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gnu: python-anndata: Move to python-science.
* gnu/packages/python-xyz.scm (python-anndata): Move from here ... * gnu/packages/python-science.scm: ... to here. Change-Id: I3d968728de04610984c08884bd29cd9c055fa284
This commit is contained in:
Sharlatan Hellseher
parent
aaeb42f675
commit
f9f378224d
2 changed files with 80 additions and 80 deletions
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@ -249,6 +249,86 @@ possibility to differentiate functions that contain matrix functions as
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+,-,*,/, dot, solve, qr, eigh, cholesky.")
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(license license:bsd-3)))
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(define-public python-anndata
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(package
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(name "python-anndata")
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(version "0.11.1")
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(source
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(origin
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;; The tarball from PyPi doesn't include tests.
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(method git-fetch)
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(uri (git-reference
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(url "https://github.com/theislab/anndata")
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(commit version)))
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(file-name (git-file-name name version))
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(sha256
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(base32
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"0skmjjvxk5gdsx6fkplszff92jsb4l45j23c6mhq1vdi3wqhqhcw"))))
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(build-system pyproject-build-system)
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(arguments
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(list
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#:test-flags
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#~(list "-k" #$(string-append
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;; This one test seemingly freezes
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"not test_read_lazy_h5_cluster"
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;; Fails with a numpy deprecation warning
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;; but not an actual failure
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" and not test_read_write_X"))
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#:phases
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#~(modify-phases %standard-phases
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;; Doctests require scanpy from (gnu packages bioinformatics)
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(add-after 'unpack 'disable-doctests
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(lambda _
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(substitute* "pyproject.toml"
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(("--doctest-modules") ""))))
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(add-before 'build 'set-version
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(lambda _
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(setenv "SETUPTOOLS_SCM_PRETEND_VERSION" #$version)
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;; ZIP does not support timestamps before 1980.
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(setenv "SOURCE_DATE_EPOCH" "315532800")))
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;; Numba needs a writable dir to cache functions.
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(add-before 'check 'set-numba-cache-dir
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(lambda _
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(setenv "NUMBA_CACHE_DIR" "/tmp"))))))
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(propagated-inputs
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(list python-array-api-compat
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python-exceptiongroup ;only for Python <3.11
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python-h5py
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python-importlib-metadata
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python-natsort
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python-numcodecs
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python-packaging
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python-pandas
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python-scipy
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python-scikit-learn
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python-setuptools ; For pkg_resources.
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python-zarr))
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(native-inputs
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(list python-awkward
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python-boltons
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python-dask
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python-distributed
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python-hatchling
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python-hatch-vcs
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python-joblib
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python-loompy
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python-matplotlib
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python-pytest
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python-pytest-mock
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python-pytest-doctestplus
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python-pytest-xdist
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python-toml
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python-flit
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python-setuptools-scm))
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(home-page "https://github.com/theislab/anndata")
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(synopsis "Annotated data for data analysis pipelines")
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(description "Anndata is a package for simple (functional) high-level APIs
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for data analysis pipelines. In this context, it provides an efficient,
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scalable way of keeping track of data together with learned annotations and
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reduces the code overhead typically encountered when using a mostly
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object-oriented library such as @code{scikit-learn}.")
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(license license:bsd-3)))
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(define-public python-aplus
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(package
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(name "python-aplus")
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@ -30070,86 +30070,6 @@ codecs for use in data storage and communication applications.")
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N-dimensional arrays for Python.")
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(license license:expat)))
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(define-public python-anndata
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(package
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(name "python-anndata")
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(version "0.11.1")
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(source
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(origin
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;; The tarball from PyPi doesn't include tests.
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(method git-fetch)
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(uri (git-reference
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(url "https://github.com/theislab/anndata")
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(commit version)))
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(file-name (git-file-name name version))
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(sha256
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(base32
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"0skmjjvxk5gdsx6fkplszff92jsb4l45j23c6mhq1vdi3wqhqhcw"))))
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(build-system pyproject-build-system)
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(arguments
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(list
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#:test-flags
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#~(list "-k" #$(string-append
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;; This one test seemingly freezes
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"not test_read_lazy_h5_cluster"
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;; Fails with a numpy deprecation warning
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;; but not an actual failure
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" and not test_read_write_X"))
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#:phases
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#~(modify-phases %standard-phases
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;; Doctests require scanpy from (gnu packages bioinformatics)
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(add-after 'unpack 'disable-doctests
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(lambda _
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(substitute* "pyproject.toml"
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(("--doctest-modules") ""))))
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(add-before 'build 'set-version
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(lambda _
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(setenv "SETUPTOOLS_SCM_PRETEND_VERSION" #$version)
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;; ZIP does not support timestamps before 1980.
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(setenv "SOURCE_DATE_EPOCH" "315532800")))
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;; Numba needs a writable dir to cache functions.
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(add-before 'check 'set-numba-cache-dir
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(lambda _
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(setenv "NUMBA_CACHE_DIR" "/tmp"))))))
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(propagated-inputs
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(list python-array-api-compat
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python-exceptiongroup ;only for Python <3.11
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python-h5py
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python-importlib-metadata
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python-natsort
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python-numcodecs
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python-packaging
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python-pandas
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python-scipy
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python-scikit-learn
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python-setuptools ; For pkg_resources.
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python-zarr))
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(native-inputs
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(list python-awkward
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python-boltons
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python-dask
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python-distributed
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python-hatchling
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python-hatch-vcs
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python-joblib
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python-loompy
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python-matplotlib
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python-pytest
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python-pytest-mock
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python-pytest-doctestplus
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python-pytest-xdist
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python-toml
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python-flit
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python-setuptools-scm))
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(home-page "https://github.com/theislab/anndata")
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(synopsis "Annotated data for data analysis pipelines")
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(description "Anndata is a package for simple (functional) high-level APIs
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for data analysis pipelines. In this context, it provides an efficient,
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scalable way of keeping track of data together with learned annotations and
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reduces the code overhead typically encountered when using a mostly
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object-oriented library such as @code{scikit-learn}.")
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(license license:bsd-3)))
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(define-public python-dill
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(package
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(name "python-dill")
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