guix_mirror_bot pushed a commit to branch python-team
in repository guix.
commit 56c54f69c19d34ea5bb2df987a45e104b9c27880
Author: Sharlatan Hellseher <[email protected]>
AuthorDate: Thu Feb 5 12:19:10 2026 +0000
gnu: python-celltypist: Update to 1.7.1.
* gnu/packages/bioinformatics.scm (python-celltypist): Update to 1.7.1.
[arguments] <tests?>: Enable simple runtime regression check.
<phases>: Remove 'set-home and 'set-numba-cache-dir; add
'set-environment; use custom 'check phase.
[native-inputs]: Remove python-wheel; add python-setuptools.
Change-Id: I7ec16da8c6d3af8ad0d8eb96d5f9b50d9858eae3
---
gnu/packages/bioinformatics.scm | 32 +++++++++++++++++---------------
1 file changed, 17 insertions(+), 15 deletions(-)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index aa4d11fd10..a5721e601a 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -2548,30 +2548,33 @@ from high-throughput single-cell RNA sequencing
(scRNA-seq) data.")
(define-public python-celltypist
(package
(name "python-celltypist")
- (version "1.6.2")
+ (version "1.7.1")
(source
(origin
(method git-fetch)
(uri (git-reference
- (url "https://github.com/Teichlab/celltypist";)
- (commit version)))
+ (url "https://github.com/Teichlab/celltypist";)
+ (commit version)))
(file-name (git-file-name name version))
(sha256
- (base32
- "0c42cx01zkxr0dk5f1d7q71qdi18v2smlc3wpvwyjlzplya7k2iy"))))
+ (base32 "1ha19wak8lnbm2j929lswncswygl1qiv53b8fs321s6708gyhv4v"))))
(build-system pyproject-build-system)
(arguments
(list
- #:tests? #false ;there are none
#:phases
- '(modify-phases %standard-phases
- (add-before 'check 'set-home
- ;; The sanity check requires a HOME directory, because celltypist
- ;; wants to write settings.
- (lambda _ (setenv "HOME" "/tmp")))
- ;; Numba needs a writable dir to cache functions.
- (add-before 'build 'set-numba-cache-dir
- (lambda _ (setenv "NUMBA_CACHE_DIR" "/tmp"))))))
+ #~(modify-phases %standard-phases
+ (add-before 'build 'set-environment
+ (lambda _
+ (setenv "HOME" "/tmp")
+ (setenv "NUMBA_CACHE_DIR" "/tmp")))
+ (replace 'check
+ ;; Simple regression check, taken from project's Dockerfile,
+ ;; "--update-models" requires network access.
+ (lambda* (#:key tests? #:allow-other-keys)
+ (when tests?
+ (invoke "celltypist" "--help")))))))
+ (native-inputs
+ (list python-setuptools))
(propagated-inputs
(list python-click
python-leidenalg
@@ -2581,7 +2584,6 @@ from high-throughput single-cell RNA sequencing
(scRNA-seq) data.")
python-scanpy
python-scikit-learn
python-requests))
- (native-inputs (list python-wheel))
(home-page "https://github.com/Teichlab/celltypist";)
(synopsis "Tool for semi-automatic cell type classification")
(description
