GNU bug report logs - #58012
[PATCH 0/7] Update python-networkx.

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

From: Greg Hogan <code <at> greghogan.com>
To: guix-patches <at> gnu.org
Cc: Greg Hogan <code <at> greghogan.com>
Subject: [PATCH 0/7] Update python-networkx.
Date: Thu, 22 Sep 2022 19:39:27 +0000

A version update to python-networkx and build fixes for several
packages.

The only dependent failing to build is python-hyperopt, which has
likewise been failing to build upstream:
  https://ci.guix.gnu.org/search?query=python-hyperopt

Greg Hogan (7):
  gnu: python-networkx: Update to 2.8.6.
  gnu: python-aws-sam-translator: Update to 1.51.0.
  gnu: Add python-jschema-to-python.
  gnu: Add python-sarif-om.
  gnu: python-cfn-lint: Update to 0.65.0.
  gnu: python-setools: Update to 4.4.0.
  gnu: python-louvain: Fix test.

 gnu/local.mk                                  |  1 +
 gnu/packages/graph.scm                        |  1 +
 .../patches/python-louvain-fix-test.patch     | 15 +++++
 gnu/packages/python-web.scm                   | 55 +++++++++++++++++--
 gnu/packages/python-xyz.scm                   |  4 +-
 gnu/packages/selinux.scm                      | 13 +++--
 6 files changed, 77 insertions(+), 12 deletions(-)
 create mode 100644 gnu/packages/patches/python-louvain-fix-test.patch

-- 
2.37.3

Message #8 received at 58012 <at> debbugs.gnu.org (full text, mbox):

From: Greg Hogan <code <at> greghogan.com>
To: 58012 <at> debbugs.gnu.org
Cc: Greg Hogan <code <at> greghogan.com>
Subject: [core-updates PATCH 2/7] gnu: python-aws-sam-translator: Update to
 1.51.0.
Date: Thu, 22 Sep 2022 19:44:05 +0000

* gnu/packages/python-web.scm (python-aws-sam-translator): Update to 1.51.0.
---
 gnu/packages/python-web.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/python-web.scm b/gnu/packages/python-web.scm
index 94544e1e74..be780e5d3c 100644
--- a/gnu/packages/python-web.scm
+++ b/gnu/packages/python-web.scm
@@ -563,13 +563,13 @@ (define-public python-css-html-js-minify
 (define-public python-aws-sam-translator
   (package
     (name "python-aws-sam-translator")
-    (version "1.40.0")
+    (version "1.51.0")
     (source (origin
               (method url-fetch)
               (uri (pypi-uri "aws-sam-translator" version))
               (sha256
                (base32
-                "1hq5ggbzcq4k3ks439hki493w4sasgaxns6j5x57xsj822acalmf"))))
+                "1ywzchc3nk13xh593j7b14qp3y0fdx7cfbdhnm34p39av66xffac"))))
     (build-system python-build-system)
     (arguments
      `(;; XXX: Tests are not distributed with the PyPI archive, and would
-- 
2.37.3

Message #11 received at 58012 <at> debbugs.gnu.org (full text, mbox):

From: Greg Hogan <code <at> greghogan.com>
To: 58012 <at> debbugs.gnu.org
Cc: Greg Hogan <code <at> greghogan.com>
Subject: [core-updates PATCH 1/7] gnu: python-networkx: Update to 2.8.6.
Date: Thu, 22 Sep 2022 19:44:04 +0000

* gnu/packages/python-xyz.scm (python-networkx): Update to 2.8.6.
---
 gnu/packages/python-xyz.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index 92e0c9dbe8..bcf28d54ce 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -9497,13 +9497,13 @@ (define-public python-netifaces
 (define-public python-networkx
   (package
     (name "python-networkx")
-    (version "2.6.2")
+    (version "2.8.6")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "networkx" version))
        (sha256
-        (base32 "1fqrq7gc0nn4rd4zqibw96cap75vb5nlixapkajwawp71jaz21i3"))))
+        (base32 "19h18f5j79l7kmwm5cvm75fadjgmkzw5m3pyvb9cnq0860q7faxx"))))
     (build-system python-build-system)
     (arguments
      '(#:phases (modify-phases %standard-phases
-- 
2.37.3

Message #14 received at 58012 <at> debbugs.gnu.org (full text, mbox):

From: Greg Hogan <code <at> greghogan.com>
To: 58012 <at> debbugs.gnu.org
Cc: Greg Hogan <code <at> greghogan.com>
Subject: [core-updates PATCH 3/7] gnu: Add python-jschema-to-python.
Date: Thu, 22 Sep 2022 19:44:06 +0000

* gnu/packages/python-web.scm (python-jschema-to-python): New variable.
---
 gnu/packages/python-web.scm | 19 +++++++++++++++++++
 1 file changed, 19 insertions(+)

diff --git a/gnu/packages/python-web.scm b/gnu/packages/python-web.scm
index be780e5d3c..6a7c4be531 100644
--- a/gnu/packages/python-web.scm
+++ b/gnu/packages/python-web.scm
@@ -757,6 +757,25 @@ (define-public python-cfn-lint
 for resource properties and best practices.")
     (license license:expat)))
 
