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2473 Commits

Author SHA1 Message Date
Vinicius Monego
c4b9f726e3
gnu: python-pymc: Update to 5.7.1. 
* gnu/packages/statistics.scm (python-pymc): Update to 5.7.1.
 2023-08-05 18:40:01 -03:00
Vinicius Monego
02a36d939a
gnu: python-pymc: Update to 5.6.1. 
* gnu/packages/statistics.scm (python-pymc): Update to 5.6.1.
 2023-07-29 14:25:03 -03:00
Vinicius Monego
26e24d8018
gnu: python-arviz: Update to 0.16.1. 
* gnu/packages/statistics.scm (python-arviz): Update to 0.16.1.
 2023-07-29 14:25:03 -03:00
Nicolas Goaziou
7a18bd9e74
gnu: Rationalize texlive-updmap.cfg and texlive-tiny inputs. 
TEXLIVE-UPDMAP.CFG and TEXLIVE-TINY should only be used as native inputs.
Also remove texlive packages already provided by them.

* doc/build.scm (pdf-manual):
* gnu/packages/algebra.scm (pari-gp):
* gnu/packages/bioinformatics.scm (discrover):
(phyml):
(velvet):
* gnu/packages/chemistry.scm (yaehmop):
* gnu/packages/chez.scm (stex-bootstrap):
(chez-web):
(chez-sockets):
* gnu/packages/cran.scm (r-prereg):
* gnu/packages/docbook.scm (dblatex):
* gnu/packages/emacs-xyz.scm (emacs-auctex):
* gnu/packages/engineering.scm (fastcap):
* gnu/packages/fsf.scm (book-faif):
* gnu/packages/graphviz.scm (dot2tex):
* gnu/packages/maths.scm (hypre):
* gnu/packages/ocaml.scm (unison):
(ocaml-bibtex2html):
* gnu/packages/plotutils.scm (asymptote):
* gnu/packages/python-xyz.scm (python-nbconvert):
(python-pypandoc):
* gnu/packages/radio.scm (gnuradio):
(libosmo-dsp):
* gnu/packages/statistics.scm (r-with-tests):
* gnu/packages/tex.scm (texlive-makecmds):
(texlive-innerscript):
(teximpatient):
(texlive-xkeyval): Remove texlive packages already provided by
TEXLIVE-UPDMAP.CFG.  Don't add TEXLIVE-TINY or TEXLIVE-UPDMAP.CFG as inputs.
 2023-07-18 18:16:47 +02:00
Nicolas Goaziou
520551a596
gnu: Replace texlive-latex-base with texlive-latex-bin. 
Although `latex-base' is clearly defined on CTAN, it isn't a proper TeX Live
package.  Since we're trying to follow as closely as possible this TeX
distribution, we replace the package with the closest one, which is
`texlive-latex-bin'.  As a consequence, the #:TEXLIVE-LATEX-BASE argument
becomes #:TEXLIVE-LATEX-BIN?, emphasizing the fact that the meaningful values
for it are booleans.

* gnu/packages/graphviz.scm (dot2tex)[propagated-inputs]: Remove
TEXLIVE-GRAPHICS, TEXLIVE-LATEX-BASE.  Add TEXLIVE-LATEX-BIN.
* gnu/packages/plotutils.scm (asymptote)[native-inputs]: Remove
TEXLIVE-LATEX-BASE, TEXLIVE-GRAPHICS, TEXLIVE-L3BACKEND.  Use
TEXLIVE-UPDMAP.CFG.
* gnu/packages/sphinx.scm (python-sphinx)[propagated-inputs]: Remove
TEXLIVE-GRAPHICS, TEXLIVE-LATEX-BASE.  Add TEXLIVE-LATEX-BIN.
* gnu/packages/tex.scm (texlive-latex-base): Deprecate variable.
