[PATCH] Fix pbtranscript-tofu runtime errors.

[PATCH] Fix pbtranscript-tofu runtime errors.

[Ricardo Wurmus]

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Hi Guix,

pbtranscript-tofu has a few more dependencies that the install script
didn't check for.  The four patches add packages for as yet unpackaged
dependencies (python-decorator and python-networkx), remove even more
pre-built stuff from the pbtranscript-tofu tarball, and finally add all
missing inputs.

~~ Ricardo


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From 1e18e4a855659f674203777b454035cbee1a8da6 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
Date: Tue, 31 Mar 2015 12:34:37 +0200
Subject: [PATCH 1/4] gnu: Add python-decorator.

* gnu/packages/python.scm (python-decorator, python2-decorator): New
  variables.
---
 gnu/packages/python.scm | 28 ++++++++++++++++++++++++++++
 1 file changed, 28 insertions(+)

diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm
index 23afec7..f7eb478 100644
--- a/gnu/packages/python.scm
+++ b/gnu/packages/python.scm
@@ -2837,6 +2837,34 @@ PNG, PostScript, PDF, and SVG file output.")
 (define-public python2-cairocffi
   (package-with-python2 python-cairocffi))
 
+(define-public python-decorator
+  (package
+    (name "python-decorator")
+    (version "3.4.2")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append
+             "https://pypi.python.org/packages/source/d/decorator/decorator-"
+             version ".tar.gz"))
+       (sha256
+        (base32 "0i2bnlkh0p9gs76hb28mafandcrig2fmv56w9ai6mshxwqn0083k"))))
+    (build-system python-build-system)
+    (arguments '(#:tests? #f)) ; no test target
+    (native-inputs
+     `(("python-setuptools" ,python-setuptools)))
+    (home-page "http://pypi.python.org/pypi/decorator/")
+    (synopsis "Python module to simplify usage of decorators")
+    (description
+      "The aim of the decorator module is to simplify the usage of decorators
+for the average programmer, and to popularize decorators usage giving examples
+of useful decorators, such as memoize, tracing, redirecting_stdout, locked,
+etc.  The core of this module is a decorator factory.")
+    (license license:expat)))
+
+(define-public python2-decorator
+  (package-with-python2 python-decorator))
+
 (define-public python-ipython
   (package
     (name "python-ipython")
-- 
2.1.0


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From cebbfa900aaba3468654f173cda38bbeb2df31a6 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
Date: Tue, 31 Mar 2015 12:35:09 +0200
Subject: [PATCH 2/4] gnu: Add python-networkx.

* gnu/packages/python.scm (python-networkx, python2-networkx): New variables.
---
 gnu/packages/python.scm | 29 +++++++++++++++++++++++++++++
 1 file changed, 29 insertions(+)

diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm
index f7eb478..c5cae6d 100644
--- a/gnu/packages/python.scm
+++ b/gnu/packages/python.scm
@@ -3335,6 +3335,35 @@ interfaces in an easy and portable manner.")
 (define-public python2-netifaces
   (package-with-python2 python-netifaces))
 
+(define-public python-networkx
+  (package
+    (name "python-networkx")
+    (version "1.9.1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append
+             "https://pypi.python.org/packages/source/n/networkx/networkx-"
+             version ".tar.gz"))
+       (sha256
+        (base32 "0n8wy0yq1kmdq4wh68mlhwhkndvwzx48lg41a1z0sxxms0wfp033"))))
+    (build-system python-build-system)
+    ;; python-decorator is needed at runtime
+    (propagated-inputs
+     `(("python-decorator" ,python-decorator)))
+    (native-inputs
+     `(("python-setuptools" ,python-setuptools)
+       ("python-nose" ,python-nose)))
+    (home-page "http://networkx.github.io/")
+    (synopsis "Python module for creating and manipulating graphs and networks")
+    (description
+      "NetworkX is a Python package for the creation, manipulation, and study
+of the structure, dynamics, and functions of complex networks.")
+    (license bsd-3)))
+
+(define-public python2-networkx
+  (package-with-python2 python-networkx))
+
 (define-public snakemake
   (package
     (name "snakemake")
-- 
2.1.0


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From aad74ddc7c66fdb1c58dc89afa7078288ebeb918 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
Date: Tue, 31 Mar 2015 12:37:31 +0200
Subject: [PATCH 3/4] gnu: pbtranscript-tofu: delete pre-built libraries.

