diff options
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 29 |
1 files changed, 13 insertions, 16 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index e94fca2935..cab61ef45a 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -24552,48 +24552,45 @@ populations.") (license license:bsd-3))) (define-public scregseg + ;; 0.1.3 was released in 2023, there are a lot of comparability fixes on + ;; master branch, use the latest commit for now. + (let ((commit "78ebff8c3507752c3bfbc4db3f72f7e8a733e92f") + (revision "0")) (package (name "scregseg") - (version "0.1.3") + (version (git-version "0.1.3" revision commit)) (source (origin (method git-fetch) (uri (git-reference (url "https://github.com/BIMSBbioinfo/scregseg") - (commit (string-append "v" version)))) + (commit commit))) (file-name (git-file-name name version)) (sha256 (base32 - "07g2barywa1wi8mggbxkbxqjw1fzd0a0l9cjdbkx4s40imb1dbxb")) + "19iasx6zh305cn8p390ack78f4iklyk61xmnf99c2b8ibml7jmzj")) (snippet '(delete-file "src/scregseg/_utils.c")))) (build-system pyproject-build-system) (arguments (list + #:test-flags + #~(list "--pyargs" "scregseg") #:phases '(modify-phases %standard-phases ;; Numba needs a writable dir to cache functions. (add-before 'check 'set-numba-cache-dir (lambda _ (setenv "NUMBA_CACHE_DIR" "/tmp"))) - ;; Cython extensions have to be built before running the tests. - (add-before 'check 'build-extensions - (lambda _ - (invoke "python" "setup.py" "build_ext" "--inplace"))) ;; NumPy 1.20 deprecated the type wrappers for int and float. (add-after 'unpack 'compatibility (lambda _ (substitute* "src/scregseg/_utils.pyx" - (("np.float") "float")))) - (add-after 'unpack 'do-not-fail-to-find-sklearn - (lambda _ - ;; XXX: I have no idea why it cannot seem to find sklearn. - (substitute* "setup.py" - (("'sklearn',") ""))))))) + (("np.float") "float"))))))) (native-inputs (list python-cython - python-wheel)) + python-setuptools)) (propagated-inputs - (list python-scikit-learn + (list python-scikit-learn-1.6 python-scipy python-numpy python-hmmlearn @@ -24615,7 +24612,7 @@ Dirichlet-Multinomial emission probabilities to segment the genome either according to distinct relative cross-cell accessibility profiles or (after collapsing the single-cell tracks to pseudo-bulk tracks) to capture distinct cross-cluster accessibility profiles.") - (license license:gpl3+))) + (license license:gpl3+)))) (define-public megadepth (package |