* gnu/packages/bioinformatics.scm (python-hic2cool): Update to 0.8.3. --- gnu/packages/bioinformatics.scm | 28 ++++++++++++++++++++++------ 1 file changed, 22 insertions(+), 6 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index dab097381a..66e69ff2c8 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -11892,18 +11892,34 @@ pyGenomeTracks can make plots with or without Hi-C data.") (define-public python-hic2cool (package (name "python-hic2cool") - (version "0.4.2") + (version "0.8.3") + ;; pypi sources do not contain the test_data directory and no test can be + ;; run (source (origin - (method url-fetch) - (uri (pypi-uri "hic2cool" version)) + (method git-fetch) + (uri (git-reference + (url "https://github.com/4dn-dcic/hic2cool") + (commit version))) + (file-name (git-file-name name version)) (sha256 (base32 - "0xy6mhfns2lzib1kcr6419jjp6pmh0qx8z8na55lmiwn0ds8q9cl")))) + "0dlnf0qfcp4jrc1nyya32a035c13xicyq16bwfnwhbb9s47mz7gl")))) (build-system python-build-system) - (arguments '(#:tests? #f)) ; no tests included + (arguments + `(#:phases + (modify-phases %standard-phases + ;;two of the test-data files need to be writable + (add-after 'unpack 'patch-test-data + (lambda* (#:key inputs outputs #:allow-other-keys) + (chmod "test_data/hic2cool_0.4.2_single_res.cool" #o600) + (chmod "test_data/hic2cool_0.7.0_multi_res.mcool" #o600)))))) (propagated-inputs - `(("python-cooler" ,python-cooler))) + `(("python-cooler" ,python-cooler) + ("python-h5py" ,python-h5py) + ("python-numpy" ,python-numpy) + ("python-pandas" ,python-pandas) + ("python-scipy" ,python-scipy))) (home-page "https://github.com/4dn-dcic/hic2cool") (synopsis "Converter for .hic and .cool files") (description -- 2.31.1
Hey Guix,
I made some changes to the commit message, I omitted some important
information.
I will send another patch. Sorry for this!
All the best,
Mădălin!
On 06.06.2021 07:15, GNU bug Tracking System wrote:
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* gnu/packages/bioinformatics.scm (python-hic2cool): Update to 0.8.3. [source]: Changed from pypi to github, pypi sources do not contain tests. [arguments]: Add build phase "patch-test-data" and removed #:tests? #f. [propagated-inputs]: Add python-h5py, python-numpy, python-pandas and python-scipy. --- gnu/packages/bioinformatics.scm | 28 ++++++++++++++++++++++------ 1 file changed, 22 insertions(+), 6 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index dab097381a..66e69ff2c8 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -11892,18 +11892,34 @@ pyGenomeTracks can make plots with or without Hi-C data.") (define-public python-hic2cool (package (name "python-hic2cool") - (version "0.4.2") + (version "0.8.3") + ;; pypi sources do not contain the test_data directory and no test can be + ;; run (source (origin - (method url-fetch) - (uri (pypi-uri "hic2cool" version)) + (method git-fetch) + (uri (git-reference + (url "https://github.com/4dn-dcic/hic2cool") + (commit version))) + (file-name (git-file-name name version)) (sha256 (base32 - "0xy6mhfns2lzib1kcr6419jjp6pmh0qx8z8na55lmiwn0ds8q9cl")))) + "0dlnf0qfcp4jrc1nyya32a035c13xicyq16bwfnwhbb9s47mz7gl")))) (build-system python-build-system) - (arguments '(#:tests? #f)) ; no tests included + (arguments + `(#:phases + (modify-phases %standard-phases + ;;two of the test-data files need to be writable + (add-after 'unpack 'patch-test-data + (lambda* (#:key inputs outputs #:allow-other-keys) + (chmod "test_data/hic2cool_0.4.2_single_res.cool" #o600) + (chmod "test_data/hic2cool_0.7.0_multi_res.mcool" #o600)))))) (propagated-inputs - `(("python-cooler" ,python-cooler))) + `(("python-cooler" ,python-cooler) + ("python-h5py" ,python-h5py) + ("python-numpy" ,python-numpy) + ("python-pandas" ,python-pandas) + ("python-scipy" ,python-scipy))) (home-page "https://github.com/4dn-dcic/hic2cool") (synopsis "Converter for .hic and .cool files") (description -- 2.31.1
[-- Attachment #1: Type: text/plain, Size: 2748 bytes --] I made a few changes before pushing the patch. On Sun, Jun 06, 2021 at 07:14:07AM +0200, Mădălin Ionel Patrașcu wrote: > * gnu/packages/bioinformatics.scm (python-hic2cool): Update to 0.8.3. I mentioned that the download changed to use git-fetch, the added phase and enabled tests, and the added inputs. > --- > gnu/packages/bioinformatics.scm | 28 ++++++++++++++++++++++------ > 1 file changed, 22 insertions(+), 6 deletions(-) > > diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm > index dab097381a..66e69ff2c8 100644 > --- a/gnu/packages/bioinformatics.scm > +++ b/gnu/packages/bioinformatics.scm > @@ -11892,18 +11892,34 @@ pyGenomeTracks can make plots with or without Hi-C data.") > (define-public python-hic2cool > (package > (name "python-hic2cool") > - (version "0.4.2") > + (version "0.8.3") > + ;; pypi sources do not contain the test_data directory and no test can be > + ;; run > (source > (origin > - (method url-fetch) > - (uri (pypi-uri "hic2cool" version)) > + (method git-fetch) > + (uri (git-reference > + (url "https://github.com/4dn-dcic/hic2cool") > + (commit version))) > + (file-name (git-file-name name version)) > (sha256 > (base32 > - "0xy6mhfns2lzib1kcr6419jjp6pmh0qx8z8na55lmiwn0ds8q9cl")))) > + "0dlnf0qfcp4jrc1nyya32a035c13xicyq16bwfnwhbb9s47mz7gl")))) > (build-system python-build-system) > - (arguments '(#:tests? #f)) ; no tests included > + (arguments > + `(#:phases > + (modify-phases %standard-phases > + ;;two of the test-data files need to be writable > + (add-after 'unpack 'patch-test-data > + (lambda* (#:key inputs outputs #:allow-other-keys) > + (chmod "test_data/hic2cool_0.4.2_single_res.cool" #o600) > + (chmod "test_data/hic2cool_0.7.0_multi_res.mcool" #o600)))))) I changed this one to be 'lambda _' and I changed the chmods to make-file-writable. > (propagated-inputs > - `(("python-cooler" ,python-cooler))) > + `(("python-cooler" ,python-cooler) > + ("python-h5py" ,python-h5py) > + ("python-numpy" ,python-numpy) > + ("python-pandas" ,python-pandas) > + ("python-scipy" ,python-scipy))) > (home-page "https://github.com/4dn-dcic/hic2cool") > (synopsis "Converter for .hic and .cool files") > (description > -- > 2.31.1 > > > > -- Efraim Flashner <efraim@flashner.co.il> אפרים פלשנר GPG key = A28B F40C 3E55 1372 662D 14F7 41AA E7DC CA3D 8351 Confidentiality cannot be guaranteed on emails sent or received unencrypted [-- Attachment #2: signature.asc --] [-- Type: application/pgp-signature, Size: 833 bytes --]