GNU bug report logs - #29018
[PATCH 0/3] Update snakemake (and python-configargparse)

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Message #5 received at submit <at> debbugs.gnu.org (full text, mbox):

From: Kyle Meyer <kyle <at> kyleam.com>
To: guix-patches <at> gnu.org
Cc: Kyle Meyer <kyle <at> kyleam.com>
Subject: [PATCH 0/3] Update snakemake (and python-configargparse)
Date: Thu, 26 Oct 2017 16:59:48 -0400

  gnu: python-configargparse: Update to 0.12.0.
  gnu: Add python-ratelimiter.
  gnu: snakemake: Update to 4.2.0.

 gnu/packages/python.scm | 58 ++++++++++++++++++++++++++++++++++++++++---------
 1 file changed, 48 insertions(+), 10 deletions(-)

-- 
2.14.3

Message #8 received at 29018 <at> debbugs.gnu.org (full text, mbox):

From: Kyle Meyer <kyle <at> kyleam.com>
To: 29018 <at> debbugs.gnu.org
Cc: Kyle Meyer <kyle <at> kyleam.com>
Subject: [PATCH 1/3] gnu: python-configargparse: Update to 0.12.0.
Date: Thu, 26 Oct 2017 17:02:28 -0400

* gnu/packages/python.scm (python-configargparse, python2-configargparse):
Update to 0.12.0.
[arguments]: Enable tests.
[native-inputs]: Add python-pyyaml, which is an optional dependency but
required to run the tests.
---
 gnu/packages/python.scm | 24 +++++++++++++++++-------
 1 file changed, 17 insertions(+), 7 deletions(-)

diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm
index f003cb2ef..3f92da44d 100644
--- a/gnu/packages/python.scm
+++ b/gnu/packages/python.scm
@@ -15,7 +15,7 @@
 ;;; Copyright © 2015, 2017 Ben Woodcroft <donttrustben <at> gmail.com>
 ;;; Copyright © 2015, 2016 Erik Edrosa <erik.edrosa <at> gmail.com>
 ;;; Copyright © 2015, 2016, 2017 Efraim Flashner <efraim <at> flashner.co.il>
-;;; Copyright © 2015 Kyle Meyer <kyle <at> kyleam.com>
+;;; Copyright © 2015, 2017 Kyle Meyer <kyle <at> kyleam.com>
 ;;; Copyright © 2015, 2016 Chris Marusich <cmmarusich <at> gmail.com>
 ;;; Copyright © 2016 Danny Milosavljevic <dannym+a <at> scratchpost.org>
 ;;; Copyright © 2016 Lukas Gradl <lgradl <at> openmailbox.org>
@@ -9279,20 +9279,30 @@ config files.")
 (define-public python-configargparse
   (package
     (name "python-configargparse")
-    (version "0.10.0")
+    (version "0.12.0")
     (source (origin
               (method url-fetch)
               (uri (string-append
-                    "https://pypi.python.org/packages/source/C/ConfigArgParse/"
+                    "https://pypi.io/packages/source/C/ConfigArgParse/"
                     "ConfigArgParse-" version ".tar.gz"))
               (sha256
                (base32
-                "19wh919gbdbzxzpagg52q3lm62yicm95ddlcx77dyjc1slyshl1v"))))
+                "0fgkiqh6r3rbkdq3k8c48m85g52k96686rw3a6jg4lcncrkpvk98"))))
     (build-system python-build-system)
+    (native-inputs
+     `(("python-pyyaml" ,python-pyyaml)))
     (arguments
-     ;; FIXME: Bug in test suite filed upstream:
-     ;; https://github.com/bw2/ConfigArgParse/issues/32
-     '(#:tests? #f))
+     `(#:phases
+       (modify-phases %standard-phases
+         (replace 'check
+           (lambda _
+             ;; Bypass setuptools-shim because one test relies on "setup.py"
+             ;; being the first argument passed to the python call.
+             ;;
+             ;; NOTE: Many tests do not run because they rely on Python's
+             ;; built-in test.test_argparse, but we remove the unit tests from
+             ;; our Python installation.
+             (zero? (system* "python" "setup.py" "test")))))))
     (synopsis "Replacement for argparse")
     (description "A drop-in replacement for argparse that allows options to also
 be set via config files and/or environment variables.")
-- 
2.14.3

Message #11 received at 29018 <at> debbugs.gnu.org (full text, mbox):

From: Kyle Meyer <kyle <at> kyleam.com>
To: 29018 <at> debbugs.gnu.org
Cc: Kyle Meyer <kyle <at> kyleam.com>
Subject: [PATCH 2/3] gnu: Add python-ratelimiter.
Date: Thu, 26 Oct 2017 17:02:29 -0400

* gnu/packages/python.scm (python-ratelimiter, python2-ratelimiter): New
variables.
---
 gnu/packages/python.scm | 24 ++++++++++++++++++++++++
 1 file changed, 24 insertions(+)

diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm
index 3f92da44d..fed7394d7 100644
--- a/gnu/packages/python.scm
+++ b/gnu/packages/python.scm
@@ -16843,3 +16843,27 @@ interpreter when it prints a stack trace.")
 
