From: Ricardo Wurmus <rekado@elephly.net>
To: 60009@debbugs.gnu.org
Cc: Ricardo Wurmus <rekado@elephly.net>
Subject: [bug#60009] [PATCH 06/18] gnu: python-hicexplorer: Update to 3.7.2.
Date: Mon, 12 Dec 2022 15:27:04 +0100 [thread overview]
Message-ID: <20221212142716.9460-6-rekado@elephly.net> (raw)
In-Reply-To: <20221212142716.9460-1-rekado@elephly.net>
* gnu/packages/bioinformatics.scm (python-hicexplorer): Update to 3.7.2.
[build-system]: Use pyproject-build-system.
[arguments]: Use gexp; remove phase "loosen-up-requirements"; add test-flags
to skip some tests; add phase "remove-dependency-on-krbalancing" to remove a
dependency on an unlicensed package; add phase "fix-references"; add phase
"run-only-low-mem-tests".
[propagated-inputs]: Remove python-configparser and python-six; add
python-biopython, python-cleanlab-1, python-fit-nbinom, python-graphviz,
python-hic2cool, python-hicmatrix, python-hyperopt, python-imbalanced-learn,
python-ipykernel, python-psutil, python-pybedtools, python-pygenometracks,
python-scikit-learn, and python-tqdm.
[native-inputs]: Add graphviz.
---
gnu/packages/bioinformatics.scm | 106 ++++++++++++++++++++++++++++----
1 file changed, 94 insertions(+), 12 deletions(-)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index e6a8789ea6..ea33311a2c 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -13413,7 +13413,7 @@ (define-public python-hicmatrix
(define-public python-hicexplorer
(package
(name "python-hicexplorer")
- (version "2.1.4")
+ (version "3.7.2")
(source
(origin
;; The latest version is not available on Pypi.
@@ -13424,32 +13424,114 @@ (define-public python-hicexplorer
(file-name (git-file-name name version))
(sha256
(base32
- "0q5gpbzmrkvygqgw524q36b4nrivcmyi5v194vsx0qw7b3gcmq08"))))
- (build-system python-build-system)
+ "1yavgxry38g326z10bclvdf8glmma05fxj5m73h15m1r2l9xmw3v"))))
+ (build-system pyproject-build-system)
(arguments
- `(#:phases
- (modify-phases %standard-phases
- (add-after 'unpack 'loosen-up-requirements
- (lambda _
- (substitute* "setup.py"
- (("==") ">="))
- #t)))))
+ (list
+ #:test-flags
+ '(list "hicexplorer/test/general/"
+ "--ignore" "hicexplorer/test/general/test_hicTADClassifier.py"
+ "--ignore" "hicexplorer/test/general/test_hicTrainTADClassifier.py"
+ "-k"
+ (string-append
+ ;; Unknown chromosome: ChrX
+ "not test_build_matrix_restrictionCutFile_two"
+ ;; fixture 'keepSelfLigation' not found
+ " and not test_build_matrix_restrictionCutFile_six"
+ ;; ValueError: object dtype is not supported by sparse matrices
+ " and not test_hic_transfer_obs_exp_perChromosome"
+
+ ;; No KR balancing available
+ " and not test_correct_matrix_KR_partial_cool"
+ " and not test_correct_matrix_KR_cool"
+ " and not test_correct_matrix_KR_H5"))
+ #:phases
+ #~(modify-phases %standard-phases
+ ;; See https://github.com/deeptools/Knight-Ruiz-Matrix-balancing-algorithm/issues/23
+ (add-after 'unpack 'remove-dependency-on-krbalancing
+ (lambda _
+ (substitute* "hicexplorer/hicCorrectMatrix.py"
+ (("from krbalancing import.*") "")
+ (("( *)assert\\(args.correctionMethod == 'KR'\\)" m indent)
+ (string-append m "\n"
+ indent "log.error('krbalancing not available')\n"
+ indent "exit(1)")))
+ (substitute* "setup.py"
+ (("\"krbalancing >= 0.0.5\",") ""))
+ (substitute* "requirements.txt"
+ (("krbalancing >= 0.0.5") ""))))
+ (add-after 'unpack 'fix-references
+ (lambda _
+ (let ((site (string-append #$output "/lib/python"
+ #$(version-major+minor
+ (package-version python))
+ "/site-packages")))
+ (substitute* "hicexplorer/lib/tadClassifier.py"
+ (("model_location = site.getsitepackages\\(\\)\\[0\\]")
+ (string-append "model_location = \"" site "\""))))
+ (substitute* "hicexplorer/hicFindRestSite.py"
+ (("subprocess.check_output\\(\\[\"cat\"")
+ (string-append "subprocess.check_output([\""
+ (which "cat") "\""))
+ (("cmd = 'sort -k1")
+ (string-append "cmd = '" (which "sort") " -k1")))))
+ ;; The tests aim to detect available memory and run more tests when
+ ;; there is more available memory. Let's run them deterministically
+ ;; instead and don't run any tests that require more than 1GB of
+ ;; RAM.
