* gnu/packages/bioinformatics.scm (python-hicmatrix): Update to 15. [source]: Changed from pypi to github, pypi sources do not contain tests. [arguments]: Removed build phase "relax-requirements" and replaced the pahse "check". [native-inputs]: Add python-pytest. --- gnu/packages/bioinformatics.scm | 37 ++++++++++++++++----------------- 1 file changed, 18 insertions(+), 19 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 2de8a59d3c..02da131fdf 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -11786,29 +11786,26 @@ such as Hi-C contact matrices.") (define-public python-hicmatrix (package (name "python-hicmatrix") - (version "12") - (source - (origin - ;; Version 12 is not available on pypi. - (method git-fetch) - (uri (git-reference - (url "https://github.com/deeptools/HiCMatrix") - (commit version))) - (file-name (git-file-name name version)) - (sha256 - (base32 - "1xhdyx16f3brgxgxybixdi64ki8nbbkq5vk4h9ahi11pzpjfn1pj")))) + (version "15") + (source + (origin + ;;Pypi sources do not contain any test + (method git-fetch) + (uri (git-reference + (url "https://github.com/deeptools/HiCMatrix") + (commit version))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "1dshjxgb16sdfg9k1bhw2yhyngac04k4ca7aqy8g3i3pprr068r5")))) (build-system python-build-system) (arguments `(#:phases (modify-phases %standard-phases - (add-after 'unpack 'relax-requirements - (lambda _ - (substitute* '("requirements.txt" - "setup.py") - (("cooler *=+ *0.8.5") - "cooler==0.8.*")) - #t))))) + (replace 'check + (lambda* (#:key tests? #:allow-other-keys) + (when tests? + (invoke "python" "-m" "pytest" "-v"))))))) (propagated-inputs `(("python-cooler" ,python-cooler) ("python-intervaltree" ,python-intervaltree) @@ -11816,6 +11813,8 @@ such as Hi-C contact matrices.") ("python-pandas" ,python-pandas) ("python-scipy" ,python-scipy) ("python-tables" ,python-tables))) + (native-inputs + `(("python-pytest" ,python-pytest))) (home-page "https://github.com/deeptools/HiCMatrix/") (synopsis "HiCMatrix class for HiCExplorer and pyGenomeTracks") (description -- 2.31.1
* gnu/packages/bioinformatics.scm (python-hicmatrix): Update to 15. [source]: Download via git-fetch. [arguments]: Enabled tests. Remove 'relax-requirements phase. [native-inputs]: Add python-pytest. --- gnu/packages/bioinformatics.scm | 37 ++++++++++++++++----------------- 1 file changed, 18 insertions(+), 19 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 2de8a59d3c..02da131fdf 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -11786,29 +11786,26 @@ such as Hi-C contact matrices.") (define-public python-hicmatrix (package (name "python-hicmatrix") - (version "12") - (source - (origin - ;; Version 12 is not available on pypi. - (method git-fetch) - (uri (git-reference - (url "https://github.com/deeptools/HiCMatrix") - (commit version))) - (file-name (git-file-name name version)) - (sha256 - (base32 - "1xhdyx16f3brgxgxybixdi64ki8nbbkq5vk4h9ahi11pzpjfn1pj")))) + (version "15") + (source + (origin + ;;Pypi sources do not contain any test + (method git-fetch) + (uri (git-reference + (url "https://github.com/deeptools/HiCMatrix") + (commit version))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "1dshjxgb16sdfg9k1bhw2yhyngac04k4ca7aqy8g3i3pprr068r5")))) (build-system python-build-system) (arguments `(#:phases (modify-phases %standard-phases - (add-after 'unpack 'relax-requirements - (lambda _ - (substitute* '("requirements.txt" - "setup.py") - (("cooler *=+ *0.8.5") - "cooler==0.8.*")) - #t))))) + (replace 'check + (lambda* (#:key tests? #:allow-other-keys) + (when tests? + (invoke "python" "-m" "pytest" "-v"))))))) (propagated-inputs `(("python-cooler" ,python-cooler) ("python-intervaltree" ,python-intervaltree) @@ -11816,6 +11813,8 @@ such as Hi-C contact matrices.") ("python-pandas" ,python-pandas) ("python-scipy" ,python-scipy) ("python-tables" ,python-tables))) + (native-inputs + `(("python-pytest" ,python-pytest))) (home-page "https://github.com/deeptools/HiCMatrix/") (synopsis "HiCMatrix class for HiCExplorer and pyGenomeTracks") (description -- 2.31.1
Hi Guix!