* gnu/packages/bioinformatics.scm (pbtranscript-tofu)[arguments]: Delete
  "build" directory and any shared objects after unpacking.
---
 gnu/packages/bioinformatics.scm | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 93dc542..f124732 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -830,12 +830,15 @@ files and writing bioinformatics applications.")
             (chdir "pbtranscript-tofu/pbtranscript/")
             ;; Delete clutter
             (delete-file-recursively "dist/")
+            (delete-file-recursively "build/")
             (delete-file-recursively "setuptools_cython-0.2.1-py2.6.egg/")
             (delete-file-recursively "pbtools.pbtranscript.egg-info")
             (delete-file "Cython-0.20.1.tar.gz")
             (delete-file "setuptools_cython-0.2.1-py2.7.egg")
             (delete-file "setuptools_cython-0.2.1.tar.gz")
             (delete-file "setup.cfg")
+            (for-each delete-file
+                      (find-files "." "\\.so"))
             ;; files should be writable for install phase
             (for-each (lambda (f) (chmod f #o755))
                       (find-files "." "\\.py")))
-- 
2.1.0


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From 8c6999e039048e9dd5063cc1fa4c76b59e5263c0 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
Date: Tue, 31 Mar 2015 13:46:27 +0200
Subject: [PATCH 4/4] gnu: pbtranscript-tofu: add missing inputs.

* gnu/packages/bioinformatics.scm (pbtranscript-tofu)[inputs]: Add missing
  runtime inputs.
---
 gnu/packages/bioinformatics.scm | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index f124732..76dd2cd 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -847,6 +847,8 @@ files and writing bioinformatics applications.")
        `(("python-cython" ,python2-cython)
          ("python-numpy" ,python2-numpy)
          ("python-bx-python" ,python2-bx-python)
+         ("python-networkx" ,python2-networkx)
+         ("python-scipy" ,python2-scipy)
          ("python-pbcore" ,python2-pbcore)))
       (native-inputs
        `(("python-nose" ,python2-nose)
-- 
2.1.0

Re: [PATCH] Fix pbtranscript-tofu runtime errors.

[Mark H Weaver]

Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de> writes:

> From 1e18e4a855659f674203777b454035cbee1a8da6 Mon Sep 17 00:00:00 2001
> From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
> Date: Tue, 31 Mar 2015 12:34:37 +0200
> Subject: [PATCH 1/4] gnu: Add python-decorator.

Looks good.

> From cebbfa900aaba3468654f173cda38bbeb2df31a6 Mon Sep 17 00:00:00 2001
> From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
> Date: Tue, 31 Mar 2015 12:35:09 +0200
> Subject: [PATCH 2/4] gnu: Add python-networkx.

Looks good.

> From aad74ddc7c66fdb1c58dc89afa7078288ebeb918 Mon Sep 17 00:00:00 2001
> From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
> Date: Tue, 31 Mar 2015 12:37:31 +0200
> Subject: [PATCH 3/4] gnu: pbtranscript-tofu: delete pre-built libraries.

Please capitalize "Delete".

> diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
> index 93dc542..f124732 100644
> --- a/gnu/packages/bioinformatics.scm
> +++ b/gnu/packages/bioinformatics.scm
> @@ -830,12 +830,15 @@ files and writing bioinformatics applications.")
>              (chdir "pbtranscript-tofu/pbtranscript/")
>              ;; Delete clutter
>              (delete-file-recursively "dist/")
> +            (delete-file-recursively "build/")
>              (delete-file-recursively "setuptools_cython-0.2.1-py2.6.egg/")
>              (delete-file-recursively "pbtools.pbtranscript.egg-info")
>              (delete-file "Cython-0.20.1.tar.gz")
>              (delete-file "setuptools_cython-0.2.1-py2.7.egg")
>              (delete-file "setuptools_cython-0.2.1.tar.gz")
>              (delete-file "setup.cfg")
> +            (for-each delete-file
> +                      (find-files "." "\\.so"))
>              ;; files should be writable for install phase
>              (for-each (lambda (f) (chmod f #o755))
>                        (find-files "." "\\.py")))

In the calls to 'find-files', the patterns should be "\\.so$" and
"\\.py$", respectively.

> From 8c6999e039048e9dd5063cc1fa4c76b59e5263c0 Mon Sep 17 00:00:00 2001
> From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
> Date: Tue, 31 Mar 2015 13:46:27 +0200
> Subject: [PATCH 4/4] gnu: pbtranscript-tofu: add missing inputs.

Please capitalize "Add".

Otherwise these patches look good to me.  Okay to push with these
changes.

     Thanks!
       Mark

Re: [PATCH] Fix pbtranscript-tofu runtime errors.

