* [bug#48863] [PATCH] gnu: python-hicmatrix: Update to 15.
@ 2021-06-06 8:31 Mădălin Ionel Patrașcu
2021-06-07 11:53 ` [bug#48863] [PATCH v2] " Mădălin Ionel Patrașcu
2021-06-07 11:54 ` [bug#48863] [PATCH] " Mădălin Ionel Patrașcu
0 siblings, 2 replies; 4+ messages in thread
From: Mădălin Ionel Patrașcu @ 2021-06-06 8:31 UTC (permalink / raw)
To: 48863; +Cc: rekado, Mădălin Ionel Patrașcu
* 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
^ permalink raw reply related [flat|nested] 4+ messages in thread* [bug#48863] [PATCH v2] gnu: python-hicmatrix: Update to 15.
2021-06-06 8:31 [bug#48863] [PATCH] gnu: python-hicmatrix: Update to 15 Mădălin Ionel Patrașcu
@ 2021-06-07 11:53 ` Mădălin Ionel Patrașcu
2021-06-08 8:47 ` bug#48863: " Ricardo Wurmus
2021-06-07 11:54 ` [bug#48863] [PATCH] " Mădălin Ionel Patrașcu
1 sibling, 1 reply; 4+ messages in thread
From: Mădălin Ionel Patrașcu @ 2021-06-07 11:53 UTC (permalink / raw)
To: 48863; +Cc: rekado, Mădălin Ionel Patrașcu
* 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
^ permalink raw reply related [flat|nested] 4+ messages in thread* bug#48863: [PATCH v2] gnu: python-hicmatrix: Update to 15.
2021-06-07 11:53 ` [bug#48863] [PATCH v2] " Mădălin Ionel Patrașcu
@ 2021-06-08 8:47 ` Ricardo Wurmus
0 siblings, 0 replies; 4+ messages in thread
From: Ricardo Wurmus @ 2021-06-08 8:47 UTC (permalink / raw)
To: Mădălin Ionel Patrașcu; +Cc: 48863-done
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
^ permalink raw reply [flat|nested] 4+ messages in thread
* [bug#48863] [PATCH] gnu: python-hicmatrix: Update to 15.
2021-06-06 8:31 [bug#48863] [PATCH] gnu: python-hicmatrix: Update to 15 Mădălin Ionel Patrașcu
2021-06-07 11:53 ` [bug#48863] [PATCH v2] " Mădălin Ionel Patrașcu
@ 2021-06-07 11:54 ` Mădălin Ionel Patrașcu
1 sibling, 0 replies; 4+ messages in thread
From: Mădălin Ionel Patrașcu @ 2021-06-07 11:54 UTC (permalink / raw)
To: 48863; +Cc: rekado
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
^ permalink raw reply [flat|nested] 4+ messages in thread
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2021-06-06 8:31 [bug#48863] [PATCH] gnu: python-hicmatrix: Update to 15 Mădălin Ionel Patrașcu
2021-06-07 11:53 ` [bug#48863] [PATCH v2] " Mădălin Ionel Patrașcu
2021-06-08 8:47 ` bug#48863: " Ricardo Wurmus
2021-06-07 11:54 ` [bug#48863] [PATCH] " Mădălin Ionel Patrașcu
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