I changed the commit message!
All the best!
On 06.06.2021 10:31, Mădălin Ionel Patrașcu wrote:
> * gnu/packages/bioinformatics.scm (python-hicmatrix): Update to 15.
> [source]: Changed from pypi to github, pypi sources do not contain tests.
> [arguments]: Removed build phase "relax-requirements" and replaced the
> pahse "check".
> [native-inputs]: Add python-pytest.
> ---
> gnu/packages/bioinformatics.scm | 37 ++++++++++++++++-----------------
> 1 file changed, 18 insertions(+), 19 deletions(-)
>
> diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
> index 2de8a59d3c..02da131fdf 100644
> --- a/gnu/packages/bioinformatics.scm
> +++ b/gnu/packages/bioinformatics.scm
> @@ -11786,29 +11786,26 @@ such as Hi-C contact matrices.")
> (define-public python-hicmatrix
> (package
> (name "python-hicmatrix")
> - (version "12")
> - (source
> - (origin
> - ;; Version 12 is not available on pypi.
> - (method git-fetch)
> - (uri (git-reference
> - (url "https://github.com/deeptools/HiCMatrix")
> - (commit version)))
> - (file-name (git-file-name name version))
> - (sha256
> - (base32
> - "1xhdyx16f3brgxgxybixdi64ki8nbbkq5vk4h9ahi11pzpjfn1pj"))))
> + (version "15")
> + (source
> + (origin
> + ;;Pypi sources do not contain any test
> + (method git-fetch)
> + (uri (git-reference
> + (url "https://github.com/deeptools/HiCMatrix")
> + (commit version)))
> + (file-name (git-file-name name version))
> + (sha256
> + (base32
> + "1dshjxgb16sdfg9k1bhw2yhyngac04k4ca7aqy8g3i3pprr068r5"))))
> (build-system python-build-system)
> (arguments
> `(#:phases
> (modify-phases %standard-phases
> - (add-after 'unpack 'relax-requirements
> - (lambda _
> - (substitute* '("requirements.txt"
> - "setup.py")
> - (("cooler *=+ *0.8.5")
> - "cooler==0.8.*"))
> - #t)))))
> + (replace 'check
> + (lambda* (#:key tests? #:allow-other-keys)
> + (when tests?
> + (invoke "python" "-m" "pytest" "-v")))))))
> (propagated-inputs
> `(("python-cooler" ,python-cooler)
> ("python-intervaltree" ,python-intervaltree)
> @@ -11816,6 +11813,8 @@ such as Hi-C contact matrices.")
> ("python-pandas" ,python-pandas)
> ("python-scipy" ,python-scipy)
> ("python-tables" ,python-tables)))
> + (native-inputs
> + `(("python-pytest" ,python-pytest)))
> (home-page "https://github.com/deeptools/HiCMatrix/")
> (synopsis "HiCMatrix class for HiCExplorer and pyGenomeTracks")
> (description
--
System Administrator
Bioinformatics and Omics Data Science
BIMSB - MDC
Mădălin Ionel Patrașcu <madalinionel.patrascu@mdc-berlin.de>
writes:
> * gnu/packages/bioinformatics.scm (python-hicmatrix): Update to
> 15.
> [source]: Download via git-fetch.
> [arguments]: Enabled tests. Remove 'relax-requirements phase.
> [native-inputs]: Add python-pytest.
Applied as commit 8d9652beca7e3fc5b445c5d51d954193a11999b2.
Thank you!
--
Ricardo