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gnu: python-anndata: Move to python-science.

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* gnu/packages/python-xyz.scm (python-anndata): Move from here ...
* gnu/packages/python-science.scm: ... to here.

Change-Id: I3d968728de04610984c08884bd29cd9c055fa284
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Sharlatan Hellseher 2025-07-24 15:33:45 +01:00
parent aaeb42f675
commit f9f378224d
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2 changed files with 80 additions and 80 deletions
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80
gnu/packages/python-science.scm
View file

@ -249,6 +249,86 @@ possibility to differentiate functions that contain matrix functions as
+,-,*,/, dot, solve, qr, eigh, cholesky.") +,-,*,/, dot, solve, qr, eigh, cholesky.")
(license license:bsd-3))) (license license:bsd-3)))
(define-public python-anndata
(package
(name "python-anndata")
(version "0.11.1")
(source
(origin
;; The tarball from PyPi doesn't include tests.
(method git-fetch)
(uri (git-reference
(url "https://github.com/theislab/anndata")
(commit version)))
(file-name (git-file-name name version))
(sha256
(base32
"0skmjjvxk5gdsx6fkplszff92jsb4l45j23c6mhq1vdi3wqhqhcw"))))
(build-system pyproject-build-system)
(arguments
(list
#:test-flags
#~(list "-k" #$(string-append
;; This one test seemingly freezes
"not test_read_lazy_h5_cluster"
;; Fails with a numpy deprecation warning
;; but not an actual failure
" and not test_read_write_X"))
#:phases
#~(modify-phases %standard-phases
;; Doctests require scanpy from (gnu packages bioinformatics)
(add-after 'unpack 'disable-doctests
(lambda _
(substitute* "pyproject.toml"
(("--doctest-modules") ""))))
(add-before 'build 'set-version
(lambda _
(setenv "SETUPTOOLS_SCM_PRETEND_VERSION" #$version)
;; ZIP does not support timestamps before 1980.
(setenv "SOURCE_DATE_EPOCH" "315532800")))
;; Numba needs a writable dir to cache functions.
(add-before 'check 'set-numba-cache-dir
(lambda _
(setenv "NUMBA_CACHE_DIR" "/tmp"))))))
(propagated-inputs
(list python-array-api-compat
python-exceptiongroup ;only for Python <3.11
python-h5py
python-importlib-metadata
python-natsort
python-numcodecs
python-packaging
python-pandas
python-scipy
python-scikit-learn
python-setuptools ; For pkg_resources.
python-zarr))
(native-inputs
(list python-awkward
python-boltons
python-dask
python-distributed
python-hatchling
python-hatch-vcs
python-joblib
python-loompy
python-matplotlib
python-pytest
python-pytest-mock
python-pytest-doctestplus
python-pytest-xdist
python-toml
python-flit
python-setuptools-scm))
(home-page "https://github.com/theislab/anndata")
(synopsis "Annotated data for data analysis pipelines")
(description "Anndata is a package for simple (functional) high-level APIs
for data analysis pipelines. In this context, it provides an efficient,
scalable way of keeping track of data together with learned annotations and
reduces the code overhead typically encountered when using a mostly
object-oriented library such as @code{scikit-learn}.")
(license license:bsd-3)))
(define-public python-aplus (define-public python-aplus
(package (package
(name "python-aplus") (name "python-aplus")

80
gnu/packages/python-xyz.scm
View file

@ -30070,86 +30070,6 @@ codecs for use in data storage and communication applications.")
N-dimensional arrays for Python.") N-dimensional arrays for Python.")
(license license:expat))) (license license:expat)))
(define-public python-anndata
(package
(name "python-anndata")
(version "0.11.1")
(source
(origin
;; The tarball from PyPi doesn't include tests.
(method git-fetch)
(uri (git-reference
(url "https://github.com/theislab/anndata")
(commit version)))
(file-name (git-file-name name version))
(sha256
(base32
"0skmjjvxk5gdsx6fkplszff92jsb4l45j23c6mhq1vdi3wqhqhcw"))))
(build-system pyproject-build-system)
(arguments
(list
#:test-flags
#~(list "-k" #$(string-append
;; This one test seemingly freezes
"not test_read_lazy_h5_cluster"
;; Fails with a numpy deprecation warning
;; but not an actual failure
" and not test_read_write_X"))
#:phases
#~(modify-phases %standard-phases
;; Doctests require scanpy from (gnu packages bioinformatics)
(add-after 'unpack 'disable-doctests
(lambda _
(substitute* "pyproject.toml"
(("--doctest-modules") ""))))
(add-before 'build 'set-version
(lambda _
(setenv "SETUPTOOLS_SCM_PRETEND_VERSION" #$version)
;; ZIP does not support timestamps before 1980.
(setenv "SOURCE_DATE_EPOCH" "315532800")))
;; Numba needs a writable dir to cache functions.
(add-before 'check 'set-numba-cache-dir
(lambda _
(setenv "NUMBA_CACHE_DIR" "/tmp"))))))
(propagated-inputs
(list python-array-api-compat
python-exceptiongroup ;only for Python <3.11
python-h5py
python-importlib-metadata
python-natsort
python-numcodecs
python-packaging
python-pandas
python-scipy
python-scikit-learn
python-setuptools ; For pkg_resources.
python-zarr))
(native-inputs
(list python-awkward
python-boltons
python-dask
python-distributed
python-hatchling
python-hatch-vcs
python-joblib
python-loompy
python-matplotlib
python-pytest
python-pytest-mock
python-pytest-doctestplus
python-pytest-xdist
python-toml
python-flit
python-setuptools-scm))
(home-page "https://github.com/theislab/anndata")
(synopsis "Annotated data for data analysis pipelines")
(description "Anndata is a package for simple (functional) high-level APIs
for data analysis pipelines. In this context, it provides an efficient,
scalable way of keeping track of data together with learned annotations and
reduces the code overhead typically encountered when using a mostly
object-oriented library such as @code{scikit-learn}.")
(license license:bsd-3)))
(define-public python-dill (define-public python-dill
(package (package
(name "python-dill") (name "python-dill")