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

1 files changed, 80 insertions, 0 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")