Message ID | 20210606051407.6535-1-madalinionel.patrascu@mdc-berlin.de |
---|---|
State | Accepted |
Headers | show |
Series | [bug#48862] gnu: python-hic2cool: Update to 0.8.3. | expand |
Context | Check | Description |
---|---|---|
cbaines/applying patch | fail | View Laminar job |
cbaines/issue | success | View issue |
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: > Thank you for filing a new bug report with debbugs.gnu.org. > > This is an automatically generated reply to let you know your message > has been received. > > Your message is being forwarded to the package maintainers and other > interested parties for their attention; they will reply in due course. > > Your message has been sent to the package maintainer(s): > guix-patches@gnu.org > > If you wish to submit further information on this problem, please > send it to 48862@debbugs.gnu.org. > > Please do not send mail to help-debbugs@gnu.org unless you wish > to report a problem with the Bug-tracking system. >
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 > > > >
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