(texlive-hyphen-complete):
(texlive-tex):
(texlive-latex):
(texlive-docstrip):
(texlive-unicode-data):
(texlive-hyphen-base):
(texlive-tex-ini-files):
(texlive-metafont):
(texlive-modes):
(texlive-knuth-lib):
(texlive-latex-fonts):
(texlive-etex):
(texlive-plain):
(texlive-kpathsea):
(texlive-latexconfig):
(texlive-latex-bin):
(texlive-l3kernel):
(texlive-l3backend):
(texlive-l3packages):
(texlive-luatex):
(texlive-luahbtex):
(texlive-babel):
(texlive-cyrillic):
(texlive-pdftex):
(texlive-cm)[arguments]: Replace #:TEXLIVE-LATEX-BASE with #:TEXLIVE-LATEX-BIN?.
(texlive-lm):
(texlive-lua-alt-getopt):
(texlive-luaotfload):
(texlive-graphics-def):
(texlive-graphics-cfg): Set #:TEXLIVE-LATEX-BIN? to #F.
(texlive-graphics):
(texlive-lualibs):
(texlive-firstaid):
(texlive-atveryend)[arguments]: Set #:TEXLIVE-LATEX-BIN? to #F.
[native-inputs]: Add TEXLIVE-DOCSTRIP, TEXLIVE-PDFTEX.
(texlive-updmap.cfg): Remove TEXLIVE-CM, TEXLIVE-GRAPHICS,
TEXLIVE-LATEX-BASE.  Add TEXLIVE-LATEX-BIN.
(texlive-atbegshi)[arguments]: Set #:TEXLIVE-LATEX-BIN? to #F.
[native-inputs]: Add TEXLIVE-DOCSTRIP, TEXLIVE-PDFTEX.
[propagated-inputs]: Remove TEXLIVE-IFTEX, TEXLIVE-INFWARERR and
TEXLIVE-LTXCMDS.
(texlive-everyshi)[arguments]: Build package with a temporary "latex.fmt"
file.
(texlive-cyrillic): Set #:TEXLIVE-LATEX-BIN? to #T.
* guix/build-system/texlive.scm (default-texlive-latex-base): Rename to
TEXLIVE-LATEX-BIN.
(lower): Set default value for TEXLIVE-LATEX-BIN? to #TRUE.
* gnu/packages/statistics.scm (r-with-tests): Remove TEXLIVE-LATEX-BASE and
TEXLIVE-GRAPHICS.
* doc/guix.texi (Build Systems): Document #:TEXLIVE-LATEX-BIN? argument.
Remove reference to #:TEXLIVE-LATEX-BASE.
 2023-07-18 18:15:03 +02:00
Nicolas Goaziou
36d7acf003
gnu: Deprecate texlive-base in favor of texlive-scheme-basic. 
* gnu/packages/tex.scm (texlive-base): Deprecate variable.
(texlive-updmap.cfg): Use default packages from now deprecated TEXLIVE-BASE.
Also remove already implemented TODO.
* doc/build.scm (pdf-manual):
* gnu/packages/statistics.scm: Replace TEXLIVE-BASE with call to
TEXLIVE-UPDMAP.CFG.
* guix/profiles.scm (texlive-font-maps): Trigger TeX Live hook whenever
a texlive package is included in the manifest.
 2023-07-18 18:15:02 +02:00
Nicolas Goaziou
eab3b80369
gnu: texlive-jknappen: Deprecate package. 
* gnu/packages/tex.scm (texlive-jknappen): Deprecate variable.
(texlive-paralist):
(texlive-jadetex):
(texlive-xindy):
* gnu/packages/maths.scm (hypre):
* gnu/packages/python-xyz.scm (python-nbconvert): Use TEXLIVE-JKNAPLTX instead.
 2023-07-18 18:11:41 +02:00
Nicolas Goaziou
402f256f81
gnu: texlive-latex-xkeyval -> texlive-xkeyval. 
* gnu/packages/tex.scm (texlive-xkeyval): New variable.
(texlive-latex-xkeyval): Deprecate variable.
