaml.scm b/gnu/packages/ocaml.scm index 22767ee2a2..0117f6dca2 100644 --- a/gnu/packages/ocaml.scm +++ b/gnu/packages/ocaml.scm @@ -6799,6 +6799,34 @@ in the documentation always stays up-to-date. compatibility.") (license license:isc))) +(define-public ocaml-mparser + (package + (name "ocaml-mparser") + (version "1.3") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/murmour/mparser") + (commit version))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "16j19v16r42gcsii6a337zrs5cxnf12ig0vaysxyr7sq5lplqhkx")))) + (build-system dune-build-system) + (arguments + ;; No tests. + '(#:package "mparser" + #:tests? #f)) + (home-page "https://github.com/murmour/mparser") + (synopsis "Simple monadic parser combinator library") + (description + "This library implements a rather complete and efficient monadic parser +combinator library similar to the Parsec library for Haskell by Daan Leijen and +the FParsec library for FSharp by Stephan Tolksdorf.") + ;; With static linking exception. + (license license:lgpl2.1+))) + (define-public lablgtk3 (package (name "lablgtk") From 620b4e8ad3b8a6c3a770a5a3ab69b546d7570df7 Mon Sep 17 00:00:00 2001 From: Xinglu Chen Date: Sat, 19 Jun 2021 17:50:40 +0200 Subject: [PATCH 016/144] gnu: Add ocaml-mparser-re. * gnu/packages/ocaml.scm (ocaml-mparser-re): New variable. Signed-off-by: Julien Lepiller --- gnu/packages/ocaml.scm | 15 +++++++++++++++ 1 file changed, 15 insertions(+) diff --git a/gnu/packages/ocaml.scm b/gnu/packages/ocaml.scm index 0117f6dca2..f795f8d918 100644 --- a/gnu/packages/ocaml.scm +++ b/gnu/packages/ocaml.scm @@ -6827,6 +6827,21 @@ the FParsec library for FSharp by Stephan Tolksdorf.") ;; With static linking exception. (license license:lgpl2.1+))) +(define-public ocaml-mparser-re + (package + (inherit ocaml-mparser) + (name "ocaml-mparser-re") + (arguments + ;; No tests. + '(#:package "mparser-re" + #:tests? #f)) + (propagated-inputs + `(("ocaml-mparser" ,ocaml-mparser) + ("ocaml-re" ,ocaml-re))) + (synopsis "MParser plugin for RE-based regular expressions") + (description "This package provides RE-based regular expressions +support for Mparser."))) + (define-public lablgtk3 (package (name "lablgtk") From dcd94ee855fa03596a8e84b7cffe1344bb6206ef Mon Sep 17 00:00:00 2001 From: Xinglu Chen Date: Sat, 19 Jun 2021 17:50:41 +0200 Subject: [PATCH 017/144] gnu: Add ocaml-mparser-pcre. * gnu/packages/ocaml.scm (ocaml-mparser-pcre): New variable. Signed-off-by: Julien Lepiller --- gnu/packages/ocaml.scm | 15 +++++++++++++++ 1 file changed, 15 insertions(+) diff --git a/gnu/packages/ocaml.scm b/gnu/packages/ocaml.scm index f795f8d918..4e0c6458b6 100644 --- a/gnu/packages/ocaml.scm +++ b/gnu/packages/ocaml.scm @@ -6842,6 +6842,21 @@ the FParsec library for FSharp by Stephan Tolksdorf.") (description "This package provides RE-based regular expressions support for Mparser."))) +(define-public ocaml-mparser-pcre + (package + (inherit ocaml-mparser) + (name "ocaml-mparser-pcre") + (arguments + ;; No tests. + '(#:package "mparser-pcre" + #:tests? #f)) + (propagated-inputs + `(("ocaml-mparser" ,ocaml-mparser) + ("ocaml-pcre" ,ocaml-pcre))) + (synopsis "MParser plugin for PCRE-based regular expressions") + (description "This package provides PCRE-based regular expressions +support for Mparser."))) + (define-public lablgtk3 (package (name "lablgtk") From 019c862a67b677ceeb0d91c9440f5ed8d9c149a4 Mon Sep 17 00:00:00 2001 From: Nicolas Goaziou Date: Sun, 20 Jun 2021 08:22:37 +0200 Subject: [PATCH 018/144] gnu: tectonic: Update to 0.7.0. * gnu/packages/rust-apps.scm (tectonic): Update to 0.7.0. --- gnu/packages/rust-apps.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/rust-apps.scm b/gnu/packages/rust-apps.scm index 82afb01998..5108ade3c9 100644 --- a/gnu/packages/rust-apps.scm +++ b/gnu/packages/rust-apps.scm @@ -587,14 +587,14 @@ gitignore rules.") (define-public tectonic (package (name "tectonic") - (version "0.6.4") + (version "0.7.0") (source (origin (method url-fetch) (uri (crate-uri "tectonic" version)) (file-name (string-append name "-" version ".tar.gz")) (sha256 - (base32 "1h6m0mxqd8580c82dknja7qqhkg1pbvwmw4rlzfr1ndfjrcbk3al")))) + (base32 "1x6i97dl28y6wxpq2r4dcsa853sa4yw5vhl79qdb44q5wsd6ba1f")))) (build-system cargo-build-system) (arguments `(#:rust ,rust-1.52 From 7ab6907448002d7049f01f320300a9daa2388e69 Mon Sep 17 00:00:00 2001 From: Solene Rapenne Date: Sat, 19 Jun 2021 19:04:08 +0200 Subject: [PATCH 019/144] gnu: openvpn: Update to 2.5.3. * gnu/packages/vpn.scm (openvpn): Update to 2.5.3. Signed-off-by: Brice Waegeneire --- gnu/packages/vpn.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/vpn.scm b/gnu/packages/vpn.scm index 5b10d92f0f..8272a3a26e 100644 --- a/gnu/packages/vpn.scm +++ b/gnu/packages/vpn.scm @@ -513,7 +513,7 @@ this process. It is compatible with Fortinet VPNs.") (define-public openvpn (package (name "openvpn") - (version "2.5.2") + (version "2.5.3") (source (origin (method url-fetch) (uri (string-append @@ -521,7 +521,7 @@ this process. It is compatible with Fortinet VPNs.") version ".tar.xz")) (sha256 (base32 - "1j0xkiya20hhvalfjg5l3v1226vyjs9j9aw2mzpnbwq1d61l69xi")))) + "0zlski66mw10klmwvg445z051mld7xjng4iyl4f9b883qr1rjspv")))) (build-system gnu-build-system) (arguments '(#:configure-flags '("--enable-iproute2=yes"))) From 0bfafa49fa387c6a58f79178fc6344b2ce0bf02d Mon Sep 17 00:00:00 2001 From: Xinglu Chen Date: Sun, 20 Jun 2021 12:41:52 +0200 Subject: [PATCH 020/144] gnu: ocaml-menhir: Update to 20210419. * gnu/packages/ocaml.scm (ocaml-menhir): Update to 20210419. Signed-off-by: Julien Lepiller --- gnu/packages/ocaml.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/ocaml.scm b/gnu/packages/ocaml.scm index 4e0c6458b6..a49ee8370b 100644 --- a/gnu/packages/ocaml.scm +++ b/gnu/packages/ocaml.scm @@ -1030,7 +1030,7 @@ Emacs.") (define-public ocaml-menhir (package (name "ocaml-menhir") - (version "20200211") + (version "20210419") (source (origin (method git-fetch) @@ -1039,7 +1039,7 @@ Emacs.") (commit version))) (file-name (git-file-name name version)) (sha256 - (base32 "019izf51kdc7pzkw68zg8a2alc8lxw1gwdp7in970mr90n16b5zj")))) + (base32 "0jcbr7s3iwfr7xxfybs3h407g76yfp5yq5r9i0wg2ahvvbqh03ky")))) (build-system dune-build-system) (inputs `(("ocaml" ,ocaml))) From 6e6769dde0a3e613784834aeded53b3aaa2e4cec Mon Sep 17 00:00:00 2001 From: Julien Lepiller Date: Sun, 20 Jun 2021 12:59:56 +0200 Subject: [PATCH 021/144] gnu: why3: Update to 1.3.3. * gnu/packages/maths.scm (why3): Update to 1.3.3. [arguments]: Adjust for newer ocaml-num. --- gnu/packages/maths.scm | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm index a79d546abd..84540d5ffe 100644 --- a/gnu/packages/maths.scm +++ b/gnu/packages/maths.scm @@ -6289,14 +6289,14 @@ numeric differences and differences in numeric formats.") (define-public why3 (package (name "why3") - (version "1.3.1") + (version "1.3.3") (source (origin (method url-fetch) (uri (string-append "https://gforge.inria.fr/frs/download.php/file" - "/38291/why3-" version ".tar.gz")) + "/38367/why3-" version ".tar.gz")) (sha256 (base32 - "16zcrc60zz2j3gd3ww93z2z9x2jkxb3kr57y8i5rcgmacy7mw3bv")))) + "1n0a2nn1gnk0zg339lh698g4wpk7m8m1vyi2yvifd5adqvk4milw")))) (build-system ocaml-build-system) (native-inputs `(("coq" ,coq) @@ -6320,8 +6320,8 @@ numeric differences and differences in numeric formats.") (setenv "CONFIG_SHELL" (which "sh")) (substitute* "configure" ;; find ocaml-num in the correct directory - (("\\$DIR/nums.cma") "$DIR/../nums.cma") - (("\\$DIR/num.cmi") "$DIR/../num.cmi")) + (("\\$DIR/nums.cma") "$DIR/num.cma") + (("\\$DIR/num.cmi") "$DIR/core/num.cmi")) #t)) (add-after 'configure 'fix-makefile (lambda _ From a211078f992bc5a26eaf787c6b01caa41de67597 Mon Sep 17 00:00:00 2001 From: Xinglu Chen Date: Sun, 20 Jun 2021 12:42:43 +0200 Subject: [PATCH 022/144] gnu: ocaml-ppxlib: Update to 0.22.1. * gnu/packages/ocaml.scm (ocaml-ppxlib): Update to 0.22.1. Signed-off-by: Julien Lepiller --- gnu/packages/ocaml.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/ocaml.scm b/gnu/packages/ocaml.scm index a49ee8370b..047d504a0a 100644 --- a/gnu/packages/ocaml.scm +++ b/gnu/packages/ocaml.scm @@ -5025,7 +5025,7 @@ as part of the same ocaml-migrate-parsetree driver.") (define-public ocaml-ppxlib (package (name "ocaml-ppxlib") - (version "0.22.0") + (version "0.22.1") (home-page "https://github.com/ocaml-ppx/ppxlib") (source (origin @@ -5036,7 +5036,7 @@ as part of the same ocaml-migrate-parsetree driver.") (file-name (git-file-name name version)) (sha256 (base32 - "0kf7lgcwygf6zlx7rwddqpqvasa6v7xiq0bqal8vxlib6lpg074q")))) + "0cpfg634if1py1b2rljk3cagq9gj68dl2gk1kdg76f9rapvl2i4g")))) (build-system dune-build-system) (propagated-inputs `(("ocaml-base" ,ocaml-base) From ef3f38ea0027f48feb6a29df131ac58bfbb46b7d Mon Sep 17 00:00:00 2001 From: Brice Waegeneire Date: Sun, 20 Jun 2021 15:15:55 +0200 Subject: [PATCH 023/144] services: openssh: Replace 'without-password' by 'prohibit-password'. For some time, OpenSSH's option 'PermitRootLogin' has deprecated the ambiguous argument 'without-password' with 'prohibit-password'. * doc/guix.texi (Network Services): Replace 'without-password by 'prohibit-password. * gnu/machine/digital-ocean.scm (guix-infect): Change system configuration to use 'prohibit-password. * gnu/services/ssh.scm (openssh-configuration): Change comment to use 'prohibit-password. (openssh-config-file): Add support for 'prohibit-password to 'permit-root-login'. Warn about deprecated 'without-password usage. * gnu/tests/ganeti.scm (%ganeti-os): Replace 'without-password by 'prohibit-password. Signed-off-by: Tobias Geerinckx-Rice --- doc/guix.texi | 6 +++--- gnu/machine/digital-ocean.scm | 3 ++- gnu/services/ssh.scm | 11 +++++++++-- gnu/tests/ganeti.scm | 3 ++- 4 files changed, 16 insertions(+), 7 deletions(-) diff --git a/doc/guix.texi b/doc/guix.texi index efeb176e3d..66c6adc4f5 100644 --- a/doc/guix.texi +++ b/doc/guix.texi @@ -17070,7 +17070,7 @@ shell daemon, @command{sshd}. Its value must be an (service openssh-service-type (openssh-configuration (x11-forwarding? #t) - (permit-root-login 'without-password) + (permit-root-login 'prohibit-password) (authorized-keys `(("alice" ,(local-file "alice.pub")) ("bob" ,(local-file "bob.pub")))))) @@ -17104,7 +17104,7 @@ TCP port on which @command{sshd} listens for incoming connections. @item @code{permit-root-login} (default: @code{#f}) This field determines whether and when to allow logins as root. If @code{#f}, root logins are disallowed; if @code{#t}, they are allowed. -If it's the symbol @code{'without-password}, then root logins are +If it's the symbol @code{'prohibit-password}, then root logins are permitted but not with password-based authentication. @item @code{allow-empty-passwords?} (default: @code{#f}) @@ -29333,7 +29333,7 @@ cluster node that supports multiple storage backends, and installs the ;; Ganeti uses SSH to communicate between nodes. (service openssh-service-type (openssh-configuration - (permit-root-login 'without-password))) + (permit-root-login 'prohibit-password))) (service ganeti-service-type (ganeti-configuration diff --git a/gnu/machine/digital-ocean.scm b/gnu/machine/digital-ocean.scm index 82383a8c7c..d97c300d18 100644 --- a/gnu/machine/digital-ocean.scm +++ b/gnu/machine/digital-ocean.scm @@ -1,5 +1,6 @@ ;;; GNU Guix --- Functional package management for GNU ;;; Copyright © 2019 Jakob L. Kreuze +;;; Copyright © 2020 Brice Waegeneire ;;; ;;; This file is part of GNU Guix. ;;; @@ -256,7 +257,7 @@ cat > /etc/bootstrap-config.scm << EOF (service openssh-service-type (openssh-configuration (log-level 'debug) - (permit-root-login 'without-password)))) + (permit-root-login 'prohibit-password)))) %base-services))) EOF # guix pull diff --git a/gnu/services/ssh.scm b/gnu/services/ssh.scm index 1891db0487..a018052eeb 100644 --- a/gnu/services/ssh.scm +++ b/gnu/services/ssh.scm @@ -6,6 +6,8 @@ ;;; Copyright © 2019 Ricardo Wurmus ;;; Copyright © 2020 pinoaffe ;;; Copyright © 2020 Oleg Pykhalov +;;; Copyright © 2020 Brice Waegeneire +;;; Copyright © 2021 Tobias Geerinckx-Rice ;;; ;;; This file is part of GNU Guix. ;;; @@ -30,6 +32,7 @@ #:use-module (gnu services web) #:use-module (gnu system pam) #:use-module (gnu system shadow) + #:use-module (guix deprecation) #:use-module (guix gexp) #:use-module (guix records) #:use-module (guix modules) @@ -288,7 +291,7 @@ The other options should be self-descriptive." ;; integer (port-number openssh-configuration-port-number (default 22)) - ;; Boolean | 'without-password + ;; Boolean | 'prohibit-password (permit-root-login openssh-configuration-permit-root-login (default #f)) ;; Boolean @@ -441,7 +444,11 @@ of user-name/file-like tuples." #$(match (openssh-configuration-permit-root-login config) (#t "yes") (#f "no") - ('without-password "without-password"))) + ('without-password (warn-about-deprecation + 'without-password #f + #:replacement 'prohibit-password) + "prohibit-password") + ('prohibit-password "prohibit-password"))) (format port "PermitEmptyPasswords ~a\n" #$(if (openssh-configuration-allow-empty-passwords? config) "yes" "no")) diff --git a/gnu/tests/ganeti.scm b/gnu/tests/ganeti.scm index ff853a7149..19c26b86dd 100644 --- a/gnu/tests/ganeti.scm +++ b/gnu/tests/ganeti.scm @@ -1,5 +1,6 @@ ;;; GNU Guix --- Functional package management for GNU ;;; Copyright © 2020 Marius Bakke . +;;; Copyright © 2020 Brice Waegeneire ;;; ;;; This file is part of GNU Guix. ;;; @@ -65,7 +66,7 @@ (service openssh-service-type (openssh-configuration - (permit-root-login 'without-password))) + (permit-root-login 'prohibit-password))) (service ganeti-service-type (ganeti-configuration From 6b8552fd5af1a794a355cf0f3279a82b8267a202 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sun, 20 Jun 2021 16:38:54 +0200 Subject: [PATCH 024/144] gnu: knot: Update to 3.0.7. * gnu/packages/dns.scm (knot): Update to 3.0.7. --- gnu/packages/dns.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/dns.scm b/gnu/packages/dns.scm index 199b876369..dc6b101e3c 100644 --- a/gnu/packages/dns.scm +++ b/gnu/packages/dns.scm @@ -817,7 +817,7 @@ Extensions} (DNSSEC).") (define-public knot (package (name "knot") - (version "3.0.6") + (version "3.0.7") (source (origin (method git-fetch) @@ -826,7 +826,7 @@ Extensions} (DNSSEC).") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 - (base32 "0mjgjx43yb3w688jw16g5m1724wb0wnv4y7di2rslrp0s11wl2a9")) + (base32 "0ihd0lfh0r1nzz2di2rqkrx5j1017xv7m54irlhccx21inwv6g3y")) (modules '((guix build utils))) (snippet '(begin From df68e5c65ae015639566baf5cce1faf96a2d0ed4 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sun, 20 Jun 2021 16:39:29 +0200 Subject: [PATCH 025/144] gnu: rsnapshot: Update to 1.4.4. * gnu/packages/backup.scm (rsnapshot): Update to 1.4.4. --- gnu/packages/backup.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/backup.scm b/gnu/packages/backup.scm index 5e0009472e..d425243848 100644 --- a/gnu/packages/backup.scm +++ b/gnu/packages/backup.scm @@ -451,7 +451,7 @@ rdiff-backup is easy to use and settings have sensible defaults.") (define-public rsnapshot (package (name "rsnapshot") - (version "1.4.3") + (version "1.4.4") (source (origin (method url-fetch) @@ -459,7 +459,7 @@ rdiff-backup is easy to use and settings have sensible defaults.") "https://github.com/rsnapshot/rsnapshot/releases/download/" version "/rsnapshot-" version ".tar.gz")) (sha256 - (base32 "1lavqmmsf53pim0nvming7fkng6p0nk2a51k2c2jdq0l7snpl31b")))) + (base32 "0yc5k2fhm54ypxgm1fsaf8vrg5b7qbvbsqk371n6baf592vprjy1")))) (build-system gnu-build-system) (arguments `(#:phases From eca228eb09fd54021af98347aeeb92e5c3dd629e Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sun, 20 Jun 2021 16:39:36 +0200 Subject: [PATCH 026/144] gnu: tcpdump: Update to 4.99.1. * gnu/packages/admin.scm (tcpdump): Update to 4.99.1. --- gnu/packages/admin.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/admin.scm b/gnu/packages/admin.scm index ea5cd91e38..16fcdfcb8c 100644 --- a/gnu/packages/admin.scm +++ b/gnu/packages/admin.scm @@ -1319,14 +1319,14 @@ network statistics collection, security monitoring, network debugging, etc.") (define-public tcpdump (package (name "tcpdump") - (version "4.99.0") + (version "4.99.1") (source (origin (method url-fetch) (uri (string-append "https://www.tcpdump.org/release/tcpdump-" version ".tar.gz")) (sha256 (base32 - "0hmqh2fx8rgs9v1mk3vpywj61xvkifz260q685xllxr8jmxg3wlc")))) + "1ghfs5gifzrk3813zf9zalfbjs70wg6llz6q31k180r7zf2nkcvr")))) (build-system gnu-build-system) (inputs `(("libpcap" ,libpcap) ("openssl" ,openssl))) From d027858e70c4a37aca90b1d4ecb2f0421a95d987 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sun, 20 Jun 2021 16:43:50 +0200 Subject: [PATCH 027/144] gnu: corsix-th: Update to 0.65. * gnu/packages/games.scm (corsix-th): Update to 0.65. --- gnu/packages/games.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/games.scm b/gnu/packages/games.scm index 6b3a6f0e1f..fca25294db 100644 --- a/gnu/packages/games.scm +++ b/gnu/packages/games.scm @@ -946,7 +946,7 @@ allows users to brew while offline.") (define-public corsix-th (package (name "corsix-th") - (version "0.64") + (version "0.65") (source (origin (method git-fetch) @@ -955,7 +955,7 @@ allows users to brew while offline.") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 - (base32 "0chh9cv2kdc39sr0x8hclcyzd8dz2y6grgagqzkvr7j570wa5cqh")))) + (base32 "0hp7da7b73dpn1h22rw3h8w6aaj9azn18qnp3ap3lrlqhj4fzcb3")))) (build-system cmake-build-system) (arguments `(#:phases From 5ae0d2c24737572ba3e0619a0176a07758078e1d Mon Sep 17 00:00:00 2001 From: Xinglu Chen Date: Sun, 20 Jun 2021 16:52:14 +0200 Subject: [PATCH 028/144] gnu: ocaml-dot-merlin-reader: Update to 4.2-411. * gnu/packages/ocaml.scm (ocaml-dot-merlin-reader): Update to 4.2-411. Signed-off-by: Julien Lepiller --- gnu/packages/ocaml.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/ocaml.scm b/gnu/packages/ocaml.scm index 047d504a0a..58b34d4293 100644 --- a/gnu/packages/ocaml.scm +++ b/gnu/packages/ocaml.scm @@ -4540,7 +4540,7 @@ format}. @code{craml} is released as a single binary (called @code{craml}).") (define-public ocaml-dot-merlin-reader (package (name "ocaml-dot-merlin-reader") - (version "3.4.2") + (version "4.2-411") (source (origin (method git-fetch) @@ -4550,7 +4550,7 @@ format}. @code{craml} is released as a single binary (called @code{craml}).") (file-name (git-file-name name version)) (sha256 (base32 - "0i2nwkdh6cfzmnsdsr8aw86vs8j1k5jkjzrs61b9384wnffdbbmj")))) + "1vl6p8m2pag5j283h5g2gzxxfm599k6qhyrjkdf3kyc476fc9lw8")))) (build-system dune-build-system) (arguments '(#:package "dot-merlin-reader" #:tests? #f)) ; no tests From 980c33bd3f16e44a123ef21408a56e59ebb76373 Mon Sep 17 00:00:00 2001 From: Xinglu Chen Date: Sun, 20 Jun 2021 16:52:16 +0200 Subject: [PATCH 029/144] =?UTF-8?q?gnu:=20ocaml-merlin:=20Inherit=20from?= =?UTF-8?q?=20=E2=80=98ocaml-dot-merlin-reader=E2=80=99.?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/packages/ocaml.scm (ocaml-merlin): Inherit from ‘ocaml-dot-merlin-reader’, thus also updating it to 4.2-411. [version, source, build-system, home-page]: Remove. [arguments]<#:phases>: Use custom test phase. Signed-off-by: Julien Lepiller --- gnu/packages/ocaml.scm | 24 +++++++++--------------- 1 file changed, 9 insertions(+), 15 deletions(-) diff --git a/gnu/packages/ocaml.scm b/gnu/packages/ocaml.scm index 58b34d4293..21d16a46a1 100644 --- a/gnu/packages/ocaml.scm +++ b/gnu/packages/ocaml.scm @@ -4566,21 +4566,16 @@ format}. @code{craml} is released as a single binary (called @code{craml}).") (define-public ocaml-merlin (package + (inherit ocaml-dot-merlin-reader) (name "ocaml-merlin") - (version "3.4.2") - (source - (origin - (method git-fetch) - (uri (git-reference - (url "https://github.com/ocaml/merlin") - (commit (string-append "v" version)))) - (file-name (git-file-name name version)) - (sha256 - (base32 - "0i2nwkdh6cfzmnsdsr8aw86vs8j1k5jkjzrs61b9384wnffdbbmj")))) - (build-system dune-build-system) - (arguments '(#:package "merlin" - #:test-target "tests")) + (arguments + '(#:package "merlin" + #:phases + (modify-phases %standard-phases + (replace 'check + (lambda* (#:key tests? #:allow-other-keys) + (when tests? + (invoke "dune" "runtest" "-p" "merlin,dot-merlin-reader"))))))) (inputs `(("ocaml-yojson" ,ocaml-yojson) ("ocaml-csexp" ,ocaml-csexp) @@ -4589,7 +4584,6 @@ format}. @code{craml} is released as a single binary (called @code{craml}).") `(("ocaml-dot-merlin-reader" ,ocaml-dot-merlin-reader) ; required for tests ("ocaml-mdx" ,ocaml-mdx) ("jq" ,jq))) - (home-page "https://ocaml.github.io/merlin/") (synopsis "Context sensitive completion for OCaml in Vim and Emacs") (description "Merlin is an editor service that provides modern IDE features for OCaml. Emacs and Vim support is provided out-of-the-box. From 4ebc965edea519c884b4a643f970b235cd0ff37f Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Sun, 20 Jun 2021 23:40:36 +0200 Subject: [PATCH 030/144] gnu: whois: Update to 5.5.10. * gnu/packages/networking.scm (whois): Update to 5.5.10. --- gnu/packages/networking.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/networking.scm b/gnu/packages/networking.scm index da4ede06f2..5bdbe3bc9d 100644 --- a/gnu/packages/networking.scm +++ b/gnu/packages/networking.scm @@ -1399,7 +1399,7 @@ and up to 1 Mbit/s downstream.") (define-public whois (package (name "whois") - (version "5.5.9") + (version "5.5.10") (source (origin (method git-fetch) @@ -1408,7 +1408,7 @@ and up to 1 Mbit/s downstream.") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 - (base32 "0l9dhyciylh14lqw8j5mrk0y2hl95cnj8pyvvabbgwxpsdn0yvbb")))) + (base32 "179hgmh9yqk8jq26ybik4cr3lgryd5p6kdwccc3r7mfssk3yp8lz")))) (build-system gnu-build-system) (arguments `(#:tests? #f ; no test suite From 2955fec1c9a97f6468a3a36580f70256103d708c Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Mon, 21 Jun 2021 01:13:38 +0200 Subject: [PATCH 031/144] gnu: asio: Update to 1.18.2. * gnu/packages/networking.scm (asio): Update to 1.18.2. --- gnu/packages/networking.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/networking.scm b/gnu/packages/networking.scm index 5bdbe3bc9d..34369e892e 100644 --- a/gnu/packages/networking.scm +++ b/gnu/packages/networking.scm @@ -3033,14 +3033,14 @@ asynchronous model using a modern C++ approach.") (define-public asio (package (inherit asio-1.12) - (version "1.18.1") + (version "1.18.2") (source (origin (method url-fetch) (uri (string-append "mirror://sourceforge/asio/asio/" version " (Stable)/asio-" version ".tar.bz2")) (sha256 - (base32 "04wi69d72l1p5c7d63z1dz06zn8pdqsbgx1if98dszs9ymfqgyaa")))))) + (base32 "1wpr4ymv63a192fmymwyxd7v0bv575v022gz53y0mcflhr2mvh1s")))))) (define-public shadowsocks ;; There are some security fixes after the last release. From 8b9b707674bf0ad11e0d773ec6939685900f9683 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Mon, 21 Jun 2021 01:13:51 +0200 Subject: [PATCH 032/144] gnu: kirc: Update to 0.2.7. * gnu/packages/irc.scm (kirc): Update to 0.2.7. --- gnu/packages/irc.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/irc.scm b/gnu/packages/irc.scm index 3d1753bff4..7f5394c03c 100644 --- a/gnu/packages/irc.scm +++ b/gnu/packages/irc.scm @@ -378,7 +378,7 @@ for the IRCv3 protocol.") (define-public kirc (package (name "kirc") - (version "0.2.6") + (version "0.2.7") (source (origin (method git-fetch) (uri (git-reference @@ -386,7 +386,7 @@ for the IRCv3 protocol.") (commit version))) (file-name (git-file-name name version)) (sha256 - (base32 "11pwbil44q7sm3mp1khgw8wmwln2n03f1qawlgmg168jzyxqrs16")))) + (base32 "0phx00lr7ya8rx1hskv1wdwbq2vlihiqhnplqdvk1r3m23is7al9")))) (build-system gnu-build-system) (arguments `(#:tests? #f ; no tests From 3a67aafc557f37c7c224149168d7db77acfc1a37 Mon Sep 17 00:00:00 2001 From: "Boris A. Dekshteyn" Date: Tue, 15 Jun 2021 01:31:13 +1200 Subject: [PATCH 033/144] gnu: font-terminus: Build Open Type Bitmap. * gnu/packages/fonts.scm (font-terminus)[outputs]: Add otb. [arguments]: Add 'build-otb, 'install-otb phases. Signed-off-by: Efraim Flashner --- gnu/packages/fonts.scm | 11 ++++++++++- 1 file changed, 10 insertions(+), 1 deletion(-) diff --git a/gnu/packages/fonts.scm b/gnu/packages/fonts.scm index 4d57bbd514..9297256f8e 100644 --- a/gnu/packages/fonts.scm +++ b/gnu/packages/fonts.scm @@ -426,7 +426,7 @@ The unified Libertinus family consists of: (sha256 (base32 "0yggffiplk22lgqklfmd2c0rw8gwchynjh5kz4bz8yv2h6vw2qfr")))) (build-system gnu-build-system) - (outputs (list "out" "pcf-8bit")) + (outputs (list "out" "pcf-8bit" "otb")) (arguments `(#:tests? #f ; no test target in tarball #:phases @@ -441,6 +441,15 @@ The unified Libertinus family consists of: (let ((pcf-8bit (assoc-ref outputs "pcf-8bit"))) (apply invoke "make" "install-pcf-8bit" (string-append "prefix=" pcf-8bit) + make-flags)))) + (add-after 'build-more-bits 'build-otb + ;; Build Open Type Bitmap + (lambda* (#:key make-flags #:allow-other-keys) + (apply invoke "make" "otb" make-flags))) + (add-after 'install 'install-otb + (lambda* (#:key make-flags outputs #:allow-other-keys) + (let ((otb (assoc-ref outputs "otb"))) + (apply invoke "make" "install-otb" (string-append "prefix=" otb) make-flags))))))) (native-inputs `(("bdftopcf" ,bdftopcf) From 5bf6b88ef39e192d1a433d5fb61824626a2954e3 Mon Sep 17 00:00:00 2001 From: Nicolas Goaziou Date: Mon, 21 Jun 2021 08:07:09 +0200 Subject: [PATCH 034/144] gnu: emacs-corfu: Update to 0.9. * gnu/packages/emacs-xyz.scm (emacs-corfu): Update to 0.9. --- gnu/packages/emacs-xyz.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index 2a319ef2aa..6a93fe41bc 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -2817,7 +2817,7 @@ of bibliographic references.") (define-public emacs-corfu (package (name "emacs-corfu") - (version "0.8") + (version "0.9") (source (origin (method git-fetch) (uri (git-reference @@ -2826,7 +2826,7 @@ of bibliographic references.") (file-name (git-file-name name version)) (sha256 (base32 - "007r1l3ian2bfj4h2xkd2qwh1d1m7kda1p6pj51dikbzaphglh1r")))) + "0265kld5vg870n1zaks42qdawl03zi6rjhffrkkngwgs9i9ap30i")))) (build-system emacs-build-system) (home-page "https://github.com/minad/corfu") (synopsis "Completion overlay region function") From 0f1e95746b89878f7e8debc3d9f435c13948568d Mon Sep 17 00:00:00 2001 From: Nicolas Goaziou Date: Mon, 21 Jun 2021 08:08:41 +0200 Subject: [PATCH 035/144] gnu: emacs-vertico: Update to 0.12. * gnu/packages/emacs-xyz.scm (emacs-vertico): Update to 0.12. --- gnu/packages/emacs-xyz.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index 6a93fe41bc..046a861f6c 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -28501,7 +28501,7 @@ and preferred services can easily be configured.") (define-public emacs-vertico (package (name "emacs-vertico") - (version "0.11") + (version "0.12") (source (origin (method git-fetch) @@ -28510,7 +28510,7 @@ and preferred services can easily be configured.") (commit version))) (file-name (git-file-name name version)) (sha256 - (base32 "0vx23csk1nsrcazifwjxchqdmp3qbg2mwbvkqxn134g89qi8pqkw")))) + (base32 "1qb5qmspc7042r366d73j26hrzmrsdwscv8ly9glsa4gbdxcjkln")))) (build-system emacs-build-system) (native-inputs `(("texinfo" ,texinfo))) From a7495b04b5c606c900ceb76202fdeb5785dea0f7 Mon Sep 17 00:00:00 2001 From: Nicolas Goaziou Date: Mon, 21 Jun 2021 08:10:05 +0200 Subject: [PATCH 036/144] gnu: emacs-marginalia: Update to 0.7. * gnu/packages/emacs-xyz.scm (emacs-marginalia): Update to 0.7. --- gnu/packages/emacs-xyz.