[PATCH] gnu: Add Cython

[PATCH] gnu: Add Cython

[Federico Beffa]

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In preparing this package I've found that the python-build-system (not
sure about the others) defines the environment variable HOME as
"/homeless-shelter". However, that directory does not exist in the
build chroot. This is a problem for cython, because it wants to access
$HOME/.cython. Wouldn't it be better to point HOME to an existing
directory (created in the chroot) with suitable permissions?

I'm a little bit unsure about the name of the package. I've not
prefixed it with "python[2]-" as the program extends the Python
language and can work with both (2 and 3) Python version series.
However, the package installs files in
".../lib/python${version}/site-packages/...". The naming is in-line
with Debian naming.


Regards,
Fede

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From b9e7cdb367518547be3d8bc535828a0d1f1ac96e Mon Sep 17 00:00:00 2001
From: Federico Beffa <beffa@fbengineering.ch>
Date: Mon, 20 Oct 2014 19:52:45 +0200
Subject: [PATCH] gnu: Add Cython

* gnu/packages/python.scm(cython,cython2): New variables
---
 gnu/packages/python.scm | 50 +++++++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 50 insertions(+)

diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm
index 897e248..f8503c3 100644
--- a/gnu/packages/python.scm
+++ b/gnu/packages/python.scm
@@ -37,6 +37,7 @@
   #:use-module (gnu packages pkg-config)
   #:use-module (gnu packages databases)
   #:use-module (gnu packages zip)
+  #:use-module (gnu packages gcc)
   #:use-module (gnu packages multiprecision)
   #:use-module (guix packages)
   #:use-module (guix download)
@@ -1832,3 +1833,52 @@ sources.")
 
 (define-public python2-sphinx
   (package-with-python2 python-sphinx))
+
+(define-public cython
+  (package
+    (name "cython")
+    (version "0.21.1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append
+             "http://cython.org/release/Cython-"
+             version ".tar.gz"))
+       (sha256
+        (base32
+         "0ddz2l2dvcy5hdkxx4xlfiwpccvwia7ixgcy4h0pdv46a4i4vxj3"))))
+    (build-system python-build-system)
+    (inputs
+     `(("python" ,python))) ; otherwise ld doesn't find libpython3.3m.so
+    (arguments
+     `(#:phases
+       (alist-replace
+        'build
+        (lambda* (#:key outputs inputs 
+                  #:allow-other-keys #:rest args)
+          (let ((build (assoc-ref %standard-phases 'build)))
+            (setenv "HOME" "/tmp") ; some tests require access to "$HOME/.cython"
+            (apply build args)))
+        (alist-replace
+         'check
+         (lambda _ (zero? 
+                    (system* "python" 
+                             "runtests.py" 
+                             "-vv")))
+         %standard-phases))))
+    (home-page "http://cython.org/")
+    (synopsis "C extensions for Python")
+    (description "Cython is an optimising static compiler for both the Python
+programming language and the extended Cython programming language.  It makes
+writing C extensions for Python as easy as Python itself.")
+    (license asl2.0)))
+
+(define-public cython2
+  (package 
+    (inherit cython)
+    (name "cython2")
+    (build-system python-build-system)
+    (inputs
+     `(("python-2" ,python-2)))
+    (arguments
+     `(#:python ,python-2 ,@(package-arguments cython)))))
-- 
1.8.4

Re: [PATCH] gnu: Add Cython

[Eric Bavier]

Federico Beffa writes:

> In preparing this package I've found that the python-build-system (not
> sure about the others) defines the environment variable HOME as
> "/homeless-shelter". However, that directory does not exist in the
> build chroot. This is a problem for cython, because it wants to access
> $HOME/.cython. Wouldn't it be better to point HOME to an existing
> directory (created in the chroot) with suitable permissions?

It's not a common need when building packages.  There are a few other
packages that need an existing, writable $HOME when building or testing.

> I'm a little bit unsure about the name of the package. I've not
> prefixed it with "python[2]-" as the program extends the Python
> language and can work with both (2 and 3) Python version series.
> However, the package installs files in
> ".../lib/python${version}/site-packages/...". The naming is in-line
> with Debian naming.

What you did seems reasonable to me.

> From b9e7cdb367518547be3d8bc535828a0d1f1ac96e Mon Sep 17 00:00:00 2001
> From: Federico Beffa <beffa@fbengineering.ch>
> Date: Mon, 20 Oct 2014 19:52:45 +0200
> Subject: [PATCH] gnu: Add Cython
> 
> * gnu/packages/python.scm(cython,cython2): New variables

Period "." at the end.
 
