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

Previous Next

To add a comment to this bug, you must first unarchive it, by sending
a message to control AT debbugs.gnu.org, with unarchive 27922 in the body.
You can then email your comments to 27922 AT debbugs.gnu.org in the normal way.

Toggle the display of automated, internal messages from the tracker.

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

From: Leo Famulari <leo <at> famulari.name>
To: guix-patches <at> gnu.org
Subject: [PATCH] gnu: python-numpy: Update to 1.12.1.
Date: Wed,  2 Aug 2017 15:49:00 -0400

* 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

Message #8 received at 27922 <at> debbugs.gnu.org (full text, mbox):

From: Marius Bakke <mbakke <at> fastmail.com>
To: Leo Famulari <leo <at> famulari.name>, 27922 <at> debbugs.gnu.org
Subject: Re: [bug#27922] [PATCH] gnu: python-numpy: Update to 1.12.1.
Date: Wed, 02 Aug 2017 22:12:21 +0200

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

Leo Famulari <leo <at> 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?

[signature.asc (application/pgp-signature, inline)]

Message #11 received at 27922 <at> debbugs.gnu.org (full text, mbox):

From: Leo Famulari <leo <at> famulari.name>
To: Marius Bakke <mbakke <at> fastmail.com>
Cc: 27922 <at> debbugs.gnu.org
Subject: Re: [bug#27922] [PATCH] gnu: python-numpy: Update to 1.12.1.
Date: Wed, 2 Aug 2017 18:48:34 -0400

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

On Wed, Aug 02, 2017 at 10:12:21PM +0200, Marius Bakke wrote:
> Leo Famulari <leo <at> 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.

[signature.asc (application/pgp-signature, inline)]

Message #14 received at 27922 <at> debbugs.gnu.org (full text, mbox):

From: ludo <at> gnu.org (Ludovic Courtès)
To: Leo Famulari <leo <at> famulari.name>
Cc: 27922 <at> debbugs.gnu.org, Marius Bakke <mbakke <at> fastmail.com>
Subject: Re: [bug#27922] [PATCH] gnu: python-numpy: Update to 1.12.1.
Date: Mon, 04 Sep 2017 15:19:05 +0200

Leo Famulari <leo <at> famulari.name> skribis:

> On Wed, Aug 02, 2017 at 10:12:21PM +0200, Marius Bakke wrote:
>> Leo Famulari <leo <at> 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'.

Message #17 received at 27922 <at> debbugs.gnu.org (full text, mbox):

From: Thomas Danckaert <post <at> thomasdanckaert.be>
To: ludo <at> gnu.org (Ludovic Courtès)
Cc: 27922 <at> debbugs.gnu.org, Marius Bakke <mbakke <at> fastmail.com>,
 Leo Famulari <leo <at> famulari.name>
Subject: Re: [bug#27922] [PATCH] gnu: python-numpy: Update to 1.12.1.
Date: Tue, 26 Sep 2017 11:53:55 +0200

ludo <at> gnu.org (Ludovic Courtès) writes:

> Leo Famulari <leo <at> famulari.name> skribis:
>
>> On Wed, Aug 02, 2017 at 10:12:21PM +0200, Marius Bakke wrote:
>>> Leo Famulari <leo <at> 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

Message #20 received at 27922 <at> debbugs.gnu.org (full text, mbox):

From: ludo <at> gnu.org (Ludovic Courtès)
To: Thomas Danckaert <post <at> thomasdanckaert.be>
Cc: 27922 <at> debbugs.gnu.org, Marius Bakke <mbakke <at> fastmail.com>,
 Leo Famulari <leo <at> famulari.name>
Subject: Re: [bug#27922] [PATCH] gnu: python-numpy: Update to 1.12.1.
Date: Tue, 26 Sep 2017 13:48:45 +0200

Thomas Danckaert <post <at> thomasdanckaert.be> skribis:

> ludo <at> gnu.org (Ludovic Courtès) writes:
>
>> Leo Famulari <leo <at> famulari.name> skribis:
>>
>>> On Wed, Aug 02, 2017 at 10:12:21PM +0200, Marius Bakke wrote:
>>>> Leo Famulari <leo <at> 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’.

