GNU bug report logs - #50105
[core-updates] Python sitecustomize issue.

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Package: guix; Severity: important; Reported by: Mathieu Othacehe <othacehe@HIDDEN>; Keywords: patch; dated Wed, 18 Aug 2021 09:54:02 UTC; Maintainer for guix is bug-guix@HIDDEN.
Added tag(s) patch. Request was from Maxim Cournoyer <maxim.cournoyer@HIDDEN> to control <at> debbugs.gnu.org. Full text available.
Severity set to 'important' from 'normal' Request was from Maxim Cournoyer <maxim.cournoyer@HIDDEN> to control <at> debbugs.gnu.org. Full text available.

Message received at 50105 <at> debbugs.gnu.org:


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From: Maxim Cournoyer <maxim.cournoyer@HIDDEN>
To: Mathieu Othacehe <othacehe@HIDDEN>
Subject: Re: bug#50105: [core-updates] Python sitecustomize issue.
References: <878s0zoz98.fsf@HIDDEN>
Date: Tue, 31 Aug 2021 00:03:23 -0400
In-Reply-To: <878s0zoz98.fsf@HIDDEN> (Mathieu Othacehe's message of "Wed, 18
 Aug 2021 11:53:07 +0200")
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--=-=-=
Content-Type: text/plain

Hi Mathieu,

[...]

> I think the issue here lies in the sitecustomize.py file introduced with
> cb72f9a773e0931ee3758c851d96007ded034e4c.
>
> python_root = os.path.realpath(sys.executable).split('/bin/')[0]
>
>
> When using the Python C library, sys.executable is not the expected
> python binary but the test binary.
>
> So when we try to find the associated libraries in the Python search
> path, this way:
>
> index = sys_path_absolute.index(python_site)
> sys.path = sys.path[:index] + matching_sites + sys.path[index:]
>
>
> we get:
>
> ValueError: '/home/mathieu/glade-3.38.2/build/lib/python3.9/site-packages' is not in list
>
>
> Running the test with the PYTHONPATH set to:
>
> PYTHONPATH=/home/mathieu/glade-3.38.2/build/lib/python3.9/site-packages:$PYTHONPATH 
>
> is a way to work around this issue.
>
> The fix here would be to replace sys.executable in the sitecustomize.py
> with something more adequate, but I have no idea what could it be.

From the doc [0], sys.prefix seems to be more correct.  This had been
suggested by Hartmut some time ago and I had this patch ready recently.
Perhaps it already addresses the issue at hand?

You'll find it attached.  It hasn't gotten much testing yet.

[0]  https://docs.python.org/3/library/sys.html#sys.prefix


--=-=-=
Content-Type: text/x-patch
Content-Disposition: attachment;
 filename=0001-aux-files-sitecustomize-Cleanup-and-add-explanatory-.patch

From e693b38a6d5c370e13f795c6303f50871ec78ae4 Mon Sep 17 00:00:00 2001
From: Maxim Cournoyer <maxim.cournoyer@HIDDEN>
Date: Tue, 3 Aug 2021 20:41:20 -0400
Subject: [PATCH] aux-files: sitecustomize: Cleanup and add explanatory
 comments.

* gnu/packages/aux-files/python/sitecustomize.py: Add a comment explaining the
general idea.

(major_minor): Use the unpacking operator (*) to provide the arguments.
(site_packages_prefix): Use os.path.join to form the path.
(python_site): Likewise.
(all_sites_raw): Split on os.path.pathsep.
(sys.path): Directly splice the result in the list.

Suggested-by: Hartmut Goebel <h.goebel@HIDDEN>
---
 .../aux-files/python/sitecustomize.py         | 28 ++++++++++++++-----
 1 file changed, 21 insertions(+), 7 deletions(-)

diff --git a/gnu/packages/aux-files/python/sitecustomize.py b/gnu/packages/aux-files/python/sitecustomize.py
index 65d3c7d554..71e328b9ac 100644
--- a/gnu/packages/aux-files/python/sitecustomize.py
+++ b/gnu/packages/aux-files/python/sitecustomize.py
@@ -20,13 +20,26 @@
 import os
 import sys
 
-python_root = os.path.realpath(sys.executable).split('/bin/')[0]
-major_minor = '{}.{}'.format(sys.version_info[0], sys.version_info[1])
-site_packages_prefix = 'lib/python' + major_minor + '/site-packages'
-python_site = python_root + '/' + site_packages_prefix
+# Commentary:
+#
+# Site-specific customization for Guix.
+#
+# The program below honors the GUIX_PYTHONPATH environment variable to
+# discover Python packages.  File names appearing in this variable that match
+# a predefined versioned installation prefix are added to the sys.path.  To be
+# considered, a Python package must be installed under the
+# 'lib/pythonX.Y/site-packages' directory, where X and Y are the major and
+# minor version numbers of the Python interpreter.
+#
+# Code:
+
+major_minor = '{}.{}'.format(*sys.version_info)
+site_packages_prefix = os.path.join(
+    'lib', 'python' + major_minor, 'site-packages')
+python_site = os.path.join(sys.prefix, site_packages_prefix)
 
 try:
-    all_sites_raw = os.environ['GUIX_PYTHONPATH'].split(':')
+    all_sites_raw = os.environ['GUIX_PYTHONPATH'].split(os.path.pathsep)
 except KeyError:
     all_sites_raw = []
 # Normalize paths, otherwise a trailing slash would cause it to not match.
@@ -35,7 +48,8 @@ matching_sites = [p for p in all_sites_norm
                   if p.endswith(site_packages_prefix)]
 
 # Insert sites matching the current version into sys.path, right before
-# Python's own site.
+# Python's own site.  This way, the user can override the libraries provided
+# by Python itself.
 sys_path_absolute = [os.path.realpath(p) for p in sys.path]
 index = sys_path_absolute.index(python_site)
-sys.path = sys.path[:index] + matching_sites + sys.path[index:]
+sys.path[index:index] = matching_sites
-- 
2.32.0


--=-=-=--




Information forwarded to bug-guix@HIDDEN:
bug#50105; Package guix. Full text available.

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From: Mathieu Othacehe <othacehe@HIDDEN>
To: bug-guix@HIDDEN
Subject: [core-updates] Python sitecustomize issue.
Date: Wed, 18 Aug 2021 11:53:07 +0200
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Acknowledgement sent to Mathieu Othacehe <othacehe@HIDDEN>:
New bug report received and forwarded. Copy sent to bug-guix@HIDDEN. Full text available.
Report forwarded to bug-guix@HIDDEN:
bug#50105; Package guix. Full text available.
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Copyright (C) 1999 Darren O. Benham, 1997 nCipher Corporation Ltd, 1994-97 Ian Jackson.