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index 046a861f6c..e73ebfa2e5 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -8031,7 +8031,7 @@ list of candidates.") (define-public emacs-marginalia (package (name "emacs-marginalia") - (version "0.6") + (version "0.7") (source (origin (method git-fetch) @@ -8040,7 +8040,7 @@ list of candidates.") (commit version))) (file-name (git-file-name name version)) (sha256 - (base32 "1lisns2vghmqlg8wiv6jy15cfgnc8j83khz0vfnmrjwgcmjw3bbz")))) + (base32 "0yn6dybvsdhr37hnadmbfqi7pf7scxr9z6a6ghsqbrghycddd0mc")))) (build-system emacs-build-system) (home-page "https://github.com/minad/marginalia") (synopsis "Marginalia in the minibuffer completions") From 30a04c00beb3b0bc3799f27caf05bedb5094c0c5 Mon Sep 17 00:00:00 2001 From: Jack Hill Date: Fri, 18 Jun 2021 18:15:46 +0200 Subject: [PATCH 037/144] gnu: Add tlf. * gnu/packages/patches/tlf-support-hamlib-4.2+.patch: New file. * gnu/local.mk: Add it. * gnu/packages/radio.scm (tlf): New variable. Signed-off-by: Guillaume Le Vaillant --- gnu/local.mk | 1 + .../patches/tlf-support-hamlib-4.2+.patch | 66 +++++++++++++++++++ gnu/packages/radio.scm | 62 +++++++++++++++++ 3 files changed, 129 insertions(+) create mode 100644 gnu/packages/patches/tlf-support-hamlib-4.2+.patch diff --git a/gnu/local.mk b/gnu/local.mk index 375883de03..f7ff9af997 100644 --- a/gnu/local.mk +++ b/gnu/local.mk @@ -1753,6 +1753,7 @@ dist_patch_DATA = \ %D%/packages/patches/tipp10-qt5.patch \ %D%/packages/patches/tk-find-library.patch \ %D%/packages/patches/tla2tools-build-xml.patch \ + %D%/packages/patches/tlf-support-hamlib-4.2+.patch \ %D%/packages/patches/tor-fix-build-with-gcc-7.patch \ %D%/packages/patches/transcode-ffmpeg.patch \ %D%/packages/patches/transmission-honor-localedir.patch \ diff --git a/gnu/packages/patches/tlf-support-hamlib-4.2+.patch b/gnu/packages/patches/tlf-support-hamlib-4.2+.patch new file mode 100644 index 0000000000..3c5db10010 --- /dev/null +++ b/gnu/packages/patches/tlf-support-hamlib-4.2+.patch @@ -0,0 +1,66 @@ +From 295fa956f899af37acb6bda9c76ad77748eb9a4a Mon Sep 17 00:00:00 2001 +From: Ervin Hegedus +Date: Sat, 5 Jun 2021 09:23:06 +0200 +Subject: [PATCH] Quick fix for changing of Hamlib's FILPATHLEN macro + +This patch was prepared for Guix by Jack Hill by +squashing together the changes from upstream #268 +. + +It allows the released version of Tlf to build against the version 4.2 of +hamlib in Guix. + +--- + src/sendqrg.c | 6 +++--- + src/sendqrg.h | 10 ++++++++++ + 2 files changed, 13 insertions(+), 3 deletions(-) + +diff --git a/src/sendqrg.c b/src/sendqrg.c +index ceeb356..5d4420e 100644 +--- a/src/sendqrg.c ++++ b/src/sendqrg.c +@@ -87,7 +87,7 @@ int init_tlf_rig(void) { + + rigportname[strlen(rigportname) - 1] = '\0'; // remove '\n' + strncpy(my_rig->state.rigport.pathname, rigportname, +- FILPATHLEN - 1); ++ TLFFILPATHLEN - 1); + + caps = my_rig->caps; + +@@ -104,9 +104,9 @@ int init_tlf_rig(void) { + if (dcd_type != RIG_DCD_NONE) + my_rig->state.dcdport.type.dcd = dcd_type; + if (ptt_file) +- strncpy(my_rig->state.pttport.pathname, ptt_file, FILPATHLEN); ++ strncpy(my_rig->state.pttport.pathname, ptt_file, TLFFILPATHLEN); + if (dcd_file) +- strncpy(my_rig->state.dcdport.pathname, dcd_file, FILPATHLEN); ++ strncpy(my_rig->state.dcdport.pathname, dcd_file, TLFFILPATHLEN); + + my_rig->state.rigport.parm.serial.rate = serial_rate; + +diff --git a/src/sendqrg.h b/src/sendqrg.h +index 8c53f2e..1ef85a6 100644 +--- a/src/sendqrg.h ++++ b/src/sendqrg.h +@@ -23,6 +23,16 @@ + + #include + ++#ifdef HAMLIB_FILPATHLEN ++ #define TLFFILPATHLEN HAMLIB_FILPATHLEN ++#else ++ #ifdef FILPATHLEN ++ #define TLFFILPATHLEN FILPATHLEN ++ #else ++ #error "(HAMLIB_)FILPATHLEN macro not found" ++ #endif ++#endif ++ + int init_tlf_rig(void); + void close_tlf_rig(RIG *my_rig); + +-- +2.32.0 + diff --git a/gnu/packages/radio.scm b/gnu/packages/radio.scm index 618b2cfeaa..991d2e3a2e 100644 --- a/gnu/packages/radio.scm +++ b/gnu/packages/radio.scm @@ -7,6 +7,7 @@ ;;; Copyright © 2020 Charlie Ritter ;;; Copyright © 2020, 2021 Tobias Geerinckx-Rice ;;; Copyright © 2021 João Pedro Simas +;;; Copyright © 2021 Jack Hill ;;; ;;; This file is part of GNU Guix. ;;; @@ -29,6 +30,7 @@ #:use-module (guix download) #:use-module (guix git-download) #:use-module (guix utils) + #:use-module (gnu packages) #:use-module (gnu packages admin) #:use-module (gnu packages algebra) #:use-module (gnu packages astronomy) @@ -68,6 +70,7 @@ #:use-module (gnu packages multiprecision) #:use-module (gnu packages ncurses) #:use-module (gnu packages networking) + #:use-module (gnu packages perl) #:use-module (gnu packages pkg-config) #:use-module (gnu packages pulseaudio) #:use-module (gnu packages python) @@ -1065,6 +1068,65 @@ users.") "--with-tcl-binding" "--with-xml-support"))))) +(define-public tlf + (package + (name "tlf") + (version "1.4.1") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/tlf/tlf") + (commit (string-append "tlf-" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "1xpgs4k27pjd9mianfknknp6mf34365bcp96wrv5xh4dhph573rj")) + (patches + (search-patches "tlf-support-hamlib-4.2+.patch")))) + (build-system gnu-build-system) + (arguments + '(#:configure-flags + (list "--enable-fldigi-xmlrpc"))) + (native-inputs + `(("autoconf" ,autoconf) + ("automake" ,automake) + ("perl" ,perl) + ("pkg-config" ,pkg-config))) + (inputs + `(("cmocka" ,cmocka) + ("glib" ,glib) + ("hamlib" ,hamlib) + ("libusb" ,libusb) ;`Requires.private: libusb-1.0` in hamlib pkg-config + ("ncurses" ,ncurses) + ("xmlrpc-c" ,xmlrpc-c))) + (home-page "https://tlf.github.io/") + (synopsis "Amateur radio contest logging for the terminal") + (description "TLF is a @acronym{Text User Interface, TUI} amateur radio +contest logging program. It integrates with radios supported by hamlib and +other ham radio programs like fldigi. Many contests are supported including: + +@itemize +@item CQWW (SO, M/S and M/M) +@item WPX (SO, M/S and M/M) +@item ARRL Sweepstakes (SO, M/S ) +@item EU SPRINT +@item EUHFC +@item ARRL-DX (both sides) +@item ARRL-FD +@item ARRL 10m +@item ARRL 160m +@item Region1 field day +@item SP DX contest +@item PACC (both sides) +@item NRAU - scandinavian +@item Wysiwyg mults mode (per band or per contest) +@item WAEDX +@end itemize + +It also supports connecting to DX clusters, log synchronization with other TLF +instances over the network, and general QSO and DXpedition logging.") + (license license:gpl2+))) + (define-public wsjtx (package (name "wsjtx") From 659cc959b3d028edb1e1f1d931ccc10983285f1d Mon Sep 17 00:00:00 2001 From: Pierre Neidhardt Date: Mon, 21 Jun 2021 09:00:59 +0200 Subject: [PATCH 038/144] gnu: Add forgotten ecl-stmx and cl-stmx definitions. * gnu/packages/lisp-xyz.scm (cl-ecl-stmx, ecl-ecl-stmx): New variables. --- gnu/packages/lisp-xyz.scm | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/gnu/packages/lisp-xyz.scm b/gnu/packages/lisp-xyz.scm index 1bd35d5812..2e95d5c694 100644 --- a/gnu/packages/lisp-xyz.scm +++ b/gnu/packages/lisp-xyz.scm @@ -17471,3 +17471,9 @@ Memory transactions give freedom from deadlocks, are immune to thread-safety bugs and race conditions, provide automatic roll-back on failure, and aim at resolving the tension between granularity and concurrency.") (license license:llgpl)))) + +(define-public ecl-stmx + (sbcl-package->ecl-package sbcl-stmx)) + +(define-public cl-stmx + (sbcl-package->cl-source-package sbcl-stmx)) From 9d48a179d19ffa32c3255bbc5c573afad0b2cc3a Mon Sep 17 00:00:00 2001 From: Pierre Neidhardt Date: Mon, 21 Jun 2021 09:14:04 +0200 Subject: [PATCH 039/144] gnu: Add binding-arrows. * gnu/packages/lisp-xyz.scm (cl-binding-arrows, ecl-binding-arrows, sbcl-binding-arrows): New variables. --- gnu/packages/lisp-xyz.scm | 37 +++++++++++++++++++++++++++++++++++++ 1 file changed, 37 insertions(+) diff --git a/gnu/packages/lisp-xyz.scm b/gnu/packages/lisp-xyz.scm index 2e95d5c694..f0073b80b9 100644 --- a/gnu/packages/lisp-xyz.scm +++ b/gnu/packages/lisp-xyz.scm @@ -17477,3 +17477,40 @@ resolving the tension between granularity and concurrency.") (define-public cl-stmx (sbcl-package->cl-source-package sbcl-stmx)) + +(define-public sbcl-binding-arrows + ;; Fork of sbcl-arrows that does not have a new tag. + (let ((commit "d19364ec8850880ed6e42078ccaa2ed9114dc83a") + (revision "1")) + (package + (name "sbcl-binding-arrows") + (version (git-version "1.0.0" revision commit)) + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/phoe/binding-arrows") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 "0hqikgzic7kjq2n1d924yldfm30qz67cmsk6gghi9cbmxkwdlwp8")))) + (build-system asdf-build-system/sbcl) + (native-inputs + `(("hu.dwim.stefil" ,sbcl-hu.dwim.stefil))) + (home-page "https://github.com/phoe/binding-arrows") + (synopsis "Threading macros based on binding anonymous variables") + (description + "This system implements binding threading macros -- a kind of threading +macros with different semantics than classical, Clojure core threading macros +or their extension, swiss-arrows. Two Common Lisp implementations of those are +@code{arrows} and @code{arrow-macros}. + +This system is a fork of @code{arrows} with changes in semantics that make it +impossible to merge back upstream.") + (license license:expat)))) + +(define-public ecl-binding-arrows + (sbcl-package->ecl-package sbcl-binding-arrows)) + +(define-public cl-binding-arrows + (sbcl-package->cl-source-package sbcl-binding-arrows)) From 9903342ac822c7e569e6b0425945cfacfb40c4e6 Mon Sep 17 00:00:00 2001 From: Pierre Neidhardt Date: Mon, 21 Jun 2021 09:41:10 +0200 Subject: [PATCH 040/144] gnu: Add atomics. * gnu/packages/lisp-xyz.scm (cl-atomics, ecl-atomics, sbcl-atomics): New variables. --- gnu/packages/lisp-xyz.scm | 35 +++++++++++++++++++++++++++++++++++ 1 file changed, 35 insertions(+) diff --git a/gnu/packages/lisp-xyz.scm b/gnu/packages/lisp-xyz.scm index f0073b80b9..f5a4f2f1de 100644 --- a/gnu/packages/lisp-xyz.scm +++ b/gnu/packages/lisp-xyz.scm @@ -17514,3 +17514,38 @@ impossible to merge back upstream.") (define-public cl-binding-arrows (sbcl-package->cl-source-package sbcl-binding-arrows)) + +(define-public sbcl-atomics + ;; No release in years. + (let ((commit "9ee0bdebcd2bb9b242671a75460db13fbf45454c") + (revision "1")) + (package + (name "sbcl-atomics") + (version (git-version "1.0.0" revision commit)) + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/Shinmera/atomics") + (commit commit))) + (file-name (git-file-name "atomics" version)) + (sha256 + (base32 "0mp5jdqq0aamdhgnvw149cqqi3zg7dkkibp25qi4rafw1fnpd40z")))) + (build-system asdf-build-system/sbcl) + (inputs + `(("documentation-utils" ,sbcl-documentation-utils))) + (native-inputs + `(("parachute" ,sbcl-parachute))) + (home-page "https://shinmera.github.io/atomics/") + (synopsis "Common Lisp portability layer for atomic operations") + (description + "This is a library for access to atomic operation primitives such as +compare-and-swap. It aims to be a rather thin layer over what the +implementations offer.") + (license license:zlib)))) + +(define-public ecl-atomics + (sbcl-package->ecl-package sbcl-atomics)) + +(define-public cl-atomics + (sbcl-package->cl-source-package sbcl-atomics)) From 3b45aa167dba93196bf0908e32f744b6b10734e5 Mon Sep 17 00:00:00 2001 From: Pierre Neidhardt Date: Mon, 21 Jun 2021 10:02:17 +0200 Subject: [PATCH 041/144] gnu: Add cl-mock. * gnu/packages/lisp-xyz.scm (cl-mock, ecl-cl-mock, sbcl-cl-mock): New variables. --- gnu/packages/lisp-xyz.scm | 35 +++++++++++++++++++++++++++++++++++ 1 file changed, 35 insertions(+) diff --git a/gnu/packages/lisp-xyz.scm b/gnu/packages/lisp-xyz.scm index f5a4f2f1de..83ca4c17ab 100644 --- a/gnu/packages/lisp-xyz.scm +++ b/gnu/packages/lisp-xyz.scm @@ -17549,3 +17549,38 @@ implementations offer.") (define-public cl-atomics (sbcl-package->cl-source-package sbcl-atomics)) + +(define-public sbcl-cl-mock + ;; .asd version only got updated recently, despired the old GitHug "1.0.1" release. + (let ((commit "7988dca2093358911b67597a2cd1570c785dfe76")) + (package + (name "sbcl-cl-mock") + (version (git-version "1.0.1" "1" commit)) + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/Ferada/cl-mock/") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 "0f40wikcf783jx26ip0nnhwjjfjvjiw7njqsqrb6kaphc8bgw0i1")))) + (build-system asdf-build-system/sbcl) + (inputs + `(("alexandria" ,sbcl-alexandria) + ("closer-mop" ,sbcl-closer-mop) + ("trivia" ,sbcl-trivia))) + (native-inputs + `(("fiveam" ,sbcl-fiveam))) + (home-page "https://github.com/Ferada/cl-mock") + (synopsis "Mocking functions for Common Lisp testing") + (description + "This small library provides a way to replace the actual implementation +of either regular or generic functions with mocks.") + (license license:agpl3)))) + +(define-public ecl-cl-mock + (sbcl-package->ecl-package sbcl-cl-mock)) + +(define-public cl-mock + (sbcl-package->cl-source-package sbcl-cl-mock)) From 40098148bdc0a6abe8d99dbcc6c9113661fd38e7 Mon Sep 17 00:00:00 2001 From: Pierre Neidhardt Date: Mon, 21 Jun 2021 11:11:36 +0200 Subject: [PATCH 042/144] gnu: Add cl-murmurhash. * gnu/packages/lisp-xyz.scm (cl-murmurhash, ecl-cl-murmurhash, sbcl-cl-murmurhash): New variables. --- gnu/packages/lisp-xyz.scm | 36 ++++++++++++++++++++++++++++++++++++ 1 file changed, 36 insertions(+) diff --git a/gnu/packages/lisp-xyz.scm b/gnu/packages/lisp-xyz.scm index 83ca4c17ab..e16ea33d0a 100644 --- a/gnu/packages/lisp-xyz.scm +++ b/gnu/packages/lisp-xyz.scm @@ -17584,3 +17584,39 @@ of either regular or generic functions with mocks.") (define-public cl-mock (sbcl-package->cl-source-package sbcl-cl-mock)) + +(define-public sbcl-cl-murmurhash + ;; No release. + (let ((commit "5433f5e95f1cce63a81259a471150834c6a59364") + (revision "1")) + (package + (name "sbcl-cl-murmurhash") + (version (git-version "0.0.0" revision commit)) + (home-page "https://github.com/ruricolist/cl-murmurhash/") + (source + (origin + (method git-fetch) + (uri (git-reference + (url home-page) + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "0251r0mpjm0y3qsm4lm7ncvrkxvgwc53spdm1p2mpayhvkkqqsws")))) + (build-system asdf-build-system/sbcl) + (inputs + `(("babel" ,sbcl-babel))) + (native-inputs + `(("fiveam" ,sbcl-fiveam))) + (synopsis "32-bit version of Murmurhash3 for Common Lisp") + (description + "This Common Lisp package offers an implementation of the 32-bit +variant of MurmurHash3 (@url{https://github.com/aappleby/smhasher}), a fast +non-crytographic hashing algorithm.") + (license license:expat)))) + +(define-public ecl-cl-murmurhash + (sbcl-package->ecl-package sbcl-cl-murmurhash)) + +(define-public cl-murmurhash + (sbcl-package->cl-source-package sbcl-cl-murmurhash)) From 008da15880c80a905e2b9e34e0f0abadb7eefda1 Mon Sep 17 00:00:00 2001 From: Pierre Neidhardt Date: Mon, 21 Jun 2021 11:14:10 +0200 Subject: [PATCH 043/144] gnu: Add cl-hamt. * gnu/packages/lisp-xyz.scm (cl-hamt, ecl-cl-hamt, sbcl-cl-hamt): New variables. --- gnu/packages/lisp-xyz.scm | 33 +++++++++++++++++++++++++++++++++ 1 file changed, 33 insertions(+) diff --git a/gnu/packages/lisp-xyz.scm b/gnu/packages/lisp-xyz.scm index e16ea33d0a..81bb1dad2e 100644 --- a/gnu/packages/lisp-xyz.scm +++ b/gnu/packages/lisp-xyz.scm @@ -17620,3 +17620,36 @@ non-crytographic hashing algorithm.") (define-public cl-murmurhash (sbcl-package->cl-source-package sbcl-cl-murmurhash)) + +(define-public sbcl-cl-hamt + ;; No release + (let ((commit "7a99eaaca1f952029def9ad5a2b80a612a712208")) + (package + (name "sbcl-cl-hamt") + (version (git-version "0.0.0" "1" commit)) + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/danshapero/cl-hamt/") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 "1ycbd73ykfj5j9sdhlzamyv18qbjj6xqf7fhm4fa0nsyr6sr3rf5")))) + (build-system asdf-build-system/sbcl) + (inputs + `(("cl-murmurhash" ,sbcl-cl-murmurhash))) + (native-inputs + `(("fiveam" ,sbcl-fiveam))) + (home-page "https://github.com/danshapero/cl-hamt") + (synopsis "Dictionary & set data structure using hash array-mapped tries") + (description + "This library provides purely functional dictionaries and sets in +Common Lisp based on the hash array-mapped trie data structure.") + (license license:bsd-3)))) + +(define-public ecl-cl-hamt + (sbcl-package->ecl-package sbcl-cl-hamt)) + +(define-public cl-hamt + (sbcl-package->cl-source-package sbcl-cl-hamt)) From 71c3f954194770956b39d311fab44ee6ddb4f666 Mon Sep 17 00:00:00 2001 From: Pierre Neidhardt Date: Mon, 21 Jun 2021 11:17:37 +0200 Subject: [PATCH 044/144] gnu: Add cl-gserver. * gnu/packages/lisp-xyz.scm (cl-gserver, ecl-cl-gserver, sbcl-cl-gserver): New variables. --- gnu/packages/lisp-xyz.scm | 42 +++++++++++++++++++++++++++++++++++++++ 1 file changed, 42 insertions(+) diff --git a/gnu/packages/lisp-xyz.scm b/gnu/packages/lisp-xyz.scm index 81bb1dad2e..f2fe9c93d1 100644 --- a/gnu/packages/lisp-xyz.scm +++ b/gnu/packages/lisp-xyz.scm @@ -17653,3 +17653,45 @@ Common Lisp based on the hash array-mapped trie data structure.") (define-public cl-hamt (sbcl-package->cl-source-package sbcl-cl-hamt)) + +(define-public sbcl-cl-gserver + (package + (name "sbcl-cl-gserver") + (version "1.7.2") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/mdbergmann/cl-gserver") + (commit version))) + (file-name (git-file-name "cl-gserver" version)) + (sha256 + (base32 "1vkxs6ybi1pkpji2crmhq8c71zg0dn2ji0lcwhs0rivphz5jxk24")))) + (build-system asdf-build-system/sbcl) + (inputs + `(("alexandria" ,sbcl-alexandria) + ("bordeaux-threads" ,sbcl-bordeaux-threads) + ("lparallel" ,sbcl-lparallel) + ("cl-speedy-queue" ,sbcl-cl-speedy-queue) + ("log4cl" ,sbcl-log4cl) + ("str" ,sbcl-cl-str) + ("blackbird" ,sbcl-blackbird) + ("cl-hamt" ,sbcl-cl-hamt) + ("binding-arrows" ,sbcl-binding-arrows) + ("atomics" ,sbcl-atomics))) + (native-inputs + `(("fiveam" ,sbcl-fiveam) + ("mock" ,sbcl-cl-mock))) + (home-page "https://mdbergmann.github.io/cl-gserver/index.html") + (synopsis "Actor framework for easy access to state and async operations") + (description + "@code{cl-gserver} is a 'message passing' library / framework with actors +similar to Erlang or Akka. It supports creating reactive systems for parallel +computing and event based message handling.") + (license license:agpl3))) + +(define-public ecl-cl-gserver + (sbcl-package->ecl-package sbcl-cl-gserver)) + +(define-public cl-gserver + (sbcl-package->cl-source-package sbcl-cl-gserver)) From bf0f9dd051919f1f66d7f48b1724a1e4a0e37795 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 21 Jun 2021 12:15:52 +0200 Subject: [PATCH 045/144] gnu: apache-arrow: Update to 4.0.1. * gnu/packages/databases.scm (apache-arrow): Update to 4.0.1. [arguments]: Remove trailing boolean; ensure that xsimd is not downloaded and built anew. [inputs]: Add xsimd. --- gnu/packages/databases.scm | 14 +++++++++----- 1 file changed, 9 insertions(+), 5 deletions(-) diff --git a/gnu/packages/databases.scm b/gnu/packages/databases.scm index f90b6e1bd8..e963789695 100644 --- a/gnu/packages/databases.scm +++ b/gnu/packages/databases.scm @@ -81,6 +81,7 @@ #:use-module (gnu packages check) #:use-module (gnu packages cmake) #:use-module (gnu packages compression) + #:use-module (gnu packages cpp) #:use-module (gnu packages crypto) #:use-module (gnu packages curl) #:use-module (gnu packages cyrus-sasl) @@ -3655,7 +3656,7 @@ the SQL language using a syntax that reflects the resulting query.") (define-public apache-arrow (package (name "apache-arrow") - (version "3.0.0") + (version "4.0.1") (source (origin (method git-fetch) @@ -3665,21 +3666,22 @@ the SQL language using a syntax that reflects the resulting query.") (file-name (git-file-name name version)) (sha256 (base32 - "03ngddh3r1g6f9aja2jlfksgvgyzmxmfy4bxvzjrcv5fvl5x8ii0")))) + "1lcd9gdpwlrr92rm812a5p4l6zx0arwd0zj72a4ga699s1psz8yv")))) (build-system cmake-build-system) (arguments `(#:tests? #f #:phases (modify-phases %standard-phases (add-before 'configure 'enter-source-directory - (lambda _ (chdir "cpp") #t)) + (lambda _ (chdir "cpp"))) (add-after 'unpack 'set-env (lambda _ + (substitute* "cpp/cmake_modules/ThirdpartyToolchain.cmake" + (("set\\(xsimd_SOURCE.*") "")) (setenv "BOOST_ROOT" (assoc-ref %build-inputs "boost")) (setenv "BROTLI_HOME" (assoc-ref %build-inputs "brotli")) (setenv "FLATBUFFERS_HOME" (assoc-ref %build-inputs "flatbuffers")) - (setenv "RAPIDJSON_HOME" (assoc-ref %build-inputs "rapidjson")) - #t))) + (setenv "RAPIDJSON_HOME" (assoc-ref %build-inputs "rapidjson"))))) #:build-type "Release" #:configure-flags (list "-DARROW_PYTHON=ON" @@ -3701,6 +3703,7 @@ the SQL language using a syntax that reflects the resulting query.") ;; function, or using pkg-config for packages that do not ;; have this feature "-DARROW_DEPENDENCY_SOURCE=SYSTEM" + "-Dxsimd_SOURCE=SYSTEM" ;; Split output into its component packages. (string-append "-DCMAKE_INSTALL_PREFIX=" @@ -3759,6 +3762,7 @@ the SQL language using a syntax that reflects the resulting query.") ("re2" ,re2) ("snappy" ,snappy) ("utf8proc" ,utf8proc) + ("xsimd" ,xsimd) ("zlib" ,zlib) ("zstd" ,zstd "lib"))) (native-inputs From 42d8257e03f8ba89313c0fa298eb7e9d53c63811 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 21 Jun 2021 12:16:36 +0200 Subject: [PATCH 046/144] gnu: r-arrow: Add arrow libraries. * gnu/packages/cran.scm (r-arrow)[inputs]: Add the lib output of apache-arrow. --- gnu/packages/cran.scm | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index e01b2417d2..f8c2258c34 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -17760,7 +17760,8 @@ colored by the number of neighboring points. This is useful to visualize the (properties `((upstream-name . "arrow"))) (build-system r-build-system) (inputs - `(("zlib" ,zlib))) + `(("apache-arrow" ,apache-arrow "lib") + ("zlib" ,zlib))) (propagated-inputs `(("r-assertthat" ,r-assertthat) ("r-bit64" ,r-bit64) From 38d829cf24cd56499dcc1010c9c40bc8dc93ab18 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 21 Jun 2021 12:25:21 +0200 Subject: [PATCH 047/144] gnu: python-argh: Remove python-tox. * gnu/packages/python-xyz.scm (python-argh)[propagated-inputs]: Remove python-tox. --- gnu/packages/python-xyz.scm | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index bb263a6f20..7270aefa1b 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -22805,8 +22805,7 @@ standard error channel (stderr) in your program.") ("python-mock" ,python-mock) ("python-pytest" ,python-pytest) ("python-pytest-cov" ,python-pytest-cov) - ("python-pytest-xdist" ,python-pytest-xdist) - ("python-tox" ,python-tox))) + ("python-pytest-xdist" ,python-pytest-xdist))) (home-page "https://github.com/neithere/argh/") (synopsis "Argparse wrapper with natural syntax") (description From 8a62d8685af8eb0b913c86a9a664692fa3399bc0 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 21 Jun 2021 13:02:39 +0200 Subject: [PATCH 048/144] gnu: Add python-iced. * gnu/packages/bioinformatics.scm (python-iced): New variable. --- gnu/packages/bioinformatics.scm | 24 ++++++++++++++++++++++++ 1 file changed, 24 insertions(+) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 7a1c8cc8e3..85d4e5a185 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -11957,6 +11957,30 @@ options), bedgraph, links (represented as arcs), and Hi-C matrices. pyGenomeTracks can make plots with or without Hi-C data.") (license license:gpl3+))) +(define-public python-iced + (package + (name "python-iced") + (version "0.5.8") + (source + (origin + (method url-fetch) + (uri (pypi-uri "iced" version)) + (sha256 + (base32 + "1avcjmpyyvhgbj5qca4l70ipiz7j3xmcw9p6rd9c06j99faa0r71")))) + (build-system python-build-system) + (arguments `(#:tests? #false)) ; there are none + (propagated-inputs + `(("python-numpy" ,python-numpy) + ("python-pandas" ,python-pandas) + ("python-scipy" ,python-scipy) + ("python-scikit-learn" ,python-scikit-learn))) + (home-page "https://github.com/hiclib/iced") + (synopsis "ICE normalization") + (description "This is a package for normalizing Hi-C contact counts +efficiently.") + (license license:bsd-3))) + (define-public python-hic2cool (package (name "python-hic2cool") From 7e2afc6ac33ffbedd4c3bff2edf1c2e8d523785e Mon Sep 17 00:00:00 2001 From: Sergey Trofimov Date: Thu, 17 Jun 2021 07:31:11 +0200 Subject: [PATCH 049/144] gnu: moreutils: Remove obsolete source uri. * gnu/packages/moreutils.scm (moreutils): Remove obsolete origin uri as it returns 404. Signed-off-by: Efraim Flashner --- gnu/packages/moreutils.scm | 10 +++------- 1 file changed, 3 insertions(+), 7 deletions(-) diff --git a/gnu/packages/moreutils.scm b/gnu/packages/moreutils.scm index 9e3bf0fc29..47bda32126 100644 --- a/gnu/packages/moreutils.scm +++ b/gnu/packages/moreutils.scm @@ -34,13 +34,9 @@ (source (origin (method url-fetch) - (uri (list - (string-append - "https://git.joeyh.name/index.cgi/moreutils.git/snapshot/" - name "-" version ".tar.gz") - (string-append - "http://drabczyk.org/" - name "-" version ".tar.gz"))) + (uri (string-append + "https://git.joeyh.name/index.cgi/moreutils.git/snapshot/" + name "-" version ".tar.gz")) (sha256 (base32 "10c8b4bwnli4gxwvgmgkc5kin1ksrxsnxmigs7y4rrh4aaszdjb0")))) (build-system gnu-build-system) From 5e6abeee989db65fb235e76b64b2f3f0e3bb7d74 Mon Sep 17 00:00:00 2001 From: Vinicius Monego Date: Sun, 25 Apr 2021 18:15:01 +0000 Subject: [PATCH 050/144] gnu: mlt: Update license. * gnu/packages/video.scm (mlt)[license]: Change from gpl3 to lgpl2.1+. Signed-off-by: Efraim Flashner --- gnu/packages/video.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/video.scm b/gnu/packages/video.scm index 6e6f84ec68..55d1967444 100644 --- a/gnu/packages/video.scm +++ b/gnu/packages/video.scm @@ -42,7 +42,7 @@ ;;; Copyright © 2020 Guillaume Le Vaillant ;;; Copyright © 2020 Alex McGrath ;;; Copyright © 2020, 2021 Michael Rohleder -;;; Copyright © 2020 Vinicius Monego +;;; Copyright © 2020, 2021 Vinicius Monego ;;; Copyright © 2020 Brett Gilio ;;; Copyright © 2020 Alexandru-Sergiu Marton ;;; Copyright © 2020 Ivan Kozlov @@ -3041,7 +3041,7 @@ broadcasting. It provides a toolkit for broadcasters, video editors, media players, transcoders, web streamers and many more types of applications. The functionality of the system is provided via an assortment of ready to use tools, XML authoring components, and an extensible plug-in based API.") - (license license:gpl3))) + (license license:lgpl2.1+))) (define-public v4l-utils (package From 6b183cd47d620428f0286faa6fdeffcdd89e9a77 Mon Sep 17 00:00:00 2001 From: Vinicius Monego Date: Sun, 25 Apr 2021 18:17:22 +0000 Subject: [PATCH 051/144] gnu: mlt: Update to 6.26.1. * gnu/packages/video.scm (mlt): Update to 6.26.1. Signed-off-by: Efraim Flashner --- gnu/packages/video.