guix_mirror_bot pushed a commit to branch python-team
in repository guix.
commit 220eb165ba52d500340974aa67f1f16f121e86a7
Author: Sharlatan Hellseher <[email protected]>
AuthorDate: Sun Dec 14 15:26:26 2025 +0000
gnu: python-arboreto: Update to 0.1.6-0.79f916b.
* gnu/packages/bioinformatics.scm (python-arboreto): Update to
79f916b0ea25c00989331b8db243826049c3d66c commit.
[arguments] <tests?, test-backend> Enable.
<phases>: Add 'disable-failing-tests.
[propagated-inputs]: Remove python-lz4, python-pyarrow, and
python-tornado-6.
[native-inputs]: Remove python-wheel.
Change-Id: If380a31f7a27832c0e0fd1dda80d5dfd3e539345
---
gnu/packages/bioinformatics.scm | 40 ++++++++++++++++++++++++++--------------
1 file changed, 26 insertions(+), 14 deletions(-)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index b19ca1b77e..7ee57344fc 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -21916,34 +21916,46 @@ pycisTarget and SCENIC.")
(define-public python-arboreto
(package
(name "python-arboreto")
- (version "0.1.6")
+ ;; 0.1.6 was released in 2021
+ (properties '((commit . "79f916b0ea25c00989331b8db243826049c3d66c")
+ (revision . "0")))
+ (version (git-version "0.1.6"
+ (assoc-ref properties 'revision)
+ (assoc-ref properties 'commit)))
(source (origin
(method git-fetch)
(uri (git-reference
- (url "https://github.com/aertslab/arboreto";)
- (commit "2f475dca08f47a60acc2beb8dd897e77b7495ca4")))
+ (url "https://github.com/aertslab/arboreto";)
+ (commit (assoc-ref properties 'commit))))
(file-name (git-file-name name version))
(sha256
(base32
- "0l0im8ay7l2d24f7vaha454vsaha9s36bfqhbijg3b8ir8apsd7l"))))
+ "10h1xzvp5r4612icxd5mfhvmwyw57mlvw6z9nwgh37qpzjcnvddd"))))
(build-system pyproject-build-system)
- ;; Lots of tests fail because python-distributed fails to start the
- ;; "Nanny" process.
- (arguments '(#:tests? #false))
+ (arguments
+ (list
+ ;; tests: 38 tests (skipped=2)
+ #:test-backend #~'unittest
+ #:phases
+ #~(modify-phases %standard-phases
+ (add-after 'unpack 'disable-failing-tests
+ (lambda _
+ (substitute* "tests/test_algo.py"
+ ;; AssertionError: 'Timed out trying to connect to
+ ;; tcp://127.0.0.2:12345 after 10 s' not found in 'Timed out
+ ;; trying to connect to tcp://127.0.0.2:12345 after 30 s'
+ (("def test_address")
+ "def __off_test_address")))))))
(native-inputs
- (list python-setuptools
- python-wheel))
+ (list python-setuptools))
(propagated-inputs
- (list python-bokeh
+ (list python-bokeh ;XXX: for python-dask
python-dask
python-distributed
- python-lz4
python-numpy
python-pandas
- python-pyarrow
python-scikit-learn
- python-scipy
- python-tornado-6))
+ python-scipy))
(home-page "https://github.com/aertslab/arboreto";)
(synopsis "Gene regulatory network inference using tree-based ensemble
regressors")
(description