> ---
>  gnu/packages/python.scm | 50
>  +++++++++++++++++++++++++++++++++++++++++++++++++
>  1 file changed, 50 insertions(+)
> 
> diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm
> index 897e248..f8503c3 100644
> --- a/gnu/packages/python.scm
> +++ b/gnu/packages/python.scm
> @@ -37,6 +37,7 @@
>    #:use-module (gnu packages pkg-config)
>    #:use-module (gnu packages databases)
>    #:use-module (gnu packages zip)
> +  #:use-module (gnu packages gcc)

I don't see what prompts this new module.  Leftover from development?

>  (define-public python2-sphinx
>    (package-with-python2 python-sphinx))
> +
> +(define-public cython
> +  (package
> +    (name "cython")
> +    (version "0.21.1")
> +    (source
> +     (origin
> +       (method url-fetch)
> +       (uri (string-append
> +             "http://cython.org/release/Cython-"
> +             version ".tar.gz"))

The style in the rest of the file would dictate that the uri begin on
the same line as string-append.

> +       (sha256
> +        (base32
> +         "0ddz2l2dvcy5hdkxx4xlfiwpccvwia7ixgcy4h0pdv46a4i4vxj3"))))
> +    (build-system python-build-system)
> +    (inputs
> +     `(("python" ,python))) ; otherwise ld doesn't find libpython3.3m.so
> +    (arguments
> +     `(#:phases
> +       (alist-replace
> +        'build
> +        (lambda* (#:key outputs inputs 
> +                  #:allow-other-keys #:rest args)
> +          (let ((build (assoc-ref %standard-phases 'build)))
> +            (setenv "HOME" "/tmp") ; some tests require access to "$HOME/.cython"
> +            (apply build args)))

If $HOME is only required for tests only, please make the setenv a
separate phase that comes just before the check phase.  See
e.g. duplicity or rdup in gnu/packages/backup.scm, or the definition of
python-2 itself.  We try to avoid "wrapping" phases with (apply <phase>
args).

> +        (alist-replace
> +         'check
> +         (lambda _ (zero? 
> +                    (system* "python" 
> +                             "runtests.py" 
> +                             "-vv")))

Nitpicky: the lambda could probably go on a single line
(e.g. python-parse or python-enum34).

> +         %standard-phases))))
> +    (home-page "http://cython.org/")
> +    (synopsis "C extensions for Python")
> +    (description "Cython is an optimising static compiler for both the Python
> +programming language and the extended Cython programming language.  It makes
> +writing C extensions for Python as easy as Python itself.")
> +    (license asl2.0)))
> +
> +(define-public cython2
> +  (package 
> +    (inherit cython)
> +    (name "cython2")
> +    (build-system python-build-system)
> +    (inputs
> +     `(("python-2" ,python-2)))
> +    (arguments
> +     `(#:python ,python-2 ,@(package-arguments cython)))))

Does package-with-python2 not work here?  You might be able to do::

(define-public cython2
  (package (inherit (package-with-python2 cython))
    (name "cython2")))

-- 
Eric Bavier

Re: [PATCH] gnu: Add Cython

[Federico Beffa]

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On Mon, Oct 20, 2014 at 11:15 PM, Eric Bavier <ericbavier@gmail.com> wrote:
>
> It's not a common need when building packages.  There are a few other
> packages that need an existing, writable $HOME when building or testing.

OK. But if the directory would exist, then the build system would
cover more packages with no extra tweaking required.

> I don't see what prompts this new module.  Leftover from development?

Yes.

> Does package-with-python2 not work here?  You might be able to do::
>
> (define-public cython2
>   (package (inherit (package-with-python2 cython))
>     (name "cython2")))

Yes, that's nicer. Changed.

Thanks for the comments!
Fede

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From 28ff33bea638e9d8182b013624acbc7dedd68b4a Mon Sep 17 00:00:00 2001
From: Federico Beffa <beffa@fbengineering.ch>
Date: Mon, 20 Oct 2014 19:52:45 +0200
Subject: [PATCH] gnu: Add Cython

* gnu/packages/python.scm(cython,cython2): New variables.
---
 gnu/packages/python.scm | 36 ++++++++++++++++++++++++++++++++++++
 1 file changed, 36 insertions(+)

diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm
index 897e248..63bc588 100644
--- a/gnu/packages/python.scm
+++ b/gnu/packages/python.scm
@@ -1832,3 +1832,39 @@ sources.")
 
