lbraun pushed a commit to branch wip-python-pep517
in repository guix.
commit 3f4520315eff9d346881f110b6aa3fa732995eaa
Author: Lars-Dominik Braun <[email protected]>
AuthorDate: Sun Jan 9 10:33:10 2022 +0100
gnu: python-anndata: Remove custom build phases, disable failing test.
* gnu/packages/python-xyz.scm (python-anndata)[arguments]: Disable failing
test, remove custom 'build and 'install phases, but keep environment
variable for setuptools-scm.
[propagated-inputs]: Add python-pytoml.
[native-inputs]: Use python-flit-core instead of python-flit, add
python-boltons.
---
gnu/packages/python-xyz.scm | 34 +++++++++-------------------------
1 file changed, 9 insertions(+), 25 deletions(-)
diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index fcc658b49b..3bfedd4418 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -21912,31 +21912,12 @@ N-dimensional arrays for Python.")
"1q30bsfsq9xfqm8nmabg3bjh9gix3yng0170xiiyw1lin4xncf0q"))))
(build-system python-build-system)
(arguments
- `(#:phases
+ `(#:test-flags '("-vv" "-k" "not concatenation.rst") ; needs
python-scanpy.
+ #:phases
(modify-phases %standard-phases
- (delete 'check)
- (add-before 'build 'relax-dependency-requirements
- (lambda _
- ;; We need to upgrade python-pandas to avoid
- ;; https://github.com/pandas-dev/pandas/issues/35446
- (substitute* "pyproject.toml"
- (("pandas>=1.1.1") "pandas>=1.0.5"))))
- (replace 'build
+ (add-before 'build 'set-version
(lambda _
- (setenv "SETUPTOOLS_SCM_PRETEND_VERSION" ,version)
- ;; 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$")))
- #t)))))
+ (setenv "SETUPTOOLS_SCM_PRETEND_VERSION" ,version))))))
(propagated-inputs
(list python-h5py
python-importlib-metadata
@@ -21945,10 +21926,13 @@ N-dimensional arrays for Python.")
python-packaging
python-pandas
python-scipy
+ python-pytoml
python-zarr))
(native-inputs
- (list python-joblib python-pytest python-toml python-flit
- python-setuptools-scm))
+ ;; Missing: python-scanpy, which is part of bioinformatics module,
+ ;; which cannot be imported here.
+ (list python-joblib python-pytest python-toml python-flit-core
+ python-setuptools-scm python-boltons))
(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
