diff options
Diffstat (limited to 'gnu/packages/python-xyz.scm')
| -rw-r--r-- | gnu/packages/python-xyz.scm | 49 |
1 files changed, 26 insertions, 23 deletions
diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 579105e263..f5c4e3e9f7 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -201,6 +201,7 @@ #:use-module (gnu packages libusb) #:use-module (gnu packages linux) #:use-module (gnu packages llvm) + #:use-module (gnu packages machine-learning) #:use-module (gnu packages man) #:use-module (gnu packages markup) #:use-module (gnu packages maths) @@ -23601,29 +23602,26 @@ N-dimensional arrays for Python.") (sha256 (base32 "0v7npqrg1rdm8jzw22a45c0mqrmsv05r3k88i3lhzi0pzzxca1i1")))) - (build-system python-build-system) + (build-system pyproject-build-system) (arguments - `(#:phases - (modify-phases %standard-phases - (delete 'check) - (replace 'build - (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") - (invoke "flit" "build"))) - (replace 'install - (lambda* (#:key inputs outputs #:allow-other-keys) - (add-installed-pythonpath inputs outputs) - (let ((out (assoc-ref outputs "out"))) - (for-each (lambda (wheel) - (format #true wheel) - (invoke "python" "-m" "pip" "install" - wheel (string-append "--prefix=" out))) - (find-files "dist" "\\.whl$")))))))) + (list + #:test-flags + '(list "-k" "not concatenation.rst") + #:phases + #~(modify-phases %standard-phases + ;; Doctests require scanpy from (gnu packages bioinformatics) + (add-after 'unpack 'disable-doctests + (lambda _ + (substitute* "pyproject.toml" + (("--doctest-modules") "")))) + (add-before 'build 'set-version + (lambda _ + (setenv "SETUPTOOLS_SCM_PRETEND_VERSION" #$version) + (substitute* "anndata/_metadata.py" + (("__version__ =.*") + (string-append "__version__ = \"" #$version "\"\n"))) + ;; ZIP does not support timestamps before 1980. + (setenv "SOURCE_DATE_EPOCH" "315532800")))))) (propagated-inputs (list python-h5py python-importlib-metadata @@ -23632,9 +23630,14 @@ N-dimensional arrays for Python.") python-packaging python-pandas python-scipy + python-scikit-learn python-zarr)) (native-inputs - (list python-joblib python-pytest python-toml python-flit + (list python-boltons + python-joblib + python-pytest + python-toml + python-flit python-setuptools-scm)) (home-page "https://github.com/theislab/anndata") (synopsis "Annotated data for data analysis pipelines") |