gnu: Add python-optparse-pretty and python-mgatk.

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3 participants
  • MadalinIonel.Patrascu@mdc-berlin.de
  • Mădălin Ionel Patrașcu
  • Ricardo Wurmus
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MadalinIonel.Patrascu@mdc-berlin.de
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MadalinIonel.Patrascu@mdc-berlin.de wrote 2 years ago
(name . guix-patches@gnu.org)(address . guix-patches@gnu.org)
271d6a24b07a43ce8258824917b6630a@mdc-berlin.de
* gnu/packages/python-xyz.scm (python-optparse-pretty): New variable.

* gnu/packages/bioinformatics.scm (python-mgatk): New variable.
Attachment: file
Mădălin Ionel Patrașcu wrote 2 years ago
[PATCH 2/2] gnu: Add python-mgatk.
(address . 63448@debbugs.gnu.org)
20230511183412.27180-2-madalinionel.patrascu@mdc-berlin.de
* gnu/packages/bioinformatics.scm (python-mgatk): New variable.
---
gnu/packages/bioinformatics.scm | 35 +++++++++++++++++++++++++++++++++
1 file changed, 35 insertions(+)

Toggle diff (48 lines)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index afca5ab93b..92017b3a07 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -12628,6 +12628,41 @@ (define-public python-biothings-client
API services.")
(license license:bsd-3)))
+(define-public python-mgatk
+ (package
+ (name "python-mgatk")
+ (version "0.6.7")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (pypi-uri "mgatk" version))
+ (sha256
+ (base32 "0bxxk3v8lmqcdnm97468p7p3kzb59i5bpgayx7kqzl2p8lfwzi9h"))))
+ (build-system pyproject-build-system)
+ (arguments
+ (list #:tests? #f)) ; There are no tests in the pypi archive.
+ (propagated-inputs
+ (list python-biopython
+ python-click
+ python-numpy
+ python-optparse-pretty
+ python-pandas
+ python-pysam
+ python-regex
+ python-ruamel.yaml
+ snakemake))
+ (native-inputs
+ (list python-pytest))
+ (home-page "https://github.com/caleblareau/mgatk")
+ (synopsis "Mitochondrial genome analysis toolkit.")
+ (description "This package is a python-based command line interface for
+processing .bam files with mitochondrial reads and generating high-quality
+heteroplasmy estimation from sequencing data. The mgatk package places a
+special emphasis on mitochondrial genotypes generated from single-cell genomics
+data, primarily @acronym{mtscATAC-seq, mitochondrial single-cell ATAC-sequence},
+but is generally applicable across other assays.")
+ (license license:expat)))
+
(define-public python-multivelo
(package
(name "python-multivelo")
--
2.39.2
Mădălin Ionel Patrașcu wrote 2 years ago
[PATCH 1/2] gnu: Add python-optparse-pretty.
(address . 63448@debbugs.gnu.org)
20230511183412.27180-1-madalinionel.patrascu@mdc-berlin.de
* gnu/packages/python-xyz.scm (python-optparse-pretty): New variable
---
gnu/packages/python-xyz.scm | 23 ++++++++++++++++++++++-
1 file changed, 22 insertions(+), 1 deletion(-)

Toggle diff (45 lines)
diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index 4f48d80eb6..9fabfce79f 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -66,7 +66,7 @@
;;; Copyright © 2019, 2020, 2021 Giacomo Leidi <goodoldpaul@autistici.org>
;;; Copyright © 2019 Wiktor Żelazny <wzelazny@vurv.cz>
;;; Copyright © 2019, 2020, 2021, 2022 Tanguy Le Carrour <tanguy@bioneland.org>
-;;; Copyright © 2019, 2021, 2022 Mădălin Ionel Patrașcu <madalinionel.patrascu@mdc-berlin.de>
+;;; Copyright © 2019, 2021-2023 Mădălin Ionel Patrașcu <madalinionel.patrascu@mdc-berlin.de>
;;; Copyright © 2020 Riku Viitanen <riku.viitanen@protonmail.com>
;;; Copyright © 2020 Jakub Kądziołka <kuba@kadziolka.net>
;;; Copyright © 2020 sirgazil <sirgazil@zoho.com>
@@ -2690,6 +2690,27 @@ (define-public python-diskcache
(description "DiskCache is a disk and file backed persistent cache.")
(license license:asl2.0)))
+(define-public python-optparse-pretty
+ (package
+ (name "python-optparse-pretty")
+ (version "0.1.1")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (pypi-uri "optparse-pretty" version))
+ (sha256
+ (base32 "1920wbh2b7a8qn7zx2iiqbcdaax335l81a73x9pp8h11yzs2jdmh"))))
+ (build-system pyproject-build-system)
+ (arguments
+ (list #:tests? #f)) ; There are no tests in the pypi archive.
+ (home-page "https://github.com/gvalkov/optparse-pretty")
+ (synopsis "Compact help formatter for optparse")
+ (description
+ "This module provides two help formatters for optparse. They provide
+terser and more customizable option formatting in comparison to the default
+help formatter.")
+ (license license:bsd-3)))
+
(define-public python-orjson
(package
(name "python-orjson")

