[bug#73173] [PATCH] gnu: Update python-rdflib to 7.0.0.

[bug#73173] [PATCH] gnu: Update python-rdflib to 7.0.0.

[Roel Janssen]

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Dear Guix,

I'd like to update python-rdflib to 7.0.0. When building the reverse-
dependent packages, I found that python-prov and cwltool don't support
version 7.  So the attached patch keeps 6.1.1 around but upgrades all
the others. I built the following packages successful after the
upgrade:
- carla
- ardour
- zeitgeist
- python-schema-salad
- python-sparqlwrapper
- python-cfgraph
- python-pyrdfa3
- python-sparqlkernel

The following package failed to build, but I believe it's unrelated to
the upgrade:
- python-pytorch-geometric

Keeping python-prov and cwltool at python-rdflib-6 doesn't affect the
successful builds of these packages.  So I believe the impact is
minimal.

Let me know if/what I can do to improve the patch.
Thank you for your time in advance.

Kind regards,
Roel Janssen

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[-- Type: text/x-patch, Size: 4099 bytes --]

From 5c1857e08a25c9ca00d3c3acf7fade67e523fbe3 Mon Sep 17 00:00:00 2001
Message-ID: <5c1857e08a25c9ca00d3c3acf7fade67e523fbe3.1725996315.git.roel@gnu.org>
From: Roel Janssen <roel@gnu.org>
Date: Tue, 10 Sep 2024 21:19:50 +0200
Subject: [PATCH] gnu: Update python-rdflib to 7.0.0.

* gnu/packages/rdf.scm: Add updated recipe for python-rdflib; Keep
  python-rdflib-6 for compatibility.
* gnu/packages/python-xyz.scm: Build python-prov with python-rdflib-6 because
  rdflib-7 is not supported.
* gnu/packages/bioinformatics.scm: Build cwltool with python-rdflib-6 because
  it fails to build with rdflib-7.

Change-Id: Ibc40c16ede20e69e702915488d6b2f0a7e70b868
---
 gnu/packages/bioinformatics.scm |  2 +-
 gnu/packages/python-xyz.scm     |  2 +-
 gnu/packages/rdf.scm            | 43 +++++++++++++++++++++++++++++++++
 3 files changed, 45 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 4653360792..db8befd144 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -5786,7 +5786,7 @@ (define-public cwltool
            python-prov
            python-pydot
            python-psutil
-           python-rdflib
+           python-rdflib-6
            python-requests
            python-ruamel.yaml
            python-schema-salad
diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index 21e04e75e9..2fbdd32cf3 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -24995,7 +24995,7 @@ (define-public python-prov
                 (("\\.serialize\\(format=\"nt\"\\)")
                  ".serialize(format=\"nt\", encoding=\"utf-8\")")))))))
     (propagated-inputs
-     (list python-dateutil python-lxml python-networkx python-rdflib))
+     (list python-dateutil python-lxml python-networkx python-rdflib-6))
     (native-inputs
      (list graphviz python-pydot))
     (home-page "https://github.com/trungdong/prov")
diff --git a/gnu/packages/rdf.scm b/gnu/packages/rdf.scm
index f10b530861..9a02a71d81 100644
--- a/gnu/packages/rdf.scm
+++ b/gnu/packages/rdf.scm
@@ -328,6 +328,49 @@ (define-public sord
     (license license:isc)))
 
 (define-public python-rdflib
+  (package
+    (name "python-rdflib")
+    (version "7.0.0")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (pypi-uri "rdflib" version))
+        (sha256
+         (base32
+          "1blmx4v003afr3l9qg84ymj0sldcbsr2dzdgq6w5k022d62yp5cr"))))
+    (build-system pyproject-build-system)
+    (arguments
+     '(#:phases
+       (modify-phases %standard-phases
+         (add-after 'unpack 'adjust-tests
+           (lambda _
+             (for-each delete-file
+                       '(;; The tests in this file miss a test fixture.
+                         ;; fixture 'no_cover' not found
+                         "test/test_misc/test_plugins.py"
+                         ;; These tests need internet access.
+                         "test/jsonld/test_onedotone.py"
+                         "test/test_examples.py"
+                         "test/test_extras/test_infixowl/test_basic.py"
+                         "test/test_extras/test_infixowl/test_context.py"
+                         "test/test_sparql/test_service.py"))))
+         (replace 'check
+           (lambda* (#:key tests? #:allow-other-keys)
+             (when tests?
+               (invoke "pytest" "-vv" "test/")))))))
+    (native-inputs
+     (list python-pytest python-poetry-core))
+    (propagated-inputs
+      (list python-html5lib python-isodate python-pyparsing))
+    (home-page "https://github.com/RDFLib/rdflib")
+    (synopsis "Python RDF library")
+    (description
+      "RDFLib is a Python library for working with RDF, a simple yet
+powerful language for representing information.")
+    (license (license:non-copyleft "file://LICENSE"
+                                   "See LICENSE in the distribution."))))
+
+(define-public python-rdflib-6
   (package
     (name "python-rdflib")
     (version "6.1.1")

base-commit: b82c8ceae14d5d0f4584452f34f5103ffd0e0f8d
-- 
2.46.0

[bug#73173] [PATCH] gnu: Update python-rdflib to 7.0.0.