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/video.scm b/gnu/packages/video.scm index 55d1967444..04c79dffb5 100644 --- a/gnu/packages/video.scm +++ b/gnu/packages/video.scm @@ -2984,7 +2984,7 @@ from sites like Twitch.tv and pipes them into a video player of choice.") (define-public mlt (package (name "mlt") - (version "6.22.1") + (version "6.26.1") (source (origin (method git-fetch) (uri (git-reference @@ -2993,7 +2993,7 @@ from sites like Twitch.tv and pipes them into a video player of choice.") (file-name (git-file-name name version)) (sha256 (base32 - "0jxv848ykw0csbnayrd710ylw46m0picfv7rpzsxz1vh4jzs395k")))) + "1gz79xvs5jrzqhwhfk0dqdd3xiavnjp4q957h7nb02rij32byb39")))) (build-system gnu-build-system) (arguments `(#:tests? #f ; no tests From 49e8fa4a3d0e170788338dea9a5d2e2fd33adec1 Mon Sep 17 00:00:00 2001 From: Vinicius Monego Date: Sun, 25 Apr 2021 18:17:23 +0000 Subject: [PATCH 052/144] gnu: mlt: Add optional dependencies. * gnu/packages/video.scm (mlt)[inputs]: Add alsa-plugins:pulseaudio, libebur128, rtaudio, sdl2, sdl2-image, sox, vidstab. Remove sdl. Signed-off-by: Efraim Flashner --- gnu/packages/video.scm | 9 +++++++-- 1 file changed, 7 insertions(+), 2 deletions(-) diff --git a/gnu/packages/video.scm b/gnu/packages/video.scm index 04c79dffb5..987d75f0b7 100644 --- a/gnu/packages/video.scm +++ b/gnu/packages/video.scm @@ -3014,6 +3014,7 @@ from sites like Twitch.tv and pipes them into a video player of choice.") #t))))) (inputs `(("alsa-lib" ,alsa-lib) + ("alsa-plugins" ,alsa-plugins "pulseaudio") ("ffmpeg" ,ffmpeg) ("fftw" ,fftw) ("frei0r-plugins" ,frei0r-plugins) @@ -3022,6 +3023,7 @@ from sites like Twitch.tv and pipes them into a video player of choice.") ("libxml2" ,libxml2) ("jack" ,jack-1) ("ladspa" ,ladspa) + ("libebur128" ,libebur128) ("libexif" ,libexif) ("libvorbis" ,libvorbis) ("rubberband" ,rubberband) @@ -3029,8 +3031,11 @@ from sites like Twitch.tv and pipes them into a video player of choice.") ("pulseaudio" ,pulseaudio) ("qtbase" ,qtbase-5) ("qtsvg" ,qtsvg) - ("sdl" ,sdl) - ("sox" ,sox))) + ("rtaudio" ,rtaudio) + ("sdl2" ,sdl2) + ("sdl2-image" ,sdl2-image) + ("sox" ,sox) + ("vidstab" ,vidstab))) (native-inputs `(("pkg-config" ,pkg-config))) (home-page "https://www.mltframework.org/") From 0b1cf40dce8e2f2d8651a2a2dc00cfb7026c8014 Mon Sep 17 00:00:00 2001 From: Vinicius Monego Date: Sun, 25 Apr 2021 18:17:24 +0000 Subject: [PATCH 053/144] gnu: Add shotcut. * gnu/packages/video.scm (shotcut): New variable. Signed-off-by: Efraim Flashner --- gnu/packages/video.scm | 77 ++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 77 insertions(+) diff --git a/gnu/packages/video.scm b/gnu/packages/video.scm index 987d75f0b7..444eee849e 100644 --- a/gnu/packages/video.scm +++ b/gnu/packages/video.scm @@ -86,6 +86,7 @@ #:use-module (guix build-system meson) #:use-module (guix build-system perl) #:use-module (guix build-system python) + #:use-module (guix build-system qt) #:use-module (guix build-system waf) #:use-module (guix build-system trivial) #:use-module (gnu packages) @@ -4607,6 +4608,82 @@ helps you create the film you have always dreamed of. Easily add sub-titles, transitions, and effects and then export your film to many common formats.") (license license:gpl3+))) +(define-public shotcut + (package + (name "shotcut") + (version "21.03.21") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/mltframework/shotcut") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "0jb488vynn0vmq22z51bg4hb4617732nva9rg52lzl89v5n8gmsi")))) + (build-system qt-build-system) + (arguments + `(#:tests? #f ;there are no tests + #:phases + (modify-phases %standard-phases + (replace 'configure + (lambda* (#:key outputs #:allow-other-keys) + (let* ((out (assoc-ref outputs "out"))) + (invoke "qmake" + (string-append "PREFIX=" out) + "QMAKE_LRELEASE=lrelease" + "QMAKE_LUPDATE=lupdate" + "shotcut.pro")))) + (add-after 'install 'wrap-executable + (lambda* (#:key inputs outputs #:allow-other-keys) + (let* ((out (assoc-ref outputs "out")) + (frei0r (assoc-ref inputs "frei0r-plugins")) + (ffmpeg (assoc-ref inputs "ffmpeg")) + (jack (assoc-ref inputs "jack")) + (sdl2 (assoc-ref inputs "sdl2"))) + (wrap-program (string-append out "/bin/shotcut") + `("PATH" ":" prefix + ,(list (string-append ffmpeg "/bin"))) + `("LD_LIBRARY_PATH" ":" prefix + ,(list (string-append jack "/lib" ":" sdl2 "/lib"))) + `("FREI0R_PATH" ":" = + (,(string-append frei0r "/lib/frei0r-1/"))) + `("MLT_PREFIX" ":" = + (,(assoc-ref inputs "mlt"))))) + #t))))) + (native-inputs + `(("pkg-config" ,pkg-config) + ("python" ,python-wrapper) + ("qttools" ,qttools))) + (inputs + `(("ffmpeg" ,ffmpeg) + ("frei0r-plugins" ,frei0r-plugins) + ("jack" ,jack-1) + ("ladspa" ,ladspa) + ("lame" ,lame) + ("libvpx" ,libvpx) + ("libx264" ,libx264) + ("mlt" ,mlt) + ("pulseaudio" ,pulseaudio) + ("qtbase" ,qtbase-5) + ("qtdeclarative" ,qtdeclarative) + ("qtgraphicaleffects" ,qtgraphicaleffects) + ("qtmultimedia" ,qtmultimedia) + ("qtquickcontrols" ,qtquickcontrols) + ("qtquickcontrols2" ,qtquickcontrols2) + ("qtsvg" ,qtsvg) + ("qtwebkit" ,qtwebkit) + ("qtwebsockets" ,qtwebsockets) + ("qtx11extras" ,qtx11extras) + ("sdl2" ,sdl2))) + (home-page "https://www.shotcut.org/") + (synopsis "Video editor built on the MLT framework") + (description + "Shotcut is a video editor built on the MLT framework. Features include +a wide range of formats through @code{ffmpeg}, 4k resolution support, webcam +and audio capture, network stream playback, and many more.") + (license license:gpl3+))) + (define-public dav1d (package (name "dav1d") From 5506b841d18fa415321c22b7e2b7eec9f6ce50d9 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Mon, 21 Jun 2021 17:08:14 +0300 Subject: [PATCH 054/144] gnu: mlt: Don't hardcode gcc value. * gnu/packages/video.scm (mlt)[arguments]: Adjust make-flags to use cc-for-target, cxx-for-target. --- gnu/packages/video.scm | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/gnu/packages/video.scm b/gnu/packages/video.scm index 444eee849e..fbc468eab7 100644 --- a/gnu/packages/video.scm +++ b/gnu/packages/video.scm @@ -2998,7 +2998,8 @@ from sites like Twitch.tv and pipes them into a video player of choice.") (build-system gnu-build-system) (arguments `(#:tests? #f ; no tests - #:make-flags '("CC=gcc" "CXX=g++") + #:make-flags '(,(string-append "CC=" (cc-for-target)) + ,(string-append "CXX=" (cxx-for-target))) #:configure-flags (list "--enable-gpl3" "--enable-gpl") From 6acc04eca75fccd517e33b9aa7f5a02a300ec74a Mon Sep 17 00:00:00 2001 From: Jack Hill Date: Fri, 23 Apr 2021 16:05:06 -0400 Subject: [PATCH 055/144] gnu: Add eovim. * gnu/packages/vim (eovim): New variable. Signed-off-by: Efraim Flashner --- gnu/packages/vim.scm | 45 +++++++++++++++++++++++++++++++++++++++++++- 1 file changed, 44 insertions(+), 1 deletion(-) diff --git a/gnu/packages/vim.scm b/gnu/packages/vim.scm index 238c25d486..7a37162116 100644 --- a/gnu/packages/vim.scm +++ b/gnu/packages/vim.scm @@ -8,7 +8,7 @@ ;;; Copyright © 2019 HiPhish ;;; Copyright © 2019 Julien Lepiller ;;; Copyright © 2019, 2020 Jakub Kądziołka -;;; Copyright © 2020 Jack Hill +;;; Copyright © 2020, 2021 Jack Hill ;;; Copyright © 2021 Simon Tournier ;;; Copyright © 2021 Tissevert ;;; @@ -43,6 +43,7 @@ #:use-module (gnu packages attr) #:use-module (gnu packages autotools) #:use-module (gnu packages base) + #:use-module (gnu packages enlightenment) #:use-module (gnu packages fontutils) #:use-module (gnu packages gawk) #:use-module (gnu packages gettext) @@ -746,6 +747,48 @@ refactor Vim in order to: ;; except for parts that were contributed under the Vim license. (license (list license:asl2.0 license:vim)))) +(define-public eovim + (package + (name "eovim") + (version "0.2.0") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/jeanguyomarch/eovim/") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "06b7crmz3wvvq15ncl0jk20s8j1pmna2jin0k5y5n5qxpafbgp3k")))) + (build-system cmake-build-system) + (arguments + '(#:tests? #false ;no tests + #:phases + (modify-phases %standard-phases + (add-after 'configure 'reference-nvim + (lambda* (#:key inputs #:allow-other-keys) + (let ((nvim (string-append (assoc-ref inputs "neovim") + "/bin/nvim"))) + ;; This substitution should change one line, and replaces the default + ;; value in the struct of options with an absolute store reference. + (substitute* "../source/src/main.c" + (("(^[[:blank:]]+\\.nvim = \")nvim" _ start) + (string-append start nvim)))))) + (add-before 'build 'set-home + (lambda _ (setenv "HOME" "/tmp")))))) + (native-inputs + `(("pkg-config" ,pkg-config))) + (inputs + `(("efl" ,efl) + ("msgpack" ,msgpack) + ("neovim" ,neovim))) + (home-page "https://github.com/jeanguyomarch/eovim/") + (synopsis "EFL GUI for Neovim") + (description "Graphical Neovim interface based on the @acronym{EFL, Enlightenment +Foundation Libraries} toolkit. Its features include customizable appearance +and support for fonts with ligatures.") + (license license:expat))) + (define-public vifm (package (name "vifm") From 91defaf245aad937a604c0549bcb3652252241ab Mon Sep 17 00:00:00 2001 From: Andreas Enge Date: Mon, 21 Jun 2021 16:44:26 +0200 Subject: [PATCH 056/144] gnu: mpfrcx: Update to 0.6.2. * gnu/packages/algebra.scm (mpfrcx): Update to 0.6.2. --- gnu/packages/algebra.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/algebra.scm b/gnu/packages/algebra.scm index d8ed9e8f1e..e7938b45db 100644 --- a/gnu/packages/algebra.scm +++ b/gnu/packages/algebra.scm @@ -76,7 +76,7 @@ (define-public mpfrcx (package (name "mpfrcx") - (version "0.6.1") + (version "0.6.2") (source (origin (method url-fetch) (uri (string-append @@ -84,7 +84,7 @@ version ".tar.gz")) (sha256 (base32 - "0gk2l40awp3q1lh828dhcjshcldy3b1l2v51glaq0lj1h7w34sin")))) + "165syd6kihwp6bry9hvr3v0908cgadsz5w5h5ry4mjnchrklnb7w")))) (build-system gnu-build-system) (propagated-inputs `(("gmp" ,gmp) From cfe79af7e6798e26d4676cd0158ba37b80370665 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Mon, 21 Jun 2021 18:01:54 +0300 Subject: [PATCH 057/144] gnu: rust-openssl-sys-0.9: Update to 0.9.64. * gnu/packages/crates-io.scm (rust-openssl-sys-0.9): Update to 0.9.64. --- gnu/packages/crates-io.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/crates-io.scm b/gnu/packages/crates-io.scm index ecdc813292..930ab5d4e4 100644 --- a/gnu/packages/crates-io.scm +++ b/gnu/packages/crates-io.scm @@ -29687,14 +29687,14 @@ system for OpenSSL.") (define-public rust-openssl-sys-0.9 (package (name "rust-openssl-sys") - (version "0.9.60") + (version "0.9.64") (source (origin (method url-fetch) (uri (crate-uri "openssl-sys" version)) (file-name (string-append name "-" version ".tar.gz")) (sha256 - (base32 "1rpkfl0rmdcvxzyzp3n24g9clplh4avgzpi5c2a3hx96hcccf7wj")) + (base32 "1bsim2zk69q1dw6rixn48l1ci8bmz5kvbkgsks2ci079w0pzr7i0")) (patches (search-patches "rust-openssl-sys-no-vendor.patch")))) (build-system cargo-build-system) (arguments From 5c9f614e699342e9e8afb38287c089e6282a99a1 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 21 Jun 2021 14:37:46 +0200 Subject: [PATCH 058/144] gnu: python-aws-sam-translator: Update to 1.36.0. * gnu/packages/python-web.scm (python-aws-sam-translator): Update to 1.36.0. --- gnu/packages/python-web.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/python-web.scm b/gnu/packages/python-web.scm index 86a732fa1b..43454d4b59 100644 --- a/gnu/packages/python-web.scm +++ b/gnu/packages/python-web.scm @@ -362,13 +362,13 @@ WSGI. This package includes libraries for implementing ASGI servers.") (define-public python-aws-sam-translator (package (name "python-aws-sam-translator") - (version "1.30.1") + (version "1.36.0") (source (origin (method url-fetch) (uri (pypi-uri "aws-sam-translator" version)) (sha256 (base32 - "0d9ppd94x2kw404m49ajswmmxgdngbs4p5ajyrdvnlivfzqbv7dx")))) + "115mcbb4r205c1hln199llqrvvbijfqz075rwx991l99jc6rj6zs")))) (build-system python-build-system) (arguments `(;; XXX: Tests are not distributed with the PyPI archive, and would From ac02d423d3fcb11048ee2e4a02626fca40cf1419 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 21 Jun 2021 14:38:00 +0200 Subject: [PATCH 059/144] gnu: python-pyyaml: Update to 5.4.1. * gnu/packages/python-xyz.scm (python-pyyaml): Update to 5.4.1. --- gnu/packages/python-xyz.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 7270aefa1b..1268ff257a 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -3551,14 +3551,14 @@ environments and back.") (define-public python-pyyaml (package (name "python-pyyaml") - (version "5.3.1") + (version "5.4.1") (source (origin (method url-fetch) (uri (pypi-uri "PyYAML" version)) (sha256 (base32 - "0pb4zvkfxfijkpgd1b86xjsqql97ssf1knbd1v53wkg1qm9cgsmq")))) + "0pm440pmpvgv5rbbnm8hk4qga5a292kvlm1bh3x2nwr8pb5p8xv0")))) (build-system python-build-system) (inputs `(("libyaml" ,libyaml))) From 35b31a18beed9b0492d0eb09d03927c30e7b23f9 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 21 Jun 2021 14:38:06 +0200 Subject: [PATCH 060/144] gnu: python-cfn-lint: Update to 0.51.0. * gnu/packages/python-web.scm (python-cfn-lint): Update to 0.51.0. [arguments]: Delete another test that attempts to access the internet. --- gnu/packages/python-web.scm | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/gnu/packages/python-web.scm b/gnu/packages/python-web.scm index 43454d4b59..d0a4ee9c16 100644 --- a/gnu/packages/python-web.scm +++ b/gnu/packages/python-web.scm @@ -465,7 +465,7 @@ emit information from within their applications to the AWS X-Ray service.") (define-public python-cfn-lint (package (name "python-cfn-lint") - (version "0.41.0") + (version "0.51.0") (home-page "https://github.com/aws-cloudformation/cfn-python-lint") (source (origin (method git-fetch) @@ -475,7 +475,7 @@ emit information from within their applications to the AWS X-Ray service.") (file-name (git-file-name name version)) (sha256 (base32 - "0nqs0fmj3hd7pnd9hkb4z57jvi2iv82hh6n3xxba6i6p8zgx75q4")))) + "1027s243sik25c6sqw6gla7k7vl3jdicrik5zdsa8pafxh2baja4")))) (build-system python-build-system) (arguments `(#:phases (modify-phases %standard-phases @@ -486,6 +486,8 @@ emit information from within their applications to the AWS X-Ray service.") ;; to avoid a dependency on 'git'. (delete-file "test/unit/module/maintenance/test_update_documentation.py") + (delete-file + "test/unit/module/maintenance/test_update_resource_specs.py") (setenv "PYTHONPATH" (string-append "./build/lib:" (getenv "PYTHONPATH"))) From 111aa862ec204f619143ffc93c0c55560916b294 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 21 Jun 2021 17:20:12 +0200 Subject: [PATCH 061/144] gnu: r-monocle3: Add missing input. * gnu/packages/bioconductor.scm (r-monocle3)[propagated-inputs]: Add r-assertthat. --- gnu/packages/bioconductor.scm | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 35fb43b3cd..6845894e97 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -6313,7 +6313,8 @@ qPCR data, but could be used with other types as well.") "1cjxqfw3qvy269hsf5v80d4kshl932wrl949iayas02saj6f70ls")))) (build-system r-build-system) (propagated-inputs - `(("r-biobase" ,r-biobase) + `(("r-assertthat" ,r-assertthat) + ("r-biobase" ,r-biobase) ("r-biocgenerics" ,r-biocgenerics) ("r-delayedmatrixstats" ,r-delayedmatrixstats) ("r-dplyr" ,r-dplyr) From 278e1c090e8b567169934de293649abf268eae53 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 21 Jun 2021 17:51:27 +0200 Subject: [PATCH 062/144] gnu: Add r-residualmatrix. * gnu/packages/bioconductor.scm (r-residualmatrix): New variable. --- gnu/packages/bioconductor.scm | 31 +++++++++++++++++++++++++++++++ 1 file changed, 31 insertions(+) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 6845894e97..1d4a033038 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -6205,6 +6205,37 @@ classification (assignment) methods. It also contains a Shiny application for interactive exploration of results.") (license license:gpl2+))) +(define-public r-residualmatrix + (package + (name "r-residualmatrix") + (version "1.2.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "ResidualMatrix" version)) + (sha256 + (base32 + "0p7va19aw0j6anx7ck879kbi5cn7dy712h5ia94adr38ssismv1v")))) + (properties + `((upstream-name . "ResidualMatrix"))) + (build-system r-build-system) + (propagated-inputs + `(("r-delayedarray" ,r-delayedarray) + ("r-matrix" ,r-matrix) + ("r-s4vectors" ,r-s4vectors))) + (native-inputs + `(("r-knitr" ,r-knitr))) + (home-page "https://github.com/LTLA/ResidualMatrix") + (synopsis "Create a DelayedMatrix of regression residuals") + (description + "This package implements tools for delayed computation of a matrix of +residuals after fitting a linear model to each column of an input matrix. It +also supports partial computation of residuals where selected factors are to +be preserved in the output matrix. It implements a number of efficient +methods for operating on the delayed matrix of residuals, most notably matrix +multiplication and calculation of row/column sums or means.") + (license license:gpl3))) + (define-public r-mast (package (name "r-mast") From a41bddd29d60ba37ce13f3f34b466ae8008db27e Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 21 Jun 2021 17:51:43 +0200 Subject: [PATCH 063/144] gnu: Add r-batchelor. * gnu/packages/bioconductor.scm (r-batchelor): New variable. --- gnu/packages/bioconductor.scm | 43 +++++++++++++++++++++++++++++++++++ 1 file changed, 43 insertions(+) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 1d4a033038..fd9d80cbdf 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -6236,6 +6236,49 @@ methods for operating on the delayed matrix of residuals, most notably matrix multiplication and calculation of row/column sums or means.") (license license:gpl3))) +(define-public r-batchelor + (package + (name "r-batchelor") + (version "1.8.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "batchelor" version)) + (sha256 + (base32 + "1xm204wp3m3mmlc1s59lscbbjvwm5nj32vvf16njcg7pb32lsiqa")))) + (properties `((upstream-name . "batchelor"))) + (build-system r-build-system) + (propagated-inputs + `(("r-beachmat" ,r-beachmat) + ("r-biocgenerics" ,r-biocgenerics) + ("r-biocneighbors" ,r-biocneighbors) + ("r-biocparallel" ,r-biocparallel) + ("r-biocsingular" ,r-biocsingular) + ("r-delayedarray" ,r-delayedarray) + ("r-delayedmatrixstats" ,r-delayedmatrixstats) + ("r-igraph" ,r-igraph) + ("r-matrix" ,r-matrix) + ("r-rcpp" ,r-rcpp) + ("r-residualmatrix" ,r-residualmatrix) + ("r-s4vectors" ,r-s4vectors) + ("r-scaledmatrix" ,r-scaledmatrix) + ("r-scuttle" ,r-scuttle) + ("r-singlecellexperiment" ,r-singlecellexperiment) + ("r-summarizedexperiment" ,r-summarizedexperiment))) + (native-inputs `(("r-knitr" ,r-knitr))) + (home-page "https://bioconductor.org/packages/batchelor") + (synopsis "Single-Cell Batch Correction Methods") + (description + "This package implements a variety of methods for batch correction of +single-cell (RNA sequencing) data. This includes methods based on detecting +mutually nearest neighbors, as well as several efficient variants of linear +regression of the log-expression values. Functions are also provided to +perform global rescaling to remove differences in depth between batches, and +to perform a principal components analysis that is robust to differences in +the numbers of cells across batches.") + (license license:gpl3))) + (define-public r-mast (package (name "r-mast") From 7209beb694401a0a180c43e11f1d7efd9807aafc Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 21 Jun 2021 17:52:00 +0200 Subject: [PATCH 064/144] gnu: Add r-leidenbase. * gnu/packages/bioconductor.scm (r-leidenbase): New variable. --- gnu/packages/bioconductor.scm | 34 ++++++++++++++++++++++++++++++++++ 1 file changed, 34 insertions(+) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index fd9d80cbdf..f218fd1285 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -6371,6 +6371,40 @@ tasks on single cell expression data. It is designed to work with RNA-Seq and qPCR data, but could be used with other types as well.") (license license:artistic2.0))) +(define-public r-leidenbase + (let ((commit "430f22af6982cc7d2e6e77f6b0df47bc970dcbce") + (revision "1")) + (package + (name "r-leidenbase") + (version (git-version "0.1.3" revision commit)) + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/cole-trapnell-lab/leidenbase") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "0ylqsmdpv4xq6f6ldxvwkhk33a9i1jcgk60zvksk3iplykfzd6c0")))) + (properties `((upstream-name . "leidenbase"))) + (build-system r-build-system) + (inputs + `(("zlib" ,zlib))) + (native-inputs + `(("gfortran" ,gfortran))) + (propagated-inputs + `(("r-igraph" ,r-igraph))) + (home-page "https://github.com/cole-trapnell-lab/leidenbase") + (synopsis "R and C wrappers to run the Leiden find_partition function") + (description + "This package provides an R to C interface that runs the Leiden +community detection algorithm to find a basic partition. It runs the +equivalent of the @code{find_partition} function. This package includes the +required source code files from the official Leidenalg distribution and +several functions from the R igraph package.") + (license license:gpl3+)))) + (define-public r-monocle3 (package (name "r-monocle3") From c44271445a7bee2b3873743128f7f27ff9a1320f Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Mon, 21 Jun 2021 17:52:10 +0200 Subject: [PATCH 065/144] gnu: r-monocle3: Update to 1.0.0. * gnu/packages/bioconductor.scm (r-monocle3): Update to 1.0.0. [propagated-inputs]: Add r-batchelor, r-leidenbase, and r-rsample. --- gnu/packages/bioconductor.scm | 7 +++++-- 1 file changed, 5 insertions(+), 2 deletions(-) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index f218fd1285..e8d353f49a 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -6408,7 +6408,7 @@ several functions from the R igraph package.") (define-public r-monocle3 (package (name "r-monocle3") - (version "0.1.2") + (version "1.0.0") (source (origin (method git-fetch) @@ -6418,10 +6418,11 @@ several functions from the R igraph package.") (file-name (git-file-name name version)) (sha256 (base32 - "1cjxqfw3qvy269hsf5v80d4kshl932wrl949iayas02saj6f70ls")))) + "16vpvlbms8fdvpfwzcig0rkg2mxnsq1h80d2l7q3953wm91qc9x4")))) (build-system r-build-system) (propagated-inputs `(("r-assertthat" ,r-assertthat) + ("r-batchelor" ,r-batchelor) ("r-biobase" ,r-biobase) ("r-biocgenerics" ,r-biocgenerics) ("r-delayedmatrixstats" ,r-delayedmatrixstats) @@ -6432,6 +6433,7 @@ several functions from the R igraph package.") ("r-htmlwidgets" ,r-htmlwidgets) ("r-igraph" ,r-igraph) ("r-irlba" ,r-irlba) + ("r-leidenbase" ,r-leidenbase) ("r-limma" ,r-limma) ("r-lmtest" ,r-lmtest) ("r-mass" ,r-mass) @@ -6451,6 +6453,7 @@ several functions from the R igraph package.") ("r-reshape2" ,r-reshape2) ("r-reticulate" ,r-reticulate) ("r-rhpcblasctl" ,r-rhpcblasctl) + ("r-rsample" ,r-rsample) ("r-rtsne" ,r-rtsne) ("r-shiny" ,r-shiny) ("r-slam" ,r-slam) From 23e3d2d9befa6ace742868244ec282e0d5786ad5 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Mon, 21 Jun 2021 14:32:13 +0200 Subject: [PATCH 066/144] gnu: font-overpass: Fix typo in description. * gnu/packages/fonts.scm (font-overpass)[description]: Fix typo. --- gnu/packages/fonts.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/gnu/packages/fonts.scm b/gnu/packages/fonts.scm index 9297256f8e..a1d7abd435 100644 --- a/gnu/packages/fonts.scm +++ b/gnu/packages/fonts.scm @@ -2264,6 +2264,6 @@ half of the twentieth century.") (description "Overpass is a sans-serif typeface based on the U.S. interstate highway road signage typefaces, adapted for on-screen display and user interfaces. -Overpass includes proprotional and monospace variants.") +Overpass includes proportional and monospace variants.") (license (list license:silofl1.1 license:lgpl2.1)))) From 98ae5c9d8493189007221e2f9ac5dacbcd2a1a3b Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Mon, 21 Jun 2021 14:33:57 +0200 Subject: [PATCH 067/144] gnu: lxcfs: Fix typos in description. * gnu/packages/virtualization.scm (lxcfs)[synopsis, description]: Fix typos. --- gnu/packages/virtualization.scm | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/gnu/packages/virtualization.scm b/gnu/packages/virtualization.scm index 600e4f401a..f144671709 100644 --- a/gnu/packages/virtualization.scm +++ b/gnu/packages/virtualization.scm @@ -1063,10 +1063,10 @@ manage system or application containers.") (inputs `(("fuse" ,fuse))) (build-system gnu-build-system) - (synopsis "FUSE based filesystem for LXC") - (description "LXCFS is a small FUSE filesystem written with the intention + (synopsis "FUSE-based file system for LXC") + (description "LXCFS is a small FUSE file system written with the intention of making Linux containers feel more like a virtual machine. -It started as a side-project of LXC but is useable by any runtime.") +It started as a side project of LXC but can be used by any run-time.") (license license:lgpl2.1+))) (define-public libvirt From 885d05acb9339f860f03efe41b44b8cf4fe9d987 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Mon, 21 Jun 2021 14:34:55 +0200 Subject: [PATCH 068/144] gnu: capnproto: Fix typo in phase name. * gnu/packages/serialization.scm (capnproto)[arguments]: Rename the 'use-tmp-for-tempory-files phase to 'use-tmp-for-temporary-files. --- gnu/packages/serialization.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/serialization.scm b/gnu/packages/serialization.scm index 7ea25b886c..8f292ae408 100644 --- a/gnu/packages/serialization.scm +++ b/gnu/packages/serialization.scm @@ -424,9 +424,9 @@ it a convenient format to store user input files.") ;; /etc/services, which is not present in build environment. (substitute* "src/kj/async-io-test.c++" ((":http") ":80")) #t)) - (add-before 'check 'use-tmp-for-tempory-files + (add-before 'check 'use-tmp-for-temporary-files (lambda _ - ;; Use /tmp for tempory files, as the default /var/tmp directory + ;; Use /tmp for temporary files, as the default /var/tmp directory ;; doesn't exist. (substitute* "src/kj/filesystem-disk-test.c++" (("VAR\\_TMP \"/var/tmp\"") From fe255fb8bc87125524207db6115d25a0417a99d5 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Mon, 21 Jun 2021 14:44:47 +0200 Subject: [PATCH 069/144] import: egg: Edit egg->guix-package docstring. * guix/import/egg.scm (egg->guix-package): Edit docstring. --- guix/import/egg.scm | 12 ++++++++---- 1 file changed, 8 insertions(+), 4 deletions(-) diff --git a/guix/import/egg.scm b/guix/import/egg.scm index 26f8364732..107894ddcf 100644 --- a/guix/import/egg.scm +++ b/guix/import/egg.scm @@ -1,5 +1,6 @@ ;;; GNU Guix --- Functional package management for GNU ;;; Copyright © 2021 Xinglu Chen +;;; Copyright © 2021 Tobias Geerinckx-Rice ;;; ;;; This file is part of GNU Guix. ;;; @@ -173,10 +174,13 @@ return the package metadata in FILE." ;;; (define* (egg->guix-package name #:key (file #f) (source #f)) - "Import CHICKEN egg NAME from and return a record type for the -egg, or #f on failure. FILE is the filepath to the NAME.egg file. SOURCE is -the a ``file-like'' object containing the source code corresonding to the egg. -If SOURCE is not specified, the tarball for the egg will be downloaded. + "Import a CHICKEN egg called NAME from either the given .egg FILE, or from +the latest NAME metadata downloaded from the official repository if FILE is #f. +Return a record or #f on failure. + +SOURCE is a ``file-like'' object containing the source code corresponding to +the egg. If SOURCE is not specified, the latest tarball for egg NAME will be +downloaded. Specifying the SOURCE argument is mainly useful for developing a CHICKEN egg locally. Note that if FILE and SOURCE are specified, recursive import will From 18968a7752b47ee003a93b8c27cecbc3ae44ac54 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Mon, 21 Jun 2021 18:37:04 +0200 Subject: [PATCH 070/144] gnu: dovecot: Update to 2.3.15 [fixes CVE-2021-29157 & CVE-2021-33515]. * gnu/packages/mail.scm (dovecot): Update to 2.3.15. --- gnu/packages/mail.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/mail.scm b/gnu/packages/mail.scm index 5a1ca62a4f..9160284fdf 100644 --- a/gnu/packages/mail.scm +++ b/gnu/packages/mail.scm @@ -1832,7 +1832,7 @@ facilities for checking incoming mail.") (package (name "dovecot") ;; Also update dovecot-pigeonhole when updating to a new minor version. - (version "2.3.14") + (version "2.3.15") (source (origin (method url-fetch) @@ -1840,7 +1840,7 @@ facilities for checking incoming mail.") (version-major+minor version) "/" "dovecot-" version ".tar.gz")) (sha256 - (base32 "0jm3p52z619v7ajh533g2g7d790k82fk0w7ry0zqlm8ymzrxgcy8")))) + (base32 "141manrh54cy8xizr7f8fsa3vdzc2ccfgdz87l9rjylm8mfxvfr1")))) (build-system gnu-build-system) (native-inputs `(("pkg-config" ,pkg-config))) From 4343476a3bffeb3714ad50ff7559c4b7f7c81551 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Mon, 21 Jun 2021 18:37:40 +0200 Subject: [PATCH 071/144] gnu: dovecot-pigeonhole: Update to 0.5.15 [fixes CVE-2020-28200]. * gnu/packages/mail.scm (dovecot-pigeonhole): Update to 0.5.15. --- gnu/packages/mail.