* [bug#38637] [PATCH 2/4] gnu: Add python-argh.
2019-12-16 15:25 ` [bug#38637] [PATCH 1/4] gnu: Add python-iocapture Mădălin Ionel Patrașcu
@ 2019-12-16 15:25 ` Mădălin Ionel Patrașcu
2019-12-16 16:31 ` Ricardo Wurmus
2019-12-16 15:25 ` [bug#38637] [PATCH 3/4] gnu: python-pyfaidx: Update to 0.5.7 Mădălin Ionel Patrașcu
` (2 subsequent siblings)
3 siblings, 1 reply; 9+ messages in thread
From: Mădălin Ionel Patrașcu @ 2019-12-16 15:25 UTC (permalink / raw)
To: 38637; +Cc: 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
^ permalink raw reply related [flat|nested] 9+ messages in thread* [bug#38637] [PATCH 3/4] gnu: python-pyfaidx: Update to 0.5.7.
2019-12-16 15:25 ` [bug#38637] [PATCH 1/4] gnu: Add python-iocapture Mădălin Ionel Patrașcu
2019-12-16 15:25 ` [bug#38637] [PATCH 2/4] gnu: Add python-argh Mădălin Ionel Patrașcu
@ 2019-12-16 15:25 ` Mădălin Ionel Patrașcu
2019-12-16 22:26 ` Ricardo Wurmus
2019-12-16 15:25 ` [bug#38637] [PATCH 4/4] gnu: Add python-gffutils Mădălin Ionel Patrașcu
2019-12-16 16:27 ` [bug#38637] [PATCH 1/4] gnu: Add python-iocapture Ricardo Wurmus
3 siblings, 1 reply; 9+ messages in thread
From: Mădălin Ionel Patrașcu @ 2019-12-16 15:25 UTC (permalink / raw)
To: 38637; +Cc: 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
^ permalink raw reply related [flat|nested] 9+ messages in thread* [bug#38637] [PATCH 4/4] gnu: Add python-gffutils.
2019-12-16 15:25 ` [bug#38637] [PATCH 1/4] gnu: Add python-iocapture Mădălin Ionel Patrașcu
2019-12-16 15:25 ` [bug#38637] [PATCH 2/4] gnu: Add python-argh Mădălin Ionel Patrașcu
2019-12-16 15:25 ` [bug#38637] [PATCH 3/4] gnu: python-pyfaidx: Update to 0.5.7 Mădălin Ionel Patrașcu
@ 2019-12-16 15:25 ` Mădălin Ionel Patrașcu
2019-12-16 22:33 ` bug#38637: " Ricardo Wurmus
2019-12-16 16:27 ` [bug#38637] [PATCH 1/4] gnu: Add python-iocapture Ricardo Wurmus
3 siblings, 1 reply; 9+ messages in thread
From: Mădălin Ionel Patrașcu @ 2019-12-16 15:25 UTC (permalink / raw)
To: 38637; +Cc: 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
^ permalink raw reply related [flat|nested] 9+ messages in thread* [bug#38637] [PATCH 1/4] gnu: Add python-iocapture.
2019-12-16 15:25 ` [bug#38637] [PATCH 1/4] gnu: Add python-iocapture Mădălin Ionel Patrașcu
` (2 preceding siblings ...)
2019-12-16 15:25 ` [bug#38637] [PATCH 4/4] gnu: Add python-gffutils Mădălin Ionel Patrașcu
@ 2019-12-16 16:27 ` Ricardo Wurmus
3 siblings, 0 replies; 9+ messages in thread
From: Ricardo Wurmus @ 2019-12-16 16:27 UTC (permalink / raw)
To: Mădălin Ionel Patrașcu; +Cc: 38637
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
^ permalink raw reply [flat|nested] 9+ messages in thread