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33/55: gnu: python-cooler: Update to 0.9.1.
From: |
guix-commits |
Subject: |
33/55: gnu: python-cooler: Update to 0.9.1. |
Date: |
Mon, 15 Jan 2024 07:42:24 -0500 (EST) |
rekado pushed a commit to branch wip-python-science
in repository guix.
commit 935191fb705c4daf664fde905b156f5b0d64c335
Author: Ricardo Wurmus <rekado@elephly.net>
AuthorDate: Tue Jan 9 14:33:23 2024 +0100
gnu: python-cooler: Update to 0.9.1.
* gnu/packages/bioinformatics.scm (python-cooler): Update to 0.9.1.
[build-system]: Use pyproject-build-system.
[arguments]: Remove custom build phases; disable tests via #:test-flags.
[propagated-inputs]: Remove python-six and python-sparse.
[native-inputs]: Remove python-codecov, python-mock, and
python-pytest-flake8;
add python-coverage, python-hatchling, and python-isort.
Change-Id: I48b6a9c07a2bc1c213971585d7191573fd5d5aca
---
gnu/packages/bioinformatics.scm | 66 ++++++++++++-----------------------------
1 file changed, 19 insertions(+), 47 deletions(-)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 5d0c53d45e..9f33caa8e0 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -16917,55 +16917,26 @@ fasta subsequences.")
(define-public python-cooler
(package
(name "python-cooler")
- (version "0.8.11")
+ (version "0.9.1")
(source
(origin
(method url-fetch)
(uri (pypi-uri "cooler" version))
(sha256
(base32
- "1i96fmpsimj4wrx51rxn8lw2gqxf5a2pvrj5rwdd6ivnm3pmhyrn"))))
- (build-system python-build-system)
+ "0capn4jj3mkxfwcc65cg644zvrv4sqr2wxr0ylx5w767jx3yb7p2"))))
+ (build-system pyproject-build-system)
(arguments
- `(#:phases
- (modify-phases %standard-phases
- ;; cooler requests cytoolz<0.11. It only uses cytoolz for "compose",
- ;; which composes two functions.
- (add-after 'unpack 'use-recent-cytoolz
- (lambda _
- (substitute* '("requirements.txt"
- "cooler.egg-info/requires.txt")
- (("cytoolz.*<.*0.11") "cytoolz"))))
- ;; This version of flake8 just won't work with this version of
- ;; pytest, because of dependency pinning.
- (add-after 'unpack 'do-not-use-flake8
- (lambda _
- (substitute* "setup.cfg"
- (("addopts = --flake8") "addopts = "))))
- (add-after 'unpack 'patch-tests
- (lambda _
- (substitute* "tests/test_create.py"
- (("def test_roundtrip")
- (string-append "@pytest.mark.skip(reason=\"requires network "
- "access to genome.ucsc.edu\")\n"
- "def test_roundtrip")))
- (substitute* "tests/test_util.py"
- (("def test_fetch_chromsizes")
- (string-append "@pytest.mark.skip(reason=\"requires network "
- "access to genome.ucsc.edu\")\n"
- "def test_fetch_chromsizes"))
- ;; See https://github.com/open2c/cooler/issues/287
- (("skipif\\(six.PY2, reason=\"Scipy on Py2 is too old\"")
- "skip(reason=\"Scipy is too new\""))
- ;; This test depends on ipytree, which contains a lot of minified
- ;; JavaScript.
- (substitute* "tests/test_fileops.py"
- (("def test_print_trees")
- "def _test_print_trees"))))
- (replace 'check
- (lambda* (#:key tests? #:allow-other-keys)
- (when tests?
- (invoke "python" "-m" "pytest" "-v")))))))
+ (list
+ #:test-flags
+ '(list "-k"
+ (string-append
+ ;; These tests download files from the internet.
+ "not test_fetch_chromsizes"
+ " and not test_roundtrip"
+ ;; This test depends on ipytree, which contains a lot of
+ ;; minified JavaScript.
+ " and not test_print_trees"))))
(propagated-inputs
(list python-asciitree
python-biopython
@@ -16981,12 +16952,13 @@ fasta subsequences.")
python-pysam
python-pyyaml
python-scipy
- python-simplejson
- python-six
- python-sparse))
+ python-simplejson))
(native-inputs
- (list python-codecov python-mock python-pytest python-pytest-cov
- python-pytest-flake8))
+ (list python-coverage
+ python-hatchling
+ python-isort
+ python-pytest
+ python-pytest-cov))
;; Almost all the projects of the Mirnylab are moved under Open2C umbrella
(home-page "https://github.com/open2c/cooler")
(synopsis "Sparse binary format for genomic interaction matrices")
- 32/55: gnu: python-plastid: Update to 0.6.1., (continued)
- 32/55: gnu: python-plastid: Update to 0.6.1., guix-commits, 2024/01/15
- 35/55: gnu: python-demuxem: Disable tests., guix-commits, 2024/01/15
- 38/55: gnu: python-fit-nbinom: Disable tests., guix-commits, 2024/01/15
- 36/55: gnu: python-cartopy: Update to 0.22.0., guix-commits, 2024/01/15
- 42/55: gnu: python-pint: Add missing input., guix-commits, 2024/01/15
- 08/55: gnu: python-tifffile: Update to 2023.12.9., guix-commits, 2024/01/15
- 15/55: gnu: python-pynndescent: Update to 0.5.11., guix-commits, 2024/01/15
- 24/55: gnu: python-cleanlab: Disable test_aux_inputs, enable other tests., guix-commits, 2024/01/15
- 12/55: gnu: python-pypng: Update to 0.20220715.0., guix-commits, 2024/01/15
- 31/55: gnu: cnvkit: Update to 0.9.10., guix-commits, 2024/01/15
- 33/55: gnu: python-cooler: Update to 0.9.1.,
guix-commits <=
- 34/55: gnu: python-pint: Update to 0.23., guix-commits, 2024/01/15
- 41/55: gnu: python-hicexplorer: Make compatible with latest scipy., guix-commits, 2024/01/15
- 45/55: gnu: datasette: Update to 1.0a7., guix-commits, 2024/01/15
- 49/55: gnu: python-adjusttext: Disable tests., guix-commits, 2024/01/15
- 50/55: gnu: python-mysql-connector-python: Defuse time bomb., guix-commits, 2024/01/15
- 52/55: gnu: python-xarray: Update to 2023.12.0., guix-commits, 2024/01/15
- 51/55: gnu: python-telomerecat: Disable tests., guix-commits, 2024/01/15
- 53/55: gnu: python-dask: Propagate click., guix-commits, 2024/01/15
- 39/55: gnu: python-scikit-optimize: Make compatible with latest sklearn., guix-commits, 2024/01/15
- 43/55: gnu: python-metpy: Update to 1.6.0., guix-commits, 2024/01/15