[Ludovic Courtès]

Hi Roel,

Roel Janssen <roel@gnu.org> skribis:

> Dear Guix,
>
> I'd like to update python-rdflib to 7.0.0. When building the reverse-
> dependent packages, I found that python-prov and cwltool don't support
> version 7.  So the attached patch keeps 6.1.1 around but upgrades all
> the others. I built the following packages successful after the
> upgrade:
> - carla
> - ardour
> - zeitgeist
> - python-schema-salad
> - python-sparqlwrapper
> - python-cfgraph
> - python-pyrdfa3
> - python-sparqlkernel
>
> The following package failed to build, but I believe it's unrelated to
> the upgrade:
> - python-pytorch-geometric

Indeed.  According to <https://qa.guix.gnu.org/issue/73173>, it’s all
good (it lacks armhf-linux build results, but that’s okay).

So feel free to push, thanks!

Ludo’.

[bug#73173] [PATCH] gnu: Update python-rdflib to 7.0.0.

[Roel Janssen]

Dear Ludo’,

On Wed, 2024-09-25 at 18:05 +0200, Ludovic Courtès wrote:
> Hi Roel,
> 
> Roel Janssen <roel@gnu.org> skribis:
> 
> > Dear Guix,
> > 
> > I'd like to update python-rdflib to 7.0.0. When building the
> > reverse-
> > dependent packages, I found that python-prov and cwltool don't
> > support
> > version 7.  So the attached patch keeps 6.1.1 around but upgrades
> > all
> > the others. I built the following packages successful after the
> > upgrade:
> > - carla
> > - ardour
> > - zeitgeist
> > - python-schema-salad
> > - python-sparqlwrapper
> > - python-cfgraph
> > - python-pyrdfa3
> > - python-sparqlkernel
> > 
> > The following package failed to build, but I believe it's unrelated
> > to
> > the upgrade:
> > - python-pytorch-geometric
> 
> Indeed.  According to <https://qa.guix.gnu.org/issue/73173>, it’s all
> good (it lacks armhf-linux build results, but that’s okay).
> 
> So feel free to push, thanks!
> 

Thank you for your time and efforts!

Upon invoking 'git push', I'm receiving this error message:
  All 109 channel news entries are valid.
  guix git: error: unknown introductory commit and signer
  error: failed to push some refs to  
'ssh://git.savannah.gnu.org/srv/git/guix.git'

My GPG key is still the same, although I updated the expiration date
(and updated the key on Savannah). It looks like the key information in
.guix-authorizations for me is still correct.

Since it's been a while, where should I start reading the documentation
on understanding/overcoming this problem?

Kind regards,
Roel Janssen

[bug#73173] [PATCH] gnu: Update python-rdflib to 7.0.0.

[Ludovic Courtès]

Hi,

Roel Janssen <roel@gnu.org> skribis:

> Upon invoking 'git push', I'm receiving this error message:
>   All 109 channel news entries are valid.
>   guix git: error: unknown introductory commit and signer
>   error: failed to push some refs to  
> 'ssh://git.savannah.gnu.org/srv/git/guix.git'
>
> My GPG key is still the same, although I updated the expiration date
> (and updated the key on Savannah). It looks like the key information in
> .guix-authorizations for me is still correct.
>
> Since it's been a while, where should I start reading the documentation
> on understanding/overcoming this problem?

Oh.  The message comes from ‘guix git authenticate’, and it’s admittedly
unclear.

To fix it, you must first manually run:

  guix git authenticate 9edb3f66fd807b096b48283debdcddccfea34bad \
    "BBB0 2DDF 2CEA F6A8 0D1D  E643 A2A0 6DF2 A33A 54FA"

This will record the introductory commit and signer (the two hex strings
above) in ‘.git/config’, and from there you should be all set.

This is only briefly mentioned in
<https://guix.gnu.org/manual/devel/en/html_node/Building-from-Git.html>.

HTH,
Ludo’.

bug#73173: [PATCH] gnu: Update python-rdflib to 7.0.0.

[Roel Janssen]

On Mon, 2024-09-30 at 21:47 +0200, Ludovic Courtès wrote:
> Hi,
> 
> Roel Janssen <roel@gnu.org> skribis:
> 
> > Upon invoking 'git push', I'm receiving this error message:
> >   All 109 channel news entries are valid.
> >   guix git: error: unknown introductory commit and signer
> >   error: failed to push some refs to  
> > 'ssh://git.savannah.gnu.org/srv/git/guix.git'
> > 
> > My GPG key is still the same, although I updated the expiration
> > date
> > (and updated the key on Savannah). It looks like the key
> > information in
> > .guix-authorizations for me is still correct.
> > 
> > Since it's been a while, where should I start reading the
> > documentation
> > on understanding/overcoming this problem?
> 
> Oh.  The message comes from ‘guix git authenticate’, and it’s
> admittedly
> unclear.
> 
> To fix it, you must first manually run:
> 
>   guix git authenticate 9edb3f66fd807b096b48283debdcddccfea34bad \
>     "BBB0 2DDF 2CEA F6A8 0D1D  E643 A2A0 6DF2 A33A 54FA"
> 
> This will record the introductory commit and signer (the two hex
> strings
> above) in ‘.git/config’, and from there you should be all set.
> 
> This is only briefly mentioned in
> <
> https://guix.gnu.org/manual/devel/en/html_node/Building-from-Git.html>
> .
> 
> HTH,
> Ludo’.
> 

Ha! I was thinking about it wrong.  Thank you for your help.  This, and
the CI system, including the checks performed when doing a "git push",
is impressive to see.

I pushed the patch in d057d59170446fe47ddedd7eb281ca2a1dfc05e9

Kind regards,
Roel