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/mail.scm b/gnu/packages/mail.scm index 9160284fdf..6ed1c04c9e 100644 --- a/gnu/packages/mail.scm +++ b/gnu/packages/mail.scm @@ -1901,7 +1901,7 @@ It supports mbox/Maildir and its own dbox/mdbox formats.") (let ((dovecot-version (version-major+minor (package-version dovecot)))) (package (name "dovecot-pigeonhole") - (version "0.5.14") + (version "0.5.15") (source (origin (method url-fetch) @@ -1909,7 +1909,7 @@ It supports mbox/Maildir and its own dbox/mdbox formats.") "https://pigeonhole.dovecot.org/releases/" dovecot-version "/" "dovecot-" dovecot-version "-pigeonhole-" version ".tar.gz")) (sha256 - (base32 "1lmjzz4kd90wbdslacybizd1dks4bhwmrx39lj8b19naldw0zjk8")) + (base32 "1l2h0p8ddsl3ja2lnwk0mfqplqh8n0iw8k27awd3ak7prr88yjg1")) (modules '((guix build utils))) (snippet '(begin From a03912ed864be7002d7b6496b1df0992f8b651b3 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Mon, 21 Jun 2021 23:46:04 +0200 Subject: [PATCH 072/144] gnu: ungoogled-chromium: Update to 91.0.4472.114-0.a9eb6fd. * gnu/packages/chromium.scm (%chromium-version): Set to 91.0.4472.114. (%ungoogled-revision): Set to a9eb6fd. (%ungoogled-origin, ungoogled-chromium): Update hashes. --- gnu/packages/chromium.scm | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/gnu/packages/chromium.scm b/gnu/packages/chromium.scm index 8d7326e1c4..596a84a0d6 100644 --- a/gnu/packages/chromium.scm +++ b/gnu/packages/chromium.scm @@ -322,11 +322,11 @@ (string-append "ungoogled-chromium-" category "-" name)))) (sha256 (base32 hash)))) -(define %chromium-version "91.0.4472.106") +(define %chromium-version "91.0.4472.114") (define %debian-revision "debian/90.0.4430.85-1") ;; Note: use 'git describe --long' even for exact tags to placate the ;; custom version format for ungoogled-chromium. -(define %ungoogled-revision "91.0.4472.101-1-2-gbd0ffd1") +(define %ungoogled-revision "91.0.4472.114-1-0-ga9eb6fd") (define %debian-patches (list (debian-patch "fixes/nomerge.patch" @@ -346,7 +346,7 @@ (file-name (git-file-name "ungoogled-chromium" %ungoogled-revision)) (sha256 (base32 - "0676wkk1zlccwwwk4hi8ifhrk2x5s66fi0amsj30b7lnydzwpfv9")))) + "1xb5g3hybaiwn3y1zw1fxd3g0zwmvplrs06sdqnxzsr1qm8b874h")))) (define %guix-patches (list (local-file @@ -488,7 +488,7 @@ %chromium-version ".tar.xz")) (sha256 (base32 - "1fxy1l2dl0f6v8566lykcng18ma6fv4nlwxmdb0hh06fgp6khpjl")) + "0wbyiwbdazgjjgj9vs56x26q3g9r80a57gfl0f2rfl1j7xwgxiy1")) (modules '((guix build utils))) (snippet (force ungoogled-chromium-snippet)))) (build-system gnu-build-system) From a1c7537548bdffa1bcb023311dfbce40914d6003 Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Mon, 21 Jun 2021 23:52:11 +0200 Subject: [PATCH 073/144] gnu: uBlock Origin: Update to 1.36.0. * gnu/packages/browser-extensions.scm (uassets): Update to 20d21ad7e. (ublock-origin): Update to 1.36.0. --- gnu/packages/browser-extensions.scm | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/gnu/packages/browser-extensions.scm b/gnu/packages/browser-extensions.scm index a5f0472c7e..a6120baf96 100644 --- a/gnu/packages/browser-extensions.scm +++ b/gnu/packages/browser-extensions.scm @@ -49,7 +49,7 @@ supported content to the Kodi media center.") (make-chromium-extension play-to-kodi)) (define uassets - (let ((commit "f521473026f5f60cc753fa4a533af41badfc700e")) + (let ((commit "20d21ad7e92539660c7cde4c5884b3e234854264")) (origin (method git-fetch) (uri (git-reference @@ -58,12 +58,12 @@ supported content to the Kodi media center.") (file-name (git-file-name "uAssets" (string-take commit 9))) (sha256 (base32 - "0ms0xxj6rcfkib33wjbki631wix17vvzr4m6z0phqmaj49bla4kz"))))) + "1xcl4qnvjb4pv3fajpmycg1i0xqsah2qakhq2figvyrq991pldy1"))))) (define ublock-origin (package (name "ublock-origin") - (version "1.35.2") + (version "1.36.0") (home-page "https://github.com/gorhill/uBlock") (source (origin (method git-fetch) @@ -71,7 +71,7 @@ supported content to the Kodi media center.") (file-name (git-file-name name version)) (sha256 (base32 - "0w4rfwgvkjvdfccxi9b4qhp0hylnd946diri19cp3fd72zkjlcky")))) + "1r3aic18zkz8s3v1a2kffidp4swzbxnq0h8444bif9myjffnpxpj")))) (build-system gnu-build-system) (outputs '("xpi" "firefox" "chromium")) (arguments From e3a468b2069ea1822914a415165efdb783ce47d7 Mon Sep 17 00:00:00 2001 From: Raghav Gururajan Date: Wed, 16 Jun 2021 20:20:53 -0400 Subject: [PATCH 074/144] gnu: dino: Remove duplicate inputs. * gnu/packages/messaging.scm (dino)[inputs]: Remove duplicate gpgme, gtk+, glib-networking and gsettings-desktop-schemas. --- gnu/packages/messaging.scm | 6 +----- 1 file changed, 1 insertion(+), 5 deletions(-) diff --git a/gnu/packages/messaging.scm b/gnu/packages/messaging.scm index fe678d89fd..1a2ba971c3 100644 --- a/gnu/packages/messaging.scm +++ b/gnu/packages/messaging.scm @@ -1261,11 +1261,7 @@ Encryption to Gajim.") ("libsignal-protocol-c" ,libsignal-protocol-c) ("libsoup" ,libsoup) ("qrencode" ,qrencode) - ("sqlite" ,sqlite) - ("gpgme" ,gpgme) - ("gtk+" ,gtk+) - ("glib-networking" ,glib-networking) - ("gsettings-desktop-schemas" ,gsettings-desktop-schemas))) + ("sqlite" ,sqlite))) (synopsis "Graphical Jabber/XMPP Client using GTK+/Vala") (description "Dino is a chat client for the desktop. It focuses on providing a minimal yet reliable Jabber/XMPP experience and having encryption enabled by From 43cec0d117b4969ba2fc63c79a241c5e06c78f3d Mon Sep 17 00:00:00 2001 From: Raghav Gururajan Date: Wed, 16 Jun 2021 20:20:54 -0400 Subject: [PATCH 075/144] gnu: dino: Add missing inputs. These new inputs are referenced by the package but was missing in the package definition. Some of these inputs might have been used by the package indirectly via propagation from other inputs. * gnu/packages/messaging.scm (dino)[native-inputs]: Add gobject-introspection. [inputs]: Add atk, cairo, gdk-pixbug+svg, libnice and pango. --- gnu/packages/messaging.scm | 8 +++++++- 1 file changed, 7 insertions(+), 1 deletion(-) diff --git a/gnu/packages/messaging.scm b/gnu/packages/messaging.scm index 1a2ba971c3..1a6a065e0f 100644 --- a/gnu/packages/messaging.scm +++ b/gnu/packages/messaging.scm @@ -1247,19 +1247,25 @@ Encryption to Gajim.") (native-inputs `(("gettext" ,gettext-minimal) ("glib:bin" ,glib "bin") + ("gobject-introspection" ,gobject-introspection) ("gtk+:bin" ,gtk+ "bin") ("pkg-config" ,pkg-config) ("vala" ,vala))) (inputs - `(("glib" ,glib) + `(("atk" ,atk) + ("cairo" ,cairo) + ("gdk-pixbuf" ,gdk-pixbuf+svg) + ("glib" ,glib) ("glib-networking" ,glib-networking) ("gpgme" ,gpgme) ("gsettings-desktop-schemas" ,gsettings-desktop-schemas) ("gtk+" ,gtk+) ("libgcrypt" ,libgcrypt) ("libgee" ,libgee) + ("libnice" ,libnice) ("libsignal-protocol-c" ,libsignal-protocol-c) ("libsoup" ,libsoup) + ("pango" ,pango) ("qrencode" ,qrencode) ("sqlite" ,sqlite))) (synopsis "Graphical Jabber/XMPP Client using GTK+/Vala") From adf485c815fc8edf67e21fe349da838eae345e32 Mon Sep 17 00:00:00 2001 From: Raghav Gururajan Date: Wed, 16 Jun 2021 20:20:55 -0400 Subject: [PATCH 076/144] gnu: dino: Enable some features. * gnu/packages/messaging.scm (dino): Add comments for v0.3.0 release. [inputs]: Add gspell and icu4c. --- gnu/packages/messaging.scm | 17 +++++++++++++++++ 1 file changed, 17 insertions(+) diff --git a/gnu/packages/messaging.scm b/gnu/packages/messaging.scm index 1a6a065e0f..22e1c370aa 100644 --- a/gnu/packages/messaging.scm +++ b/gnu/packages/messaging.scm @@ -1242,6 +1242,14 @@ Encryption to Gajim.") (guix build glib-or-gtk-build-system)) #:phases (modify-phases %standard-phases + ;; To be enabled in v0.3.0, for A/V support. + ;;(add-after 'install 'wrap + ;;(lambda* (#:key outputs #:allow-other-keys) + ;;(let* ((out (assoc-ref outputs "out")) + ;;(dino (string-append out "/bin/dino")) + ;;(gst-plugin-path (getenv "GST_PLUGIN_SYSTEM_PATH"))) + ;;(wrap-program dino + ;;`("GST_PLUGIN_SYSTEM_PATH" ":" prefix (,gst-plugin-path)))))) (add-after 'install 'glib-or-gtk-wrap (assoc-ref glib-or-gtk:%standard-phases 'glib-or-gtk-wrap))))) (native-inputs @@ -1252,6 +1260,7 @@ Encryption to Gajim.") ("pkg-config" ,pkg-config) ("vala" ,vala))) (inputs + ;; NOTE: Commented-out lines are to be enabled in v0.3.0. `(("atk" ,atk) ("cairo" ,cairo) ("gdk-pixbuf" ,gdk-pixbuf+svg) @@ -1259,15 +1268,23 @@ Encryption to Gajim.") ("glib-networking" ,glib-networking) ("gpgme" ,gpgme) ("gsettings-desktop-schemas" ,gsettings-desktop-schemas) + ("gspell" ,gspell) ;for spell-check support + ;;("gstreamer" ,gstreamer) ;for A/V support + ;;("gst-plugins-base" ,gst-plugins-base) + ;;("gst-plugins-good" ,gst-plugins-good) ("gtk+" ,gtk+) + ("icu4c" ,icu4c) ;for emoji support + ;;("libcanberra" ,libcanberra) ;for sound-notification support ("libgcrypt" ,libgcrypt) ("libgee" ,libgee) ("libnice" ,libnice) ("libsignal-protocol-c" ,libsignal-protocol-c) ("libsoup" ,libsoup) + ;;("libsrtp" ,libsrtp) ;for calls support ("pango" ,pango) ("qrencode" ,qrencode) ("sqlite" ,sqlite))) + ;;("webrtc-audio-processing" ,webrtc-audio-processing))) ;for A/V support (synopsis "Graphical Jabber/XMPP Client using GTK+/Vala") (description "Dino is a chat client for the desktop. It focuses on providing a minimal yet reliable Jabber/XMPP experience and having encryption enabled by From d534d076f005310895c5fbad77cc590714991189 Mon Sep 17 00:00:00 2001 From: Nicolas Goaziou Date: Tue, 22 Jun 2021 07:58:57 +0200 Subject: [PATCH 077/144] gnu: emacs-which-key: Update to 3.5.3. * gnu/packages/emacs-xyz.scm (emacs-which-key): Update to 3.5.3. --- gnu/packages/emacs-xyz.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index e73ebfa2e5..a9889745c7 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -14363,7 +14363,7 @@ or @code{treemacs}, but leveraging @code{Dired} to do the job of display.") (define-public emacs-which-key (package (name "emacs-which-key") - (version "3.5.2") + (version "3.5.3") (source (origin (method git-fetch) @@ -14372,7 +14372,7 @@ or @code{treemacs}, but leveraging @code{Dired} to do the job of display.") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 - (base32 "1wgygby4zwlbx6ry6asraaixl169qdz092zgk1brvg63w7f8vkkb")))) + (base32 "144i3hkgm36wnfmqk5vq390snziy3zhwifbh6q6dzs99ic77d5g6")))) (build-system emacs-build-system) (arguments `(#:tests? #t From 14f72bd48dcba8b626091d4afe8e7106eca6d7d0 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 22 Jun 2021 08:34:51 +0200 Subject: [PATCH 078/144] gnu: python-ddt: Update to 1.4.2. * gnu/packages/python-xyz.scm (python-ddt): Update to 1.4.2. --- gnu/packages/python-xyz.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 1268ff257a..a989158036 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -16713,14 +16713,14 @@ can even create animations with the cursor controls.") (define-public python-ddt (package (name "python-ddt") - (version "1.4.1") + (version "1.4.2") (source (origin (method url-fetch) (uri (pypi-uri "ddt" version)) (sha256 (base32 - "1niqpzc26sxdbyi46r07n4pma5fjx6crww2539vpfmsf0w6yg585")))) + "0y2k756qjz1rhpivi60hy29b4bf0bh3wck39i1mn6pkil9k779k4")))) (build-system python-build-system) (native-inputs `(("python-pytest" ,python-pytest))) From 44bccf414b6ba285035fa3e22512b4b99b853776 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 22 Jun 2021 08:40:56 +0200 Subject: [PATCH 079/144] gnu: Add perl-cworld-dekker. * gnu/packages/bioinformatics.scm (perl-cworld-dekker): New variable. --- gnu/packages/bioinformatics.scm | 94 +++++++++++++++++++++++++++++++++ 1 file changed, 94 insertions(+) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 85d4e5a185..13c97af8c5 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -14260,6 +14260,100 @@ researchers to design and build computational workflows for the analysis of large-scale data-analysis.") (license license:expat))) +(define-public perl-cworld-dekker + (package + (name "perl-cworld-dekker") + (version "1.01") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/dekkerlab/cworld-dekker.git") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "1dvh23fx52m59y6304xi2j2pl2hiqadlqg8jyv2pm14j1hy71ych")))) + (build-system perl-build-system) + (arguments + `(#:modules ((guix build perl-build-system) + (guix build utils) + (srfi srfi-26)) + #:phases + (modify-phases %standard-phases + (add-after 'unpack 'hardcode-references + (lambda* (#:key inputs #:allow-other-keys) + (let ((bedtools (assoc-ref inputs "bedtools")) + (r (assoc-ref inputs "r-minimal"))) + (substitute* '("scripts/python/getEigenVectors.py" + "scripts/python/matrix2EigenVectors.py") + (("bedtools intersect") + (string-append bedtools "/bin/bedtools intersect"))) + (substitute* "lib/cworld/dekker.pm" + (("bedtools --version") + (string-append bedtools "/bin/bedtools --version"))) + (substitute* '("scripts/perl/correlateMatrices.pl" + "scripts/perl/matrix2scaling.pl" + "scripts/perl/matrix2distance.pl" + "scripts/perl/coverageCorrect.pl" + "scripts/perl/matrix2anchorPlot.pl" + "scripts/python/matrix2EigenVectors.py" + "scripts/python/matrix2insulation-lite.py" + "scripts/perl/matrix2compartment.pl" + "scripts/perl/anchorPurge.pl" + "scripts/perl/applyCorrection.pl" + "scripts/perl/compareInsulation.pl" + "scripts/perl/fillMissingData.pl" + "scripts/perl/matrix2loess.pl" + "scripts/python/getEigenVectors.py" + "scripts/perl/aggregateBED.pl" + "scripts/perl/collapseMatrix.pl" + "scripts/perl/matrix2direction.pl" + "scripts/perl/singletonRemoval.pl" + "lib/cworld/dekker.pm" + "scripts/perl/matrix2insulation.pl") + (("(`|\")Rscript" _ pre) + (string-append pre r "/bin/Rscript")))))) + (add-after 'install 'install-scripts + (lambda* (#:key outputs #:allow-other-keys) + (let* ((out (assoc-ref outputs "out")) + (share (string-append out "/share/cworld-dekker"))) + (mkdir-p share) + (copy-recursively "scripts" share) + + ;; Make all scripts executable and wrap them. + (let ((r (find-files share "\\.R$")) + (py (find-files share "\\.py$")) + (pl (find-files share "\\.pl$")) + (wrap (lambda* (script var #:optional (extra "")) + (let ((path (string-append (getenv var) + extra))) + (wrap-program script + `(,var ":" prefix (,path))))))) + (for-each (cut chmod <> #o555) (append r py pl)) + (for-each (cut wrap <> "PERL5LIB" + (string-append ":" out + "/lib/perl5/site_perl")) + pl) + (for-each (cut wrap <> "PYTHONPATH") py)))))))) + (inputs + `(("libgd" ,gd) + ("perl-gd" ,perl-gd) + ("bedtools" ,bedtools) + ("python" ,python-wrapper) + ("python-scipy" ,python-scipy) + ("python-numpy" ,python-numpy) + ("python-matplotlib" ,python-matplotlib) + ("python-h5py" ,python-h5py) + ("python-scikit-learn" ,python-scikit-learn) + ("r-minimal" ,r-minimal))) + (native-inputs + `(("perl-module-build" ,perl-module-build))) + (home-page "https://github.com/dekkerlab/cworld-dekker") + (synopsis "Utility and analysis scripts for 3C, 4C, 5C, and Hi-C data") + (description "This package is a collection of Perl, Python, and R +scripts for manipulating 3C/4C/5C/Hi-C data.") + (license license:asl2.0))) + (define-public ensembl-vep (let* ((api-version "103") (api-module From b6fc274637c69929e7811b40bf9b99d3e8df8360 Mon Sep 17 00:00:00 2001 From: Felix Gruber Date: Fri, 18 Jun 2021 15:33:59 +0000 Subject: [PATCH 080/144] gnu: widelands: Update to 1.0. * gnu/packages/games.scm (widelands): Update to 1.0. [source]: Download from github as there is no tarball for v1.0 on their website. [inputs]: Add curl. * gnu/packages/patches/widelands-system-wide_minizip.patch: Adjust for 1.0. CmakeLists.txt now already defines CMAKE_MODULE_PATH, so I've moved FindMinizip.cmake to this path. Signed-off-by: Nicolas Goaziou --- gnu/packages/games.scm | 16 ++++--- .../widelands-system-wide_minizip.patch | 44 +++++++------------ 2 files changed, 25 insertions(+), 35 deletions(-) diff --git a/gnu/packages/games.scm b/gnu/packages/games.scm index fca25294db..9944c0dcc6 100644 --- a/gnu/packages/games.scm +++ b/gnu/packages/games.scm @@ -5215,15 +5215,16 @@ tactics.") (define-public widelands (package (name "widelands") - (version "21") + (version "1.0") (source (origin - (method url-fetch) - (uri (string-append "https://launchpad.net/widelands/" - "build" version "/build" version "/+download/" - "widelands-build" version "-source.tar.gz")) + (method git-fetch) + (uri (git-reference + (url "https://github.com/widelands/widelands") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) (sha256 - (base32 "0mz3jily0w1zxxqbnkqrp6hl88xhrwzbil9crq7gpcwidx60w7k0")) + (base32 "1hw51binnbia15mj1gzx1cbk3cw9r91sisqci2qzcy4ahxiadnw0")) (modules '((guix build utils))) (snippet '(begin @@ -5263,7 +5264,8 @@ tactics.") `(("gettext" ,gettext-minimal) ("python" ,python-wrapper))) (inputs - `(("boost" ,boost) + `(("curl" ,curl) + ("boost" ,boost) ("glew" ,glew) ("icu4c" ,icu4c) ("libpng" ,libpng) diff --git a/gnu/packages/patches/widelands-system-wide_minizip.patch b/gnu/packages/patches/widelands-system-wide_minizip.patch index 1fac0d5396..b59fed7531 100644 --- a/gnu/packages/patches/widelands-system-wide_minizip.patch +++ b/gnu/packages/patches/widelands-system-wide_minizip.patch @@ -2,41 +2,29 @@ Description: use the system-wide minizip instead of the embeeded one if found. Forwarded-Upstream: It was provided by upstream: http://bazaar.launchpad.net/~widelands-dev/widelands/b19-debian/revision/8147 . Thanks to Fòram na Gàidhlig for the patch. - -I just added this line to make its use easier: - set(CMAKE_MODULE_PATH ${CMAKE_MODULE_PATH} ${CMAKE_HOME_DIRECTORY}/Modules) === modified file 'CMakeLists.txt' --- - CMakeLists.txt | 3 +++ - Modules/FindMinizip.cmake | 37 +++++++++++++++++++++++++++++++++++++ - cmake/WlFunctions.cmake | 7 +++++++ - src/io/CMakeLists.txt | 2 +- - src/third_party/CMakeLists.txt | 20 +++++++++++--------- - src/third_party/minizip/README.txt | 4 ++++ - 6 files changed, 63 insertions(+), 10 deletions(-) + CMakeLists.txt | 1 + + cmake/Modules/FindMinizip.cmake | 37 +++++++++++++++++++++++++++++++++++++ + cmake/WlFunctions.cmake | 8 ++++++++ + src/io/filesystem/CMakeLists.txt | 2 +- + src/io/filesystem/zip_filesystem.h | 6 ++++++ + src/third_party/CMakeLists.txt | 20 +++++++++++--------- + 6 files changed, 64 insertions(+), 10 deletions(-) --- a/CMakeLists.txt +++ b/CMakeLists.txt -@@ -43,6 +43,7 @@ - endif(POLICY CMP0074) - - include("${CMAKE_SOURCE_DIR}/cmake/WlFunctions.cmake") -+set(CMAKE_MODULE_PATH ${CMAKE_MODULE_PATH} ${CMAKE_HOME_DIRECTORY}/Modules) - - option(OPTION_USE_GLBINDING "Use glbinding instead of GLEW" OFF) - option(OPTION_GLEW_STATIC "Use static GLEW Library" OFF) -@@ -105,6 +106,8 @@ +@@ -142,6 +142,7 @@ + find_package(SDL2_mixer REQUIRED) find_package(SDL2_ttf REQUIRED) find_package(ZLIB REQUIRED) - find_package(ICU REQUIRED) +find_package(Minizip) -+ - if(OPTION_USE_GLBINDING) - find_package(glbinding REQUIRED) + if(${CMAKE_VERSION} VERSION_LESS 3.9.0) + find_package(ICU_old REQUIRED) else() --- /dev/null -+++ b/Modules/FindMinizip.cmake ++++ b/cmake/Modules/FindMinizip.cmake @@ -0,0 +1,37 @@ +# - Try to find Minizip +# Once done this will define @@ -77,10 +65,10 @@ I just added this line to make its use easier: + --- a/cmake/WlFunctions.cmake +++ b/cmake/WlFunctions.cmake -@@ -81,6 +81,14 @@ +@@ -84,6 +84,14 @@ + if(ARG_USES_ZLIB) - wl_include_system_directories(${NAME} ${ZLIB_INCLUDE_DIRS}) - target_link_libraries(${NAME} ${ZLIB_LIBRARY}) + target_link_libraries(${NAME} ZLIB::ZLIB) + if (MINIZIP_FOUND) + wl_include_system_directories(${NAME} ${MINIZIP_INCLUDE_DIR}) + target_link_libraries(${NAME} ${MINIZIP_LIBRARY}) @@ -136,7 +124,7 @@ I just added this line to make its use easier: ) --- a/src/io/filesystem/zip_filesystem.h +++ b/src/io/filesystem/zip_filesystem.h -@@ -28,8 +28,14 @@ +@@ -25,8 +25,14 @@ #include "io/filesystem/filesystem.h" #include "io/streamread.h" #include "io/streamwrite.h" From 662316b0d6edcb838a4a70fc329660d425f5fe79 Mon Sep 17 00:00:00 2001 From: Nicolas Goaziou Date: Tue, 22 Jun 2021 10:35:58 +0200 Subject: [PATCH 081/144] gnu: widelands: Ensure Guix catches versioning scheme switch. * gnu/packages/games.scm (widelands-21): New variable. "21" was the last beta release. Upstream has now switched to a new versioning scheme, with lesser numbers. --- gnu/packages/games.scm | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/gnu/packages/games.scm b/gnu/packages/games.scm index 9944c0dcc6..1da5fa468d 100644 --- a/gnu/packages/games.scm +++ b/gnu/packages/games.scm @@ -5303,6 +5303,12 @@ of war. Widelands also offers an Artificial Intelligence to challenge you.") license:silofl1.1 ;Widelands.ttf license:cc-by-sa3.0)))) ;some music files +(define-public widelands-21 + (package + (inherit widelands) + (version "21") + (properties `((superseded . ,widelands))))) + (define-public starfighter (package (name "starfighter") From 61a9ba398f39258e603ba7eaf107ecf051d4f462 Mon Sep 17 00:00:00 2001 From: Nicolas Goaziou Date: Tue, 22 Jun 2021 10:39:40 +0200 Subject: [PATCH 082/144] gnu: widelands: Update description. * gnu/packages/games.scm (widelands)[description]: Update to mirror changes in the stable release. --- gnu/packages/games.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/games.scm b/gnu/packages/games.scm index 1da5fa468d..d365301534 100644 --- a/gnu/packages/games.scm +++ b/gnu/packages/games.scm @@ -5284,8 +5284,8 @@ nothing but your headquarters, where all your resources are stored. In the course of the game, you will build an ever growing settlement. Every member of your clan will do his or her part to produce more resources---wood, food, iron, gold and more---to further this growth. The economic network is -complex and different in the four tribes (Barbarians, Empire, Atlanteans, and -Frisians). +complex and different in the five tribes (Barbarians, Empire, Atlanteans, +Frisians and Amazons). As you are not alone in the world, you will meet other clans sooner or later. Some of them may be friendly and you may eventually trade with them. However, From 17972082ccb05cce550bc095d23bd6dcaf3ec5a7 Mon Sep 17 00:00:00 2001 From: Sharlatan Hellseher Date: Fri, 18 Jun 2021 20:27:27 +0100 Subject: [PATCH 083/144] gnu: Add gopkg.in/yaml.v3. * gnu/packages/golang.scm (go-gopkg-in-yml-v3): New variable Signed-off-by: Nicolas Goaziou --- gnu/packages/golang.scm | 27 +++++++++++++++++++++++++++ 1 file changed, 27 insertions(+) diff --git a/gnu/packages/golang.scm b/gnu/packages/golang.scm index 8c3c81ceda..1d17f02cdd 100644 --- a/gnu/packages/golang.scm +++ b/gnu/packages/golang.scm @@ -25,6 +25,7 @@ ;;; Copyright © 2020 Martin Becze ;;; Copyright © 2021 Ricardo Wurmus ;;; Copyright © 2021 Guillaume Le Vaillant +;;; Copyright © 2021 Sharlatan Hellseher ;;; ;;; This file is part of GNU Guix. ;;; @@ -2413,6 +2414,32 @@ which satisfies the cron expression.") values.") (license license:asl2.0))) +(define-public go-gopkg-in-yaml-v3 + (package + (name "go-gopkg-in-yaml-v3") + (version "3") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://gopkg.in/yaml.v3") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "06f4lnrp494wqaygv09dggr2dwf3z2bawqhnlnnwiamg5y787k4g")))) + (build-system go-build-system) + (arguments + '(#:import-path "gopkg.in/yaml.v3")) + (native-inputs + `(("go-gopkg-in-check-v1" ,go-gopkg-in-check-v1))) + (home-page "https://gopkg.in/yaml.v3") + (synopsis "YAML reader and writer for the Go language") + (description + "This package provides a Go library for encode and decode YAML values. +The yaml package supports most of YAML 1.2, but preserves some behavior from +1.1 for backwards compatibility.") + (license license:asl2.0))) + (define-public go-github-com-mattn-go-isatty (package (name "go-github-com-mattn-go-isatty") From 9ba41ea8231c44cf4d7312891b8d9add277e5d89 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Vin=C3=ADcius=20dos=20Santos=20Oliveira?= Date: Fri, 18 Jun 2021 20:20:01 -0300 Subject: [PATCH 084/144] gnu: emilua: Update to 0.3.2. * gnu/packages/lua.scm (emilua): Update to 0.3.2. Signed-off-by: Nicolas Goaziou --- gnu/packages/lua.scm | 13 +++++-------- 1 file changed, 5 insertions(+), 8 deletions(-) diff --git a/gnu/packages/lua.scm b/gnu/packages/lua.scm index 54d2ba400d..0ecc91294f 100644 --- a/gnu/packages/lua.scm +++ b/gnu/packages/lua.scm @@ -1108,23 +1108,20 @@ shell command executions.") (define-public emilua (package (name "emilua") - (version "0.3.0") + (version "0.3.2") (source (origin (method git-fetch) (uri (git-reference (url "https://gitlab.com/emilua/emilua.git") (commit (string-append "v" version)) - ;; Current version requires bundled CLI11, but at some future - ;; release the one found in the system could be used - ;; instead. Current version also requires Trial.Protocol and - ;; the HTTP lib developed as part of GSoC 2014 for Boost, but - ;; these are dependencies unlikely to be "unbundled" in future - ;; releases. + ;; Current version requires Trial.Protocol and the HTTP lib + ;; developed as part of GSoC 2014 for Boost, and these are + ;; dependencies unlikely to be "unbundled" in future releases. (recursive? #t))) (file-name (git-file-name name version)) (sha256 (base32 - "124fj73722c03znwdyqp1i0jygwv3s11f6s1j9rzym513qrf7fnd")))) + "1999bgrh52124a5g4qizav3x257ff2brjr855srpm1jv1nxzbygv")))) (build-system meson-build-system) (arguments `(#:meson ,meson-0.55 From 400f1caf3f9c3534a858db1f46618e791506465d Mon Sep 17 00:00:00 2001 From: Vinicius Monego Date: Mon, 21 Jun 2021 10:43:45 +0000 Subject: [PATCH 085/144] gnu: Add rust-uom-0.31. * gnu/packages/crates-io.scm (rust-uom-0.31): New variable. Signed-off-by: Nicolas Goaziou --- gnu/packages/crates-io.scm | 34 ++++++++++++++++++++++++++++++++++ 1 file changed, 34 insertions(+) diff --git a/gnu/packages/crates-io.scm b/gnu/packages/crates-io.scm index 930ab5d4e4..ab3dda6dda 100644 --- a/gnu/packages/crates-io.scm +++ b/gnu/packages/crates-io.scm @@ -17,6 +17,7 @@ ;;; Copyright © 2021 Alexandru-Sergiu Marton ;;; Copyright © 2021 Antero Mejr ;;; Copyright © 2021 Maxim Cournoyer +;;; Copyright © 2021 Vinicius Monego ;;; ;;; This file is part of GNU Guix. ;;; @@ -51618,6 +51619,39 @@ untrusted inputs in Rust.") (sha256 (base32 "0byf88b7ca1kb5aap8f6npp6xncvg95dnma8ipmnmd4n9r5izkam")))))) +(define-public rust-uom-0.31 + (package + (name "rust-uom") + (version "0.31.1") + (source + (origin + (method url-fetch) + (uri (crate-uri "uom" version)) + (file-name + (string-append name "-" version ".tar.gz")) + (sha256 + (base32 "0dwih0bclq18gfdf7if6kqip82w8yrf076l0ad1n3gr71bynpvmi")))) + (build-system cargo-build-system) + (arguments + `(#:cargo-inputs + (("rust-num-bigint" ,rust-num-bigint-0.3) + ("rust-num-rational" ,rust-num-rational-0.3) + ("rust-num-traits" ,rust-num-traits-0.2) + ("rust-serde" ,rust-serde-1) + ("rust-typenum" ,rust-typenum-1)) + #:cargo-development-inputs + (("rust-approx" ,rust-approx-0.3) + ("rust-quickcheck" ,rust-quickcheck-0.9) + ("rust-serde-json" ,rust-serde-json-1) + ("rust-static-assertions" + ,rust-static-assertions-1)))) + (home-page "https://github.com/iliekturtles/uom") + (synopsis "Units of measurement") + (description "Units of measurement is a crate that does automatic +type-safe zero-cost dimensional analysis.") + ;; Dual-licensed, either license applies. + (license (list license:asl2.0 license:expat)))) + (define-public rust-url-2 (package (name "rust-url") From f80f7329ceff50a8ca2a339a0ebb490450c26c20 Mon Sep 17 00:00:00 2001 From: Vinicius Monego Date: Mon, 21 Jun 2021 10:43:46 +0000 Subject: [PATCH 086/144] gnu: Add rust-uom-0.30. * gnu/packages/crates-io.scm (rust-uom-0.30): New variable. Signed-off-by: Nicolas Goaziou --- gnu/packages/crates-io.scm | 13 +++++++++++++ 1 file changed, 13 insertions(+) diff --git a/gnu/packages/crates-io.scm b/gnu/packages/crates-io.scm index ab3dda6dda..c8df916e2b 100644 --- a/gnu/packages/crates-io.scm +++ b/gnu/packages/crates-io.scm @@ -51652,6 +51652,19 @@ type-safe zero-cost dimensional analysis.") ;; Dual-licensed, either license applies. (license (list license:asl2.0 license:expat)))) +(define-public rust-uom-0.30 + (package + (inherit rust-uom-0.31) + (name "rust-uom") + (version "0.30.0") + (source + (origin + (method url-fetch) + (uri (crate-uri "uom" version)) + (file-name (string-append name "-" version ".tar.gz")) + (sha256 + (base32 "1vg59hnb7hh0p8kjjhgmrsnn3597722lkfdkp481wksq6vk06rg7")))))) + (define-public rust-url-2 (package (name "rust-url") From 2de5297a08c51e7d2c126068181a21424131c95f Mon Sep 17 00:00:00 2001 From: Vinicius Monego Date: Mon, 21 Jun 2021 10:43:47 +0000 Subject: [PATCH 087/144] gnu: Add rust-mach-0.3. * gnu/packages/crates-io.scm (rust-mach-0.3): New variable. (rust-mach-0.2): Inherit from above. Signed-off-by: Nicolas Goaziou --- gnu/packages/crates-io.scm | 19 ++++++++++++++++--- 1 file changed, 16 insertions(+), 3 deletions(-) diff --git a/gnu/packages/crates-io.scm b/gnu/packages/crates-io.scm index c8df916e2b..588c1b8b90 100644 --- a/gnu/packages/crates-io.scm +++ b/gnu/packages/crates-io.scm @@ -24874,17 +24874,17 @@ lexer.") "This package provides a collection of great and ubiqutitous macros.") (license (list license:asl2.0 license:expat)))) -(define-public rust-mach-0.2 +(define-public rust-mach-0.3 (package (name "rust-mach") - (version "0.2.3") + (version "0.3.0") (source (origin (method url-fetch) (uri (crate-uri "mach" version)) (file-name (string-append name "-" version ".tar.gz")) (sha256 - (base32 "1qdhs16cl1j3w7kvy6ak7h8lbyqmr6i3i15qfzpnv9gyrn3j9pc6")))) + (base32 "0a895rhg3a1l3ws4qf83s5mx0g29v1fzgjmbag1h36v62hmg1vi8")))) (build-system cargo-build-system) (arguments `(#:skip-build? #t @@ -24897,6 +24897,19 @@ lexer.") Mach 3.0 kernel that underlies OSX.") (license (list license:asl2.0 license:expat license:bsd-2)))) +(define-public rust-mach-0.2 + (package + (inherit rust-mach-0.3) + (name "rust-mach") + (version "0.2.3") + (source + (origin + (method url-fetch) + (uri (crate-uri "mach" version)) + (file-name (string-append name "-" version ".tar.gz")) + (sha256 + (base32 "1qdhs16cl1j3w7kvy6ak7h8lbyqmr6i3i15qfzpnv9gyrn3j9pc6")))))) + (define-public rust-mach-o-sys-0.1 (package (name "rust-mach-o-sys") From d07bade71e5ddb5ac606f5e8b6b2c7630cc557d3 Mon Sep 17 00:00:00 2001 From: Vinicius Monego Date: Mon, 21 Jun 2021 10:43:48 +0000 Subject: [PATCH 088/144] gnu: rust-lazycell-1: Update to 1.3.0. * gnu/packages/crates-io.scm (rust-lazycell-1): Update to 1.3.0. [arguments]: Remove #:skip-build. Signed-off-by: Nicolas Goaziou --- gnu/packages/crates-io.scm | 7 +++---- 1 file changed, 3 insertions(+), 4 deletions(-) diff --git a/gnu/packages/crates-io.scm b/gnu/packages/crates-io.scm index 588c1b8b90..0e90e566e3 100644 --- a/gnu/packages/crates-io.scm +++ b/gnu/packages/crates-io.scm @@ -23160,7 +23160,7 @@ requires non-const function calls to be computed.") (define-public rust-lazycell-1 (package (name "rust-lazycell") - (version "1.2.1") + (version "1.3.0") (source (origin (method url-fetch) @@ -23169,11 +23169,10 @@ requires non-const function calls to be computed.") (string-append name "-" version ".tar.gz")) (sha256 (base32 - "0gvqycmpv7parc98i6y64ai7rvxrn1947z2a6maa02g4kvxdd55j")))) + "0m8gw7dn30i0zjjpjdyf6pc16c34nl71lpv461mix50x3p70h3c3")))) (build-system cargo-build-system) (arguments - `(#:skip-build? #t - #:cargo-inputs (("rust-clippy" ,rust-clippy-0.0)))) + `(#:cargo-inputs (("rust-clippy" ,rust-clippy-0.0)))) (home-page "https://github.com/indiv0/lazycell") (synopsis "Lazily filled Cell struct") (description From e88f205876afc8f0cee2dd4ac1071b81042d4a80 Mon Sep 17 00:00:00 2001 From: Vinicius Monego Date: Mon, 21 Jun 2021 10:43:49 +0000 Subject: [PATCH 089/144] gnu: Add rust-battery-0.7. * gnu/packages/crates-io.scm (rust-battery-0.7): New variable. Signed-off-by: Nicolas Goaziou --- gnu/packages/crates-io.scm | 36 ++++++++++++++++++++++++++++++++++++ 1 file changed, 36 insertions(+) diff --git a/gnu/packages/crates-io.scm b/gnu/packages/crates-io.scm index 0e90e566e3..82a09b8b2a 100644 --- a/gnu/packages/crates-io.scm +++ b/gnu/packages/crates-io.scm @@ -4206,6 +4206,42 @@ c6e7d37. However, this package works only up to 128 bytes.") (description "This library provides for encoding and decoding any base.") (license license:expat))) +(define-public rust-battery-0.7 + (package + (name "rust-battery") + (version "0.7.8") + (source + (origin + (method url-fetch) + (uri (crate-uri "battery" version)) + (file-name + (string-append name "-" version ".tar.gz")) + (sha256 + (base32 "1r1641dyks76p39i1iihswhc6iz5z51pihmpxniy1h1pi4k29dml")))) + (build-system cargo-build-system) + (arguments + `(#:tests? #f ;; Tests fail with "No such file or directory". + #:cargo-inputs + (("rust-cfg-if" ,rust-cfg-if-1) + ("rust-core-foundation" + ,rust-core-foundation-0.7) + ("rust-lazycell" ,rust-lazycell-1) + ("rust-libc" ,rust-libc-0.2) + ("rust-mach" ,rust-mach-0.3) + ("rust-nix" ,rust-nix-0.19) + ("rust-num-traits" ,rust-num-traits-0.2) + ("rust-uom" ,rust-uom-0.30) + ("rust-winapi" ,rust-winapi-0.3)) + #:cargo-development-inputs + (("rust-approx" ,rust-approx-0.3) + ("rust-tempfile" ,rust-tempfile-3)))) + (home-page "https://github.com/svartalf/rust-battery") + (synopsis "Information about the notebook batteries") + (description + "@code{battery} provides a unified API to a notebook batteries state.") + ;; Dual licensed, either license applies. + (license (list license:asl2.0 license:expat)))) + (define-public rust-beef-0.5 (package (name "rust-beef") From bc6c99e52c283df606d9df2efb0f6db01b3f19bc Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Tue, 22 Jun 2021 09:25:03 +0300 Subject: [PATCH 090/144] gnu: libreoffice: Add vendor string. Previously: This release was supplied by nixbld. Now: This release was supplied by GNU Guix. * gnu/packages/libreoffice.scm (libreoffice)[arguments]: Add configure-flag to set vendor to 'GNU Guix'. --- gnu/packages/libreoffice.scm | 1 + 1 file changed, 1 insertion(+) diff --git a/gnu/packages/libreoffice.scm b/gnu/packages/libreoffice.scm index e03047c3fd..57a7d7b190 100644 --- a/gnu/packages/libreoffice.scm +++ b/gnu/packages/libreoffice.scm @@ -1278,6 +1278,7 @@ converting QuarkXPress file format. It supports versions 3.1 to 4.1.") #:configure-flags (list "--enable-release-build" + "--with-vendor=GNU Guix" ;; Avoid using all cpu cores by default (format #f "--with-parallelism=~d" (parallel-job-count)) "--disable-fetch-external" ; disable downloads From 920a36392a40fad1e6e42aec2bbe9292e0d2202d Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Tue, 22 Jun 2021 09:26:55 +0300 Subject: [PATCH 091/144] gnu: Add box2d. * gnu/packages/game-development.scm (box2d): New variable. --- gnu/packages/game-development.scm | 35 ++++++++++++++++++++++++++++++- 1 file changed, 34 insertions(+), 1 deletion(-) diff --git a/gnu/packages/game-development.scm b/gnu/packages/game-development.scm index 78983cd991..f1205e5407 100644 --- a/gnu/packages/game-development.scm +++ b/gnu/packages/game-development.scm @@ -4,7 +4,7 @@ ;;; Copyright © 2015, 2018 Ludovic Courtès ;;; Copyright © 2015, 2018 Alex Kost ;;; Copyright © 2015, 2016, 2017 David Thompson -;;; Copyright © 2016, 2017, 2018, 2019, 2020 Efraim Flashner +;;; Copyright © 2016, 2017, 2018, 2019, 2020, 2021 Efraim Flashner ;;; Copyright © 2016, 2017, 2020 Kei Kebreau ;;; Copyright © 2016, 2018, 2019 Ricardo Wurmus ;;; Copyright © 2016, 2017, 2018 Julian Graham @@ -2289,6 +2289,39 @@ computer games, 3D authoring tools and simulation tools.") rigid body physics library written in C.") (license license:expat))) +(define-public box2d + (package + (name "box2d") + (version "2.4.1") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/erincatto/box2d") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "1ja9cahf3z9zzrdaqcw44lpjmqf2ir2g4chwz0iwqwlkckwhpgvh")) + (modules '((guix build utils))) + (snippet + '(begin + ;; Bundled code only used for the testbed. + (delete-file-recursively "extern"))))) + (build-system cmake-build-system) + (arguments + `(#:test-target "unit_test" + #:configure-flags '("-DBUILD_SHARED_LIBS=ON" + "-DBOX2D_BUILD_TESTBED=OFF"))) + (inputs + `(("libx11" ,libx11))) + (home-page "https://box2d.org/") + (synopsis "2D physics engine for games") + (description "Box2D is a 2D rigid body simulation library for games. +Programmers can use it in their games to make objects move in realistic ways and +make the game world more interactive. From the game engine's point of view, a +physics engine is just a system for procedural animation.") + (license license:expat))) + (define-public libtcod (package (name "libtcod") From 07d2c72d39be5ec3ece9ac92cce006a56900cbe4 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Tue, 22 Jun 2021 11:24:26 +0300 Subject: [PATCH 092/144] gnu: ensembl-vep: Use a source file-name. * gnu/packages/bioinformatics.scm (ensembl-vep)[source]: Add a file-name field. --- gnu/packages/bioinformatics.scm | 1 + 1 file changed, 1 insertion(+) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 13c97af8c5..ae788eab99 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -14374,6 +14374,7 @@ scripts for manipulating 3C/4C/5C/Hi-C data.") (uri (git-reference (url "https://github.com/Ensembl/ensembl-vep.git") (commit (string-append "release/" version)))) + (file-name (git-file-name name version)) (sha256 (base32 "1iq7p72cv9b38jz2v8a4slzy2n8y0md487943180ym9xc8qvw09c")))) From 27f2b79db360cbafc5c0e7846580494ae3b91f00 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Tue, 22 Jun 2021 11:25:51 +0300 Subject: [PATCH 093/144] gnu: emacs-shell-command+: Use a source file-name. * gnu/packages/emacs-xyz.scm (emacs-shell-command+)[source]: Add a file-name field. --- gnu/packages/emacs-xyz.scm | 1 + 1 file changed, 1 insertion(+) diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index a9889745c7..26899f417b 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -27817,6 +27817,7 @@ Features: (uri (git-reference (url "https://git.sr.ht/~zge/bang") (commit version))) + (file-name (git-file-name name version)) (sha256 (base32 "1micvz6smhjma7qbka8h3w0crb3sgrxf9lz2548iqfgww50gb0lj")))) (build-system emacs-build-system) From 3623696db15f031ea4d9894a96ea2579e4211218 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Tue, 22 Jun 2021 11:26:53 +0300 Subject: [PATCH 094/144] gnu: ocaml-uri: Use a source file-name. * gnu/packages/ocaml.scm (ocaml-uri)[source]: Add a file-name field. --- gnu/packages/ocaml.scm | 1 + 1 file changed, 1 insertion(+) diff --git a/gnu/packages/ocaml.scm b/gnu/packages/ocaml.scm index 21d16a46a1..dd30f4cc97 100644 --- a/gnu/packages/ocaml.scm +++ b/gnu/packages/ocaml.scm @@ -3453,6 +3453,7 @@ JSON.") (uri (git-reference (url home-page) (commit (string-append "v" version)))) + (file-name (git-file-name name version)) (sha256 (base32 "10bf28my1yhj8a2d7bkgbna9j20wq0ghp92k926y29bmjj2qh0l7")))) From cb180427d09a5f1144bfd4f51db0bc8c0cec7c6b Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Tue, 22 Jun 2021 12:43:33 +0300 Subject: [PATCH 095/144] gnu: ixion: Update to 0.16.1. * gnu/packages/libreoffice.scm (ixion): Update to 0.16.1. --- gnu/packages/libreoffice.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/libreoffice.scm b/gnu/packages/libreoffice.scm index 57a7d7b190..dc59209a1b 100644 --- a/gnu/packages/libreoffice.scm +++ b/gnu/packages/libreoffice.scm @@ -88,7 +88,7 @@ (define-public ixion (package (name "ixion") - (version "0.15.0") + (version "0.16.1") (source (origin (method url-fetch) @@ -96,7 +96,7 @@ version ".tar.xz")) (sha256 (base32 - "1rmrl2zjzi4z0abf2cd54acypkccdhx2065dlyzy6xg83gv0mxmi")))) + "17q84mhy4rb3masvjw24x549irdjmccnc8n04xh58v9l7hxn8v22")))) (build-system gnu-build-system) (native-inputs `(("pkg-config" ,pkg-config))) From e1f5517c46373f10af22618eea8484a6d0f613c7 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Tue, 22 Jun 2021 12:43:18 +0300 Subject: [PATCH 096/144] gnu: orcus: Don't build static library. * gnu/packages/libreoffice.scm (orcus)[arguments]: Add configure-flag to skip static library. --- gnu/packages/libreoffice.scm | 2 ++ 1 file changed, 2 insertions(+) diff --git a/gnu/packages/libreoffice.scm b/gnu/packages/libreoffice.scm index dc59209a1b..672a5e3cd7 100644 --- a/gnu/packages/libreoffice.scm +++ b/gnu/packages/libreoffice.scm @@ -125,6 +125,8 @@ their dependencies automatically upon calculation.") (base32 "14gbnqsv5n2fm4sxa17014f440clrzls6p2w2ixk9wipg4950v9s")))) (build-system gnu-build-system) + (arguments + `(#:configure-flags '("--disable-static"))) (native-inputs `(("pkg-config" ,pkg-config))) (inputs From 4aae60711907ce2070410c6d2876a0d6c7ac2afe Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Tue, 22 Jun 2021 12:43:33 +0300 Subject: [PATCH 097/144] gnu: orcus: Update to 0.16.1. * gnu/packages/libreoffice.scm (orcus): Update to 0.16.1. --- gnu/packages/libreoffice.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/libreoffice.scm b/gnu/packages/libreoffice.scm index 672a5e3cd7..a41b8ee876 100644 --- a/gnu/packages/libreoffice.scm +++ b/gnu/packages/libreoffice.scm @@ -115,7 +115,7 @@ their dependencies automatically upon calculation.") (define-public orcus (package (name "orcus") - (version "0.15.3") + (version "0.16.1") (source (origin (method url-fetch) @@ -123,7 +123,7 @@ their dependencies automatically upon calculation.") "orcus-" version ".tar.xz")) (sha256 (base32 - "14gbnqsv5n2fm4sxa17014f440clrzls6p2w2ixk9wipg4950v9s")))) + "1bps34sqz7wlrl01ssywjd5fbmssplifs0rskivgrg801lr6pcm4")))) (build-system gnu-build-system) (arguments `(#:configure-flags '("--disable-static"))) From d89ef8a7d8c9e8219bd910f6a9a5dc1e6cfabff6 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Tue, 22 Jun 2021 12:41:27 +0300 Subject: [PATCH 098/144] gnu: libreoffice: Update to 7.1.4.2. * gnu/packages/libreoffice.scm (libreoffice)[inputs]: Add box2d, dtoa. [arguments]: Adjust custom 'prepare-src, 'bin-and-desktop-install phases. Add custom 'insert-external-tarballs phase. Adjust configure-flags to build without skia. Remove deprecated make-flag --- gnu/packages/libreoffice.scm | 39 +++++++++++++++++++++--------------- 1 file changed, 23 insertions(+), 16 deletions(-) diff --git a/gnu/packages/libreoffice.scm b/gnu/packages/libreoffice.scm index a41b8ee876..429f3647b7 100644 --- a/gnu/packages/libreoffice.scm +++ b/gnu/packages/libreoffice.scm @@ -57,6 +57,7 @@ #:use-module (gnu packages flex) #:use-module (gnu packages fontutils) #:use-module (gnu packages freedesktop) + #:use-module (gnu packages game-development) #:use-module (gnu packages ghostscript) #:use-module (gnu packages gl) #:use-module (gnu packages glib) @@ -1088,7 +1089,7 @@ converting QuarkXPress file format. It supports versions 3.1 to 4.1.") (define-public libreoffice (package (name "libreoffice") - (version "6.4.7.2") + (version "7.1.4.2") (source (origin (method url-fetch) @@ -1097,7 +1098,7 @@ converting QuarkXPress file format. It supports versions 3.1 to 4.1.") "https://download.documentfoundation.org/libreoffice/src/" (version-prefix version 3) "/libreoffice-" version ".tar.xz")) (sha256 - (base32 "0i3654rmzs8aazj8j3dmxamilslfrki0y4sksg3n1zygc2ddfk83")))) + (base32 "1jsskhnlyra7q6d12kkc8dxq5fgrnd8grl32bdck7j9hkwv6d13m")))) (build-system glib-or-gtk-build-system) (native-inputs `(("bison" ,bison) @@ -1110,6 +1111,7 @@ converting QuarkXPress file format. It supports versions 3.1 to 4.1.") (inputs `(("bluez" ,bluez) ("boost" ,boost) + ("box2d" ,box2d) ("clucene" ,clucene) ("cups" ,cups) ("dbus-glib" ,dbus-glib) @@ -1180,12 +1182,23 @@ converting QuarkXPress file format. It supports versions 3.1 to 4.1.") ("vigra" ,vigra) ("xdg-utils" ,xdg-utils) ("xmlsec" ,xmlsec-nss) - ("zip" ,zip))) + ("zip" ,zip) + ("dtoa" ; needed after version 6.4.7.2. + ,(origin + (method url-fetch) + (uri "https://dev-www.libreoffice.org/src/dtoa-20180411.tgz") + (sha256 + (base32 "1d0iwy0q5sjznv23d3nbwmy0r7m1mdzlnv5pc4izddkx9xld10h0")))))) (arguments `(#:tests? #f ; Building the tests already fails. - #:make-flags '("build-nocheck") ; Do not build unit tests, which fails. #:phases (modify-phases %standard-phases + (add-after 'unpack 'insert-external-tarballs + (lambda* (#:key inputs #:allow-other-keys) + (mkdir-p "external/tarballs") + (copy-file (assoc-ref inputs "dtoa") + "external/tarballs/dtoa-20180411.tgz") + #t)) (add-before 'configure 'prepare-src (lambda* (#:key inputs #:allow-other-keys) (substitute* @@ -1203,14 +1216,11 @@ converting QuarkXPress file format. It supports versions 3.1 to 4.1.") (list "dirname" "grep" "uname")) ;; GPGME++ headers are installed in a gpgme++ subdirectory, but - ;; files in "xmlsecurity/source/gpg/" and elsewhere expect to - ;; find them on the include path without a prefix. - (substitute* '("xmlsecurity/Library_xsec_xmlsec.mk" - "comphelper/Library_comphelper.mk") - (("\\$\\$\\(INCLUDE\\)") - (string-append "$$(INCLUDE) -I" - (assoc-ref inputs "gpgme") - "/include/gpgme++"))) + ;; configure is hardcoded to use FHS directories. + (substitute* "configure" + (("GPGMEPP_CFLAGS=-I/usr") + (string-append "GPGMEPP_CFLAGS=-I" + (assoc-ref inputs "gpgme")))) ;; /usr/bin/xdg-open doesn't exist on Guix System. (substitute* '("shell/source/unix/exec/shellexec.cxx" @@ -1261,10 +1271,6 @@ converting QuarkXPress file format. It supports versions 3.1 to 4.1.") "/bin/soffice") (symlink-output "/lib/libreoffice/program/soffice" "/bin/libreoffice") - (install "workdir/CustomTarget/sysui/share/libreoffice/openoffice.keys" - "/share/mime-info/libreoffice.keys") - (install "workdir/CustomTarget/sysui/share/libreoffice/openoffice.mime" - "/share/mime-info/libreoffice.mime") (install "workdir/CustomTarget/sysui/share/libreoffice/openoffice.org.xml" "/share/mime/packages/libreoffice.xml") @@ -1298,6 +1304,7 @@ converting QuarkXPress file format. It supports versions 3.1 to 4.1.") "--without-java" ;; FIXME: Enable once the corresponding inputs are packaged. "--disable-coinmp" + "--disable-skia" ;; This could (Debian does this) be a separate output containing only ;; program/libfirebird_sdbclo.so, if there's a way to point to it. "--enable-firebird-sdbc" From a40207bd6f27d5cfb880974b196606631efa9b4e Mon Sep 17 00:00:00 2001 From: Pierre Neidhardt Date: Tue, 22 Jun 2021 12:58:43 +0200 Subject: [PATCH 099/144] gnu: nyxt: Update to 2.1.0. * gnu/packages/web-browsers.scm (nyxt): Update to 2.1.0. --- gnu/packages/web-browsers.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/web-browsers.scm b/gnu/packages/web-browsers.scm index f70af1af50..97da3d74e3 100644 --- a/gnu/packages/web-browsers.scm +++ b/gnu/packages/web-browsers.scm @@ -604,7 +604,7 @@ driven and does not detract you from your daily work.") (define-public nyxt (package (name "nyxt") - (version "2.0.0") + (version "2.1.0") (source (origin (method git-fetch) @@ -615,7 +615,7 @@ driven and does not detract you from your daily work.") (commit version))) (sha256 (base32 - "0y91hnanf1bj378zsxhjh33qnhj09f6ixpdqmkl69k0075zls93r")) + "0f2c029213apppj6ziky3wsrpsi2gpx9s55wnfriy6hp33j241gd")) (file-name (git-file-name "nyxt" version)))) (build-system gnu-build-system) (arguments From 4c98db94b0271aa5371ff00cf98c0ebc70ab1a8d Mon Sep 17 00:00:00 2001 From: Julien Lepiller Date: Tue, 1 Jun 2021 00:44:14 +0200 Subject: [PATCH 100/144] guix: java-utils: Factorize pom.xml generation. * guix/build/java-utils.scm (generate-pom.xml): New procedure. * gnu/packages/maven.scm (java-surefire-junit4): Use it. * gnu/packages/java.scm (java-qdox, java-jsr250, java-jsr305) (java-aopalliance, java-jboss-el-api-spec) (java-jboss-interceptors-api-spec): Use it. (java-qdox-M9): Ensure the generated pom file has the correct version. --- gnu/packages/java.scm | 117 ++++++-------------------------------- gnu/packages/maven.scm | 28 ++++----- guix/build/java-utils.scm | 29 ++++++++++ 3 files changed, 58 insertions(+), 116 deletions(-) diff --git a/gnu/packages/java.scm b/gnu/packages/java.scm index 471cc5e906..59f9497ec2 100644 --- a/gnu/packages/java.scm +++ b/gnu/packages/java.scm @@ -3847,25 +3847,11 @@ documentation tools.") (arguments `(#:jar-name "qdox.jar" #:tests? #f; no tests - #:modules - ((guix build ant-build-system) - (guix build java-utils) - (guix build utils) - (sxml simple)) #:phases (modify-phases %standard-phases (add-before 'install 'create-pom - (lambda _ - (with-output-to-file "pom.xml" - (lambda _ - (sxml->xml - `((project - (modelVersion "4.0.0") - (name "QDox") - (groupId "com.thoughtworks.qdox") - (artifactId "qdox") - (version ,,version)))))) - #t)) + (generate-pom.xml "pom.xml" "com.thoughtworks.qdox" "qdox" ,version + #:name "QDox")) (replace 'install (install-from-pom "pom.xml"))))) (home-page "https://github.com/codehaus/qdox") @@ -3891,7 +3877,14 @@ documentation tools.") "/qdox-" version "-sources.jar")) (sha256 (base32 - "1s2jnmx2dkwnaha12lcj26aynywgwa8sslc47z82wx8xai13y4fg")))))) + "1s2jnmx2dkwnaha12lcj26aynywgwa8sslc47z82wx8xai13y4fg")))) + (arguments + (substitute-keyword-arguments (package-arguments java-qdox) + ((#:phases phases) + `(modify-phases ,phases + (replace 'create-pom + (generate-pom.xml "pom.xml" "com.thoughtworks.qdox" "qdox" ,version + #:name "QDox")))))))) (define-public java-jarjar (package @@ -6463,25 +6456,11 @@ bottlenecks move away from the database in an effectively cached system.") `(#:tests? #f ; no tests included #:jdk ,icedtea-8 #:jar-name "jsr250.jar" - #:modules ((guix build ant-build-system) - (guix build utils) - (guix build maven pom) - (guix build java-utils) - (sxml simple)) #:phases (modify-phases %standard-phases (add-before 'install 'create-pom - (lambda _ - (with-output-to-file "pom.xml" - (lambda _ - (sxml->xml - `((project - (modelVersion "4.0.0") - (name "jsr250") - (groupId "javax.annotation") - (artifactId "jsr250-api") - (version ,,version)))))) - #t)) + (generate-pom.xml "pom.xml" "javax.annotation" "jsr250-api" ,version + #:name "jsr250")) (replace 'install (install-from-pom "pom.xml"))))) (home-page "https://jcp.org/en/jsr/detail?id=250") @@ -6510,25 +6489,10 @@ namespaces.") (arguments `(#:tests? #f ; no tests included #:jar-name "jsr305.jar" - #:modules ((guix build ant-build-system) - (guix build java-utils) - (guix build maven pom) - (guix build utils) - (sxml simple)) #:phases (modify-phases %standard-phases (add-before 'install 'create-pom - (lambda _ - (with-output-to-file "pom.xml" - (lambda _ - (sxml->xml - `((project - (modelVersion "4.0.0") - (name "jsr305") - (groupId "com.google.code.findbugs") - (artifactId "jsr305") - (version ,,version)))))) - #t)) + (generate-pom.xml "pom.xml" "com.google.code.findbugs" "jsr305" ,version)) (replace 'install (install-from-pom "pom.xml"))))) (home-page "http://findbugs.sourceforge.net/") @@ -10559,25 +10523,10 @@ this is not a static analysis tool.)") #:jdk ,icedtea-8 #:tests? #f; no tests #:source-dir "aopalliance/src/main" - #:modules ((guix build ant-build-system) - (guix build utils) - (guix build maven pom) - (guix build java-utils) - (sxml simple)) #:phases (modify-phases %standard-phases (add-before 'install 'create-pom - (lambda _ - (with-output-to-file "pom.xml" - (lambda _ - (sxml->xml - `((project - (modelVersion "4.0.0") - (name "aopalliance") - (groupId "aopalliance") - (artifactId "aopalliance") - (version "1.0")))))) - #t)) + (generate-pom.xml "pom.xml" "aopalliance" "aopalliance" ,version)) (replace 'install (install-from-pom "pom.xml"))))) (home-page "http://aopalliance.sourceforge.net") @@ -12176,29 +12125,14 @@ sequences to format your console output which works on every platform.") (build-system ant-build-system) (arguments `(#:jar-name "java-jboss-el-api_spec.jar" - #:modules ((guix build ant-build-system) - (guix build utils) - (guix build maven pom) - (guix build java-utils) - (sxml simple)) #:phases (modify-phases %standard-phases ;; the origin of javax.el:javax.el-api is unknown, so we use this package ;; instead, which implements the same thing. We override the pom file ;; to "rename" the package so it can be found by maven. (add-before 'install 'override-pom - (lambda _ - (delete-file "pom.xml") - (with-output-to-file "pom.xml" - (lambda _ - (sxml->xml - `(project - (modelVersion "4.0.0") - (name "el-api") - (groupId "javax.el") - (artifactId "javax.el-api") - (version "3.0"))))) - #t)) + (generate-pom.xml "pom.xml" "javax.el" "javax.el-api" "3.0" + #:name "el-api")) (replace 'install (install-from-pom "pom.xml"))))) (inputs @@ -12230,11 +12164,6 @@ JavaServer Pages (JSP).") #:jdk ,icedtea-8 #:source-dir "." #:tests? #f; no tests - #:modules ((guix build ant-build-system) - (guix build utils) - (guix build maven pom) - (guix build java-utils) - (sxml simple)) #:phases (modify-phases %standard-phases ;; the origin of javax.interceptor:javax.interceptor-api is unknown, @@ -12242,18 +12171,8 @@ JavaServer Pages (JSP).") ;; We override the pom file to "rename" the package so it can be found ;; by maven. (add-before 'install 'override-pom - (lambda _ - (delete-file "pom.xml") - (with-output-to-file "pom.xml" - (lambda _ - (sxml->xml - `(project - (modelVersion "4.0.0") - (name "interceptor-api") - (groupId "javax.interceptor") - (artifactId "javax.interceptor-api") - (version "3.0"))))) - #t)) + (generate-pom.xml "pom.xml" "javax.interceptor" "javax.interceptor-api" + "3.0" #:name "interceptor-api")) (replace 'install (install-from-pom "pom.xml"))))) (home-page "https://github.com/jboss/jboss-interceptors-api_spec") diff --git a/gnu/packages/maven.scm b/gnu/packages/maven.scm index c637e5c7ae..8f63ee9be2 100644 --- a/gnu/packages/maven.scm +++ b/gnu/packages/maven.scm @@ -3424,23 +3424,17 @@ starting from JUnit 4."))) #:phases (modify-phases %standard-phases (add-before 'install 'regenerate-own-pom - (lambda _ - ;; Surefire struggles resolving artifacts because of this pom - ;; file, resulting in a NullPointerException when collecting - ;; Artifacts (and a "Failure detected." message from - ;; DefaultArtifactResolver). Replace the pom file with a much - ;; simpler one. Everything is shaded anyway (as used to be the - ;; case in 2.22), so there will not be missing dependencies. - (with-output-to-file "surefire-providers/surefire-junit4/pom.xml" - (lambda _ - (sxml->xml - `((project - (modelVersion "4.0.0") - (name "Surefire JUnit4") - (groupId "org.apache.maven.surefire") - (artifactId "surefire-junit4") - (version ,,(package-version java-surefire-common-java5))))))) - #t)) + ;; Surefire struggles resolving artifacts because of this pom + ;; file, resulting in a NullPointerException when collecting + ;; Artifacts (and a "Failure detected." message from + ;; DefaultArtifactResolver). Replace the pom file with a much + ;; simpler one. Everything is shaded anyway (as used to be the + ;; case in 2.22), so there will not be missing dependencies. + (generate-pom.xml + "surefire-providers/surefire-junit4/pom.xml" + "org.apache.maven.surefire" "surefire-junit4" + ,(package-version java-surefire-common-java5) + #:name "Surefire JUnit4")) (add-before 'build 'copy-resources (lambda _ (mkdir-p "build/classes") diff --git a/guix/build/java-utils.scm b/guix/build/java-utils.scm index a868e4d52c..6abd97e118 100644 --- a/guix/build/java-utils.scm +++ b/guix/build/java-utils.scm @@ -28,6 +28,7 @@ #:use-module (sxml simple) #:export (ant-build-javadoc generate-plugin.xml + generate-pom.xml install-jars install-javadoc install-pom-file @@ -206,3 +207,31 @@ recognize the package as a plugin, and find the entry points in the plugin." ,mojos (dependencies ,@dependencies))))))))) + +(define* (generate-pom.xml pom-file groupid artifactid version + #:key (dependencies '()) + (name artifactid)) + "Generates the @file{pom.xml} for a project. It is required by Maven to find +a package, and by the java build system to know where to install a package, when +a pom.xml doesn't already exist and installing to the maven repository." + (lambda _ + (mkdir-p (dirname pom-file)) + (with-output-to-file pom-file + (lambda _ + (sxml->xml + (sxml-indent + `(project + (modelVersion "4.0.0") + (name ,name) + (groupId ,groupid) + (artifactId ,artifactid) + (version ,version) + (dependencies + ,@(map + (match-lambda + ((groupid artifactid version) + `(dependency + (groupId ,groupid) + (artifactId ,artifactid) + (version ,version)))) + dependencies))))))))) From 573b43c11675a2a125ab8c7d930f32e11f9d3acb Mon Sep 17 00:00:00 2001 From: Julien Lepiller Date: Tue, 1 Jun 2021 00:44:15 +0200 Subject: [PATCH 101/144] guix: maven: Simplify finding version and group information. * guix/build/maven/pom.scm (pom-version, pom-groupid): Do not use inputs and local packages information anymore. Adapt file to new arguments. * guix/build/maven-build-system.scm: Adapt to new arguments. * guix/build/java-utils.scm: Adapt to new arguments. --- guix/build/java-utils.scm | 18 +++++++++--------- guix/build/maven-build-system.scm | 6 +++--- guix/build/maven/pom.scm | 26 ++++++++++++-------------- 3 files changed, 24 insertions(+), 26 deletions(-) diff --git a/guix/build/java-utils.scm b/guix/build/java-utils.scm index 6abd97e118..5a54a14c1b 100644 --- a/guix/build/java-utils.scm +++ b/guix/build/java-utils.scm @@ -2,7 +2,7 @@ ;;; Copyright © 2016 Hartmut Goebel ;;; Copyright © 2016 Ricardo Wurmus ;;; Copyright © 2018 Alex Vong -;;; Copyright © 2020 Julien Lepiller +;;; Copyright © 2020, 2021 Julien Lepiller ;;; ;;; This file is part of GNU Guix. ;;; @@ -69,9 +69,9 @@ fetched." (let* ((out (assoc-ref outputs "out")) (java-inputs (append (map cdr inputs) (map cdr outputs))) (pom-content (get-pom pom-file)) - (version (pom-version pom-content java-inputs)) + (version (pom-version pom-content)) (artifact (pom-artifactid pom-content)) - (group (group->dir (pom-groupid pom-content java-inputs))) + (group (group->dir (pom-groupid pom-content))) (repository (string-append out "/lib/m2/" group "/" artifact "/" version "/")) (pom-name (string-append repository artifact "-" version ".pom"))) @@ -87,8 +87,8 @@ to ensure that maven can find dependencies." (manifest (string-append dir "/META-INF/MANIFEST.MF")) (pom (get-pom pom-file)) (artifact (pom-artifactid pom)) - (group (pom-groupid pom inputs)) - (version (pom-version pom inputs)) + (group (pom-groupid pom)) + (version (pom-version pom)) (pom-dir (string-append "META-INF/maven/" group "/" artifact))) (mkdir-p (string-append dir "/" pom-dir)) (copy-file pom-file (string-append dir "/" pom-dir "/pom.xml")) @@ -113,9 +113,9 @@ the phase fails." (let* ((out (assoc-ref outputs "out")) (java-inputs (append (map cdr inputs) (map cdr outputs))) (pom-content (get-pom pom-file)) - (version (pom-version pom-content java-inputs)) + (version (pom-version pom-content)) (artifact (pom-artifactid pom-content)) - (group (group->dir (pom-groupid pom-content java-inputs))) + (group (group->dir (pom-groupid pom-content))) (repository (string-append out "/lib/m2/" group "/" artifact "/" version "/")) ;; We try to find the file that was built. If it was built from our @@ -180,9 +180,9 @@ recognize the package as a plugin, and find the entry points in the plugin." (name (pom-name pom-content)) (description (pom-description pom-content)) (dependencies (pom-dependencies pom-content)) - (version (pom-version pom-content java-inputs)) + (version (pom-version pom-content)) (artifact (pom-artifactid pom-content)) - (groupid (pom-groupid pom-content java-inputs)) + (groupid (pom-groupid pom-content)) (mojos `(mojos ,@(with-directory-excursion directory diff --git a/guix/build/maven-build-system.scm b/guix/build/maven-build-system.scm index 534b4ebcee..0456bfdf61 100644 --- a/guix/build/maven-build-system.scm +++ b/guix/build/maven-build-system.scm @@ -1,5 +1,5 @@ ;;; GNU Guix --- Functional package management for GNU -;;; Copyright © 2020 Julien Lepiller +;;; Copyright © 2020, 2021 Julien Lepiller ;;; ;;; This file is part of GNU Guix. ;;; @@ -82,8 +82,8 @@ (let* ((pom (get-pom pom-file)) (java-inputs (map cdr inputs)) (artifact (pom-artifactid pom)) - (group (pom-groupid pom java-inputs local-packages)) - (version (pom-version pom java-inputs local-packages))) + (group (pom-groupid pom)) + (version (pom-version pom))) (let loop ((modules (pom-ref pom "modules")) (local-packages (add-local-package local-packages group artifact version))) diff --git a/guix/build/maven/pom.scm b/guix/build/maven/pom.scm index c92d409d2b..327d5f75e8 100644 --- a/guix/build/maven/pom.scm +++ b/guix/build/maven/pom.scm @@ -1,5 +1,5 @@ ;;; GNU Guix --- Functional package management for GNU -;;; Copyright © 2019, 2020 Julien Lepiller +;;; Copyright © 2019-2021 Julien Lepiller ;;; ;;; This file is part of GNU Guix. ;;; @@ -93,13 +93,12 @@ If no result is found, the result is @code{#f}." (get-pom (car java-inputs)))) #f))) -(define* (pom-groupid content inputs #:optional local-packages) +(define* (pom-groupid content) "Find the groupID of a pom file, potentially looking at its parent pom file. See @code{find-parent} for the meaning of the arguments." (if content (let ((res (or (pom-ref content "groupId") - (pom-groupid (find-parent content inputs local-packages) - inputs)))) + (pom-ref (pom-ref content "parent") "groupId")))) (cond ((string? res) res) ((null? res) #f) @@ -114,13 +113,12 @@ See @code{find-parent} for the meaning of the arguments." (car res) #f))) -(define* (pom-version content inputs #:optional local-packages) +(define* (pom-version content) "Find the version of a pom file, potentially looking at its parent pom file. See @code{find-parent} for the meaning of the arguments." (if content (let ((res (or (pom-ref content "version") - (pom-version (find-parent content inputs local-packages) - inputs)))) + (pom-ref (pom-ref content "parent") "version")))) (cond ((string? res) res) ((null? res) #f) @@ -344,7 +342,7 @@ Returns nothing, but overrides the @var{pom-file} as a side-effect." ((tag rest ...) (match tag (('http://maven.apache.org/POM/4.0.0:plugin plugin ...) - (let ((group (or (pom-groupid plugin inputs) "org.apache.maven.plugins")) + (let ((group (or (pom-groupid plugin) "org.apache.maven.plugins")) (artifact (pom-artifactid plugin))) (if (member artifact (or (assoc-ref excludes group) '())) (fix-plugins rest optional?) @@ -355,11 +353,11 @@ Returns nothing, but overrides the @var{pom-file} as a side-effect." (define* (fix-plugin plugin #:optional optional?) (let* ((artifact (pom-artifactid plugin)) - (group (or (pom-groupid plugin inputs) "org.apache.maven.plugins")) + (group (or (pom-groupid plugin) "org.apache.maven.plugins")) (version (or (assoc-ref (assoc-ref local-packages group) artifact) (find-version inputs group artifact optional?) - (pom-version plugin inputs)))) - (if (pom-version plugin inputs) + (pom-version plugin)))) + (if (pom-version plugin) (map (lambda (tag) (match tag @@ -373,7 +371,7 @@ Returns nothing, but overrides the @var{pom-file} as a side-effect." (define* (fix-dep dep #:optional optional?) (let* ((artifact (pom-artifactid dep)) - (group (or (pom-groupid dep inputs) (pom-groupid pom inputs))) + (group (or (pom-groupid dep) (pom-groupid pom))) (scope (pom-ref dep "scope")) (is-optional? (equal? (pom-ref dep "optional") '("true")))) (format (current-error-port) "maven: ~a:~a :: ~a (optional: ~a)~%" @@ -382,8 +380,8 @@ Returns nothing, but overrides the @var{pom-file} as a side-effect." with-build-dependencies?) (let ((version (or (assoc-ref (assoc-ref local-packages group) artifact) (find-version inputs group artifact optional?) - (pom-version dep inputs)))) - (if (pom-version dep inputs) + (pom-version dep)))) + (if (pom-version dep) (map (lambda (tag) (match tag From 6ec2109ab6ea8c8503288a5729a795939e6db41e Mon Sep 17 00:00:00 2001 From: Julien Lepiller Date: Tue, 1 Jun 2021 00:44:16 +0200 Subject: [PATCH 102/144] guix: maven: Simplify finding local packages and modules. * guix/build/maven-build-system (fix-pom): Fix a single pom file without recursing (fix-pom-files): Find local packages and all submodules, and fix them all at once. (add-local-package): Move to... * guix/build/maven/pom.scm (add-local-package): ...here. (pom-and-submodules, pom-local-packages): New procedures. --- guix/build/maven-build-system.scm | 41 +++++------------------- guix/build/maven/pom.scm | 53 ++++++++++++++++++++++++++++++- 2 files changed, 60 insertions(+), 34 deletions(-) diff --git a/guix/build/maven-build-system.scm b/guix/build/maven-build-system.scm index 0456bfdf61..374fa2fdb8 100644 --- a/guix/build/maven-build-system.scm +++ b/guix/build/maven-build-system.scm @@ -60,47 +60,22 @@ (invoke "mvn" "-v") #t) -(define (add-local-package local-packages group artifact version) - (define (alist-set lst key val) - (match lst - ('() (list (cons key val))) - (((k . v) lst ...) - (if (equal? k key) - (cons (cons key val) lst) - (cons (cons k v) (alist-set lst key val)))))) - (alist-set local-packages group - (alist-set (or (assoc-ref local-packages group) '()) artifact - version))) - (define (fix-pom pom-file inputs local-packages excludes) (chmod pom-file #o644) (format #t "fixing ~a~%" pom-file) (fix-pom-dependencies pom-file (map cdr inputs) #:with-plugins? #t #:with-build-dependencies? #t #:local-packages local-packages - #:excludes excludes) - (let* ((pom (get-pom pom-file)) - (java-inputs (map cdr inputs)) - (artifact (pom-artifactid pom)) - (group (pom-groupid pom)) - (version (pom-version pom))) - (let loop ((modules (pom-ref pom "modules")) - (local-packages - (add-local-package local-packages group artifact version))) - (pk 'local-packages local-packages) - (match modules - (#f local-packages) - ('() local-packages) - (((? string? _) modules ...) - (loop modules local-packages)) - (((_ module) modules ...) - (loop - modules - (fix-pom (string-append (dirname pom-file) "/" module "/pom.xml") - inputs local-packages excludes))))))) + #:excludes excludes)) (define* (fix-pom-files #:key inputs local-packages exclude #:allow-other-keys) - (fix-pom "pom.xml" inputs local-packages exclude) + (let ((local-packages (pom-local-packages "pom.xml" #:local-packages local-packages))) + (format (current-error-port) "Fix pom files with local packages: ~a~%" local-packages) + (for-each + (lambda (pom) + (when (file-exists? pom) + (fix-pom pom inputs local-packages exclude))) + (pom-and-submodules "pom.xml"))) #t) (define* (build #:key outputs #:allow-other-keys) diff --git a/guix/build/maven/pom.scm b/guix/build/maven/pom.scm index 327d5f75e8..8f16cf4d26 100644 --- a/guix/build/maven/pom.scm +++ b/guix/build/maven/pom.scm @@ -21,7 +21,8 @@ #:use-module (system foreign) #:use-module (ice-9 match) #:use-module (srfi srfi-1) - #:export (get-pom + #:export (add-local-package + get-pom pom-ref pom-description pom-name @@ -30,8 +31,24 @@ pom-groupid pom-dependencies group->dir + pom-and-submodules + pom-local-packages fix-pom-dependencies)) +(define (add-local-package local-packages group artifact version) + "Takes @var{local-packages}, a list of local packages, and adds a new one +for @var{group}:@var{artifact} at @var{version}." + (define (alist-set lst key val) + (match lst + ('() (list (cons key val))) + (((k . v) lst ...) + (if (equal? k key) + (cons (cons key val) lst) + (cons (cons k v) (alist-set lst key val)))))) + (alist-set local-packages group + (alist-set (or (assoc-ref local-packages group) '()) artifact + version))) + (define (get-pom file) "Return the content of a @file{.pom} file." (let ((pom-content (call-with-input-file file xml->sxml))) @@ -234,6 +251,40 @@ to re-declare the namespaces in the top-level element." http://maven.apache.org/xsd/maven-4.0.0.xsd")) ,(map fix-xml sxml))))) +(define (pom-and-submodules pom-file) + "Given @var{pom-file}, the file name of a pom, return the list of pom file +names that correspond to itself and its submodules, recursively." + (define (get-modules modules) + (match modules + (#f '()) + ('() '()) + (((? string? _) rest ...) (get-modules rest)) + ((('http://maven.apache.org/POM/4.0.0:module mod) rest ...) + (let ((pom (string-append (dirname pom-file) "/" mod "/pom.xml"))) + (if (file-exists? pom) + (cons pom (get-modules rest)) + (get-modules rest)))))) + + (let* ((pom (get-pom pom-file)) + (modules (get-modules (pom-ref pom "modules")))) + (cons pom-file + (apply append (map pom-and-submodules modules))))) + +(define* (pom-local-packages pom-file #:key (local-packages '())) + "Given @var{pom-file}, a pom file name, return a list of local packages that +this repository contains." + (let loop ((modules (pom-and-submodules pom-file)) + (local-packages local-packages)) + (match modules + (() local-packages) + ((module modules ...) + (let* ((pom (get-pom module)) + (version (pom-version pom)) + (artifactid (pom-artifactid pom)) + (groupid (pom-groupid pom))) + (loop modules + (add-local-package local-packages groupid artifactid version))))))) + (define (group->dir group) "Convert a group ID to a directory path." (string-join (string-split group #\.) "/")) From 9711970c99cfbf1b5546c395d5407d67b954c343 Mon Sep 17 00:00:00 2001 From: Julien Lepiller Date: Tue, 1 Jun 2021 00:44:17 +0200 Subject: [PATCH 103/144] guix: maven: Support fixing extensions. * guix/build/maven/pom.scm (fix-pom-dependencies): Add support for fixing extension versions. --- guix/build/maven/pom.scm | 19 +++++++++++++++++++ 1 file changed, 19 insertions(+) diff --git a/guix/build/maven/pom.scm b/guix/build/maven/pom.scm index 8f16cf4d26..3a4ad7a216 100644 --- a/guix/build/maven/pom.scm +++ b/guix/build/maven/pom.scm @@ -374,8 +374,27 @@ Returns nothing, but overrides the @var{pom-file} as a side-effect." `((http://maven.apache.org/POM/4.0.0:plugins ,(fix-plugins plugins)) ,@(fix-build rest))) + (('http://maven.apache.org/POM/4.0.0:extensions extensions ...) + `((http://maven.apache.org/POM/4.0.0:extensions + ,(fix-extensions extensions)) + ,@(fix-build rest))) (tag (cons tag (fix-build rest))))))) + (define* (fix-extensions extensions #:optional optional?) + (match extensions + ('() '()) + ((tag rest ...) + (match tag + (('http://maven.apache.org/POM/4.0.0:extension extension ...) + (let ((group (or (pom-groupid extension) "org.apache.maven.plugins")) + (artifact (pom-artifactid extension))) + (if (member artifact (or (assoc-ref excludes group) '())) + (fix-extensions rest optional?) + `((http://maven.apache.org/POM/4.0.0:extension + ,(fix-plugin extension optional?)); extensions are similar to plugins + ,@(fix-extensions rest optional?))))) + (tag (cons tag (fix-extensions rest optional?))))))) + (define fix-management (match-lambda ('() '()) From 0db1393b732304220aff978676b5354bfa186a65 Mon Sep 17 00:00:00 2001 From: Julien Lepiller Date: Tue, 1 Jun 2021 00:44:18 +0200 Subject: [PATCH 104/144] guix: maven: Support fixing modules. * guix/build/maven/pom.scm (fix-pom-dependencies): Support fixing modules that do not exist. * guix/build/maven-build-system.scm (fix-pom): Fix modules. --- guix/build/maven-build-system.scm | 1 + guix/build/maven/pom.scm | 19 ++++++++++++++++++- 2 files changed, 19 insertions(+), 1 deletion(-) diff --git a/guix/build/maven-build-system.scm b/guix/build/maven-build-system.scm index 374fa2fdb8..b3d97c81ea 100644 --- a/guix/build/maven-build-system.scm +++ b/guix/build/maven-build-system.scm @@ -65,6 +65,7 @@ (format #t "fixing ~a~%" pom-file) (fix-pom-dependencies pom-file (map cdr inputs) #:with-plugins? #t #:with-build-dependencies? #t + #:with-modules? #t #:local-packages local-packages #:excludes excludes)) diff --git a/guix/build/maven/pom.scm b/guix/build/maven/pom.scm index 3a4ad7a216..ffb4515179 100644 --- a/guix/build/maven/pom.scm +++ b/guix/build/maven/pom.scm @@ -291,7 +291,8 @@ this repository contains." (define* (fix-pom-dependencies pom-file inputs #:key with-plugins? with-build-dependencies? - (excludes '()) (local-packages '())) + with-modules? (excludes '()) + (local-packages '())) "Open @var{pom-file}, and override its content, rewritting its dependencies to set their version to the latest version available in the @var{inputs}. @@ -339,8 +340,24 @@ Returns nothing, but overrides the @var{pom-file} as a side-effect." `((http://maven.apache.org/POM/4.0.0:build ,(fix-build build)) ,@(fix-pom rest)) (cons tag (fix-pom rest)))) + (('http://maven.apache.org/POM/4.0.0:modules modules ...) + (if with-modules? + `((http://maven.apache.org/POM/4.0.0:modules ,(fix-modules modules)) + ,@(fix-pom rest)) + (cons tag (fix-pom rest)))) (tag (cons tag (fix-pom rest))))))) + (define fix-modules + (match-lambda + ('() '()) + ((tag rest ...) + (match tag + (('http://maven.apache.org/POM/4.0.0:module module) + (if (file-exists? (string-append (dirname pom-file) "/" module "/pom.xml")) + `((http://maven.apache.org/POM/4.0.0:module ,module) ,@(fix-modules rest)) + (fix-modules rest))) + (tag (cons tag (fix-modules rest))))))) + (define fix-dep-management (match-lambda ('() '()) From 5bb3395c42c3475cd4d71d475ae050f1b80fbe2d Mon Sep 17 00:00:00 2001 From: Julien Lepiller Date: Tue, 1 Jun 2021 00:44:19 +0200 Subject: [PATCH 105/144] guix: maven: Look in local packages when searching for package version. * guix/build/maven/pom.scm (fix-pom-dependencies): Also look at local packages when looking for a package version. --- guix/build/maven/pom.scm | 20 +++++++++++++------- 1 file changed, 13 insertions(+), 7 deletions(-) diff --git a/guix/build/maven/pom.scm b/guix/build/maven/pom.scm index ffb4515179..9c0669c7cd 100644 --- a/guix/build/maven/pom.scm +++ b/guix/build/maven/pom.scm @@ -481,7 +481,7 @@ Returns nothing, but overrides the @var{pom-file} as a side-effect." (cons `(http://maven.apache.org/POM/4.0.0:version ,version) dep))) dep))) - (define* (find-version inputs group artifact #:optional optional?) + (define (find-packaged-version inputs group artifact) (let* ((directory (string-append "lib/m2/" (group->dir group) "/" artifact)) (java-inputs (filter @@ -493,13 +493,19 @@ Returns nothing, but overrides the @var{pom-file} as a side-effect." (versions (append-map ls java-inputs)) (versions (sort versions version>?))) (if (null? versions) - (if optional? #f - (begin - (format (current-error-port) "maven: ~a:~a is missing from inputs~%" - group artifact) - (throw 'no-such-input group artifact))) - (car versions)))) + (car versions)))) + + (define* (find-version inputs group artifact #:optional optional?) + (let ((packaged-version (find-packaged-version inputs group artifact)) + (local-version (assoc-ref (assoc-ref local-packages group) artifact))) + (or local-version packaged-version + (if optional? + #f + (begin + (format (current-error-port) "maven: ~a:~a is missing from inputs~%" + group artifact) + (throw 'no-such-input group artifact)))))) (let ((tmpfile (string-append pom-file ".tmp"))) (with-output-to-file pom-file From cc09453862d1604bbbb4a2a9487e395d9a459708 Mon Sep 17 00:00:00 2001 From: Julien Lepiller Date: Tue, 1 Jun 2021 00:44:20 +0200 Subject: [PATCH 106/144] guix: maven: Use a temporary file to fix pom files. * guix/build/maven/pom.scm (fix-pom-dependencies): Actually use the temporary file that was created. --- guix/build/maven/pom.scm | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/guix/build/maven/pom.scm b/guix/build/maven/pom.scm index 9c0669c7cd..9e35e47a7f 100644 --- a/guix/build/maven/pom.scm +++ b/guix/build/maven/pom.scm @@ -508,6 +508,7 @@ Returns nothing, but overrides the @var{pom-file} as a side-effect." (throw 'no-such-input group artifact)))))) (let ((tmpfile (string-append pom-file ".tmp"))) - (with-output-to-file pom-file + (with-output-to-file tmpfile (lambda _ - (sxml->xml (fix-maven-xml (fix-pom pom))))))) + (sxml->xml (fix-maven-xml (fix-pom pom))))) + (rename-file tmpfile pom-file))) From 7f902d368de9d5539ae0caf531fe64bca5339c5f Mon Sep 17 00:00:00 2001 From: Julien Lepiller Date: Tue, 1 Jun 2021 00:44:21 +0200 Subject: [PATCH 107/144] guix: java-utils: Look for actual jar files. * guix/build/java-utils.scm (install-from-pom): Fix `find-files` to look only for jar files. --- guix/build/java-utils.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/guix/build/java-utils.scm b/guix/build/java-utils.scm index 5a54a14c1b..87c3ac43c9 100644 --- a/guix/build/java-utils.scm +++ b/guix/build/java-utils.scm @@ -125,7 +125,7 @@ the phase fails." version ".jar")))) ;; Otherwise, we try to find any jar file. (jars (if (null? jars) - (find-files "." ".*.jar") + (find-files "." "\\.jar$") jars)) (jar-name (string-append repository artifact "-" version ".jar")) (pom-name (string-append repository artifact "-" version ".pom"))) From 01706f6e0081674dffa39a49c33e04d48aad5300 Mon Sep 17 00:00:00 2001 From: Julien Lepiller Date: Tue, 1 Jun 2021 00:44:22 +0200 Subject: [PATCH 108/144] gnu: Add java-jopt-simple-4. * gnu/packges/java.scm (java-jopt-simple-4): New variable. (java-jopt-simple): Install to maven repository structure. --- gnu/packages/java.scm | 32 ++++++++++++++++++++++++++++++-- 1 file changed, 30 insertions(+), 2 deletions(-) diff --git a/gnu/packages/java.scm b/gnu/packages/java.scm index 59f9497ec2..b34e31a612 100644 --- a/gnu/packages/java.scm +++ b/gnu/packages/java.scm @@ -3,7 +3,7 @@ ;;; Copyright © 2016 Leo Famulari ;;; Copyright © 2016, 2017 Roel Janssen ;;; Copyright © 2017, 2019, 2021 Carlo Zancanaro -;;; Copyright © 2017-2020 Julien Lepiller +;;; Copyright © 2017-2021 Julien Lepiller ;;; Copyright © 2017 Thomas Danckaert ;;; Copyright © 2016, 2017, 2018 Alex Vong ;;; Copyright © 2017, 2019, 2021 Tobias Geerinckx-Rice @@ -5781,7 +5781,13 @@ The jMock library (build-system ant-build-system) (arguments `(#:tests? #f ; there are no tests - #:jar-name "jopt-simple.jar")) + #:jar-name "jopt-simple.jar" + #:phases + (modify-phases %standard-phases + (add-before 'install 'create-pom + (generate-pom.xml "pom.xml" "net.sf.jopt-simple" "jopt-simple" ,version)) + (replace 'install + (install-from-pom "pom.xml"))))) (home-page "https://pholser.github.io/jopt-simple/") (synopsis "Java library for parsing command line options") (description "JOpt Simple is a Java library for parsing command line @@ -5793,6 +5799,28 @@ retrieval of options and their arguments simple and expressive, without being overly clever.") (license license:expat))) +;; Required by jmh +(define-public java-jopt-simple-4 + (package + (inherit java-jopt-simple) + (version "4.6") + (source (origin + (method url-fetch) + (uri (string-append "https://repo1.maven.org/maven2/" + "net/sf/jopt-simple/jopt-simple/" + version "/jopt-simple-" + version "-sources.jar")) + (sha256 + (base32 + "0ny82zczxkn201ld0b7rps0ifzjhfs8m1ncdmy1f50145ciszkpd")))) + (arguments + (substitute-keyword-arguments (package-arguments java-jopt-simple) + ((#:phases phases) + `(modify-phases ,phases + (replace 'create-pom + (generate-pom.xml "pom.xml" "net.sf.jopt-simple" "jopt-simple" + ,version)))))))) + (define-public java-commons-math3 (package (name "java-commons-math3") From 887410838628a9a1d5c15e71a6e48f4afd9ec33b Mon Sep 17 00:00:00 2001 From: Julien Lepiller Date: Tue, 1 Jun 2021 00:44:23 +0200 Subject: [PATCH 109/144] gnu: java-commons-math3: Install to maven repository. * gnu/packages/java.scm (java-commons-math3)[phases]: Use install-from-pom. --- gnu/packages/java.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/gnu/packages/java.scm b/gnu/packages/java.scm index b34e31a612..dd30e70635 100644 --- a/gnu/packages/java.scm +++ b/gnu/packages/java.scm @@ -5855,7 +5855,7 @@ overly clever.") #t)) ;; There is no install target. (replace 'install - (install-jars "target"))))) + (install-from-pom "pom.xml"))))) (native-inputs `(("java-junit" ,java-junit) ("java-hamcrest-core" ,java-hamcrest-core))) From b6b9668949ec73b45141d9002802f55c5604a3bd Mon Sep 17 00:00:00 2001 From: Julien Lepiller Date: Tue, 1 Jun 2021 00:44:24 +0200 Subject: [PATCH 110/144] gnu: maven-core: Hardcode versions we have in Guix. * gnu/packages/maven.scm (maven-core)[phases]: Replace default hardcoded versions by versions of packages we have in Guix. --- gnu/packages/maven.scm | 29 ++++++++++++++++++++++++++--- 1 file changed, 26 insertions(+), 3 deletions(-) diff --git a/gnu/packages/maven.scm b/gnu/packages/maven.scm index 8f63ee9be2..9d65e9b56d 100644 --- a/gnu/packages/maven.scm +++ b/gnu/packages/maven.scm @@ -1,5 +1,5 @@ ;;; GNU Guix --- Functional package management for GNU -;;; Copyright © 2018 Julien Lepiller +;;; Copyright © 2018-2021 Julien Lepiller ;;; Copyright © 2019 Tobias Geerinckx-Rice ;;; Copyright © 2019 Björn Höfling ;;; Copyright © 2020 Efraim Flashner @@ -1541,7 +1541,9 @@ process.")))) (add-before 'build 'modify-metainf (lambda _ (substitute* "build.xml" - (("message=\"\"") "message=\"Implementation-Version: 3.5.4\n\"")) + (("message=\"\"") + (string-append "message=\"Implementation-Version: " + (package-version maven) "\n\""))) #t)) (add-before 'build 'add-maven-files (lambda _ @@ -1590,7 +1592,28 @@ artifactId=maven-core" ,(package-version maven-core-bootstrap)))) default-bindings-xml artifact-handlers-xml))))))) #t)) - (add-after 'generate-metadata 'rebuild + (add-after 'generate-metadata 'fix-plugin-versions + (lambda _ + ;; This file controls the default plugins used by Maven. Ensure + ;; we use the versions we have packaged by default + (substitute* '("build/classes/META-INF/plexus/default-bindings.xml" + "build/classes/META-INF/plexus/components.xml") + (("maven-install-plugin:[0-9.]+") + (string-append "maven-install-plugin:" + ,(package-version maven-install-plugin))) + (("maven-resources-plugin:[0-9.]+") + (string-append "maven-resources-plugin:" + ,(package-version maven-resources-plugin))) + (("maven-compiler-plugin:[0-9.]+") + (string-append "maven-compiler-plugin:" + ,(package-version maven-compiler-plugin))) + (("maven-surefire-plugin:[0-9.]+") + (string-append "maven-surefire-plugin:" + ,(package-version maven-surefire-plugin))) + (("maven-jar-plugin:[0-9.]