From: "Mădălin Ionel Patrașcu" <madalinionel.patrascu@mdc-berlin.de>
To: <46955@debbugs.gnu.org>
Cc: rekado@elephly.net,
"Mădălin Ionel Patrașcu" <madalinionel.patrascu@mdc-berlin.de>
Subject: [bug#46955] [PATCH 3/3] gnu: python-cooler: Update to 0.8.11.
Date: Sun, 6 Jun 2021 02:06:51 +0200 [thread overview]
Message-ID: <20210606000651.28252-3-madalinionel.patrascu@mdc-berlin.de> (raw)
In-Reply-To: <20210606000651.28252-1-madalinionel.patrascu@mdc-berlin.de>
* gnu/packages/bioinformatics.scm (python-cooler): Update to 0.8.11.
---
gnu/packages/bioinformatics.scm | 38 +++++++++++++++++++++++++++------
1 file changed, 32 insertions(+), 6 deletions(-)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index dab097381a..988f663ceb 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -11717,15 +11717,34 @@ fasta subsequences.")
(define-public python-cooler
(package
(name "python-cooler")
- (version "0.8.7")
+ (version "0.8.11")
(source
(origin
(method url-fetch)
(uri (pypi-uri "cooler" version))
(sha256
(base32
- "01g6gqix9ba27sappz6nfyiwabzrlf8i5fn8kwcz8ra356cq9crp"))))
+ "1i96fmpsimj4wrx51rxn8lw2gqxf5a2pvrj5rwdd6ivnm3pmhyrn"))))
(build-system python-build-system)
+ (arguments
+ `(#:phases
+ (modify-phases %standard-phases
+ (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")))))
+ (replace 'check
+ (lambda* (#:key tests? #:allow-other-keys)
+ (when tests?
+ (invoke "python" "-m" "pytest" "-v")))))))
(propagated-inputs
`(("python-asciitree" ,python-asciitree)
("python-biopython" ,python-biopython)
@@ -11741,11 +11760,18 @@ fasta subsequences.")
("python-pysam" ,python-pysam)
("python-pyyaml" ,python-pyyaml)
("python-scipy" ,python-scipy)
- ("python-simplejson" ,python-simplejson)))
+ ("python-simplejson" ,python-simplejson)
+ ("python-six" ,python-six)
+ ("python-sparse" ,python-sparse)))
(native-inputs
- `(("python-mock" ,python-mock)
- ("python-pytest" ,python-pytest)))
- (home-page "https://github.com/mirnylab/cooler")
+ `(("python-codecov" ,python-codecov)
+ ("python-ipytree" ,python-ipytree)
+ ("python-mock" ,python-mock)
+ ("python-pytest" ,python-pytest)
+ ("python-pytest-cov" ,python-pytest-cov)
+ ("python-pytest-flake8" ,python-pytest-flake8)))
+ ;;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")
(description
"Cooler is a support library for a sparse, compressed, binary persistent
--
2.31.1
next prev parent reply other threads:[~2021-06-06 0:08 UTC|newest]
Thread overview: 17+ messages / expand[flat|nested] mbox.gz Atom feed top
2021-03-06 0:54 [bug#46955] (no subject) Mădălin Ionel Patrașcu
2021-03-06 0:57 ` [bug#46955] [PATCH 1/2] gnu: Add python-sparse Mădălin Ionel Patrașcu
2021-03-06 0:57 ` [bug#46955] [PATCH 2/2] gnu: python-cooler: Update to 0.8.10 Mădălin Ionel Patrașcu
2021-04-01 15:09 ` Ricardo Wurmus
2021-04-01 15:07 ` [bug#46955] [PATCH 1/2] gnu: Add python-sparse Ricardo Wurmus
2021-04-01 15:10 ` Ricardo Wurmus
[not found] ` <handler.46955.B.16149920915786.ack@debbugs.gnu.org>
2021-06-03 23:23 ` [bug#46955] [ext] bug#46955: Acknowledgement ((no subject)) Mădălin Ionel Patrașcu
2021-06-03 23:25 ` [bug#46955] [PATCH 1/3] gnu: Add python-sparse Mădălin Ionel Patrașcu
2021-06-03 23:25 ` [bug#46955] [PATCH 2/3] gnu: Add python-ipytree Mădălin Ionel Patrașcu
2021-06-03 23:25 ` [bug#46955] [PATCH 3/3] gnu: python-cooler: Update to 0.8.11 Mădălin Ionel Patrașcu
2021-06-05 10:06 ` Maxime Devos
2021-06-06 0:03 ` [bug#46955] [ext] " Mădălin Ionel Patrașcu
2021-06-06 0:06 ` [bug#46955] [PATCH 1/3] gnu: Add python-sparse Mădălin Ionel Patrașcu
2021-06-06 0:06 ` [bug#46955] [PATCH 2/3] gnu: Add python-ipytree Mădălin Ionel Patrașcu
2021-06-06 6:23 ` Ricardo Wurmus
2021-06-06 0:06 ` Mădălin Ionel Patrașcu [this message]
2021-06-06 6:36 ` bug#46955: [PATCH 3/3] gnu: python-cooler: Update to 0.8.11 Ricardo Wurmus
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