(texlive-bidi):
(texlive-pstool):
(texlive-polyglossia):
(texlive-zref):
(texlive-standalone):
(texlive-todonotes):
(texlive-adjustbox):
(texlive-qrcode):
(texlive-breakurl):
* gnu/packages/graphviz.scm (dot2tex):
* gnu/packages/statistics.scm (r-with-tests): Use new name.
 2023-07-18 18:10:48 +02:00
Nicolas Goaziou
76819a9655
gnu: texlive-fonts-ec -> texlive-ec. 
* gnu/packages/tex.scm (texlive-ec): New variable.
(texlive-fonts-ec): Deprecate variable.
(lyx):
(biber):
* gnu/packages/python-xyz.scm (python-pypandoc):
* gnu/packages/statistics.scm (r-with-tests):
* doc/build.scm (pdf-manual):
* gnu/packages/bioinformatics.scm (discrover):
(phyml):
(velvet):
* gnu/packages/chemistry.scm (yaehmop):
* gnu/packages/chez.scm (stex-bootstrap):
* gnu/packages/ocaml.scm (unison):
(ocaml-bibtex2html):
* gnu/packages/plotutils.scm (asymptote): Use new name.
 2023-07-18 18:10:48 +02:00
Nicolas Goaziou
9550a20361
gnu: texlive-latex-upquote -> texlive-upquote. 
* gnu/packages/tex.scm (texlive-upquote): New variable.
(texlive-latex-upquote): Deprecate variable.
* gnu/packages/cran.scm (r-prereg):
* gnu/packages/maths.scm (hypre):
* gnu/packages/python-xyz.scm (python-nbconvert):
* gnu/packages/sphinx.scm (python-sphinx):
* gnu/packages/statistics.scm (r-with-tests): Use new name.
 2023-07-18 18:10:46 +02:00
Ricardo Wurmus
ed58e991f5
gnu: r-puniform: Update to 0.2.6. 
* gnu/packages/statistics.scm (r-puniform): Update to 0.2.6.
 2023-07-17 14:19:54 +02:00
Ricardo Wurmus
a450a5aafa
gnu: r-clubsandwich: Update to 0.5.9. 
* gnu/packages/statistics.scm (r-clubsandwich): Update to 0.5.9.
 2023-07-17 14:19:54 +02:00
Ricardo Wurmus
7d6bdd1c8a
gnu: r-matrixmodels: Update to 0.5-2. 
* gnu/packages/statistics.scm (r-matrixmodels): Update to 0.5-2.
 2023-07-17 14:19:54 +02:00
Ricardo Wurmus
b5fede2809
gnu: r-deoptimr: Update to 1.1-0. 
* gnu/packages/statistics.scm (r-deoptimr): Update to 1.1-0.
 2023-07-17 14:19:54 +02:00
Ricardo Wurmus
f96c109be9
gnu: r-mgcv: Update to 1.9-0. 
* gnu/packages/statistics.scm (r-mgcv): Update to 1.9-0.
 2023-07-17 14:19:53 +02:00
Ricardo Wurmus
af6b542954
gnu: r-openssl: Update to 2.1.0. 
* gnu/packages/statistics.scm (r-openssl): Update to 2.1.0.
[properties]: Add hint to keep openssl input.
[inputs]: Add zlib.
 2023-07-17 14:18:43 +02:00
Ricardo Wurmus
8d2a016f1b
gnu: r-with-tests: Update to 4.3.1. 
* gnu/packages/statistics.scm (r-with-tests): Update to 4.3.1.
 2023-07-16 10:48:00 +02:00
Ricardo Wurmus
ff0d34a29b
gnu: r-with-tests: Fix reference to grep. 
detectCores.R fails to return the number of cores when running R in a
container without grep.

Reported-by: Jonas Freimuth.

* gnu/packages/statistics.scm (r-with-tests)[arguments]: Fix references to
grep and wc in detectCores.R.
[inputs]: Add grep.
 2023-07-16 10:48:00 +02:00
Ricardo Wurmus
ee50cae529
gnu: r-norm: Update to 1.0-11.1. 
* gnu/packages/statistics.scm (r-norm): Update to 1.0-11.1.
