diff options
Diffstat (limited to 'gnu/packages/python-xyz.scm')
| -rw-r--r-- | gnu/packages/python-xyz.scm | 38 |
1 files changed, 29 insertions, 9 deletions
diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 8f018cb512..b302a1eff1 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -180,6 +180,7 @@ #:use-module (gnu packages base) #:use-module (gnu packages bash) #:use-module (gnu packages bdw-gc) + #:use-module (gnu packages bioinformatics) #:use-module (gnu packages build-tools) #:use-module (gnu packages check) #:use-module (gnu packages cmake) @@ -27567,7 +27568,7 @@ N-dimensional arrays for Python.") (define-public python-anndata (package (name "python-anndata") - (version "0.8.0") + (version "0.10.7") (source (origin ;; The tarball from PyPi doesn't include tests. @@ -27578,29 +27579,39 @@ N-dimensional arrays for Python.") (file-name (git-file-name name version)) (sha256 (base32 - "0v7npqrg1rdm8jzw22a45c0mqrmsv05r3k88i3lhzi0pzzxca1i1")))) + "1i08rm1xnsnq12rjv4virgdx61bra1gsfagjdq0kcpz8npxqa0as")))) (build-system pyproject-build-system) (arguments (list #:test-flags - '(list "-k" "not concatenation.rst") + '(list "-k" (string-append "not concatenation.rst" + ;; fixture 'mocker' not found + " and not test_consecutive_bool")) #:phases #~(modify-phases %standard-phases ;; Doctests require scanpy from (gnu packages bioinformatics) (add-after 'unpack 'disable-doctests (lambda _ + (substitute* "conftest.py" + (("import pytest") + (string-append "import pytest\nimport _pytest\n")) + (("pytest.DoctestItem") + "_pytest.doctest.DoctestItem")) (substitute* "pyproject.toml" (("--doctest-modules") "")))) (add-before 'build 'set-version (lambda _ (setenv "SETUPTOOLS_SCM_PRETEND_VERSION" #$version) - (substitute* "anndata/_metadata.py" - (("__version__ =.*") - (string-append "__version__ = \"" #$version "\"\n"))) ;; ZIP does not support timestamps before 1980. - (setenv "SOURCE_DATE_EPOCH" "315532800")))))) + (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-h5py + (list python-array-api-compat + python-exceptiongroup ;only for Python <3.11 + python-h5py python-importlib-metadata python-natsort python-numcodecs @@ -27610,9 +27621,18 @@ N-dimensional arrays for Python.") python-scikit-learn python-zarr)) (native-inputs - (list python-boltons + (list python-awkward + python-boltons + python-dask + python-distributed + python-hatchling + python-hatch-vcs python-joblib + python-loompy + python-matplotlib python-pytest + python-pytest-doctestplus + python-pytest-xdist python-toml python-flit python-setuptools-scm)) |