[bug#63448] gnu: Add python-optparse-pretty and python-mgatk.

[bug#63448] gnu: Add python-optparse-pretty and python-mgatk.

[MadalinIonel.Patrascu]

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* gnu/packages/python-xyz.scm (python-optparse-pretty): New variable.

* gnu/packages/bioinformatics.scm (python-mgatk): New variable.


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[bug#63448] [PATCH 1/2] gnu: Add python-optparse-pretty.

[Mădălin Ionel Patrașcu]

* gnu/packages/python-xyz.scm (python-optparse-pretty): New variable
---
 gnu/packages/python-xyz.scm | 23 ++++++++++++++++++++++-
 1 file changed, 22 insertions(+), 1 deletion(-)

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

[bug#63448] [PATCH 2/2] gnu: Add python-mgatk.

[Mădălin Ionel Patrașcu]

* gnu/packages/bioinformatics.scm (python-mgatk): New variable.
---
 gnu/packages/bioinformatics.scm | 35 +++++++++++++++++++++++++++++++++
 1 file changed, 35 insertions(+)

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

[bug#63448] [PATCH 2/2] gnu: Add python-mgatk.

[Ricardo Wurmus]

Mădălin Ionel Patrașcu <madalinionel.patrascu@mdc-berlin.de> writes:

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

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

-- 
Ricardo

[bug#63448] [PATCH 1/2] gnu: Add python-optparse-pretty.

[Ricardo Wurmus]

Mădălin Ionel Patrașcu <madalinionel.patrascu@mdc-berlin.de> writes:

> * gnu/packages/python-xyz.scm (python-optparse-pretty): New variable
…
> +    (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

[bug#63448] [PATCH v2 2/2] gnu: Add python-mgatk.

[Mădălin Ionel Patrașcu]

* gnu/packages/bioinformatics.scm (python-mgatk): New variable.
---
 gnu/packages/bioinformatics.scm | 54 +++++++++++++++++++++++++++++++++
 1 file changed, 54 insertions(+)

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

[bug#63448] [PATCH v3 2/2] gnu: Add python-mgatk.

[Mădălin Ionel Patrașcu]

* gnu/packages/bioinformatics.scm (python-mgatk): New variable.
---
 gnu/packages/bioinformatics.scm | 52 +++++++++++++++++++++++++++++++++
 1 file changed, 52 insertions(+)

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

bug#63448: gnu: Add python-optparse-pretty and python-mgatk.

[Ricardo Wurmus]

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