[bug#27922] [PATCH] gnu: python-numpy: Update to 1.12.1.

[bug#27922] [PATCH] gnu: python-numpy: Update to 1.12.1.

[Leo Famulari]

* gnu/packages/python.scm (python-numpy, python2-numpy): Update to 1.12.1.
[source]: Download the "real" release tarball instead of the snapshot.
---
 gnu/packages/python.scm | 9 ++++-----
 1 file changed, 4 insertions(+), 5 deletions(-)

diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm
index cf77abdba..1a6a46143 100644
--- a/gnu/packages/python.scm
+++ b/gnu/packages/python.scm
@@ -3670,16 +3670,15 @@ between language specification and implementation aspects.")
 (define-public python-numpy
   (package
     (name "python-numpy")
-    (version "1.12.0")
+    (version "1.12.1")
     (source
      (origin
        (method url-fetch)
-       (uri (string-append
-             "https://github.com/numpy/numpy/archive/v" version ".tar.gz"))
-       (file-name (string-append name "-" version ".tar.gz"))
+       (uri (string-append "https://github.com/numpy/numpy/releases/download/v"
+                           version "/numpy-" version ".tar.gz"))
        (sha256
         (base32
-         "025d4j4aakcp8w5i5diqh812cbbjgac7jszx1j56ivrbi1i8vv7d"))))
+         "1afg2dvi764gilxsff73g1vdir8lr2030l50mw3s8i78h7zpyvfm"))))
     (build-system python-build-system)
     (inputs
      `(("openblas" ,openblas)
-- 
2.13.3

[bug#27922] [PATCH] gnu: python-numpy: Update to 1.12.1.

[Marius Bakke]

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Leo Famulari <leo@famulari.name> writes:

> * gnu/packages/python.scm (python-numpy, python2-numpy): Update to 1.12.1.

LGTM ;-)

> [source]: Download the "real" release tarball instead of the snapshot.

NumPy provides a PGP signature with the zipball on PyPi:

https://pypi.python.org/pypi/numpy

Is there a reason to prefer the GitHub release tarball?


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[bug#27922] [PATCH] gnu: python-numpy: Update to 1.12.1.

[Leo Famulari]

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On Wed, Aug 02, 2017 at 10:12:21PM +0200, Marius Bakke wrote:
> Leo Famulari <leo@famulari.name> writes:
> 
> > * gnu/packages/python.scm (python-numpy, python2-numpy): Update to 1.12.1.
> 
> LGTM ;-)
> 
> > [source]: Download the "real" release tarball instead of the snapshot.
> 
> NumPy provides a PGP signature with the zipball on PyPi:
> 
> https://pypi.python.org/pypi/numpy

Good catch!

> Is there a reason to prefer the GitHub release tarball?

Not that I know of. I only chose this tarball because I saw it on the GitHub
page. I'll try switching to PyPi.

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[bug#27922] [PATCH] gnu: python-numpy: Update to 1.12.1.

[Ludovic Courtès]

Leo Famulari <leo@famulari.name> skribis:

> On Wed, Aug 02, 2017 at 10:12:21PM +0200, Marius Bakke wrote:
>> Leo Famulari <leo@famulari.name> writes:
>> 
>> > * gnu/packages/python.scm (python-numpy, python2-numpy): Update to 1.12.1.
>> 
>> LGTM ;-)
>> 
>> > [source]: Download the "real" release tarball instead of the snapshot.
>> 
>> NumPy provides a PGP signature with the zipball on PyPi:
>> 
>> https://pypi.python.org/pypi/numpy
>
> Good catch!
>
>> Is there a reason to prefer the GitHub release tarball?
>
> Not that I know of. I only chose this tarball because I saw it on the GitHub
> page. I'll try switching to PyPi.

Leo, I think this fell through the cracks!  :-)

Ludo'.

[bug#27922] [PATCH] gnu: python-numpy: Update to 1.12.1.

[Thomas Danckaert]

ludo@gnu.org (Ludovic Courtès) writes:

> Leo Famulari <leo@famulari.name> skribis:
>
>> On Wed, Aug 02, 2017 at 10:12:21PM +0200, Marius Bakke wrote:
>>> Leo Famulari <leo@famulari.name> writes:
>>> 
>>> > * gnu/packages/python.scm (python-numpy, python2-numpy): Update to 1.12.1.
>>> 
>>> LGTM ;-)
>>> 
>>> > [source]: Download the "real" release tarball instead of the snapshot.
>>> 
>>> NumPy provides a PGP signature with the zipball on PyPi:
>>> 
>>> https://pypi.python.org/pypi/numpy
>>
>> Good catch!
>>
>>> Is there a reason to prefer the GitHub release tarball?
>>
>> Not that I know of. I only chose this tarball because I saw it on the GitHub
>> page. I'll try switching to PyPi.
>
> Leo, I think this fell through the cracks!  :-)
>
> Ludo'.

