[bug#38637] (no subject)

[bug#38637] (no subject)

[mpatras]

-- 
Mădălin Ionel Patrașcu

System Administrator
Bioinformatics and Omics Data Science
The Berlin Institute for Medical Systems Biology (BIMSB)
Max Delbrück Center (MDC)
Hannoversche Str. 28, 10115 Berlin
House 101, room 1.60

[bug#38637] [PATCH 1/4] gnu: Add python-iocapture.

[Mădălin Ionel Patrașcu]

* gnu/packages/python-xyz.scm (python-iocapture): New variable.
---
 gnu/packages/python-xyz.scm | 30 ++++++++++++++++++++++++++++++
 1 file changed, 30 insertions(+)

diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index 03dddcde43..f26bc7719b 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -67,6 +67,7 @@
 ;;; Copyright © 2019 Giacomo Leidi <goodoldpaul@autistici.org>
 ;;; Copyright © 2019 Wiktor Żelazny <wzelazny@vurv.cz>
 ;;; Copyright © 2019 Tanguy Le Carrour <tanguy@bioneland.org>
+;;; Copyright © 2019 Mădălin Ionel Patrașcu <madalinionel.patrascu@mdc-berlin.de>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -16795,3 +16796,32 @@ services to what you expect in your tests.")
 
 (define-public python2-ujson
   (package-with-python2 python-ujson))
+
+(define-public python-iocapture
+  ;; the latest is more than year newer than the latest realease
+  (let ((commit "fdc021c431d0840303908dfc3ca8769db383595c")
+        (revision "1"))
+    (package
+     (name "python-iocapture")
+     (version "0.1.2")
+     (source
+      (origin
+       (method git-fetch)
+       (uri (git-reference (url "https://github.com/oinume/iocapture.git")
+                           (commit commit)))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32
+         "1mkbhqibxvgwg0p7slr8dfraa3g2s6bsayladhax2jccwj4kcndz"))))
+     (build-system python-build-system)
+     (propagated-inputs
+      `(("python-flexmock" ,python-flexmock)
+        ("python-pytest" ,python-pytest)
+        ("python-pytest-cov" ,python-pytest-cov)
+        ("python-six" ,python-six)))
+     (home-page "https://github.com/oinume/iocapture")
+     (synopsis "Phython capuring tool for stdout and stderr")
+     (description
+      "python-iocapture helps you to capture the standard out (stdout) and the
+standard error channel (stderr) in your program.")
+     (license license:expat)))) ; MIT license
\ No newline at end of file
-- 
2.17.1

[bug#38637] [PATCH 2/4] gnu: Add python-argh.

[Mădălin Ionel Patrașcu]

* gnu/packages/python-xyz.scm (python-argh): New variable.
---
 gnu/packages/python-xyz.scm | 37 ++++++++++++++++++++++++++++++++++++-
 1 file changed, 36 insertions(+), 1 deletion(-)

diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index f26bc7719b..1f2149c9c4 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -16824,4 +16824,39 @@ services to what you expect in your tests.")
      (description
       "python-iocapture helps you to capture the standard out (stdout) and the
 standard error channel (stderr) in your program.")
-     (license license:expat)))) ; MIT license
\ No newline at end of file
+     (license license:expat)))) ; MIT license
+
+(define-public python-argh
+  ;; there are 21 commits after the latest release
+  ;; those contains important improvements
+  (let ((commit "dcd3253f2994400a6a58a700c118c53765bc50a4")
+        (revision "1"))
+    (package
+      (name "python-argh")
+      (version "0.26.2")
+      (source
+       (origin
+         (method git-fetch)
+         (uri (git-reference (url "https://github.com/neithere/argh.git")
+                             (commit commit)))
+         (file-name (git-file-name name version))
+         (sha256
+          (base32
+           "1p5h3dnpbsjmqrvil96s71asc6i3gpinmbrabqmwnrsxprz7r3ns"))))
+      (build-system python-build-system)
+      (propagated-inputs
+       `(("python-iocapture" ,python-iocapture)
+         ("python-mock" ,python-mock)
+         ("python-pytest" ,python-pytest)
+         ("python-pytest-cov" ,python-pytest-cov)
+         ("python-pytest-xdist" ,python-pytest-xdist)
+         ("python-tox" ,python-tox)))
+      (home-page "https://github.com/neithere/argh/")
+      (synopsis "Argparse wrapper with natural syntax")
+      (description
+       "python-argh is a small library that provides several layers of
+abstraction on top of python-argparse.  The layers can be mixed.  It is always
+possible to declare a command with the highest possible (and least flexible)
+layer and then tune the behaviour with any of the lower layers including the
+native API of python-argparse.")
+      (license license:lgpl3))))
-- 
2.17.1

[bug#38637] [PATCH 3/4] gnu: python-pyfaidx: Update to 0.5.7.

[Mădălin Ionel Patrașcu]

* gnu/packages/bioinformatics.scm (python-pyfaidx): Update to 0.5.7.
---
 gnu/packages/bioinformatics.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index bdb3ff761b..c8396a33dd 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -13419,14 +13419,14 @@ bgzipped text file that contains a pair of genomic coordinates per line.")
 (define-public python-pyfaidx
   (package
     (name "python-pyfaidx")
-    (version "0.5.4.2")
+    (version "0.5.7")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "pyfaidx" version))
        (sha256
         (base32
-         "0y5zyjksj1rdglj601xd2bbni5abhdh622y3ck76chyzxz9z4rx8"))))
+         "02jvdx3ksy6w5gd29i1d0g0zsabbz7c14qg482ff7pza6sdl0b2i"))))
     (build-system python-build-system)
     (propagated-inputs
      `(("python-six" ,python-six)))
-- 
2.17.1

[bug#38637] [PATCH 4/4] gnu: Add python-gffutils.

