2 files changed, 80 insertions(+), 80 deletions(-)

M gnu/packages/python-science.scm
M gnu/packages/python-xyz.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")

@@ 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")