 (define-public python2-traceback2
   (package-with-python2 python-traceback2))
+
+(define-public python-ratelimiter
+  (package
+    (name "python-ratelimiter")
+    (version "1.2.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "ratelimiter" version))
+       (sha256
+        (base32
+         "1dhz85mj5bqd2mij84ncs6pz32hgidr79hay4aqfmzaa4rbb497p"))))
+    (build-system python-build-system)
+    (arguments
+     '(#:tests? #f))          ; There are no tests in the pypi archive.
+    (home-page "https://github.com/RazerM/ratelimiter")
+    (synopsis "Simple rate limiting object")
+    (description
+     "The @code{ratelimiter} module ensures that an operation will not be
+executed more than a given number of times during a given period.")
+    (license license:asl2.0)))
+
+(define-public python2-ratelimiter
+  (package-with-python2 python-ratelimiter))
-- 
2.14.3

Message #14 received at 29018 <at> debbugs.gnu.org (full text, mbox):

From: Kyle Meyer <kyle <at> kyleam.com>
To: 29018 <at> debbugs.gnu.org
Cc: Kyle Meyer <kyle <at> kyleam.com>
Subject: [PATCH 3/3] gnu: snakemake: Update to 4.2.0.
Date: Thu, 26 Oct 2017 17:02:30 -0400

* gnu/packages/python.scm (snakemake): Update to 4.2.0.
[propagated-inputs]: Add python-appdirs, python-configargparse, python-pyyaml,
and python-ratelimiter, which are dependencies as of Snakemake 4.1.0.
---
 gnu/packages/python.scm | 10 +++++++---
 1 file changed, 7 insertions(+), 3 deletions(-)

diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm
index fed7394d7..e8a733919 100644
--- a/gnu/packages/python.scm
+++ b/gnu/packages/python.scm
@@ -6626,13 +6626,13 @@ of the structure, dynamics, and functions of complex networks.")
 (define-public snakemake
   (package
     (name "snakemake")
-    (version "3.13.3")
+    (version "4.2.0")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "snakemake" version))
        (sha256
-        (base32 "1nixb944r4hlskwkzc4wjs34b40xpxpw9gmhhm5p09gvmm22ap5d"))))
+        (base32 "0mgl44q152ws40zj2vicqark5szyd73vqy9pf26g6hk6dk0y0c79"))))
     (build-system python-build-system)
     (arguments
      ;; TODO: Package missing test dependencies.
@@ -6651,7 +6651,11 @@ of the structure, dynamics, and functions of complex networks.")
              #t)))))
     (propagated-inputs
      `(("python-wrapt" ,python-wrapt)
-       ("python-requests" ,python-requests)))
+       ("python-requests" ,python-requests)
+       ("python-appdirs" ,python-appdirs)
+       ("python-configargparse" ,python-configargparse)
+       ("python-pyyaml" ,python-pyyaml)
+       ("python-ratelimiter" ,python-ratelimiter)))
     (home-page "https://bitbucket.org/snakemake/snakemake/wiki/Home")
     (synopsis "Python-based execution environment for make-like workflows")
     (description
-- 
2.14.3

Message #19 received at 29018-done <at> debbugs.gnu.org (full text, mbox):

From: Marius Bakke <mbakke <at> fastmail.com>
To: Kyle Meyer <kyle <at> kyleam.com>, 29018-done <at> debbugs.gnu.org
Subject: Re: [bug#29018] [PATCH 0/3] Update snakemake (and
 python-configargparse)
Date: Fri, 27 Oct 2017 00:43:34 +0200

[Message part 1 (text/plain, inline)]

Kyle Meyer <kyle <at> kyleam.com> writes:

>   gnu: python-configargparse: Update to 0.12.0.
>   gnu: Add python-ratelimiter.
>   gnu: snakemake: Update to 4.2.0.

Pushed as all three, bringing 'master' to 3414ce9876.

Thank you!

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