lbraun pushed a commit to branch wip-python-pep517
in repository guix.
commit 6893d6b1b5a2dde3ce94a7e8552952252228ebbb
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 | 29 ++++++++---------------------
1 file changed, 8 insertions(+), 21 deletions(-)
diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index f6c3bc7c6a..b254e538b6 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -22934,27 +22934,12 @@ N-dimensional arrays for Python.")
"0v7npqrg1rdm8jzw22a45c0mqrmsv05r3k88i3lhzi0pzzxca1i1"))))
(build-system python-build-system)
(arguments
- `(#:phases
+ `(#:test-flags '("-vv" "-k" "not concatenation.rst") ; needs
python-scanpy.
+ #:phases
(modify-phases %standard-phases
- (delete 'check)
- (replace 'build
+ (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")
- (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$"))))))))
+ (setenv "SETUPTOOLS_SCM_PRETEND_VERSION" ,version))))))
(propagated-inputs
(list python-h5py
python-importlib-metadata
@@ -22966,8 +22951,10 @@ N-dimensional arrays for Python.")
python-xlrd-1
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
