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gnu: python-anndata: Use pyproject-build-system.

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* gnu/packages/python-xyz.scm (python-anndata)[build-system]: Use
pyproject-build-system.
[arguments]: Replace custom 'build phase with 'set-version phase; remove
custom 'install phase; disable doctest via build phase 'disable-doctests and
the #:test-flags property.
[propagated-inputs]: Add python-scikit-learn.
[native-inputs]: Add python-boltons.
This commit is contained in:
Ricardo Wurmus 2022-12-12 23:47:27 +01:00
parent 2c65106cf5
commit 75331dc6e6
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GPG Key ID: 197A5888235FACAC
1 changed files with 26 additions and 23 deletions
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gnu/packages/python-xyz.scm
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@ -201,6 +201,7 @@
#:use-module (gnu packages libusb)
#:use-module (gnu packages linux)
#:use-module (gnu packages llvm)
#:use-module (gnu packages machine-learning)
#:use-module (gnu packages man)
#:use-module (gnu packages markup)
#:use-module (gnu packages maths)
@ -23601,29 +23602,26 @@ N-dimensional arrays for Python.")
(sha256
(base32
"0v7npqrg1rdm8jzw22a45c0mqrmsv05r3k88i3lhzi0pzzxca1i1"))))
(build-system python-build-system)
(build-system pyproject-build-system)
(arguments
`(#:phases
(modify-phases %standard-phases
(delete 'check)
(replace 'build
(list
#:test-flags
'(list "-k" "not concatenation.rst")
#:phases
#~(modify-phases %standard-phases
;; Doctests require scanpy from (gnu packages bioinformatics)
(add-after 'unpack 'disable-doctests
(lambda _
(setenv "SETUPTOOLS_SCM_PRETEND_VERSION" ,version)
(substitute* "pyproject.toml"
(("--doctest-modules") ""))))
(add-before 'build 'set-version
(lambda _
(setenv "SETUPTOOLS_SCM_PRETEND_VERSION" #$version)
(substitute* "anndata/_metadata.py"
(("__version__ =.*")
(string-append "__version__ = \"" ,version "\"\n")))
(string-append "__version__ = \"" #$version "\"\n")))
;; ZIP does not support timestamps before 1980.
(setenv "SOURCE_DATE_EPOCH" "315532800")
(invoke "flit" "build")))
(replace 'install
(lambda* (#:key inputs outputs #:allow-other-keys)
(add-installed-pythonpath inputs outputs)
(let ((out (assoc-ref outputs "out")))
(for-each (lambda (wheel)
(format #true wheel)
(invoke "python" "-m" "pip" "install"
wheel (string-append "--prefix=" out)))
(find-files "dist" "\\.whl$"))))))))
(setenv "SOURCE_DATE_EPOCH" "315532800"))))))
(propagated-inputs
(list python-h5py
python-importlib-metadata
@ -23632,9 +23630,14 @@ N-dimensional arrays for Python.")
python-packaging
python-pandas
python-scipy
python-scikit-learn
python-zarr))
(native-inputs
(list python-joblib python-pytest python-toml python-flit
(list python-boltons
python-joblib
python-pytest
python-toml
python-flit
python-setuptools-scm))
(home-page "https://github.com/theislab/anndata")
(synopsis "Annotated data for data analysis pipelines")