andreas pushed a commit to branch python-team
in repository guix.
commit fbaa7a64d8bb74dcc9269963c7e0372845c1825e
Author: Nicolas Graves <ngra...@ngraves.fr>
AuthorDate: Fri Apr 4 21:16:56 2025 +0200
gnu: python-pysnptools: Fix build and enable tests.
* gnu/packages/bioinformatics.scm (python-pysnptools): Fix build and enable
tests.
[arguments]{test-flags}: Ignore failing tests.
{phases}: Add 'patch-data-path and 'loosen-requirements phases.
(pysnptools-examples-files): Add origin.
(bgen-sample-files): Add origin.
Signed-off-by: Sharlatan Hellseher <sharlata...@gmail.com>
---
gnu/packages/bioinformatics.scm | 80 ++++++++++++++++++++++++++++++++++++++---
1 file changed, 75 insertions(+), 5 deletions(-)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 520397ef6e..218f470dd9 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -3716,6 +3716,49 @@ It emphasizes modularity and performance. The API will
be immediately
familiar to anyone with experience of scikit-learn or scipy.")
(license license:asl2.0)))
+(define bgen-sample-files
+ (let* ((name "bgen-sample-files")
+ (commit "7b1bc74f58b326ca19606fa5f3c6093d48367993")
+ (revision "0")
+ (version (git-version "0.0.0" revision commit)))
+ (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/fastlmm/bgen-sample-files";)
+ (commit commit)))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32 "1b8jkscccyspfr3y1b66xvwnljcha08r2i24v9d6hcm5zii0l54w")))))
+
+(define pynsptools-examples-files
+ (let* ((name "pysnptools-examples-files")
+ ;; taken from pysnptools/util/pysnptools.hashdown.json
+ (commit "ed14e050b2b75e7f4ddb73d512fbe928bbdb2b85")
+ (revision "0")
+ (version (git-version "0.0.0" revision commit)))
+ (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/fastlmm/PySnpTools";)
+ (commit commit)))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32 "0hznpj15kx2sla16wlmcqz21n2vi2qb1493v30vz75hnm1m4iwm1"))
+ (modules '((guix build utils)
+ (ice-9 ftw)))
+ (snippet
+ #~(begin
+ ;; Delete everything except for examples directory:
+ (define (delete-except exceptions)
+ (lambda (file)
+ (unless (member file `("." ".." ,@exceptions))
+ (delete-file-recursively file))))
+ (for-each (delete-except '("pysnptools" "tests")) (scandir "."))
+ (with-directory-excursion "pysnptools"
+ (for-each (delete-except '("examples")) (scandir ".")))
+ (with-directory-excursion "tests"
+ (for-each (delete-except '("datasets")) (scandir "."))))))))
+
(define-public python-pysnptools
(package
(name "python-pysnptools")
@@ -3725,12 +3768,39 @@ familiar to anyone with experience of scikit-learn or
scipy.")
(method url-fetch)
(uri (pypi-uri "pysnptools" version))
(sha256
- (base32
- "1babnyky5fk93as1ybdvpz9x3x5099gkgscxflngzfswin23mspk"))))
+ (base32 "1babnyky5fk93as1ybdvpz9x3x5099gkgscxflngzfswin23mspk"))))
(build-system pyproject-build-system)
- ;; Tests require test data from python-bed-reader, which fetches data with
- ;; python-pooch.
- (arguments (list #:tests? #f))
+ (arguments
+ (list
+ #:test-flags
+ #~(list
+ ;; These tests require the bgen feature and an additional input.
+ "--ignore" "pysnptools/distreader/bgen.py"
+ "--ignore" "pysnptools/distreader/test_bgen2.py"
+ "--ignore" "pysnptools/distreader/distreader.py"
+ "-k" "not pysnptools.distreader.distdata.DistData.val \
+and not pysnptools.distreader.disthdf5.DistHdf5.write \
+and not pysnptools.distreader.distmemmap.DistMemMap.write"
+ ;; These tests require network connection.
+ "--ignore" "pysnptools/util/_example_file.py"
+ "--ignore" "pysnptools/util/filecache/hashdown.py")
+ #:phases
+ #~(modify-phases %standard-phases
+ (add-after 'unpack 'patch-data-path
+ (lambda _
+ (substitute* "pysnptools/util/pysnptools.hashdown.json"
+ (("https://github\\.com/fastlmm/PySnpTools/\
+raw/ed14e050b2b75e7f4ddb73d512fbe928bbdb2b85")
+ (string-append "file://" #+pynsptools-examples-files)))
+ (substitute* "pysnptools/util/bgen.hashdown.json"
+ (("https://raw\\.githubusercontent\\.com\
+/fastlmm/bgen-sample-files/7b1bc74f58b326ca19606fa5f3c6093d48367993")
+ (string-append "file://" #+bgen-sample-files)))))
+ (add-after 'unpack 'loosen-requirements
+ (lambda _
+ (substitute* "pyproject.toml"
+ (("(h5py|psutil|wheel)>=[0-9.]*" all target)
+ target)))))))
(propagated-inputs
(list python-bed-reader
python-cloudpickle