I can push a modified patch (with the pypi source) if it's ok.  Is there
any reason we would not update to version 1.13.1 rightaway?

Thomas

[bug#27922] [PATCH] gnu: python-numpy: Update to 1.12.1.

[Ludovic Courtès]

Thomas Danckaert <post@thomasdanckaert.be> skribis:

> ludo@gnu.org (Ludovic Courtès) writes:
>
>> Leo Famulari <leo@famulari.name> skribis:
>>
>>> On Wed, Aug 02, 2017 at 10:12:21PM +0200, Marius Bakke wrote:
>>>> Leo Famulari <leo@famulari.name> writes:
>>>> 
>>>> > * gnu/packages/python.scm (python-numpy, python2-numpy): Update to 1.12.1.
>>>> 
>>>> LGTM ;-)
>>>> 
>>>> > [source]: Download the "real" release tarball instead of the snapshot.
>>>> 
>>>> NumPy provides a PGP signature with the zipball on PyPi:
>>>> 
>>>> https://pypi.python.org/pypi/numpy
>>>
>>> Good catch!
>>>
>>>> Is there a reason to prefer the GitHub release tarball?
>>>
>>> Not that I know of. I only chose this tarball because I saw it on the GitHub
>>> page. I'll try switching to PyPi.
>>
>> Leo, I think this fell through the cracks!  :-)
>>
>> Ludo'.
>
> I can push a modified patch (with the pypi source) if it's ok.  Is there
> any reason we would not update to version 1.13.1 rightaway?

If the dependents of NumPy build fine, I see no reason not to upgrade to
1.13.1.

Thanks for picking this up!

Ludo’.

[bug#27922] [PATCH] gnu: python-numpy: Update to 1.12.1.

[Leo Famulari]

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On Tue, Sep 26, 2017 at 01:48:45PM +0200, Ludovic Courtès wrote:
> Thomas Danckaert <post@thomasdanckaert.be> skribis:
> > I can push a modified patch (with the pypi source) if it's ok.  Is there
> > any reason we would not update to version 1.13.1 rightaway?
> 
> If the dependents of NumPy build fine, I see no reason not to upgrade to
> 1.13.1.
> 
> Thanks for picking this up!

Yes, thank you! I got distracted and had to take a little break, which
is why this patch fell by the wayside.

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[bug#27922] [PATCH] gnu: python-numpy: Update to 1.12.1.

[Thomas Danckaert]

[-- Attachment #1: Type: Text/Plain, Size: 1234 bytes --]

From: Leo Famulari <leo@famulari.name>
Subject: Re: [bug#27922] [PATCH] gnu: python-numpy: Update to 1.12.1.
Date: Tue, 26 Sep 2017 11:46:20 -0400

> On Tue, Sep 26, 2017 at 01:48:45PM +0200, Ludovic Courtès wrote:
>> Thomas Danckaert <post@thomasdanckaert.be> skribis:
>> > I can push a modified patch (with the pypi source) if it's ok.  
>> Is there
>> > any reason we would not update to version 1.13.1 rightaway?
>>
>> If the dependents of NumPy build fine, I see no reason not to 
>> upgrade to
>> 1.13.1.
>>
>> Thanks for picking this up!
>
> Yes, thank you! I got distracted and had to take a little break, 
> which
> is why this patch fell by the wayside.

Attached patch updates to 1.13.1.  I had to add bash-minimal as a 
native input because the numpy people made their build system a 
little more convoluted ;-) (external commands such as gcc are run 
within a shell with $SHELL -c 'gcc [...]', I didn't look up the 
motivation for that).

If there are no objections, I'll push this soon.

Thomas

ps I couldn't check if matplotlib still builds with this numpy 
version, because our bluez package (on which matplotlib apparently 
depends) appears to be broken.  But that's another story.

[-- Attachment #2: 0001-gnu-python-numpy-Update-to-1.13.1.patch --]
[-- Type: Text/X-Patch, Size: 2308 bytes --]

From 2b90b6e2a9b7ac73937ee8e52b08bb715ba33fb7 Mon Sep 17 00:00:00 2001
From: Thomas Danckaert <post@thomasdanckaert.be>
Date: Tue, 26 Sep 2017 16:26:08 +0200
Subject: [PATCH] gnu: python-numpy: Update to 1.13.1.