 2023-07-12 14:29:09 +02:00
Ricardo Wurmus
c141725c65
gnu: r-logspline: Update to 2.1.20. 
* gnu/packages/statistics.scm (r-logspline): Update to 2.1.20.
 2023-07-12 14:29:09 +02:00
Ricardo Wurmus
5a1c16fa18
gnu: r-pbapply: Update to 1.7-2. 
* gnu/packages/statistics.scm (r-pbapply): Update to 1.7-2.
 2023-07-12 14:29:09 +02:00
Ricardo Wurmus
42c29d9d22
gnu: r-robust: Update to 0.7-2. 
* gnu/packages/statistics.scm (r-robust): Update to 0.7-2.
 2023-07-12 14:29:09 +02:00
Ricardo Wurmus
2108aa1975
gnu: r-rrcov: Update to 1.7-4. 
* gnu/packages/statistics.scm (r-rrcov): Update to 1.7-4.
 2023-07-12 14:29:09 +02:00
Ricardo Wurmus
387c1fafce
gnu: r-robustbase: Update to 0.99-0. 
* gnu/packages/statistics.scm (r-robustbase): Update to 0.99-0.
 2023-07-12 14:29:08 +02:00
Ricardo Wurmus
86c7032abf
gnu: r-deoptimr: Update to 1.0-14. 
* gnu/packages/statistics.scm (r-deoptimr): Update to 1.0-14.
 2023-07-12 14:29:08 +02:00
Ricardo Wurmus
f9dc378cb4
gnu: r-mvtnorm: Update to 1.2-2. 
* gnu/packages/statistics.scm (r-mvtnorm): Update to 1.2-2.
 2023-07-12 14:29:08 +02:00
Ricardo Wurmus
e8ef13993e
gnu: r-rmarkdown: Update to 2.23. 
* gnu/packages/statistics.scm (r-rmarkdown): Update to 2.23.
 2023-07-12 14:29:08 +02:00
Ricardo Wurmus
7cb71cb2fb
gnu: r-rcpparmadillo: Update to 0.12.4.1.0. 
* gnu/packages/statistics.scm (r-rcpparmadillo): Update to 0.12.4.1.0.
 2023-07-12 14:29:08 +02:00
Ricardo Wurmus
b8112b4600
gnu: r-rstudioapi: Update to 0.15.0. 
* gnu/packages/statistics.scm (r-rstudioapi): Update to 0.15.0.
 2023-07-12 14:29:08 +02:00
Ricardo Wurmus
c5c0f85b77
gnu: r-xml2: Update to 1.3.5. 
* gnu/packages/statistics.scm (r-xml2): Update to 1.3.5.
 2023-07-12 14:29:08 +02:00
Ricardo Wurmus
4ec94fe0a9
gnu: r-locfit: Update to 1.5-9.8. 
* gnu/packages/statistics.scm (r-locfit): Update to 1.5-9.8.
 2023-07-12 14:29:08 +02:00
Ricardo Wurmus
1493844a1e
gnu: r-dbplyr: Update to 2.3.3. 
* gnu/packages/statistics.scm (r-dbplyr): Update to 2.3.3.
 2023-07-12 14:29:08 +02:00
Ricardo Wurmus
6276fbb64a
gnu: r-testthat: Update to 3.1.10. 
* gnu/packages/statistics.scm (r-testthat): Update to 3.1.10.
 2023-07-12 14:29:08 +02:00
Ricardo Wurmus
b372435930
gnu: r-matrix: Update to 1.6-0. 
* gnu/packages/statistics.scm (r-matrix): Update to 1.6-0.
 2023-07-12 14:29:08 +02:00
Ricardo Wurmus
f072cd9486
gnu: r-kernsmooth: Update to 2.23-22. 
* gnu/packages/statistics.scm (r-kernsmooth): Update to 2.23-22.
 2023-07-12 14:29:08 +02:00
Ricardo Wurmus
1b09d2e9ae
gnu: r-lme4: Update to 1.1-34. 
