diff options
author | Sharlatan Hellseher <sharlatanus@gmail.com> | 2025-07-24 15:33:45 +0100 |
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committer | Sharlatan Hellseher <sharlatanus@gmail.com> | 2025-07-24 15:52:13 +0100 |
commit | f9f378224d72f20f9de9a86af4f8fa0848e5c52b (patch) | |
tree | fe768c228e7c01a0eeff2e89ef27de50c990f5c6 | |
parent | aaeb42f675dbed592b244cc4886fe6433ad3f9b8 (diff) |
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
-rw-r--r-- | gnu/packages/python-science.scm | 80 | ||||
-rw-r--r-- | gnu/packages/python-xyz.scm | 80 |
2 files changed, 80 insertions, 80 deletions
diff --git a/gnu/packages/python-science.scm b/gnu/packages/python-science.scm index f66e546df7..561f4f0936 100644 --- a/gnu/packages/python-science.scm +++ b/gnu/packages/python-science.scm @@ -249,6 +249,86 @@ possibility to differentiate functions that contain matrix functions as +,-,*,/, dot, solve, qr, eigh, cholesky.") (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 (package (name "python-aplus") diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 44b75747f6..4aa8aa2330 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -30070,86 +30070,6 @@ codecs for use in data storage and communication applications.") N-dimensional arrays for Python.") (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 (package (name "python-dill") |