GNU bug report logs - #36623
[PATCH] gnu: gdal: add python support

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From: iyzsong <at> member.fsf.org (宋文武)
To: Arne Babenhauserheide <arne_bab <at> web.de>
Cc: Ludovic Courtès <ludo <at> gnu.org>, Julien Lepiller <julien <at> lepiller.eu>, 36623 <at> debbugs.gnu.org
Subject: [bug#36623] [PATCH] gnu: gdal: add python support
Date: Sat, 20 Jul 2019 22:55:40 +0800

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

Arne Babenhauserheide <arne_bab <at> web.de> writes:

> Hello Ludo`,
>
> Ludovic Courtès <ludo <at> gnu.org> writes:
>
>>> validating RUNPATH of 6 binaries in "/gnu/store/q9sb0wv41ig429f1m1xspg22xm8pwpwh-gdal-2.2.4/lib"...
>>> /gnu/store/q9sb0wv41ig429f1m1xspg22xm8pwpwh-gdal-2.2.4/lib/python3.7/site-packages/osgeo/_gdal.cpython-37m-x86_64-linux-gnu.so:
>>> error: depends on 'libgdal.so.20', which cannot be found in RUNPATH
>>> ("/gnu/store/b7fqhszxl02g6pfm3vw6b3cjz472qrly-python-3.7.0/lib"
>>> "/gnu/store/h90vnqw0nwd0hhm1l5dgxsdrigddfmq4-glibc-2.28/lib"
>>> "/gnu/store/4sqps8dczv3g7rwbdibfz6rf5jlk7w90-gcc-5.5.0-lib/lib"
>>> "/gnu/store/4sqps8dczv3g7rwbdibfz6rf5jlk7w90-gcc-5.5.0-lib/lib/gcc/x86_64-unknown-linux-gnu/5.5.0/../../..")
>>
>> I’m not familiar with Cython so I don’t know how this was handled
>> before.  However, to me, it indicates that the resulting binaries are
>> unlikely to work.
>>
>> Namely, Python would dlopen “_gdal.cython*.so”, and that would fail to
>> find ‘libgdal.so’.

>>
>> Thoughts?
>
> Yes: It does work. But I don’t know why.

This is because the _gdal.cython*.so don't have rpath to the "lib"
directory, where libgdal.so will going.

>
> Cython runs at compile-time to generate c-code that acts as interface
> for Python. Given the paths in here, this needs gdal already installed
> in the runpath where it seems to be missing during validation.
>
> How can we fix that?

I think cython (which compile .py files to .c files) is not here..  It
has python C libraries generated by swig.
>
> Best wishes,
> Arne

In the end the python bindings for gdal can be build seperated (which
handle the missing rpath to libgdal nicely), and I prefer this way:

[0001-gnu-Add-python-gdal.patch (text/x-patch, inline)]

From 09254f646b948a5603b2b3dcb99a7f2f6ad0c8de Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?=E5=AE=8B=E6=96=87=E6=AD=A6?= <iyzsong <at> member.fsf.org>
Date: Sat, 20 Jul 2019 22:39:33 +0800
Subject: [PATCH] gnu: Add python-gdal.

For <https://issues.guix.gnu.org/issue/36623>, thank to Arne Babenhauserheide
for the original patch.

* gnu/packages/geo.scm (python-gdal): New package.
---
 gnu/packages/geo.scm | 19 +++++++++++++++++++
 1 file changed, 19 insertions(+)

diff --git a/gnu/packages/geo.scm b/gnu/packages/geo.scm
index e4b6a262c7..8005c46129 100644
--- a/gnu/packages/geo.scm
+++ b/gnu/packages/geo.scm
@@ -604,6 +604,25 @@ utilities for data translation and processing.")
                ;; frmts/mrf/libLERC
                license:asl2.0))))
 
+(define-public python-gdal
+  (package (inherit gdal)
+    (name "python-gdal")
+    (build-system python-build-system)
+    (arguments
+     '(#:tests? #f                      ; no tests
+       #:phases
+       (modify-phases %standard-phases
+         (add-before 'build 'chdir
+           (lambda _
+             (chdir "swig/python")
+             #t)))))
+    (native-inputs '())
+    (propagated-inputs
+     `(("python-numpy" ,python-numpy)))
+    (inputs
+     `(("gdal" ,gdal)))
+    (synopsis "GDAL (Geospatial Data Abstraction Library) python bindings")))
+
 (define-public postgis
   (package
     (name "postgis")
-- 
2.19.2

[Message part 3 (text/plain, inline)]

I test it with "~/src/guix/pre-inst-env guix environment --ad-hoc python
python-gdal", and in it I can run "python3 swig/python/samples/rel.py"
etc.

Does it work for you, Arne?  If so, I'll push my patch, thank you!

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