* gnu/packages/python.scm (python-numpy, python2-numpy): Update to 1.12.1.
[source]: Download the zip release from pypi instead of a git snapshot.
[native-inputs]: Add unzip and bash-minimal.
[arguments]: Set SHELL environment variable.

Co-authored by Leo Famulari <leo@famulari.name>
---
 gnu/packages/python.scm | 16 ++++++++++------
 1 file changed, 10 insertions(+), 6 deletions(-)

diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm
index 5dcb5a05c..6b9de923d 100644
--- a/gnu/packages/python.scm
+++ b/gnu/packages/python.scm
@@ -3720,22 +3720,24 @@ between language specification and implementation aspects.")
 (define-public python-numpy
   (package
     (name "python-numpy")
-    (version "1.12.0")
+    (version "1.13.1")
     (source
      (origin
        (method url-fetch)
-       (uri (string-append
-             "https://github.com/numpy/numpy/archive/v" version ".tar.gz"))
-       (file-name (string-append name "-" version ".tar.gz"))
+       (uri (pypi-uri "numpy" version ".zip"))
        (sha256
         (base32
-         "025d4j4aakcp8w5i5diqh812cbbjgac7jszx1j56ivrbi1i8vv7d"))))
+         "1fsgkhh1vdkhmlz8vmdgxnj9n9yaanckxxzz9s0b4p08fqvjic69"))))
     (build-system python-build-system)
     (inputs
      `(("openblas" ,openblas)
        ("lapack" ,lapack)))
     (native-inputs
-     `(("python-cython" ,python-cython)
+     `(("unzip" ,unzip)
+       ;; We need bash because numpy's distutils runs external commands with
+       ;; $SHELL -c '...'.
+       ("bash" ,bash-minimal)
+       ("python-cython" ,python-cython)
        ("python-nose" ,python-nose)
        ("gfortran" ,gfortran)))
     (arguments
@@ -3743,6 +3745,8 @@ between language specification and implementation aspects.")
        (modify-phases %standard-phases
         (add-before 'build 'set-environment-variables
          (lambda* (#:key inputs #:allow-other-keys)
+          (setenv "SHELL"
+                  (string-append (assoc-ref inputs "bash") "/bin/bash"))
           (call-with-output-file "site.cfg"
             (lambda (port)
               (format port
-- 
2.14.1

[bug#27922] [PATCH] gnu: python-numpy: Update to 1.12.1.

[Ludovic Courtès]

Hi,

Thomas Danckaert <post@thomasdanckaert.be> skribis:

> From: Leo Famulari <leo@famulari.name>
> Subject: Re: [bug#27922] [PATCH] gnu: python-numpy: Update to 1.12.1.
> Date: Tue, 26 Sep 2017 11:46:20 -0400
>
>> On Tue, Sep 26, 2017 at 01:48:45PM +0200, Ludovic Courtès wrote:
>>> Thomas Danckaert <post@thomasdanckaert.be> skribis:
>>> > I can push a modified patch (with the pypi source) if it's ok.
>>> Is there
>>> > any reason we would not update to version 1.13.1 rightaway?
>>>
>>> If the dependents of NumPy build fine, I see no reason not to
>>> upgrade to
>>> 1.13.1.
>>>
>>> Thanks for picking this up!
>>
>> Yes, thank you! I got distracted and had to take a little break,
>> which
>> is why this patch fell by the wayside.
>
> Attached patch updates to 1.13.1.  I had to add bash-minimal as a
> native input because the numpy people made their build system a little
> more convoluted ;-) (external commands such as gcc are run within a
> shell with $SHELL -c 'gcc [...]', I didn't look up the motivation for
> that).

This is weird: bash-minimal is an implicit input already.  What was the
error exactly?

Apart from that it looks great.

Thanks!

Ludo’.

[bug#27922] [PATCH] gnu: python-numpy: Update to 1.12.1.

[Thomas Danckaert]

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From: ludo@gnu.org (Ludovic Courtès)
Subject: Re: [bug#27922] [PATCH] gnu: python-numpy: Update to 1.12.1.
Date: Tue, 26 Sep 2017 22:08:32 +0200

> This is weird: bash-minimal is an implicit input already.  What was 
> the
> error exactly?

Oops, just setting (setenv "SHELL" "bash") is enough. Indeed, bash is 
already there.