Message #23 received at 27922 <at> debbugs.gnu.org (full text, mbox):

From: Leo Famulari <leo <at> famulari.name>
To: Ludovic Courtès <ludo <at> gnu.org>
Cc: Thomas Danckaert <post <at> thomasdanckaert.be>,
 Marius Bakke <mbakke <at> fastmail.com>, 27922 <at> debbugs.gnu.org
Subject: Re: [bug#27922] [PATCH] gnu: python-numpy: Update to 1.12.1.
Date: Tue, 26 Sep 2017 11:46:20 -0400

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

On Tue, Sep 26, 2017 at 01:48:45PM +0200, Ludovic Courtès wrote:
> Thomas Danckaert <post <at> 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.

[signature.asc (application/pgp-signature, inline)]

Message #26 received at 27922 <at> debbugs.gnu.org (full text, mbox):

From: Thomas Danckaert <post <at> thomasdanckaert.be>
To: leo <at> famulari.name
Cc: 27922 <at> debbugs.gnu.org, ludo <at> gnu.org, mbakke <at> fastmail.com
Subject: Re: [bug#27922] [PATCH] gnu: python-numpy: Update to 1.12.1.
Date: Tue, 26 Sep 2017 18:59:21 +0200 (CEST)

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

From: Leo Famulari <leo <at> 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 <at> 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.

[0001-gnu-python-numpy-Update-to-1.13.1.patch (text/x-patch, inline)]

From 2b90b6e2a9b7ac73937ee8e52b08bb715ba33fb7 Mon Sep 17 00:00:00 2001
From: Thomas Danckaert <post <at> 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 <at> 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

Message #29 received at 27922 <at> debbugs.gnu.org (full text, mbox):

From: ludo <at> gnu.org (Ludovic Courtès)
To: Thomas Danckaert <post <at> thomasdanckaert.be>
Cc: 27922 <at> debbugs.gnu.org, mbakke <at> fastmail.com, leo <at> famulari.name
Subject: Re: [bug#27922] [PATCH] gnu: python-numpy: Update to 1.12.1.
Date: Tue, 26 Sep 2017 22:08:32 +0200

Hi,

Thomas Danckaert <post <at> thomasdanckaert.be> skribis:

> From: Leo Famulari <leo <at> 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 <at> 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’.

Message #32 received at 27922 <at> debbugs.gnu.org (full text, mbox):

From: Thomas Danckaert <post <at> thomasdanckaert.be>
To: ludo <at> gnu.org
Cc: 27922 <at> debbugs.gnu.org, mbakke <at> fastmail.com, leo <at> famulari.name
Subject: Re: [bug#27922] [PATCH] gnu: python-numpy: Update to 1.12.1.
Date: Wed, 27 Sep 2017 08:36:46 +0200 (CEST)

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

From: ludo <at> 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

[0001-gnu-python-numpy-Update-to-1.13.1.patch (text/x-patch, inline)]

From f60e8593ca572477e2444a57ad508b9c558316ee Mon Sep 17 00:00:00 2001
From: Thomas Danckaert <post <at> 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 <at> 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

Message #35 received at 27922 <at> debbugs.gnu.org (full text, mbox):

From: ludo <at> gnu.org (Ludovic Courtès)
To: Thomas Danckaert <post <at> thomasdanckaert.be>
Cc: 27922 <at> debbugs.gnu.org, mbakke <at> fastmail.com, leo <at> famulari.name
Subject: Re: [bug#27922] [PATCH] gnu: python-numpy: Update to 1.12.1.
Date: Wed, 27 Sep 2017 21:35:07 +0200

Thomas Danckaert <post <at> thomasdanckaert.be> skribis:

> From: ludo <at> 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 <at> 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 <at> famulari.name>

LGTM, thank you!

Ludo’.

Message #38 received at 27922 <at> debbugs.gnu.org (full text, mbox):

From: Thomas Danckaert <post <at> thomasdanckaert.be>
To: 27922-done <at> debbugs.gnu.org
Cc: 27922 <at> debbugs.gnu.org
Subject: Re: [bug#27922] [PATCH] gnu: python-numpy: Update to 1.12.1.
Date: Thu, 28 Sep 2017 20:32:07 +0200 (CEST)

Pushed...

Previous Next

GNU bug tracking system
Copyright (C) 1999 Darren O. Benham, 1997,2003 nCipher Corporation Ltd, 1994-97 Ian Jackson.