 (define-public python2-sphinx
   (package-with-python2 python-sphinx))
+
+(define-public cython
+  (package
+    (name "cython")
+    (version "0.21.1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append "http://cython.org/release/Cython-"
+                           version ".tar.gz"))
+       (sha256
+        (base32
+         "0ddz2l2dvcy5hdkxx4xlfiwpccvwia7ixgcy4h0pdv46a4i4vxj3"))))
+    (build-system python-build-system)
+    (inputs
+     `(("python" ,python))) ; otherwise ld doesn't find libpython3.3m.so
+    (arguments
+     `(#:phases
+       (alist-cons-before
+        'check 'set-HOME
+        ;; some tests require access to "$HOME/.cython"
+        (lambda* _ (setenv "HOME" "/tmp"))
+        (alist-replace
+         'check
+         (lambda _ (zero? (system* "python" "runtests.py" "-vv")))
+         %standard-phases))))
+    (home-page "http://cython.org/")
+    (synopsis "C extensions for Python")
+    (description "Cython is an optimising static compiler for both the Python
+programming language and the extended Cython programming language.  It makes
+writing C extensions for Python as easy as Python itself.")
+    (license asl2.0)))
+
+(define-public cython2
+  (package (inherit (package-with-python2 cython))
+    (name "cython2")))
-- 
1.8.4

Re: [PATCH] gnu: Add Cython

[Andreas Enge]

On Mon, Oct 20, 2014 at 08:43:38PM +0200, Federico Beffa wrote:
> I'm a little bit unsure about the name of the package. I've not
> prefixed it with "python[2]-" as the program extends the Python
> language and can work with both (2 and 3) Python version series.
> However, the package installs files in
> ".../lib/python${version}/site-packages/...". The naming is in-line
> with Debian naming.

Since there will be two packages, I suggest to follow our python module
naming conventions although this is not a python module, and to prepend
with "python-" and "python2-". Writing "cython2" would look as if this were
a next generation cython (in particular, it would look newer than plain
cython in version 0.21.1).

Andreas

Re: [PATCH] gnu: Add Cython

[Federico Beffa]

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On Thu, Oct 23, 2014 at 8:25 AM, Andreas Enge <andreas@enge.fr> wrote:
> Since there will be two packages, I suggest to follow our python module
> naming conventions although this is not a python module, and to prepend
> with "python-" and "python2-". Writing "cython2" would look as if this were
> a next generation cython (in particular, it would look newer than plain
> cython in version 0.21.1).


Makes sense: updated.

Thanks,
Fede

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From 3155aa1ec614afb01b7bff0bbf3eabb4ee5bb0de Mon Sep 17 00:00:00 2001
From: Federico Beffa <beffa@fbengineering.ch>
Date: Mon, 20 Oct 2014 19:52:45 +0200
Subject: [PATCH] gnu: Add Cython

* gnu/packages/python.scm(cython,cython2): New variables.
---
 gnu/packages/python.scm | 41 +++++++++++++++++++++++++++++++++++++++++
 1 file changed, 41 insertions(+)

diff --git a/gnu/packages/python.scm b/gnu/packages/python.scm
index 897e248..a95d27c 100644
--- a/gnu/packages/python.scm
+++ b/gnu/packages/python.scm
@@ -4,6 +4,7 @@
 ;;; Copyright © 2013 Andreas Enge <andreas@enge.fr>
 ;;; Copyright © 2014 Mark H Weaver <mhw@netris.org>
 ;;; Copyright © 2014 Eric Bavier <bavier@member.fsf.org>
+;;; Copyright © 2014 Federico Beffa <beffa@fbengineering.ch>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -1832,3 +1833,43 @@ sources.")
 
 (define-public python2-sphinx
   (package-with-python2 python-sphinx))
+
+(define-public python-cython
+  (package
+    (name "python-cython")
+    (version "0.21.1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append "http://cython.org/release/Cython-"
+                           version ".tar.gz"))
+       (sha256
+        (base32
+         "0ddz2l2dvcy5hdkxx4xlfiwpccvwia7ixgcy4h0pdv46a4i4vxj3"))))
+    (build-system python-build-system)
+    ;; we need the full python package and not just the python-wrapper
+    ;; because we need libpython3.3m.so
+    (inputs
+     `(("python" ,python)))
+    (arguments
+     `(#:phases
+       (alist-cons-before
+        'check 'set-HOME
+        ;; some tests require access to "$HOME/.cython"
+        (lambda* _ (setenv "HOME" "/tmp"))
+        (alist-replace
+         'check
+         (lambda _ (zero? (system* "python" "runtests.py" "-vv")))
+         %standard-phases))))
+    (home-page "http://cython.org/")
+    (synopsis "C extensions for Python")
+    (description "Cython is an optimising static compiler for both the Python
+programming language and the extended Cython programming language.  It makes
+writing C extensions for Python as easy as Python itself.")
+    (license asl2.0)))
+
+(define-public python2-cython
+  (package (inherit (package-with-python2 python-cython))
+    (name "python2-cython")
+    (inputs
+     `(("python-2" ,python-2))))) ; this is not automatically changed
-- 
1.8.4

