guix_mirror_bot pushed a commit to branch master
in repository guix.
commit f9f378224d72f20f9de9a86af4f8fa0848e5c52b
Author: Sharlatan Hellseher <[email protected]>
AuthorDate: Thu Jul 24 15:33:45 2025 +0100
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
---
gnu/packages/python-science.scm | 80 +++++++++++++++++++++++++++++++++++++++++
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")