base-commit: e2eb43f945fd467e9b55a4b3c91cd186cf32e268
--
2.39.2
Ricardo Wurmus wrote 2 years ago
Re: [bug#63448] [PATCH 2/2] gnu: Add python-mgatk.
(name . Mădălin Ionel Patrașcu)(address . madalinionel.patrascu@mdc-berlin.de)(address . 63448@debbugs.gnu.org)
87jzxet2wq.fsf@elephly.net
Mădălin Ionel Patrașcu <madalinionel.patrascu@mdc-berlin.de> writes:

Toggle quote (2 lines)
> * gnu/packages/bioinformatics.scm (python-mgatk): New variable.
> ---
…
Toggle quote (3 lines)
> + (arguments
> + (list #:tests? #f)) ; There are no tests in the pypi archive.

Can you fetch the sources from https://github.com/caleblareau/mgatkinstead?
It is better to make sure this actually works by running at least some
of the tests.

--
Ricardo
Ricardo Wurmus wrote 2 years ago
Re: [bug#63448] [PATCH 1/2] gnu: Add python-optparse-pretty.
(name . Mădălin Ionel Patrașcu)(address . madalinionel.patrascu@mdc-berlin.de)(address . 63448@debbugs.gnu.org)
87fs82t2t7.fsf@elephly.net
Mădălin Ionel Patrașcu <madalinionel.patrascu@mdc-berlin.de> writes:

Toggle quote (1 lines)
> * gnu/packages/python-xyz.scm (python-optparse-pretty): New variable
…
Toggle quote (10 lines)
> + (source
> + (origin
> + (method url-fetch)
> + (uri (pypi-uri "optparse-pretty" version))
> + (sha256
> + (base32 "1920wbh2b7a8qn7zx2iiqbcdaax335l81a73x9pp8h11yzs2jdmh"))))
> + (build-system pyproject-build-system)
> + (arguments
> + (list #:tests? #f)) ; There are no tests in the pypi archive.

There are no tests at all, not just in pypi.

--
Ricardo
Mădălin Ionel Patrașcu wrote 2 years ago
[PATCH v2 2/2] gnu: Add python-mgatk.
(address . 63448@debbugs.gnu.org)
20230512103359.4111-1-madalinionel.patrascu@mdc-berlin.de
* gnu/packages/bioinformatics.scm (python-mgatk): New variable.
---
gnu/packages/bioinformatics.scm | 54 +++++++++++++++++++++++++++++++++
1 file changed, 54 insertions(+)