+") + (string-append "maven-jar-plugin:" + ,(package-version maven-jar-plugin)))))) + (add-after 'fix-plugin-versions 'rebuild (lambda _ (invoke "ant" "jar") #t)))))) From 98d2ba1a5ad517d9de184cee2fd6b9df11978d07 Mon Sep 17 00:00:00 2001 From: Julien Lepiller Date: Tue, 1 Jun 2021 00:44:25 +0200 Subject: [PATCH 111/144] gnu: maven-enforcer-parent-pom: Fix pom. * gnu/packages/maven.scm (maven-enforcer-parent-pom): Fix dependency versions in pom file. --- gnu/packages/maven.scm | 9 +++++++++ 1 file changed, 9 insertions(+) diff --git a/gnu/packages/maven.scm b/gnu/packages/maven.scm index 9d65e9b56d..f7cb168f47 100644 --- a/gnu/packages/maven.scm +++ b/gnu/packages/maven.scm @@ -2713,6 +2713,15 @@ Maven project dependencies.") (modify-phases %standard-phases (delete 'configure) (delete 'build) + (add-before 'install 'fix-pom-versions + (lambda _ + (substitute* "pom.xml" + (("3.8.1") ,(package-version java-commons-lang3)) + (("1.4.1") ,(package-version maven-resolver-util)) + (("1.12") ,(package-version java-commons-codec)) + (("2.2") + ,(string-append "" (package-version maven-dependency-tree) + ""))))) (replace 'install (install-pom-file "pom.xml"))))) (propagated-inputs From 901d48cc17ea635a34e004b1d07a2e2a9bde6188 Mon Sep 17 00:00:00 2001 From: Julien Lepiller Date: Tue, 1 Jun 2021 00:44:26 +0200 Subject: [PATCH 112/144] gnu: java-jmh: Update to 1.32. * gnu/packages/java.scm (java-jmh): Update to 1.32. [source]: Switch to the git repository. --- gnu/packages/java.scm | 14 +++++++------- 1 file changed, 7 insertions(+), 7 deletions(-) diff --git a/gnu/packages/java.scm b/gnu/packages/java.scm index dd30e70635..7a9f1c3538 100644 --- a/gnu/packages/java.scm +++ b/gnu/packages/java.scm @@ -5869,16 +5869,16 @@ available in the Java programming language or Commons Lang.") (define-public java-jmh (package (name "java-jmh") - (version "1.17.5") + (version "1.32") (source (origin - (method hg-fetch) - (uri (hg-reference - (url "http://hg.openjdk.java.net/code-tools/jmh/") - (changeset version))) - (file-name (string-append name "-" version "-checkout")) + (method git-fetch) + (uri (git-reference + (url "https://github.com/openjdk/jmh") + (commit version))) + (file-name (git-file-name name version)) (sha256 (base32 - "1fxyxhg9famwcg1prc4cgwb5wzyxqavn3cjm5vz8605xz7x5k084")))) + "0i7fa7l3gdqkkgz5ddayp6m46dgbj9rqlz35xffrcbyiz3gpljy0")))) (build-system ant-build-system) (arguments `(#:jar-name "jmh-core.jar" From 1b1eeb3b123162c4d73c939e9ca7bbbb4f79aef1 Mon Sep 17 00:00:00 2001 From: Julien Lepiller Date: Tue, 1 Jun 2021 00:44:27 +0200 Subject: [PATCH 113/144] gnu: java-jmh: Switch to maven-build-system. * gnu/packages/java.scm (java-jmh): Switch to maven-build-system. --- gnu/packages/java.scm | 34 ++++++++++++++++++---------------- 1 file changed, 18 insertions(+), 16 deletions(-) diff --git a/gnu/packages/java.scm b/gnu/packages/java.scm index 7a9f1c3538..270f2489e1 100644 --- a/gnu/packages/java.scm +++ b/gnu/packages/java.scm @@ -44,6 +44,7 @@ #:use-module (guix utils) #:use-module (guix build-system ant) #:use-module (guix build-system gnu) + #:use-module (guix build-system maven) #:use-module (guix build-system trivial) #:use-module (gnu packages) #:use-module (gnu packages attr) @@ -5879,26 +5880,27 @@ available in the Java programming language or Commons Lang.") (sha256 (base32 "0i7fa7l3gdqkkgz5ddayp6m46dgbj9rqlz35xffrcbyiz3gpljy0")))) - (build-system ant-build-system) + (build-system maven-build-system) (arguments - `(#:jar-name "jmh-core.jar" - #:source-dir "jmh-core/src/main" - #:test-dir "jmh-core/src/test" + `(#:exclude + (("org.apache.maven.plugins" . + ("maven-source-plugin" "maven-archetype-plugin" "maven-shade-plugin" + "maven-site-plugin" "maven-javadoc-plugin" "maven-eclipse-plugin")) + ("com.mycila.maven-license-plugin" . ("maven-license-plugin")) + ("org.apache.maven.wagon" . ("wagon-ssh"))) + #:maven-plugins + (("maven-enforcer-plugin" ,maven-enforcer-plugin) + ,@(default-maven-plugins)) #:phases (modify-phases %standard-phases - ;; This seems to be a bug in the JDK. It may not be necessary in - ;; future versions of the JDK. - (add-after 'unpack 'fix-bug + (add-after 'unpack 'remove-unnecessary (lambda _ - (with-directory-excursion - "jmh-core/src/main/java/org/openjdk/jmh/runner/options" - (substitute* '("IntegerValueConverter.java" - "ThreadsValueConverter.java") - (("public Class valueType") - "public Class valueType"))) - #t))))) - (inputs - `(("java-jopt-simple" ,java-jopt-simple) + ;; requires org.apache.maven.archetype:archetype-packaging. + ;; Its subprojects also require groovy, kotlin and scala, + ;; respectively. + (delete-file-recursively "jmh-archetypes")))))) + (propagated-inputs + `(("java-jopt-simple" ,java-jopt-simple-4) ("java-commons-math3" ,java-commons-math3))) (native-inputs `(("java-junit" ,java-junit) From 347846ea86e73eb34c2296d6a58edf575c543440 Mon Sep 17 00:00:00 2001 From: Julien Lepiller Date: Tue, 22 Jun 2021 14:19:34 +0200 Subject: [PATCH 114/144] gnu: java-kafka-clients: Disable failing test. * gnu/packages/java.scm (java-kafka-clients): Disable a test that fails non-deterministically. --- gnu/packages/java.scm | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/gnu/packages/java.scm b/gnu/packages/java.scm index 270f2489e1..64df5a2e24 100644 --- a/gnu/packages/java.scm +++ b/gnu/packages/java.scm @@ -11681,7 +11681,9 @@ protocol-independent framework to build mail and messaging applications.") "**/ClientUtilsTest.java" ;; End with errors that seem related to our powermock "**/KafkaProducerTest.java" - "**/BufferPoolTest.java"))) + "**/BufferPoolTest.java" + ;; Undeterministic failure, seems to affect mostly ci + "**/GarbageCollectedMemoryPoolTest.java"))) (inputs `(("java-slf4j-api" ,java-slf4j-api) ("java-lz4" ,java-lz4))) From e22a711c97e0501b398467733164da4ee140036e Mon Sep 17 00:00:00 2001 From: Vinicius Monego Date: Tue, 22 Jun 2021 09:46:32 -0300 Subject: [PATCH 115/144] gnu: libngspice: Fix KiCad compilation. * gnu/packages/engineering.scm (libngspice)[arguments]<#:configure-flags>: Pass "--with-readline=no". [inputs]: Remove readline. Signed-off-by: Guillaume Le Vaillant --- gnu/packages/engineering.scm | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/gnu/packages/engineering.scm b/gnu/packages/engineering.scm index bfd0d2f685..1ae9512df1 100644 --- a/gnu/packages/engineering.scm +++ b/gnu/packages/engineering.scm @@ -1721,14 +1721,15 @@ high-performance parallel differential evolution (DE) optimization algorithm.") "--enable-ciderlib" "--enable-xspice" "--with-ngshared" - "--with-readline=yes"))) + ;; Readline must be disabled to build KiCad with ngspice 34. See + ;; https://bugs.archlinux.org/task/70563 for reference. + "--with-readline=no"))) (native-inputs `(("bison" ,bison) ("flex" ,flex))) (inputs `(("libxaw" ,libxaw) - ("mpi" ,openmpi) - ("readline" ,readline))) + ("mpi" ,openmpi))) (home-page "http://ngspice.sourceforge.net/") (synopsis "Mixed-level/mixed-signal circuit simulator") (description From 33fa648f7561ca00d2a21bc0933d0b05ee8bf6b3 Mon Sep 17 00:00:00 2001 From: Vinicius Monego Date: Tue, 22 Jun 2021 09:53:41 -0300 Subject: [PATCH 116/144] gnu: libngspice: Delete autogenerated config.h. * gnu/packages/engineering.scm (libngspice)[arguments]<#:phases>: Rename phase 'delete-script-files to 'delete-scripts-and-config and delete config.h. Signed-off-by: Guillaume Le Vaillant --- gnu/packages/engineering.scm | 9 +++++++-- 1 file changed, 7 insertions(+), 2 deletions(-) diff --git a/gnu/packages/engineering.scm b/gnu/packages/engineering.scm index 1ae9512df1..19c15358c0 100644 --- a/gnu/packages/engineering.scm +++ b/gnu/packages/engineering.scm @@ -1711,11 +1711,16 @@ high-performance parallel differential evolution (DE) optimization algorithm.") (substitute* "man/man1/Makefile.in" (("^man_MANS = ngspice\\.1 ngnutmeg\\.1 ngsconvert\\.1 ngmultidec\\.1") "man_MANS = ")))) - (add-after 'install 'delete-script-files + (add-after 'install 'delete-scripts-and-config (lambda* (#:key outputs #:allow-other-keys) (delete-file-recursively (string-append (assoc-ref outputs "out") - "/share/ngspice/scripts"))))) + "/share/ngspice/scripts")) + ;; This file is autogenerated by the configure script and should + ;; not be distributed. It could be removed in ngspice 35. See + ;; https://bugs.archlinux.org/task/70569 for reference. + (delete-file (string-append (assoc-ref outputs "out") + "/include/config.h"))))) #:configure-flags (list "--enable-openmp" "--enable-ciderlib" From a5e6b705ac48b0294b998f73af1f23cf2b2583ac Mon Sep 17 00:00:00 2001 From: Marius Bakke Date: Tue, 22 Jun 2021 17:09:18 +0200 Subject: [PATCH 117/144] gnu: python-pika: Update to 1.2.0. * gnu/packages/python-xyz.scm (python-pika): Update to 1.2.0. [source]: Change to GIT-FETCH. [arguments]: New field. Override and disable tests. [native-inputs]: Remove PYTHON-PYEV. Add PYTHON-MOCK, PYTHON-NOSE, and PYTHON-GEVENT. (python2-pika): Remove variable. --- gnu/packages/python-xyz.scm | 36 ++++++++++++++++++++++++++++-------- 1 file changed, 28 insertions(+), 8 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index a989158036..1b7c19fdec 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -14404,17 +14404,40 @@ focus on event-based network programming and multiprotocol integration.") (define-public python-pika (package (name "python-pika") - (version "0.12.0") + (version "1.2.0") (source (origin - (method url-fetch) - (uri (pypi-uri "pika" version)) + (method git-fetch) + (uri (git-reference + (url "https://github.com/pika/pika") + (commit version))) + (file-name (git-file-name name version)) (sha256 (base32 - "0ld7akgm93s8pfa4dsx9qlzlhj76zspbr5m9ms0ns09yd2w4aq9h")))) + "0cm45xydk2jigydwszwik89qlbk6l3l18sxhzppzqmxw2rdkm22s")))) (build-system python-build-system) + (arguments + '(#:phases (modify-phases %standard-phases + (add-before 'check 'disable-live-tests + (lambda _ + ;; Disable tests that require RabbitMQ, which is not + ;; yet available in Guix. + (substitute* "setup.cfg" + (("tests/unit,tests/acceptance") + "tests/unit")) + (with-directory-excursion "tests" + (for-each delete-file + '("unit/base_connection_tests.py" + "unit/threaded_test_wrapper_test.py"))))) + (replace 'check + (lambda _ + (invoke "nosetests")))))) (native-inputs - `(("python-pyev" ,python-pyev) + `(("python-mock" ,python-mock) + ("python-nose" ,python-nose) + + ;; These are optional at runtime, and provided here for tests. + ("python-gevent" ,python-gevent) ("python-tornado" ,python-tornado) ("python-twisted" ,python-twisted))) (home-page "https://pika.readthedocs.org") @@ -14425,9 +14448,6 @@ Protocol) 0-9-1 protocol that tries to stay fairly independent of the underlying network support library.") (license license:bsd-3))) -(define-public python2-pika - (package-with-python2 python-pika)) - (define-public python-ply (package (name "python-ply") From 7c5d50f431198d08ebc4c83943748132396f666d Mon Sep 17 00:00:00 2001 From: Nicolas Goaziou Date: Tue, 22 Jun 2021 17:42:15 +0200 Subject: [PATCH 118/144] gnu: python-pikepdf: Update to 2.13.0. * gnu/packages/python-xyz.scm (python-pikepdf): Update to 2.13.0. --- gnu/packages/python-xyz.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 1b7c19fdec..744648b9f3 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -6253,13 +6253,13 @@ the OleFileIO module from PIL, the Python Image Library.") (define-public python-pikepdf (package (name "python-pikepdf") - (version "2.12.2") + (version "2.13.0") (source (origin (method url-fetch) (uri (pypi-uri "pikepdf" version)) (sha256 - (base32 "1r68zh8whp8wg4brjf5vha8h1ly8pjqyb37pfw91hyxfn6cm9wsz")))) + (base32 "1di5bbh2mr8m1aydky8ix12pkybrd0cvs8xqf5s2y1xa349r514l")))) (build-system python-build-system) (arguments `(#:tests? #false)) ;require python-xmp-toolkit From c7a5c3e0bba2ac3d197b219d21527863308b75dd Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= Date: Fri, 18 Jun 2021 18:07:21 +0200 Subject: [PATCH 119/144] gnu: petsc: Link against OpenBLAS rather than LAPACK. OpenBLAS performs better than LAPACK, the reference implementation. This is also consistent with the choice of BLAS/LAPACK implementations made in most other packages. * gnu/packages/maths.scm (petsc)[inputs]: Replace LAPACK by OPENBLAS. [arguments]: Pass "--with-openblas=1". --- gnu/packages/maths.scm | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm index 84540d5ffe..dc18536aa7 100644 --- a/gnu/packages/maths.scm +++ b/gnu/packages/maths.scm @@ -2417,7 +2417,7 @@ September 2004}") `(("python" ,python-2))) (inputs `(("gfortran" ,gfortran) - ("lapack" ,lapack) + ("openblas" ,openblas) ("superlu" ,superlu) ;; leaving out hdf5 and fftw, as petsc expects them to be built with mpi ;; leaving out opengl, as configuration seems to only be for mac @@ -2428,6 +2428,7 @@ September 2004}") #:configure-flags `("--with-mpi=0" "--with-openmp=1" + "--with-openblas=1" "--with-superlu=1") #:make-flags ;; Honor (parallel-job-count) for build. Do not use --with-make-np, From b9a95420abdf4ae7fe9a347031278a44ad6a1cce Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= Date: Tue, 22 Jun 2021 16:42:06 +0200 Subject: [PATCH 120/144] profiles: Build union of inputs in the right order. Fixes . Reported by Mathieu Othacehe and Tobias Geerinckx-Rice . Fixes a regression introduced in 8cef92d0633850d97c1a1d4521812268f56672be, whereby in case of file collisions, the "wrong" one would take precedence. * guix/build/profiles.scm (manifest-sexp->inputs+search-paths): Perform a breadth-first traversal. Reverse INPUTS and SEARCH-PATHS in the base case. * tests/profiles.scm ("profile-derivation, ordering & collisions"): New test. --- guix/build/profiles.scm | 6 +++--- tests/profiles.scm | 30 ++++++++++++++++++++++++++++++ 2 files changed, 33 insertions(+), 3 deletions(-) diff --git a/guix/build/profiles.scm b/guix/build/profiles.scm index 9249977bed..f9875ca92e 100644 --- a/guix/build/profiles.scm +++ b/guix/build/profiles.scm @@ -159,15 +159,15 @@ search path specifications." (((name version output item ('propagated-inputs deps) ('search-paths paths) _ ...) . rest) - (loop (append deps rest) + (loop (append rest deps) ;breadth-first traversal (cons item inputs) (append paths search-paths))) (() - (values inputs + (values (reverse inputs) (delete-duplicates (cons $PATH (map sexp->search-path-specification - search-paths)))))))))) + (reverse search-paths))))))))))) (define* (build-profile output manifest #:key (extra-inputs '()) (symlink symlink)) diff --git a/tests/profiles.scm b/tests/profiles.scm index 1a06ff88f3..06a0387221 100644 --- a/tests/profiles.scm +++ b/tests/profiles.scm @@ -279,6 +279,36 @@ (string=? (dirname (readlink bindir)) (derivation->output-path guile)))))) +(test-assertm "profile-derivation, ordering & collisions" + ;; ENTRY1 and ENTRY2 both provide 'bin/guile'--a collision. Make sure + ;; ENTRY1 "wins" over ENTRY2. See . + (mlet* %store-monad + ((entry1 -> (package->manifest-entry %bootstrap-guile)) + (entry2 -> (manifest-entry + (name "fake-guile") + (version "0") + (item (computed-file + "fake-guile" + #~(begin + (mkdir #$output) + (mkdir (string-append #$output "/bin")) + (call-with-output-file + (string-append #$output "/bin/guile") + (lambda (port) + (display "Fake!\n" port)))))))) + (guile (package->derivation %bootstrap-guile)) + (drv (profile-derivation (manifest (list entry1 entry2)) + #:hooks '() + #:locales? #f)) + (profile -> (derivation->output-path drv)) + (bindir -> (string-append profile "/bin")) + (file -> (string-append bindir "/guile")) + (_ (built-derivations (list drv)))) + (return (string=? (readlink file) + (string-append + (derivation->output-path guile) + "/bin/guile"))))) + (test-assertm "load-profile" (mlet* %store-monad ((entry -> (package->manifest-entry %bootstrap-guile)) From 6623d1cd7f3298f2e5c224299d11a77f7ae18bf5 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= Date: Tue, 22 Jun 2021 17:24:10 +0200 Subject: [PATCH 121/144] gnu: python-numpy, python-scipy: Remove dependency on lapack. The dependency on lapack was unused; the LAPACK interface of OpenBLAS is used instead. The dependency on lapack was added in cba256f8faaa18457fc9b77e8b401f17b89bdd75 (numpy) and 719b01c1575b8599b0dca9f245a9d759032f3168 (scipy). * gnu/packages/python-science.scm (python-scipy)[inputs]: Remove LAPACK. * gnu/packages/python-xyz.scm (python-numpy)[inputs]: Likewise. --- gnu/packages/python-science.scm | 3 +-- gnu/packages/python-xyz.scm | 5 ++--- 2 files changed, 3 insertions(+), 5 deletions(-) diff --git a/gnu/packages/python-science.scm b/gnu/packages/python-science.scm index 10fb2403e6..d2c4caac3a 100644 --- a/gnu/packages/python-science.scm +++ b/gnu/packages/python-science.scm @@ -73,8 +73,7 @@ ("python-matplotlib" ,python-matplotlib) ("python-pyparsing" ,python-pyparsing))) (inputs - `(("lapack" ,lapack) - ("openblas" ,openblas) + `(("openblas" ,openblas) ("pybind11" ,pybind11))) (native-inputs `(("python-cython" ,python-cython) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 744648b9f3..7ff7c1e4cc 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -1,6 +1,6 @@ ;;; GNU Guix --- Functional package management for GNU ;;; Copyright © 2013 Nikita Karetnikov -;;; Copyright © 2013, 2014, 2015, 2016, 2017, 2018, 2019, 2020 Ludovic Courtès +;;; Copyright © 2013, 2014, 2015, 2016, 2017, 2018, 2019, 2020, 2021 Ludovic Courtès ;;; Copyright © 2013, 2014, 2015, 2016, 2019 Andreas Enge ;;; Copyright © 2014, 2015 Mark H Weaver ;;; Copyright © 2014, 2017, 2021 Eric Bavier @@ -4950,8 +4950,7 @@ between language specification and implementation aspects.") "1ak9dmjja0q90a7fsxli51ypcwssh8c4pb6f8wkrsnf2xgdk6dy9")))) (build-system python-build-system) (inputs - `(("openblas" ,openblas) - ("lapack" ,lapack))) + `(("openblas" ,openblas))) (native-inputs `(("python-cython" ,python-cython) ("python-pytest" ,python-pytest) From 58932576263d728225b6f2b32635fb5161573769 Mon Sep 17 00:00:00 2001 From: Leo Prikler Date: Sun, 30 May 2021 18:06:49 +0200 Subject: [PATCH 122/144] gnu: Add python-soundfile. * gnu/packages/audio.scm (python-soundfile): New variable. --- gnu/packages/audio.scm | 35 +++++++++++++++++++++++++++++++++++ 1 file changed, 35 insertions(+) diff --git a/gnu/packages/audio.scm b/gnu/packages/audio.scm index 3885a22e10..9b259edfdf 100644 --- a/gnu/packages/audio.scm +++ b/gnu/packages/audio.scm @@ -85,6 +85,7 @@ #:use-module (gnu packages icu4c) #:use-module (gnu packages image) #:use-module (gnu packages libbsd) + #:use-module (gnu packages libffi) #:use-module (gnu packages libusb) #:use-module (gnu packages linux) #:use-module (gnu packages llvm) @@ -2427,6 +2428,40 @@ included are the command line utilities @code{send_osc} and @code{dump_osc}.") (define-public python2-pyliblo (package-with-python2 python-pyliblo)) +(define-public python-soundfile + (package + (name "python-soundfile") + (version "0.10.3.post1") + (source + (origin + (method url-fetch) + (uri (pypi-uri "SoundFile" version)) + (sha256 + (base32 + "0yqhrfz7xkvqrwdxdx2ydy4h467sk7z3gf984y1x2cq7cm1gy329")))) + (build-system python-build-system) + (propagated-inputs + `(("python-cffi" ,python-cffi) + ("python-numpy" ,python-numpy) + ("libsndfile" ,libsndfile))) + (native-inputs + `(("python-pytest" ,python-pytest))) + (arguments + `(#:tests? #f ; missing OGG support + #:phases + (modify-phases %standard-phases + (add-after 'unpack 'patch + (lambda* (#:key inputs #:allow-other-keys) + (substitute* "soundfile.py" + (("_find_library\\('sndfile'\\)") + (string-append "\"" (assoc-ref inputs "libsndfile") + "/lib/libsndfile.so\"")))))))) + (home-page "https://github.com/bastibe/SoundFile") + (synopsis "Python bindings for libsndfile") + (description "This package provides python bindings for libsndfile based on +CFFI and NumPy.") + (license license:expat))) + (define-public lilv (package (name "lilv") From 9e2cdf724e76cd22d50fd694c8c1d1fc7a4b2eb4 Mon Sep 17 00:00:00 2001 From: Leo Prikler Date: Sun, 30 May 2021 18:07:01 +0200 Subject: [PATCH 123/144] gnu: Add python-python3-midi. * gnu/packages/audio.scm (python-python3-midi): New variable. --- gnu/packages/audio.scm | 18 ++++++++++++++++++ 1 file changed, 18 insertions(+) diff --git a/gnu/packages/audio.scm b/gnu/packages/audio.scm index 9b259edfdf..db05735c95 100644 --- a/gnu/packages/audio.scm +++ b/gnu/packages/audio.scm @@ -2462,6 +2462,24 @@ included are the command line utilities @code{send_osc} and @code{dump_osc}.") CFFI and NumPy.") (license license:expat))) +(define-public python-python3-midi + (package + (name "python-python3-midi") + (version "0.2.5") + (source + (origin + (method url-fetch) + (uri (pypi-uri "python3_midi" version)) + (sha256 + (base32 + "1z9j1w7mpn3xhkcpxmqm5rvmj6nffb5rf14bv7n3sdh07nf6n7sf")))) + (build-system python-build-system) + (home-page "https://github.com/NFJones/python3-midi") + (synopsis "Python MIDI API") + (description "This package provides a python API to read and write MIDI +files.") + (license license:expat))) + (define-public lilv (package (name "lilv") From f356c71ade3f3d45c806d3a84eecefbfbecd526f Mon Sep 17 00:00:00 2001 From: Leo Prikler Date: Sun, 30 May 2021 18:07:06 +0200 Subject: [PATCH 124/144] gnu: Add audio-to-midi. * gnu/packages/audio.scm (audio-to-midi): New variable. --- gnu/packages/audio.scm | 40 ++++++++++++++++++++++++++++++++++++++++ 1 file changed, 40 insertions(+) diff --git a/gnu/packages/audio.scm b/gnu/packages/audio.scm index db05735c95..780a0ec996 100644 --- a/gnu/packages/audio.scm +++ b/gnu/packages/audio.scm @@ -2480,6 +2480,46 @@ CFFI and NumPy.") files.") (license license:expat))) +(define-public audio-to-midi + (package + (name "audio-to-midi") + (version "2020.7") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/NFJones/audio-to-midi") + (commit (string-append "v" version)))) + (sha256 + (base32 + "12wf17abn3psbsg2r2lk0xdnk8n5cd5rrvjlpxjnjfhd09n7qqgm")))) + (build-system python-build-system) + (propagated-inputs + `(("python-cffi" ,python-cffi) + ("python-cython" ,python-cython) + ("python-numpy" ,python-numpy) + ("python-progressbar2" ,python-progressbar2) + ("python-pycparser" ,python-pycparser) + ("python-python3-midi" ,python-python3-midi) + ("python-soundfile" ,python-soundfile))) + (native-inputs + `(("libsndfile" ,libsndfile))) + (arguments + `(#:phases + (modify-phases %standard-phases + (add-after 'unpack 'fix-versions + (lambda _ + (substitute* "requirements.txt" (("==") ">="))))))) + (home-page "https://github.com/NFJones/audio-to-midi") + (synopsis "Convert audio to multichannel MIDI.") + (description "@command{audio-to-midi} converts audio files to multichannel +MIDI files. It accomplishes this by performing FFTs on all channels of the +audio data at user-specified time steps. It then separates the resulting +frequency analysis into equivalence classes which correspond to the twelve tone +scale; the volume of each class being the average volume of its constituent +frequencies. This data is then formatted to MIDI and written to disk.") + (license license:expat))) + (define-public lilv (package (name "lilv") From b994ff128bc33091db256bc40906aa5d4e670aa1 Mon Sep 17 00:00:00 2001 From: Leo Prikler Date: Fri, 19 Mar 2021 18:54:58 +0100 Subject: [PATCH 125/144] gnu: Add apostrophe. * gnu/packages/gnome.scm (apostrophe): New variable. --- gnu/packages/gnome.scm | 64 ++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 64 insertions(+) diff --git a/gnu/packages/gnome.scm b/gnu/packages/gnome.scm index 91ffa23548..45f08b8959 100644 --- a/gnu/packages/gnome.scm +++ b/gnu/packages/gnome.scm @@ -127,6 +127,7 @@ #:use-module (gnu packages gstreamer) #:use-module (gnu packages gtk) #:use-module (gnu packages guile) + #:use-module (gnu packages haskell-xyz) #:use-module (gnu packages ibus) #:use-module (gnu packages icu4c) #:use-module (gnu packages image) @@ -11617,6 +11618,69 @@ and toolbars.") GTK+. It integrates well with the GNOME desktop environment.") (license license:gpl3+))) +(define-public apostrophe + (package + (name "apostrophe") + (version "2.4") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://gitlab.gnome.org/somas/apostrophe") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "1qzy3zhi18wf42m034s8kcmx9gl05j620x3hf6rnycq2fvy7g4gz")))) + (build-system meson-build-system) + (arguments + `(#:glib-or-gtk? #t + #:phases + (modify-phases %standard-phases + (add-after 'unpack 'patch-meson + (lambda _ + (substitute* "build-aux/meson_post_install.py" + (("gtk-update-icon-cache") "true")) + #t)) + (add-after 'glib-or-gtk-wrap 'python-and-gi-wrap + (lambda* (#:key inputs outputs #:allow-other-keys) + (let ((prog (string-append (assoc-ref outputs "out") + "/bin/apostrophe")) + (pylib (string-append (assoc-ref outputs "out") + "/lib/python" + ,(version-major+minor + (package-version python)) + "/site-packages"))) + (wrap-program prog + `("PYTHONPATH" = (,(getenv "PYTHONPATH") ,pylib)) + `("GI_TYPELIB_PATH" = (,(getenv "GI_TYPELIB_PATH"))) + `("PATH" prefix (,(string-append (assoc-ref inputs "pandoc") + "/bin")))) + #t)))))) + (inputs + `(("glib" ,glib) + ("gobject-introspection" ,gobject-introspection) + ("gspell" ,gspell) + ("gtk+" ,gtk+) + ("libhandy" ,libhandy) + ("pandoc" ,pandoc) + ("python-chardet" ,python-chardet) + ("python-levenshtein" ,python-levenshtein) + ("python-regex" ,python-regex) + ("python-pycairo" ,python-pycairo) + ("python-pygobject" ,python-pygobject) + ("python-pyenchant" ,python-pyenchant) + ("python-pypandoc" ,python-pypandoc) + ("webkitgtk" ,webkitgtk))) + (native-inputs + `(("gettext" ,gettext-minimal) + ("glib:bin" ,glib "bin") + ("pkg-config" ,pkg-config))) + (home-page "https://gitlab.gnome.org/somas/apostrophe") + (synopsis "Markdown editor written in Python with GTK+") + (description "Apostrophe is a GTK+ based distraction free Markdown editor. +It uses pandoc as back-end for parsing Markdown.") + (license license:gpl3))) + (define-public libratbag (package (name "libratbag") From 6f58ca5fb3c0abff168b2faa0a4edb8bde30f7a3 Mon Sep 17 00:00:00 2001 From: Leo Prikler Date: Tue, 11 May 2021 13:23:45 +0200 Subject: [PATCH 126/144] gnu: Add emacs-packed. * gnu/packages/emacs-xyz.scm (emacs-packed): New variable. --- gnu/packages/emacs-xyz.scm | 32 +++++++++++++++++++++++++++++++- 1 file changed, 31 insertions(+), 1 deletion(-) diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index 26899f417b..eef33fd437 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -55,7 +55,7 @@ ;;; Copyright © 2019 Jelle Licht ;;; Copyright © 2019 Björn Höfling ;;; Copyright © 2019 Stephen Webber -;;; Copyright © 2019 Leo Prikler +;;; Copyright © 2019, 2021 Leo Prikler ;;; Copyright © 2019 David Wilson ;;; Copyright © 2020 Paul Garlick ;;; Copyright © 2020 Robert Smith @@ -20485,6 +20485,36 @@ e.g. the package dependencies it requires. See function file.") (license license:gpl3+))) +(define-public emacs-packed + (package + (name "emacs-packed") + (version "3.0.3") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/emacscollective/packed") + (commit version))) + (sha256 + (base32 + "06blk8parnpq3qi6y5628q3v59c8dyi41glb289a0l16248qwphk")))) + (build-system emacs-build-system) + (home-page "https://github.com/emacscollective/packed") + (synopsis "Package manager agnostic Emacs Lisp package utilities") + (description + "Packed provides some package manager agnostic utilities to work +with Emacs Lisp packages. As far as Packed is concerned packages +are collections of Emacs Lisp libraries that are stored in a +dedicated directory such as a Git repository. And libraries are +Emacs Lisp files that provide the correct feature (matching the +filename). + +Where a package manager might depend on metadata, Packed instead +uses some heuristics to get the same information---that is slower +and might also fail at times but makes it unnecessary to maintain +package recipes.") + (license license:gpl3+))) + (define-public emacs-picpocket (let ((version "41") (commit "fa3a49f011b5ae139728548fec7375743f61c7c7")) From 4a8ca205f74dbc75bea05f08c8ed5f89168a4a6a Mon Sep 17 00:00:00 2001 From: Matthew James Kraai Date: Sun, 20 Jun 2021 17:11:33 -0700 Subject: [PATCH 127/144] gnu: tmux: Update to 3.2a. * gnu/packages/tmux.scm (tmux): Update to 3.2a. Signed-off-by: Brice Waegeneire --- gnu/packages/tmux.scm | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/gnu/packages/tmux.scm b/gnu/packages/tmux.scm index f208fbfd93..c61ecec909 100644 --- a/gnu/packages/tmux.scm +++ b/gnu/packages/tmux.scm @@ -8,6 +8,7 @@ ;;; Copyright © 2019 Oleg Pykhalov ;;; Copyright © 2020 Brice Waegeneire ;;; Copyright © 2020 Edouard Klein +;;; Copyright © 2021 Matthew James Kraai ;;; ;;; This file is part of GNU Guix. ;;; @@ -43,7 +44,7 @@ (define-public tmux (package (name "tmux") - (version "3.2") + (version "3.2a") (source (origin (method url-fetch) (uri (string-append @@ -51,7 +52,7 @@ version "/tmux-" version ".tar.gz")) (sha256 (base32 - "16d310gcpfnfh7rl5vy1lwqy54ai5awkkybzkm1bw761719k8kb6")))) + "0pyhmipg6vxvxjk7mr410007qk98rh5q0mljvkdaisibz2j565am")))) (build-system gnu-build-system) (inputs `(("libevent" ,libevent) From 83d29ccf644679f3c6cce00c674c3ed262d983ce Mon Sep 17 00:00:00 2001 From: Brice Waegeneire Date: Tue, 22 Jun 2021 08:50:20 +0200 Subject: [PATCH 128/144] gnu: tmux: Correct home-page. * gnu/packages/tmux.scm (tmux)[home-page]: Replace it with its redirection. --- gnu/packages/tmux.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/tmux.scm b/gnu/packages/tmux.scm index c61ecec909..3aaac6530d 100644 --- a/gnu/packages/tmux.scm +++ b/gnu/packages/tmux.scm @@ -6,7 +6,7 @@ ;;; Copyright © 2017 Stefan Reichör ;;; Copyright © 2019–2021 Tobias Geerinckx-Rice ;;; Copyright © 2019 Oleg Pykhalov -;;; Copyright © 2020 Brice Waegeneire +;;; Copyright © 2020, 2021 Brice Waegeneire ;;; Copyright © 2020 Edouard Klein ;;; Copyright © 2021 Matthew James Kraai ;;; @@ -57,7 +57,7 @@ (inputs `(("libevent" ,libevent) ("ncurses" ,ncurses))) - (home-page "https://tmux.github.io/") + (home-page "https://github.com/tmux/tmux/wiki") (synopsis "Terminal multiplexer") (description "tmux is a terminal multiplexer: it enables a number of terminals (or From 65c9251ef271e5a36fc5fc047e8d4c4964bb409d Mon Sep 17 00:00:00 2001 From: Solene Rapenne via Guix-patches via Date: Tue, 22 Jun 2021 20:12:35 +0200 Subject: [PATCH 129/144] gnu: wesnoth: Update to 1.14.17. * gnu/packages/games.scm (wesnoth): Update to 1.14.17. Signed-off-by: Nicolas Goaziou --- gnu/packages/games.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/games.scm b/gnu/packages/games.scm index d365301534..c38011c2e1 100644 --- a/gnu/packages/games.scm +++ b/gnu/packages/games.scm @@ -4176,7 +4176,7 @@ falling, themeable graphics and sounds, and replays.") (define-public wesnoth (package (name "wesnoth") - (version "1.14.16") + (version "1.14.17") (source (origin (method url-fetch) (uri (string-append "mirror://sourceforge/wesnoth/wesnoth-" @@ -4185,7 +4185,7 @@ falling, themeable graphics and sounds, and replays.") "wesnoth-" version ".tar.bz2")) (sha256 (base32 - "1d9hq3dcx0sgs2v4400rg2nw98v46m7bwiqqjv8z8n7vw8kx8lhg")))) + "1qc4ylhc4ab51milclzhflpmzw6bg35knwqaj3b157700jkcniin")))) (build-system cmake-build-system) (arguments `(#:tests? #f)) ;no check target From 4cb70e08b2200d0614b3dad8a6ad22c8ac0f6589 Mon Sep 17 00:00:00 2001 From: Solene Rapenne via Guix-patches via Date: Tue, 22 Jun 2021 21:22:35 +0200 Subject: [PATCH 130/144] gnu: armagetronad: Update to 0.2.9.1.0. * gnu/packages/games.scm (armagetronad): Update to 0.2.9.1.0. Signed-off-by: Nicolas Goaziou --- gnu/packages/games.