[Mădălin Ionel Patrașcu]

Co-authored-by: Ricardo Wurmus <rekado@elephly.net>

* gnu/packages/bioinformatics.scm (python-gffutils): New variable.
---
 gnu/packages/bioinformatics.scm | 51 +++++++++++++++++++++++++++++++++
 1 file changed, 51 insertions(+)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index c8396a33dd..14c0b59067 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -15370,3 +15370,54 @@ methylation metrics from them.  MethylDackel requires an indexed fasta file
 containing the reference genome as well.")
     ;; See https://github.com/dpryan79/MethylDackel/issues/85
     (license license:expat)))
+
+(define-public python-gffutils
+  ;; The latest release is older more than a year than the latest commit
+  (let ((commit "4034c54600813b1402945e12faa91b3a53162cf1")
+        (revision "1"))
+    (package
+      (name "python-gffutils")
+      (version (git-version "0.9" revision commit))
+      (source
+       (origin
+         (method git-fetch)
+         (uri (git-reference
+               (url "https://github.com/daler/gffutils.git")
+               (commit commit)))
+         (file-name (git-file-name name version))
+         (sha256
+          (base32
+           "1rwafjdnbir5wnk0ap06ww4lra3p5frhy7mfs03rlldgfnwxymsn"))))
+      (build-system python-build-system)
+      (arguments
+       `(#:phases
+         (modify-phases %standard-phases
+           (replace 'check
+             (lambda _
+               ;; Tests need to access the HOME directory
+               (setenv "HOME" "/tmp")
+               (invoke "nosetests" "-a" "!slow")))
+           (add-after 'unpack 'make-gz-files-writable
+             (lambda _
+               (for-each make-file-writable
+                         (find-files "." "\\.gz"))
+               #t)))))
+      (propagated-inputs
+       `(("python-argcomplete" ,python-argcomplete)
+         ("python-argh" ,python-argh)
+         ("python-biopython" ,python-biopython)
+         ("python-pybedtools" ,python-pybedtools)
+         ("python-pyfaidx" ,python-pyfaidx)
+         ("python-simplejson" ,python-simplejson)
+         ("python-six" ,python-six)))
+      (native-inputs
+       `(("python-nose" , python-nose)))
+      (home-page "https://github.com/daler/gffutils")
+      (synopsis "Tool for manipulation of GFF and GTF files")
+      (description
+       "python-gffutils is a Python package for working with and manipulating the
+GFF and GTF format files typically used for genomic annotations.  The files are
+loaded into a sqlite3 database, allowing much more complex manipulation of
+hierarchical features (e.g., genes, transcripts, and exons) than is possible
+with plain-text methods alone.")
+      (license license:expat)))) ;; MIT license
-- 
2.17.1

[bug#38637] [PATCH 1/4] gnu: Add python-iocapture.

[Ricardo Wurmus]

Hi Mădălin,

> * gnu/packages/python-xyz.scm (python-iocapture): New variable.

thanks for the patch!

> +(define-public python-iocapture
> +  ;; the latest is more than year newer than the latest realease

I know what you mean but that’s not what the comment says ;)  I
changed it.

> +  (let ((commit "fdc021c431d0840303908dfc3ca8769db383595c")
> +        (revision "1"))
> +    (package
> +     (name "python-iocapture")
> +     (version "0.1.2")
> +     (source
> +      (origin
> +       (method git-fetch)
> +       (uri (git-reference (url "https://github.com/oinume/iocapture.git")
> +                           (commit commit)))
> +       (file-name (git-file-name name version))
> +       (sha256
> +        (base32
> +         "1mkbhqibxvgwg0p7slr8dfraa3g2s6bsayladhax2jccwj4kcndz"))))
> +     (build-system python-build-system)
> +     (propagated-inputs
> +      `(("python-flexmock" ,python-flexmock)
> +        ("python-pytest" ,python-pytest)
> +        ("python-pytest-cov" ,python-pytest-cov)
> +        ("python-six" ,python-six)))
> +     (home-page "https://github.com/oinume/iocapture")
> +     (synopsis "Phython capuring tool for stdout and stderr")

Typos: Phython –> Python; capuring –> capturing

> +     (description
> +      "python-iocapture helps you to capture the standard out (stdout) and the
> +standard error channel (stderr) in your program.")
> +     (license license:expat)))) ; MIT license

The term “MIT license” is ambiguous, so we don’t use it, not even in a
comment.

I noticed that the tests were not actually run, so I overrode the check
phase.

I pushed this with modifications to the “master” branch with commit
dbcef44a0b.

Thanks again!

--
Ricardo

[bug#38637] [PATCH 2/4] gnu: Add python-argh.

[Ricardo Wurmus]

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

> * gnu/packages/python-xyz.scm (python-argh): New variable.

Pushed to the “master” branch (commit db6bd842aa) with minor changes,
such as this one:

> +      (license license:lgpl3))))

It’s actually LGPLv3+.

Thank you!

--
Ricardo

[bug#38637] [PATCH 3/4] gnu: python-pyfaidx: Update to 0.5.7.

[Ricardo Wurmus]

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

> * gnu/packages/bioinformatics.scm (python-pyfaidx): Update to 0.5.7.

I pushed this after upgrading some other packages to ensure that
dependent packages still build.

Thank you!

-- 
Ricardo

bug#38637: [PATCH 4/4] gnu: Add python-gffutils.

[Ricardo Wurmus]

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

> Co-authored-by: Ricardo Wurmus <rekado@elephly.net>
>
> * gnu/packages/bioinformatics.scm (python-gffutils): New variable.

I’ve pushed this to the “master” branch with commit cfd83f3282.

Thank you!

-- 
Ricardo