+ (add-after 'unpack 'run-only-low-mem-tests
+ (lambda _
+ (with-directory-excursion "hicexplorer/test"
+ (substitute* '("trivial_runs/test_hicBuildMatrix_trivial_runs_2.py"
+ "trivial_runs/test_hicAggregateContacts_trivial_runs_five.py"
+ "trivial_runs/test_hicAggregateContacts_trivial_runs_four.py"
+ "trivial_runs/test_hicAggregateContacts_trivial_runs.py"
+ "trivial_runs/test_hicAggregateContacts_trivial_runs_two_1.py"
+ "trivial_runs/test_hicBuildMatrix_trivial_runs.py"
+ "trivial_runs/test_hicAggregateContacts_trivial_runs_two_3.py"
+ "trivial_runs/test_hicAggregateContacts_trivial_runs_three.py"
+ "trivial_runs/test_hicAggregateContacts_trivial_runs_two.py"
+ "trivial_runs/test_hicAggregateContacts_trivial_runs_two_2.py"
+ "trivial_runs/test_hicAggregateContacts_trivial_runs_six.py"
+ "general/test_hicDifferentialTAD.py"
+ "general/test_hicDetectLoops.py"
+ "general/test_hicPlotMatrix.py"
+ "general/test_hicHyperoptDetectLoops.py"
+ "general/test_hicCreateThresholdFile.py"
+ "general/test_hicMergeDomains.py"
+ "general/test_hicHyperoptDetectLoopsHiCCUPS.py"
+ "general/test_hicAggregateContacts.py"
+ "general/test_hicInterIntraTAD.py")
+ (("^memory =.*") "memory = 1\n"))))))))
(propagated-inputs
(list python-biopython
- python-configparser
+ python-cleanlab-1
python-cooler
+ python-fit-nbinom
python-future
+ python-graphviz
+ python-hic2cool
+ python-hicmatrix
+ python-hyperopt
+ python-imbalanced-learn
python-intervaltree
+ python-ipykernel
python-jinja2
python-matplotlib
python-numpy
python-pandas
+ python-psutil
+ python-pybedtools
python-pybigwig
+ python-pygenometracks
python-pysam
+ python-scikit-learn
python-scipy
- python-six
python-tables
+ python-tqdm
python-unidecode))
+ (native-inputs
+ (list graphviz)) ;for hicexplorer/test/test_compute_function.py
(home-page "https://hicexplorer.readthedocs.io")
(synopsis "Process, analyze and visualize Hi-C data")
(description
--
2.36.1
next prev parent reply other threads:[~2022-12-12 14:28 UTC|newest]
Thread overview: 29+ messages / expand[flat|nested] mbox.gz Atom feed top
2022-12-12 14:22 [bug#60009] Update python-graphviz and other Python updates Ricardo Wurmus
2022-12-12 14:26 ` [bug#60009] [PATCH 01/18] gnu: python-graphviz: Update to 0.20.1 Ricardo Wurmus
2022-12-12 14:27 ` [bug#60009] [PATCH 02/18] gnu: python-hyperopt: Update to 0.2.7 Ricardo Wurmus
2022-12-12 14:27 ` [bug#60009] [PATCH 03/18] gnu: python-biopython: Update to 1.80 Ricardo Wurmus
2022-12-12 14:27 ` [bug#60009] [PATCH 04/18] gnu: python-hicmatrix: Update to 16 Ricardo Wurmus
2022-12-12 14:27 ` [bug#60009] [PATCH 05/18] gnu: python-pygenometracks: Update to 3.5 Ricardo Wurmus
2022-12-12 14:27 ` Ricardo Wurmus [this message]
2022-12-12 14:27 ` [bug#60009] [PATCH 07/18] gnu: python-dna-features-viewer: Update to 3.1.1 Ricardo Wurmus
2022-12-12 14:27 ` [bug#60009] [PATCH 08/18] gnu: python-bokeh: Skip failing PIL test Ricardo Wurmus
2022-12-12 19:10 ` zimoun
2022-12-12 20:09 ` Ricardo Wurmus
2022-12-12 20:37 ` Simon Tournier
2022-12-12 23:06 ` Ricardo Wurmus
2022-12-12 14:27 ` [bug#60009] [PATCH 09/18] gnu: sqlite-next: Update to 3.40.0 Ricardo Wurmus
2022-12-12 19:08 ` zimoun
2022-12-12 20:11 ` Ricardo Wurmus
2022-12-12 20:56 ` Simon Tournier
2022-12-12 23:02 ` Ricardo Wurmus
2022-12-12 23:21 ` Simon Tournier
2022-12-12 23:26 ` bug#60009: " Ricardo Wurmus
2022-12-12 14:27 ` [bug#60009] [PATCH 10/18] gnu: python-apsw: Update to 3.40.0.0 Ricardo Wurmus
2022-12-12 14:27 ` [bug#60009] [PATCH 11/18] gnu: python-cgatcore: Update to 0.6.14 Ricardo Wurmus
2022-12-12 14:27 ` [bug#60009] [PATCH 12/18] gnu: python-flask-restful: Update to 0.3.9 Ricardo Wurmus
2022-12-12 14:27 ` [bug#60009] [PATCH 13/18] gnu: python-marshmallow: Update to 3.19.0 Ricardo Wurmus
2022-12-12 14:27 ` [bug#60009] [PATCH 14/18] gnu: python-apispec: Update to 6.0.2 Ricardo Wurmus
2022-12-12 14:27 ` [bug#60009] [PATCH 15/18] gnu: python-pyjwt: Update to 2.6.0 Ricardo Wurmus
2022-12-12 14:27 ` [bug#60009] [PATCH 16/18] gnu: python-flasgger: Update to 0.9.5 Ricardo Wurmus
2022-12-12 14:27 ` [bug#60009] [PATCH 17/18] gnu: seqmagick: Update to 0.8.4 Ricardo Wurmus
2022-12-12 14:27 ` [bug#60009] [PATCH 18/18] gnu: cnvkit: Update to 0.9.9 Ricardo Wurmus
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