Re: [PATCH] gnu: Add Cython

[Andreas Enge]

Concerning the following problem with python-wrapper:

On Fri, Oct 24, 2014 at 05:51:12PM +0200, Federico Beffa wrote:
> +    ;; we need the full python package and not just the python-wrapper
> +    ;; because we need libpython3.3m.so

Maybe we should propagate its input python? Then python-wrapper would
also install python instead of just adding a few links to the binaries.

Andreas

Re: [PATCH] gnu: Add Cython

[Federico Beffa]

On Fri, Oct 24, 2014 at 9:50 PM, Andreas Enge <andreas@enge.fr> wrote:
> Maybe we should propagate its input python? Then python-wrapper would
> also install python instead of just adding a few links to the binaries.

From my point of view this would be desirable.  I'm having the same
problem with other packages such as numpy (which I'm preparing).

By the way, I've also noted another minor defect: the wrappers for
programs created by python-build-system puts double entries for some
directories in the definition of PYTHONPATH.  This is visible, e.g.,
in python-nose (nosetests), python-setuptools (easy_install),
python-cython and probably more.  This does not create problems, but
it would be nice to remove double entries.

Regards,
Fede

Re: [PATCH] gnu: Add Cython

[Ludovic Courtès]

Federico Beffa <beffa@ieee.org> skribis:

> From 3155aa1ec614afb01b7bff0bbf3eabb4ee5bb0de Mon Sep 17 00:00:00 2001
> From: Federico Beffa <beffa@fbengineering.ch>
> Date: Mon, 20 Oct 2014 19:52:45 +0200
> Subject: [PATCH] gnu: Add Cython
>
> * gnu/packages/python.scm(cython,cython2): New variables.

Pushed, with missing spaces in the commit log added.

Thanks!

Ludo’.

Re: [PATCH] gnu: Add Cython

[Andreas Enge]

On Mon, Nov 03, 2014 at 05:57:58PM +0100, Ludovic Courtès wrote:
> Federico Beffa <beffa@ieee.org> skribis:
> > Subject: [PATCH] gnu: Add Cython
> > * gnu/packages/python.scm(cython,cython2): New variables.
> Pushed, with missing spaces in the commit log added.

I think that should have gone on the wip-python branch eventually instead
of being pushed now... Never mind, we can always adapt it later!

Andreas

Re: [PATCH] gnu: Add Cython

[Ludovic Courtès]

Andreas Enge <andreas@enge.fr> skribis:

> On Mon, Nov 03, 2014 at 05:57:58PM +0100, Ludovic Courtès wrote:
>> Federico Beffa <beffa@ieee.org> skribis:
>> > Subject: [PATCH] gnu: Add Cython
>> > * gnu/packages/python.scm(cython,cython2): New variables.
>> Pushed, with missing spaces in the commit log added.
>
> I think that should have gone on the wip-python branch eventually instead
> of being pushed now... Never mind, we can always adapt it later!

Oh, apologies then.

But are you sure you aren’t confusing it with NumPy, which requires the
new python-wrapper?

Ludo’.

Re: [PATCH] gnu: Add Cython

[Andreas Enge]

On Mon, Nov 03, 2014 at 08:42:25PM +0100, Ludovic Courtès wrote:
> But are you sure you aren’t confusing it with NumPy, which requires the
> new python-wrapper?

Probably I am confusing things, even less problems then!

Andreas

Re: [PATCH] gnu: Add Cython

[Federico Beffa]

On Mon, Nov 3, 2014 at 8:50 PM, Andreas Enge <andreas@enge.fr> wrote:
> On Mon, Nov 03, 2014 at 08:42:25PM +0100, Ludovic Courtès wrote:
>> But are you sure you aren’t confusing it with NumPy, which requires the
>> new python-wrapper?
>
> Probably I am confusing things, even less problems then!
>

No, Andreas is right: this patch suffers from the same problem as Numpy.

Fede

Re: [PATCH] gnu: Add Cython

[Federico Beffa]

On Mon, Nov 3, 2014 at 9:12 PM, Federico Beffa <beffa@ieee.org> wrote:
> No, Andreas is right: this patch suffers from the same problem as Numpy.

Maybe I wasn't clear :-)  the patch does include python as an input.
So, it will build in master, without any change in python-wrapper.
After the changes in python-wrapper, we may want to remove the python
input.

Regards,
Fede