* gnu/packages/statistics.scm (r-lme4): Update to 1.1-34.
 2023-07-12 14:29:02 +02:00
Ricardo Wurmus
138d0dd9ad
gnu: r-digest: Update to 0.6.33. 
* gnu/packages/statistics.scm (r-digest): Update to 0.6.33.
[native-inputs]: Add r-simplermarkdown.
 2023-07-12 14:29:02 +02:00
Ricardo Wurmus
60c70a9009
gnu: r-plotly: Update to 4.10.2. 
* gnu/packages/statistics.scm (r-plotly): Update to 4.10.2.
 2023-07-12 14:29:02 +02:00
Ricardo Wurmus
8e83db0bce
gnu: python-statsmodels: Update to 0.14.0. 
* gnu/packages/statistics.scm (python-statsmodels): Update to 0.14.0.
[source]: Simplify snippet.
[build-system]: Use pyproject-build-system.
[arguments]: Remove trailing #T from build phase.
[propagated-inputs]: Add python-packaging; remove python-matplotlib.
[native-inputs]: Add python-colorama, python-flake8, python-isort,
python-joblib, python-matplotlib, python-pytest, python-pytest-randomly,
python-pytest-xdist, and python-setuptools-scm; remove python-nose and
python-sphinx.
 2023-07-07 10:13:57 +02:00
Vinicius Monego
c55611ff3f
gnu: Add python-pymc. 
* gnu/packages/statistics.scm (python-pymc): New variable.
 2023-06-25 10:48:07 -03:00
Vinicius Monego
514856e1aa
gnu: Add python-arviz. 
* gnu/packages/statistics.scm (python-arviz): New variable.
 2023-06-25 10:43:22 -03:00
Vinicius Monego
fa214b27cf
gnu: Add python-altair. 
* gnu/packages/statistics.scm (python-altair): New variable.
 2023-06-25 10:43:21 -03:00
Vinicius Monego
64e5e17d8c
gnu: Add python-vega-datasets. 
* gnu/packages/statistics.scm (python-vega-datasets): New variable.
* gnu/packages/patches/python-vega-datasets-remove-la-riots-code.patch: New
file.
* gnu/local.mk (dist_patch_DATA): Register it.
 2023-06-25 10:43:18 -03:00
Ricardo Wurmus
da71721db1
gnu: r-biased-urn: Update to 2.0.10. 
* gnu/packages/statistics.scm (r-biased-urn): Update to 2.0.10.
 2023-06-03 08:32:03 +02:00
Ricardo Wurmus
79b52c60e9
gnu: r-matrixstats: Update to 1.0.0. 
* gnu/packages/statistics.scm (r-matrixstats): Update to 1.0.0.
 2023-06-03 08:32:03 +02:00
Ricardo Wurmus
3f8a983cae
gnu: r-mvtnorm: Update to 1.2-0. 
* gnu/packages/statistics.scm (r-mvtnorm): Update to 1.2-0.
 2023-06-03 08:32:03 +02:00
Ricardo Wurmus
01d9a691be
gnu: r-rmarkdown: Update to 2.22. 
* gnu/packages/statistics.scm (r-rmarkdown): Update to 2.22.
[properties]: Add hints to the updater.
 2023-06-03 08:31:20 +02:00
Ricardo Wurmus
6ea2e1105a
gnu: r-desctools: Update to 0.99.49. 
* gnu/packages/statistics.scm (r-desctools): Update to 0.99.49.
[propagated-inputs]: Add r-withr.
 2023-05-31 18:19:55 +02:00
Ricardo Wurmus
df71989159
gnu: r-rrcov: Update to 1.7-3. 
* gnu/packages/statistics.scm (r-rrcov): Update to 1.7-3.
 2023-05-31 18:19:55 +02:00
Ricardo Wurmus
e2bc0cb1b4
gnu: r-rcpparmadillo: Update to 0.12.4.0.0. 
* gnu/packages/statistics.scm (r-rcpparmadillo): Update to 0.12.4.0.0.
 2023-05-31 18:19:55 +02:00