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/games.scm b/gnu/packages/games.scm index c38011c2e1..6ea579a04a 100644 --- a/gnu/packages/games.scm +++ b/gnu/packages/games.scm @@ -396,14 +396,14 @@ The game includes a built-in editor so you can design and share your own maps.") (define-public armagetronad (package (name "armagetronad") - (version "0.2.9.0.1") + (version "0.2.9.1.0") (source (origin (method url-fetch) (uri (string-append "mirror://sourceforge/armagetronad/stable/" version "/armagetronad-" version ".tbz")) (sha256 (base32 - "19rfhlg4gp0r7k1j8v4iw20325ciy156nmzax4xikmw22c6nmxcz")))) + "18gn4sg4j5sw38ngb90sl50raliplrsgjcvy8fjwry733k0cgdjr")))) (build-system gnu-build-system) (native-inputs `(("pkg-config" ,pkg-config))) From 35ae64b3a342de82d7bf1887dbd204aee5d5615e Mon Sep 17 00:00:00 2001 From: Solene Rapenne via Guix-patches via Date: Tue, 22 Jun 2021 22:22:42 +0200 Subject: [PATCH 131/144] gnu: odamex: Update to 0.9.3. * gnu/packages/games.scm (odamex): Update to 0.9.3. Signed-off-by: Nicolas Goaziou --- gnu/packages/games.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/gnu/packages/games.scm b/gnu/packages/games.scm index 6ea579a04a..a4c42af31d 100644 --- a/gnu/packages/games.scm +++ b/gnu/packages/games.scm @@ -7519,7 +7519,7 @@ Strife, Chex Quest, and fan-created games like Harmony, Hacx and Freedoom.") (define-public odamex (package (name "odamex") - (version "0.9.0") + (version "0.9.3") (source (origin (method url-fetch) @@ -7527,7 +7527,7 @@ Strife, Chex Quest, and fan-created games like Harmony, Hacx and Freedoom.") "mirror://sourceforge/odamex/Odamex/" version "/" "odamex-src-" version ".tar.bz2")) (sha256 - (base32 "0yfrvx8zb3chy47fyz4nik6gbh0y5608yvld4gz4y8l158qk71y1")))) + (base32 "0vmw9ijb6n4wrxjxixakn7l6a6carnvs9wbbzb4vcq1brbzyrb0p")))) (build-system cmake-build-system) (arguments `(#:tests? #f)) ; no tests (native-inputs From 4605ea1a780ff5889b7273d27a255294d7a08327 Mon Sep 17 00:00:00 2001 From: Solene Rapenne via Guix-patches via Date: Tue, 22 Jun 2021 21:48:50 +0200 Subject: [PATCH 132/144] gnu: mednafen: Update to 1.27.1. * gnu/packages/emulators.scm (mednafen): Update to 1.27.1. [inputs]: Add flac. Signed-off-by: Nicolas Goaziou --- gnu/packages/emulators.scm | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/gnu/packages/emulators.scm b/gnu/packages/emulators.scm index ec8d3d21d6..9091ef931d 100644 --- a/gnu/packages/emulators.scm +++ b/gnu/packages/emulators.scm @@ -523,14 +523,14 @@ V2.") (define-public mednafen (package (name "mednafen") - (version "1.26.1") + (version "1.27.1") (source (origin (method url-fetch) (uri (string-append "https://mednafen.github.io/releases/files/" "mednafen-" version ".tar.xz")) (sha256 - (base32 "1x7xhxjhwsdbak8l0iyb497f043xkhibk73w96xck4j2bk10fac4")))) + (base32 "1ysmb56wzr17ki6f1b486r2dzjr11igd021qb4r3437l68prpa7k")))) (build-system gnu-build-system) (arguments `(#:configure-flags @@ -541,6 +541,7 @@ V2.") `(("pkg-config" ,pkg-config))) (inputs `(("alsa" ,alsa-lib) + ("flac" ,flac) ;; ("libmpcdec" ,libmpcdec) FIXME: not recognized. ("libsndfile" ,libsndfile) ("lzo" ,lzo) From e254287b0c22fc89566bd08207dc72f4f8c9972d Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Wed, 23 Jun 2021 02:35:22 +0200 Subject: [PATCH 133/144] =?UTF-8?q?services:=20cups:=20Fix=20=E2=80=98file?= =?UTF-8?q?s-config=E2=80=99=20typo/left-over.?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * gnu/services/cups.scm (): Substitute for in documentation. * doc/guix.texi (Printing Services): Likewise. --- doc/guix.texi | 4 ++-- gnu/services/cups.scm | 21 +++++++++++---------- 2 files changed, 13 insertions(+), 12 deletions(-) diff --git a/doc/guix.texi b/doc/guix.texi index 66c6adc4f5..23c122a543 100644 --- a/doc/guix.texi +++ b/doc/guix.texi @@ -18931,7 +18931,7 @@ Specifies an access list for a job's private values. @code{@@ACL} maps to the printer's requesting-user-name-allowed or requesting-user-name-denied values. @code{@@OWNER} maps to the job's owner. @code{@@SYSTEM} maps to the groups listed for the -@code{system-group} field of the @code{files-config} configuration, +@code{system-group} field of the @code{files-configuration}, which is reified into the @code{cups-files.conf(5)} file. Other possible elements of the access list include specific user names, and @code{@@@var{group}} to indicate members of a specific group. The @@ -18953,7 +18953,7 @@ Specifies an access list for a subscription's private values. @code{@@ACL} maps to the printer's requesting-user-name-allowed or requesting-user-name-denied values. @code{@@OWNER} maps to the job's owner. @code{@@SYSTEM} maps to the groups listed for the -@code{system-group} field of the @code{files-config} configuration, +@code{system-group} field of the @code{files-configuration}, which is reified into the @code{cups-files.conf(5)} file. Other possible elements of the access list include specific user names, and @code{@@@var{group}} to indicate members of a specific group. The diff --git a/gnu/services/cups.scm b/gnu/services/cups.scm index 20e3917b93..5fe0a57e4d 100644 --- a/gnu/services/cups.scm +++ b/gnu/services/cups.scm @@ -292,11 +292,12 @@ methods. Otherwise apply to only the listed methods.") "Name of the policy.") (job-private-access (string "@OWNER @SYSTEM") - "Specifies an access list for a job's private values. @code{@@ACL} maps to -the printer's requesting-user-name-allowed or requesting-user-name-denied -values. @code{@@OWNER} maps to the job's owner. @code{@@SYSTEM} maps to the -groups listed for the @code{system-group} field of the @code{files-config} -configuration, which is reified into the @code{cups-files.conf(5)} file. + "Specifies an access list for a job's private values. +@code{@@ACL} maps to the printer's requesting-user-name-allowed or +requesting-user-name-denied values. @code{@@OWNER} maps to the job's owner. +@code{@@SYSTEM} maps to the groups listed for the @code{system-group} field of +the @code{files-configuration}, which is reified into the +@code{cups-files.conf(5)} file. Other possible elements of the access list include specific user names, and @code{@@@var{group}} to indicate members of a specific group. The access list may also be simply @code{all} or @code{default}.") @@ -312,11 +313,11 @@ may also be simply @code{all} or @code{default}.") @code{@@ACL} maps to the printer's requesting-user-name-allowed or requesting-user-name-denied values. @code{@@OWNER} maps to the job's owner. @code{@@SYSTEM} maps to the groups listed for the @code{system-group} field of -the @code{files-config} configuration, which is reified into the -@code{cups-files.conf(5)} file. Other possible elements of the access list -include specific user names, and @code{@@@var{group}} to indicate members of a -specific group. The access list may also be simply @code{all} or -@code{default}.") +the @code{files-configuration}, which is reified into the +@code{cups-files.conf(5)} file. +Other possible elements of the access list include specific user names, and +@code{@@@var{group}} to indicate members of a specific group. The access list +may also be simply @code{all} or @code{default}.") (subscription-private-values (string (string-join '("notify-events" "notify-pull-method" "notify-recipient-uri" "notify-subscriber-user-name" From ed44e62636873d2b97eff06be70799a0f679bb2b Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Mon, 21 Jun 2021 13:57:09 +0200 Subject: [PATCH 134/144] installer: Remove unused procedure. NETWORKING-SYSTEM-SERVICE? was obsoleted in commit 2e55f37c0c8fdfbc413edff61490161648a78dcc. * gnu/installer/services.scm (networking-system-service?): Remove it. --- gnu/installer/services.scm | 9 ++------- 1 file changed, 2 insertions(+), 7 deletions(-) diff --git a/gnu/installer/services.scm b/gnu/installer/services.scm index ec5ea30594..b0007218ae 100644 --- a/gnu/installer/services.scm +++ b/gnu/installer/services.scm @@ -29,7 +29,6 @@ system-service-packages desktop-system-service? - networking-system-service? %system-services system-services->configuration)) @@ -38,7 +37,7 @@ system-service make-system-service system-service? (name system-service-name) ;string - (type system-service-type) ;'desktop | 'networking + (type system-service-type) ;'desktop|'networking|… (recommended? system-service-recommended? ;Boolean (default #f)) (snippet system-service-snippet ;list of sexps @@ -46,7 +45,6 @@ (packages system-service-packages ;list of sexps (default '()))) -;; This is the list of desktop environments supported as services. (define %system-services (let-syntax ((desktop-environment (syntax-rules () ((_ fields ...) @@ -56,6 +54,7 @@ (G_ (syntax-rules () ;for xgettext ((_ str) str)))) (list + ;; This is the list of desktop environments supported as services. (desktop-environment (name "GNOME") (snippet '((service gnome-desktop-service-type)))) @@ -124,10 +123,6 @@ "Return true if SERVICE is a desktop environment service." (eq? 'desktop (system-service-type service))) -(define (networking-system-service? service) - "Return true if SERVICE is a desktop environment service." - (eq? 'networking (system-service-type service))) - (define (system-services->configuration services) "Return the configuration field for SERVICES." (let* ((snippets (append-map system-service-snippet services)) From 828ceee7db0ab74786049600108d6b15017851c5 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Wed, 23 Jun 2021 03:26:12 +0200 Subject: [PATCH 135/144] services: cups: Remove obsolete KeepAliveTimeout directive. https://github.com/apple/cups/commit/461bd4e50142b2928a0d164bd1aae274e4d34da5 * gnu/services/cups.scm (): Remove keep-alive-timeout field. * doc/guix.texi (Printing Services): Likewise. --- doc/guix.texi | 6 ------ gnu/services/cups.scm | 3 --- 2 files changed, 9 deletions(-) diff --git a/doc/guix.texi b/doc/guix.texi index 23c122a543..15e8999447 100644 --- a/doc/guix.texi +++ b/doc/guix.texi @@ -18699,12 +18699,6 @@ Specifies whether to support HTTP keep-alive connections. Defaults to @samp{#t}. @end deftypevr -@deftypevr {@code{cups-configuration} parameter} non-negative-integer keep-alive-timeout -Specifies how long an idle client connection remains open, in seconds. - -Defaults to @samp{30}. -@end deftypevr - @deftypevr {@code{cups-configuration} parameter} non-negative-integer limit-request-body Specifies the maximum size of print files, IPP requests, and HTML form data. A limit of 0 disables the limit check. diff --git a/gnu/services/cups.scm b/gnu/services/cups.scm index 5fe0a57e4d..8bcb450ddf 100644 --- a/gnu/services/cups.scm +++ b/gnu/services/cups.scm @@ -615,9 +615,6 @@ policy is @code{retry-job} or @code{retry-current-job}.") (keep-alive? (boolean #t) "Specifies whether to support HTTP keep-alive connections.") - (keep-alive-timeout - (non-negative-integer 30) - "Specifies how long an idle client connection remains open, in seconds.") (limit-request-body (non-negative-integer 0) "Specifies the maximum size of print files, IPP requests, and HTML form From ac8fb4b9f4db0cf774799b95fc176c8a80ade6cc Mon Sep 17 00:00:00 2001 From: Vinicius Monego Date: Mon, 17 May 2021 23:55:58 -0300 Subject: [PATCH 136/144] gnu: Add python-pyshp. * gnu/packages/geo.scm (python-pyshp): New variable. --- gnu/packages/geo.scm | 32 ++++++++++++++++++++++++++++++++ 1 file changed, 32 insertions(+) diff --git a/gnu/packages/geo.scm b/gnu/packages/geo.scm index a0b43308e4..af1ed3da96 100644 --- a/gnu/packages/geo.scm +++ b/gnu/packages/geo.scm @@ -15,6 +15,7 @@ ;;; Copyright © 2020 Christopher Baines ;;; Copyright © 2020, 2021 Felix Gruber ;;; Copyright © 2021 Sharlatan Hellseher +;;; Copyright © 2021 Vinicius Monego ;;; ;;; This file is part of GNU Guix. ;;; @@ -881,6 +882,37 @@ utilities for data translation and processing.") `(("gdal" ,gdal))) (synopsis "GDAL (Geospatial Data Abstraction Library) python bindings"))) +(define-public python-pyshp + (package + (name "python-pyshp") + (version "2.1.3") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/GeospatialPython/pyshp") + (commit version))) + (file-name (git-file-name name version)) + (sha256 + (base32 "0jsraqzq82pw19wvx84x7w5cs8agr44a9b5y0jjw540wim4xa73r")))) + (build-system python-build-system) + (arguments + `(#:phases + (modify-phases %standard-phases + (replace 'check + (lambda* (#:key tests? #:allow-other-keys) + (when tests? + ;; This is the only test file. + (invoke "python" "-m" "pytest" "test_shapefile.py"))))))) + (native-inputs + `(("python-pytest" ,python-pytest) + ("python-pytest-runner" ,python-pytest-runner))) + (home-page "https://github.com/GeospatialPython/pyshp") + (synopsis "Read/write support for ESRI Shapefile format") + (description + "The Python Shapefile Library (PyShp) reads and writes ESRI Shapefiles.") + (license license:expat))) + (define-public postgis (package (name "postgis") From 4b39a6fa14e5b7a4f075d8f980c974560ffc47ad Mon Sep 17 00:00:00 2001 From: Vinicius Monego Date: Tue, 25 May 2021 14:28:20 -0300 Subject: [PATCH 137/144] gnu: Add python-pykdtree. * gnu/packages/python-xyz.scm (python-pykdtree): New variable. --- gnu/packages/python-xyz.scm | 22 ++++++++++++++++++++++ 1 file changed, 22 insertions(+) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 7ff7c1e4cc..ec4209108f 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -5895,6 +5895,28 @@ operators such as union, intersection, and difference.") (define-public python2-pysnptools (package-with-python2 python-pysnptools)) +(define-public python-pykdtree + (package + (name "python-pykdtree") + (version "1.3.4") + (source + (origin + (method url-fetch) + (uri (pypi-uri "pykdtree" version)) + (sha256 + (base32 "0p8n2ljdacfixkiw092974dmhy4s1c0h032ii1z9kwi9h5h5rgmy")))) + (build-system python-build-system) + (native-inputs + `(("python-nose" ,python-nose))) + (propagated-inputs + `(("python-numpy" ,python-numpy))) + (home-page "https://github.com/storpipfugl/pykdtree") + (synopsis "Fast kd-tree implementation with OpenMP-enabled queries") + (description + "@code{pykdtree} is a kd-tree implementation for fast nearest neighbour +search in Python.") + (license license:lgpl3+))) + (define-public python-wurlitzer (package (name "python-wurlitzer") From 5ab7fbad27c652bb2a7143995970e8b5886a0cb6 Mon Sep 17 00:00:00 2001 From: Vinicius Monego Date: Tue, 18 May 2021 20:54:14 -0300 Subject: [PATCH 138/144] gnu: Add python-cartopy. * gnu/packages/geo.scm (python-cartopy): New variable. --- gnu/packages/geo.scm | 57 ++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 57 insertions(+) diff --git a/gnu/packages/geo.scm b/gnu/packages/geo.scm index af1ed3da96..546be33e55 100644 --- a/gnu/packages/geo.scm +++ b/gnu/packages/geo.scm @@ -92,6 +92,7 @@ #:use-module (gnu packages pulseaudio) #:use-module (gnu packages python) #:use-module (gnu packages python-check) + #:use-module (gnu packages python-science) #:use-module (gnu packages python-web) #:use-module (gnu packages python-xyz) #:use-module (gnu packages qt) @@ -913,6 +914,62 @@ utilities for data translation and processing.") "The Python Shapefile Library (PyShp) reads and writes ESRI Shapefiles.") (license license:expat))) +(define-public python-cartopy + (package + (name "python-cartopy") + ;; This is a post-release fix that adds build_ext to setup.py. + (version "0.19.0.post1") + (source + (origin + (method url-fetch) + (uri (pypi-uri "Cartopy" version)) + (sha256 + (base32 "0xnm8z3as3hriivdfd26s6vn5b63gb46x6vxw6gh1mwfm5rlg2sb")))) + (build-system python-build-system) + (arguments + `(#:phases + (modify-phases %standard-phases + (replace 'check + (lambda* (#:key inputs outputs tests? #:allow-other-keys) + (when tests? + (add-installed-pythonpath inputs outputs) + (invoke "python" "-m" "pytest" "--pyargs" "cartopy" + ;; These tests require online data. + "-m" "not natural_earth and not network" + ;; This one too but it's not marked as such. + "-k" "not test_gridliner_labels_bbox_style"))))))) + (propagated-inputs + `(("python-matplotlib" ,python-matplotlib) + ("python-numpy" ,python-numpy) + ("python-pykdtree" ,python-pykdtree) + ("python-pyshp" ,python-pyshp) + ("python-scipy" ,python-scipy) + ("python-shapely" ,python-shapely))) + (inputs + `(("geos" ,geos) + ("proj" ,proj))) + (native-inputs + `(("python-cython" ,python-cython) + ("python-flufl-lock" ,python-flufl-lock) + ("python-pytest" ,python-pytest))) + (home-page "https://scitools.org.uk/cartopy/docs/latest/") + (synopsis "Cartographic library for visualisation") + (description + "Cartopy is a Python package designed to make drawing maps for data +analysis and visualisation easy. + +It features: + +@itemize +@item object oriented projection definitions +@item point, line, polygon and image transformations between projections +@item integration to expose advanced mapping in Matplotlib with a simple and +intuitive interface +@item powerful vector data handling by integrating shapefile reading with +Shapely capabilities +@end itemize") + (license license:lgpl3+))) + (define-public postgis (package (name "postgis") From 6b83da96162fe212a4e306b259c2c52f17878ec5 Mon Sep 17 00:00:00 2001 From: Carlo Zancanaro Date: Wed, 23 Jun 2021 15:57:40 +1000 Subject: [PATCH 139/144] gnu: Fix references to emacs-build-system's expand-load-path phase. * gnu/packages/emacs-xyz.scm (emacs-pdf-tools)[#:phases]: Use emacs-expand-load-path instead of emacs-add-source-to-load-path. * gnu/packages/erlang.scm (emacs-erlang)[#:phases]: Use expand-load-path instead of add-source-to-load-path. * gnu/packages/protobuf.scm (emacs-protobuf-mode)[#:phases]: Use expand-load-path instead of add-source-to-load-path. Signed-off-by: Leo Prikler --- gnu/packages/emacs-xyz.scm | 2 +- gnu/packages/erlang.scm | 2 +- gnu/packages/protobuf.scm | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/gnu/packages/emacs-xyz.scm b/gnu/packages/emacs-xyz.scm index eef33fd437..28b87d49dd 100644 --- a/gnu/packages/emacs-xyz.scm +++ b/gnu/packages/emacs-xyz.scm @@ -3310,7 +3310,7 @@ during idle time, while Emacs is doing nothing else.") ("pdf-tools-handle-upgrades" '())))) (add-after 'emacs-patch-variables 'emacs-expand-load-path (assoc-ref emacs:%standard-phases 'expand-load-path)) - (add-after 'emacs-add-source-to-load-path 'emacs-install + (add-after 'emacs-expand-load-path 'emacs-install (assoc-ref emacs:%standard-phases 'install)) (add-after 'emacs-install 'emacs-build (assoc-ref emacs:%standard-phases 'build)) diff --git a/gnu/packages/erlang.scm b/gnu/packages/erlang.scm index 7b5dc70b5d..d52d5c3983 100644 --- a/gnu/packages/erlang.scm +++ b/gnu/packages/erlang.scm @@ -232,7 +232,7 @@ built-in support for concurrency, distribution and fault tolerance.") (arguments `(#:phases (modify-phases %standard-phases - (add-before 'add-source-to-load-path 'change-working-directory + (add-before 'expand-load-path 'change-working-directory (lambda _ (chdir "lib/tools/emacs") #t))))) (home-page "https://www.erlang.org/") (synopsis "Erlang major mode for Emacs") diff --git a/gnu/packages/protobuf.scm b/gnu/packages/protobuf.scm index 857adf1703..9c6dcb51cc 100644 --- a/gnu/packages/protobuf.scm +++ b/gnu/packages/protobuf.scm @@ -311,7 +311,7 @@ structured data.") (arguments `(#:phases (modify-phases %standard-phases - (add-before 'add-source-to-load-path 'change-working-directory + (add-before 'expand-load-path 'change-working-directory (lambda _ (chdir "editors") #t))))) (home-page "https://github.com/protocolbuffers/protobuf") (synopsis "Protocol buffers major mode for Emacs") From cde7068e8cb28b7245cfa07b8aa788039012f972 Mon Sep 17 00:00:00 2001 From: Nicolas Goaziou Date: Wed, 23 Jun 2021 09:36:35 +0200 Subject: [PATCH 140/144] gnu: texmacs: Update to 2.1. * gnu/packages/text-editors.scm (texmacs): Update to 2.1. [arguments]: Remove #t at the end of phases. --- gnu/packages/text-editors.scm | 10 ++++------ 1 file changed, 4 insertions(+), 6 deletions(-) diff --git a/gnu/packages/text-editors.scm b/gnu/packages/text-editors.scm index 06ae653df8..23d0484979 100644 --- a/gnu/packages/text-editors.scm +++ b/gnu/packages/text-editors.scm @@ -839,14 +839,14 @@ editors.") (define-public texmacs (package (name "texmacs") - (version "1.99.21") + (version "2.1") (source (origin (method url-fetch) (uri (string-append "https://www.texmacs.org/Download/ftp/tmftp/" "source/TeXmacs-" version "-src.tar.gz")) (sha256 - (base32 "0zmm8212cha22dp1xablj1h4anlnyhjh09n13ckqf6ppb1bkf4gm")))) + (base32 "1gl6k1bwrk1y7hjyl4xvlqvmk5crl4jvsk8wrfp7ynbdin6n2i48")))) (build-system gnu-build-system) (native-inputs `(("pkg-config" ,pkg-config) @@ -867,16 +867,14 @@ editors.") (let ((out (assoc-ref outputs "out"))) (substitute* "packages/linux/icons.sh" (("/usr/share") - (string-append out "/share"))) - #t))) + (string-append out "/share")))))) (add-after 'install 'install-desktop-file (lambda* (#:key outputs #:allow-other-keys) ;; Install desktop file. (let* ((out (assoc-ref outputs "out")) (apps (string-append out "/share/applications")) (source "TeXmacs/misc/mime/texmacs.desktop")) - (install-file source apps) - #t))) + (install-file source apps)))) (add-before 'configure 'gzip-flags (lambda _ (substitute* "Makefile.in" From 976a49bacc30ee4c77ee7e5da4ba8b4e6f32e70d Mon Sep 17 00:00:00 2001 From: Guillaume Le Vaillant Date: Wed, 23 Jun 2021 13:38:51 +0200 Subject: [PATCH 141/144] gnu: bitcoin-unlimited: Fix build. * gnu/packages/finance.scm (bitcoin-unlimited)[arguments]: Disable a test. --- gnu/packages/finance.scm | 9 ++++++++- 1 file changed, 8 insertions(+), 1 deletion(-) diff --git a/gnu/packages/finance.scm b/gnu/packages/finance.scm index d4c571d3ec..b3a8e2b732 100644 --- a/gnu/packages/finance.scm +++ b/gnu/packages/finance.scm @@ -1457,7 +1457,14 @@ following three utilities are included with the library: (substitute* "src/Makefile.test.include" (("test/utilprocess_tests.cpp") "")) - #t)) + + ;; Some transaction validation rules have changed (see upstream + ;; commit f208400825d4641b9310a1fba023d56e0862e3b0), which makes + ;; a test fail. Disable it for now. + ;; TODO: Remove this when the next version is released. + (substitute* "src/Makefile.test.include" + (("test/txvalidationcache_tests.cpp") + "")))) (add-before 'check 'set-home (lambda _ (setenv "HOME" (getenv "TMPDIR")) ; tests write to $HOME From 91b29aa37394b660117e1d79927621db1344b7fe Mon Sep 17 00:00:00 2001 From: Xinglu Chen Date: Wed, 23 Jun 2021 10:52:38 +0200 Subject: [PATCH 142/144] gnu: ocaml-dose3: Fix tests. * gnu/packages/ocaml.scm (ocaml-dose3)[arguments]<#:phases>: Add phase to patch tests script. Signed-off-by: Julien Lepiller --- gnu/packages/ocaml.scm | 9 ++++++++- 1 file changed, 8 insertions(+), 1 deletion(-) diff --git a/gnu/packages/ocaml.scm b/gnu/packages/ocaml.scm index dd30f4cc97..1262c0e303 100644 --- a/gnu/packages/ocaml.scm +++ b/gnu/packages/ocaml.scm @@ -647,7 +647,14 @@ underlying solvers like Cplex, Gurobi, Lpsolver, Glpk, CbC, SCIP or WBO.") #:make-flags (list (string-append "LIBDIR=" (assoc-ref %outputs "out") - "/lib/ocaml/site-lib")))) + "/lib/ocaml/site-lib")) + #:phases + (modify-phases %standard-phases + (add-after 'unpack 'fix-test-script + (lambda _ + (substitute* "applications/dose-tests.py" + (("warning\\(") + "from warnings import warn\nwarn("))))))) (propagated-inputs `(("ocaml-graph" ,ocaml-graph) ("ocaml-cudf" ,ocaml-cudf) From 3694c0d4fee0f7faf130ecd9386ea45932a19543 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ludovic=20Court=C3=A8s?= Date: Wed, 23 Jun 2021 15:41:42 +0200 Subject: [PATCH 143/144] .guix-authorizations: Update bavier's key. As requested at . * .guix-authorizations: Update bavier's signing key fingerprint. --- .guix-authorizations | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.guix-authorizations b/.guix-authorizations index fff75fb6d1..83606675c5 100644 --- a/.guix-authorizations +++ b/.guix-authorizations @@ -23,7 +23,7 @@ "39B3 3C8D 9448 0D2D DCC2 A498 8B44 A0CD C7B9 56F2" (name "bandali")) (;; primary: "34FF 38BC D151 25A6 E340 A0B5 3453 2F9F AFCA 8B8E" - "A0C5 E352 2EF8 EF5C 64CD B7F0 FD73 CAC7 19D3 2566" + "A3A4 B419 0074 087C A7DE 5698 BC45 CA67 E2F8 D007" (name "bavier")) ("45CC 63B8 5258 C9D5 5F34 B239 D37D 0EA7 CECC 3912" (name "biscuolo")) From 620669fd17306c2edb21c64a99fa47160fefb319 Mon Sep 17 00:00:00 2001 From: Tobias Geerinckx-Rice Date: Wed, 23 Jun 2021 12:52:21 +0200 Subject: [PATCH 144/144] gnu: cups: Add replacement to fix CVE-2020-10001. * gnu/packages/patches/cups-CVE-2020-10001.patch: New file. * gnu/local.mk (dist_patch_DATA): Add it. * gnu/packages/cups.scm (cups-minimal/fixed): New variable. (cups-minimal)[replacement]: Assign it to new field. --- gnu/local.mk | 1 + gnu/packages/cups.scm | 6 +++ .../patches/cups-CVE-2020-10001.patch | 47 +++++++++++++++++++ 3 files changed, 54 insertions(+) create mode 100644 gnu/packages/patches/cups-CVE-2020-10001.patch diff --git a/gnu/local.mk b/gnu/local.mk index f7ff9af997..fb6c25d6f9 100644 --- a/gnu/local.mk +++ b/gnu/local.mk @@ -929,6 +929,7 @@ dist_patch_DATA = \ %D%/packages/patches/crda-optional-gcrypt.patch \ %D%/packages/patches/clucene-contribs-lib.patch \ %D%/packages/patches/cube-nocheck.patch \ + %D%/packages/patches/cups-CVE-2020-10001.patch \ %D%/packages/patches/curl-use-ssl-cert-env.patch \ %D%/packages/patches/curl-7.76-use-ssl-cert-env.patch \ %D%/packages/patches/curl-7.77-tls-priority-string.patch \ diff --git a/gnu/packages/cups.scm b/gnu/packages/cups.scm index 5a15cd51b6..2dab881ae6 100644 --- a/gnu/packages/cups.scm +++ b/gnu/packages/cups.scm @@ -252,6 +252,7 @@ filters for the PDF-centric printing workflow introduced by OpenPrinting.") (package (name "cups-minimal") (version "2.3.3") + (replacement cups-minimal/fixed) (source (origin (method url-fetch) @@ -312,6 +313,11 @@ device-specific programs to convert and print many types of files.") ;; CUPS is Apache 2.0 with exceptions, see the NOTICE file. (license license:asl2.0))) +(define cups-minimal/fixed + (package-with-extra-patches + cups-minimal + (search-patches "cups-CVE-2020-10001.patch"))) + (define-public cups (package/inherit cups-minimal (name "cups") diff --git a/gnu/packages/patches/cups-CVE-2020-10001.patch b/gnu/packages/patches/cups-CVE-2020-10001.patch new file mode 100644 index 0000000000..1b16c7d97c --- /dev/null +++ b/gnu/packages/patches/cups-CVE-2020-10001.patch @@ -0,0 +1,47 @@ +From efbea1742bd30f842fbbfb87a473e5c84f4162f9 Mon Sep 17 00:00:00 2001 +From: Michael R Sweet +Date: Mon, 1 Feb 2021 15:02:32 -0500 +Subject: [PATCH] Fix a buffer (read) overflow in ippReadIO (CVE-2020-10001) + +--- + +diff --git a/cups/ipp.c b/cups/ipp.c +index 3d529346c..adbb26fba 100644 +--- a/cups/ipp.c ++++ b/cups/ipp.c +@@ -2866,7 +2866,8 @@ ippReadIO(void *src, /* I - Data source */ + unsigned char *buffer, /* Data buffer */ + string[IPP_MAX_TEXT], + /* Small string buffer */ +- *bufptr; /* Pointer into buffer */ ++ *bufptr, /* Pointer into buffer */ ++ *bufend; /* End of buffer */ + ipp_attribute_t *attr; /* Current attribute */ + ipp_tag_t tag; /* Current tag */ + ipp_tag_t value_tag; /* Current value tag */ +@@ -3441,6 +3442,7 @@ ippReadIO(void *src, /* I - Data source */ + } + + bufptr = buffer; ++ bufend = buffer + n; + + /* + * text-with-language and name-with-language are composite +@@ -3454,7 +3456,7 @@ ippReadIO(void *src, /* I - Data source */ + + n = (bufptr[0] << 8) | bufptr[1]; + +- if ((bufptr + 2 + n) >= (buffer + IPP_BUF_SIZE) || n >= (int)sizeof(string)) ++ if ((bufptr + 2 + n + 2) > bufend || n >= (int)sizeof(string)) + { + _cupsSetError(IPP_STATUS_ERROR_INTERNAL, + _("IPP language length overflows value."), 1); +@@ -3481,7 +3483,7 @@ ippReadIO(void *src, /* I - Data source */ + bufptr += 2 + n; + n = (bufptr[0] << 8) | bufptr[1]; + +- if ((bufptr + 2 + n) >= (buffer + IPP_BUF_SIZE)) ++ if ((bufptr + 2 + n) > bufend) + { + _cupsSetError(IPP_STATUS_ERROR_INTERNAL, + _("IPP string length overflows value."), 1);