(I've been looking in (guix build-system ...) to try to find out the 
default native inputs for the different build systems, but couldn't 
find it.  Where are they set?)

Thomas

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[-- Type: Text/X-Patch, Size: 2155 bytes --]

From f60e8593ca572477e2444a57ad508b9c558316ee Mon Sep 17 00:00:00 2001
From: Thomas Danckaert <post@thomasdanckaert.be>
Date: Tue, 26 Sep 2017 16:26:08 +0200
Subject: [PATCH] gnu: python-numpy: Update to 1.13.1.

* gnu/packages/python.scm (python-numpy, python2-numpy): Update to 1.13.1.
[source]: Download the zip release from pypi instead of a git snapshot.
[native-inputs]: Add unzip.
[arguments]: Set SHELL environment variable.

Co-authored by Leo Famulari <leo@famulari.name>
---
 gnu/packages/python.scm | 13 +++++++------
 1 file changed, 7 insertions(+), 6 deletions(-)

diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm
index 5dcb5a05c..6988b44a9 100644
--- a/gnu/packages/python.scm
+++ b/gnu/packages/python.scm
@@ -3720,22 +3720,21 @@ between language specification and implementation aspects.")
 (define-public python-numpy
   (package
     (name "python-numpy")
-    (version "1.12.0")
+    (version "1.13.1")
     (source
      (origin
        (method url-fetch)
-       (uri (string-append
-             "https://github.com/numpy/numpy/archive/v" version ".tar.gz"))
-       (file-name (string-append name "-" version ".tar.gz"))
+       (uri (pypi-uri "numpy" version ".zip"))
        (sha256
         (base32
-         "025d4j4aakcp8w5i5diqh812cbbjgac7jszx1j56ivrbi1i8vv7d"))))
+         "1fsgkhh1vdkhmlz8vmdgxnj9n9yaanckxxzz9s0b4p08fqvjic69"))))
     (build-system python-build-system)
     (inputs
      `(("openblas" ,openblas)
        ("lapack" ,lapack)))
     (native-inputs
-     `(("python-cython" ,python-cython)
+     `(("unzip" ,unzip)
+       ("python-cython" ,python-cython)
        ("python-nose" ,python-nose)
        ("gfortran" ,gfortran)))
     (arguments
@@ -3743,6 +3742,8 @@ between language specification and implementation aspects.")
        (modify-phases %standard-phases
         (add-before 'build 'set-environment-variables
          (lambda* (#:key inputs #:allow-other-keys)
+           ;; numpy's distutils uses $SHELL to run external commands.
+          (setenv "SHELL" "bash")
           (call-with-output-file "site.cfg"
             (lambda (port)
               (format port
-- 
2.14.1

[bug#27922] [PATCH] gnu: python-numpy: Update to 1.12.1.

[Ludovic Courtès]

Thomas Danckaert <post@thomasdanckaert.be> skribis:

> From: ludo@gnu.org (Ludovic Courtès)
> Subject: Re: [bug#27922] [PATCH] gnu: python-numpy: Update to 1.12.1.
> Date: Tue, 26 Sep 2017 22:08:32 +0200
>
>> This is weird: bash-minimal is an implicit input already.  What was
>> the
>> error exactly?
>
> Oops, just setting (setenv "SHELL" "bash") is enough. Indeed, bash is
> already there.

Wonderful.  :-)

> (I've been looking in (guix build-system ...) to try to find out the
> default native inputs for the different build systems, but couldn't
> find it.  Where are they set?)

It’s ‘standard-packages’ in (guix build-system gnu), which in turn
refers to ‘%final-inputs’ in (gnu packages commencement).

> From f60e8593ca572477e2444a57ad508b9c558316ee Mon Sep 17 00:00:00 2001
> From: Thomas Danckaert <post@thomasdanckaert.be>
> Date: Tue, 26 Sep 2017 16:26:08 +0200
> Subject: [PATCH] gnu: python-numpy: Update to 1.13.1.
>
> * gnu/packages/python.scm (python-numpy, python2-numpy): Update to 1.13.1.
> [source]: Download the zip release from pypi instead of a git snapshot.
> [native-inputs]: Add unzip.
> [arguments]: Set SHELL environment variable.
>
> Co-authored by Leo Famulari <leo@famulari.name>

LGTM, thank you!

Ludo’.

[bug#27922] [PATCH] gnu: python-numpy: Update to 1.12.1.

[Thomas Danckaert]

Pushed...