Toggle diff (69 lines)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index afca5ab93b..86e54ad5f5 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -12628,6 +12628,60 @@ (define-public python-biothings-client
API services.")
(license license:bsd-3)))
+(define-public python-mgatk
+ (let ((commit "2633903acb1fb406bb58c787f320c3641f446ee7")
+ (revision "0"))
+ (package
+ (name "python-mgatk")
+ (version "0.6.7")
+ (source
+ (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/caleblareau/mgatk")
+ (commit commit)))
+ (file-name (git-file-name name version))
+ ;(method url-fetch)
+ ;(uri (pypi-uri "mgatk" version))
+ (sha256
+ (base32 "19iklfv1brwsfg1l5lrs3z8m343nskkn1998c1fs7fdn0lgrki2p"))))
+ (build-system pyproject-build-system)
+ (arguments
+ (list
+ #:phases
+ #~(modify-phases %standard-phases
+ ;; The md5 module has beed deprecated since Python 2.5
+ (add-after 'unpack 'make-python3-compatible
+ (lambda* _
+ (substitute* "tests/test_cli.py"
+ (("import md5") ""))))
+ (replace 'check
+ (lambda* (#:key tests? #:allow-other-keys)
+ (when tests?
+ (invoke "pytest" "-vv" "-k" "not file_checksums_equal")))))))
+ (propagated-inputs
+ (list python-biopython
+ python-click
+ python-numpy
+ python-optparse-pretty
+ python-pandas
+ python-pysam
+ python-regex
+ python-ruamel.yaml
+ snakemake))
+ (native-inputs
+ (list python-minimal
+ python-pytest))
+ (home-page "https://github.com/caleblareau/mgatk")
+ (synopsis "Mitochondrial genome analysis toolkit.")
+ (description "This package is a python-based command line interface for
+processing .bam files with mitochondrial reads and generating high-quality
+heteroplasmy estimation from sequencing data. The mgatk package places a
+special emphasis on mitochondrial genotypes generated from single-cell genomics
+data, primarily @acronym{mtscATAC-seq, mitochondrial single-cell ATAC-sequence},
+but is generally applicable across other assays.")
+ (license license:expat))))
+
(define-public python-multivelo
(package
(name "python-multivelo")

base-commit: d07342b16612cfdffad6a7b3504b74e0d95d551f
--
2.39.2
Mădălin Ionel Patrașcu wrote 2 years ago
[PATCH v3 2/2] gnu: Add python-mgatk.
(address . 63448@debbugs.gnu.org)
20230512104303.4337-1-madalinionel.patrascu@mdc-berlin.de
* gnu/packages/bioinformatics.scm (python-mgatk): New variable.
---
gnu/packages/bioinformatics.scm | 52 +++++++++++++++++++++++++++++++++
1 file changed, 52 insertions(+)

Toggle diff (67 lines)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index afca5ab93b..abb7cf374a 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -12628,6 +12628,58 @@ (define-public python-biothings-client
API services.")
(license license:bsd-3)))
+(define-public python-mgatk
+ (let ((commit "2633903acb1fb406bb58c787f320c3641f446ee7")
+ (revision "0"))
+ (package
+ (name "python-mgatk")
+ (version "0.6.7")
+ (source
+ (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/caleblareau/mgatk")
+ (commit commit)))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32 "19iklfv1brwsfg1l5lrs3z8m343nskkn1998c1fs7fdn0lgrki2p"))))
+ (build-system python-build-system)
+ (arguments
+ (list
+ #:phases
+ #~(modify-phases %standard-phases
+ ;; The md5 module has beed deprecated since Python 2.5
+ (add-after 'unpack 'make-python3-compatible
+ (lambda* _
+ (substitute* "tests/test_cli.py"
+ (("import md5") ""))))
+ (replace 'check
+ (lambda* (#:key tests? #:allow-other-keys)
+ (when tests?
+ ;; This test is based on the md5 module
+ (invoke "pytest" "-vv" "-k" "not file_checksums_equal")))))))
+ (propagated-inputs
+ (list python-biopython
+ python-click
+ python-numpy
+ python-optparse-pretty
+ python-pandas
+ python-pysam
+ python-regex
+ python-ruamel.yaml
+ snakemake))
+ (native-inputs
+ (list python-pytest))
+ (home-page "https://github.com/caleblareau/mgatk")
+ (synopsis "Mitochondrial genome analysis toolkit.")
+ (description "This package is a python-based command line interface for
+processing .bam files with mitochondrial reads and generating high-quality
+heteroplasmy estimation from sequencing data. The mgatk package places a
+special emphasis on mitochondrial genotypes generated from single-cell genomics
+data, primarily @acronym{mtscATAC-seq, mitochondrial single-cell ATAC-sequence},
+but is generally applicable across other assays.")
+ (license license:expat))))
+
(define-public python-multivelo
(package
(name "python-multivelo")

base-commit: d07342b16612cfdffad6a7b3504b74e0d95d551f
--
2.39.2
Ricardo Wurmus wrote 2 years ago
gnu: Add python-optparse-pretty and python-mgatk.
(address . 63448-done@debbugs.gnu.org)
87y1ltskuw.fsf@elephly.net
I changed it back to pyproject-build-system; all Python packages should
be using pyproject-build-system, as it will replace the
python-build-system eventually.

Instead of disabling the tests I patched it to use hashlib.md5.

--
Ricardo
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