[Ricardo Wurmus]

Mark H Weaver writes:

> Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de> writes:
>
>> From 1e18e4a855659f674203777b454035cbee1a8da6 Mon Sep 17 00:00:00 2001
>> From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
>> Date: Tue, 31 Mar 2015 12:34:37 +0200
>> Subject: [PATCH 1/4] gnu: Add python-decorator.
>
> Looks good.
>
>> From cebbfa900aaba3468654f173cda38bbeb2df31a6 Mon Sep 17 00:00:00 2001
>> From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
>> Date: Tue, 31 Mar 2015 12:35:09 +0200
>> Subject: [PATCH 2/4] gnu: Add python-networkx.
>
> Looks good.
>
>> From aad74ddc7c66fdb1c58dc89afa7078288ebeb918 Mon Sep 17 00:00:00 2001
>> From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
>> Date: Tue, 31 Mar 2015 12:37:31 +0200
>> Subject: [PATCH 3/4] gnu: pbtranscript-tofu: delete pre-built libraries.
>
> Please capitalize "Delete".
>
>> diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
>> index 93dc542..f124732 100644
>> --- a/gnu/packages/bioinformatics.scm
>> +++ b/gnu/packages/bioinformatics.scm
>> @@ -830,12 +830,15 @@ files and writing bioinformatics applications.")
>>              (chdir "pbtranscript-tofu/pbtranscript/")
>>              ;; Delete clutter
>>              (delete-file-recursively "dist/")
>> +            (delete-file-recursively "build/")
>>              (delete-file-recursively "setuptools_cython-0.2.1-py2.6.egg/")
>>              (delete-file-recursively "pbtools.pbtranscript.egg-info")
>>              (delete-file "Cython-0.20.1.tar.gz")
>>              (delete-file "setuptools_cython-0.2.1-py2.7.egg")
>>              (delete-file "setuptools_cython-0.2.1.tar.gz")
>>              (delete-file "setup.cfg")
>> +            (for-each delete-file
>> +                      (find-files "." "\\.so"))
>>              ;; files should be writable for install phase
>>              (for-each (lambda (f) (chmod f #o755))
>>                        (find-files "." "\\.py")))
>
> In the calls to 'find-files', the patterns should be "\\.so$" and
> "\\.py$", respectively.
>
>> From 8c6999e039048e9dd5063cc1fa4c76b59e5263c0 Mon Sep 17 00:00:00 2001
>> From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
>> Date: Tue, 31 Mar 2015 13:46:27 +0200
>> Subject: [PATCH 4/4] gnu: pbtranscript-tofu: add missing inputs.
>
> Please capitalize "Add".
>
> Otherwise these patches look good to me.  Okay to push with these
> changes.

Thank you for the fast review.  I pushed the commits with the suggested
changes.

~~ Ricardo

Re: [PATCH] Fix pbtranscript-tofu runtime errors.

[Ludovic Courtès]

Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de> skribis:

> From 1e18e4a855659f674203777b454035cbee1a8da6 Mon Sep 17 00:00:00 2001
> From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
> Date: Tue, 31 Mar 2015 12:34:37 +0200
> Subject: [PATCH 1/4] gnu: Add python-decorator.
>
> * gnu/packages/python.scm (python-decorator, python2-decorator): New
>   variables.

OK.

> From cebbfa900aaba3468654f173cda38bbeb2df31a6 Mon Sep 17 00:00:00 2001
> From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
> Date: Tue, 31 Mar 2015 12:35:09 +0200
> Subject: [PATCH 2/4] gnu: Add python-networkx.
>
> * gnu/packages/python.scm (python-networkx, python2-networkx): New variables.

OK.

> From aad74ddc7c66fdb1c58dc89afa7078288ebeb918 Mon Sep 17 00:00:00 2001
> From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
> Date: Tue, 31 Mar 2015 12:37:31 +0200
> Subject: [PATCH 3/4] gnu: pbtranscript-tofu: delete pre-built libraries.
>
> * gnu/packages/bioinformatics.scm (pbtranscript-tofu)[arguments]: Delete
>   "build" directory and any shared objects after unpacking.

OK.  (So the tarball also contained .so files, bah!)

> From 8c6999e039048e9dd5063cc1fa4c76b59e5263c0 Mon Sep 17 00:00:00 2001
> From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
> Date: Tue, 31 Mar 2015 13:46:27 +0200
> Subject: [PATCH 4/4] gnu: pbtranscript-tofu: add missing inputs.
>
> * gnu/packages/bioinformatics.scm (pbtranscript-tofu)[inputs]: Add missing
>   runtime inputs.

OK!

Thanks,
Ludo’.

Re: [PATCH] Fix pbtranscript-tofu runtime errors.

[Ludovic Courtès]

Somehow I hadn’t seen Mark’s message.  Sorry for the noise!

Ludo’.