+(define-public python-jschema-to-python
+  (package
+    (name "python-jschema-to-python")
+    (version "1.2.3")
+    (source (origin
+              (method url-fetch)
+              (uri (pypi-uri "jschema_to_python" version))
+              (sha256
+               (base32
+                "14cvaiwm56g0v6p7zviikaa5i9ln3yqy910jmp60hirhbpz19zvn"))))
+    (build-system python-build-system)
+    (propagated-inputs (list python-attrs python-jsonpickle python-pbr))
+    (native-inputs (list python-pytest))
+    (home-page "https://github.com/microsoft/jschema-to-python")
+    (synopsis "Generate Python classes from a JSON schema.")
+    (description "This package generates source code for Python classes from a
+@url{http://jschema.org,JSchema} JSON schema.")
+    (license license:expat)))
+
 (define-public python-falcon
   (package
     (name "python-falcon")
-- 
2.37.3

Message #17 received at 58012 <at> debbugs.gnu.org (full text, mbox):

From: Greg Hogan <code <at> greghogan.com>
To: 58012 <at> debbugs.gnu.org
Cc: Greg Hogan <code <at> greghogan.com>
Subject: [core-updates PATCH 4/7] gnu: Add python-sarif-om.
Date: Thu, 22 Sep 2022 19:44:07 +0000

* gnu/packages/python-web.scm (python-sarif-om): New variable.
---
 gnu/packages/python-web.scm | 20 ++++++++++++++++++++
 1 file changed, 20 insertions(+)

diff --git a/gnu/packages/python-web.scm b/gnu/packages/python-web.scm
index 6a7c4be531..9d1fed7edd 100644
--- a/gnu/packages/python-web.scm
+++ b/gnu/packages/python-web.scm
@@ -776,6 +776,26 @@ (define-public python-jschema-to-python
 @url{http://jschema.org,JSchema} JSON schema.")
     (license license:expat)))
 
+(define-public python-sarif-om
+  (package
+    (name "python-sarif-om")
+    (version "1.0.4")
+    (source (origin
+              (method url-fetch)
+              (uri (pypi-uri "sarif_om" version))
+              (sha256
+               (base32
+                "167gb8xjm0310km3w1s12bqldbv7zyklkr4j5900vq4361ml2pyd"))))
+    (build-system python-build-system)
+    (propagated-inputs (list python-attrs))
+    (native-inputs (list python-pbr))
+    (home-page "https://github.com/microsoft/sarif-python-om")
+    (synopsis "Python implementation of the SARIF 2.1.0 object model.")
+    (description "This module contains classes for the object model defined
+by the @url{https://sarifweb.azurewebsites.net,Static Analysis Results
+Interchange Format (SARIF)} file format.")
+    (license license:expat)))
+
 (define-public python-falcon
   (package
     (name "python-falcon")
-- 
2.37.3

Message #20 received at 58012 <at> debbugs.gnu.org (full text, mbox):

From: Greg Hogan <code <at> greghogan.com>
To: 58012 <at> debbugs.gnu.org
Cc: Greg Hogan <code <at> greghogan.com>
Subject: [core-updates PATCH 5/7] gnu: python-cfn-lint: Update to 0.65.0.
Date: Thu, 22 Sep 2022 19:44:08 +0000

* gnu/packages/python-web.scm (python-cfn-lint): Update to 0.65.0.
[arguments]<#:phases>: Add 'skip-network-test.
[propagated-inputs]: Add python-importlib-resources,
python-jschema-to-python, python-sarif-om.
---
 gnu/packages/python-web.scm | 12 ++++++++++--
 1 file changed, 10 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/python-web.scm b/gnu/packages/python-web.scm
index 9d1fed7edd..2aa487d5c3 100644
--- a/gnu/packages/python-web.scm
+++ b/gnu/packages/python-web.scm
@@ -710,7 +710,7 @@ (define-public python-cbor2
 (define-public python-cfn-lint
   (package
     (name "python-cfn-lint")
-    (version "0.54.3")
+    (version "0.65.0")
     (home-page "https://github.com/aws-cloudformation/cfn-lint")
     (source (origin
               (method git-fetch)
@@ -720,11 +720,16 @@ (define-public python-cfn-lint
               (file-name (git-file-name name version))
               (sha256
                (base32
-                "106qf19n2k6sdjkb4006aidibd24qqiw901c1613xgjpnyw4dyl6"))))
+                "1rfacp39jssrbchrzb49vwrqyzhx5v7jfcgngqnb9r7qfs4bwi3w"))))
     (build-system python-build-system)
     (arguments
      `(#:phases
        (modify-phases %standard-phases
+         (add-after 'unpack 'skip-network-test
+           (lambda _
+             ;; This test requires networking.
+             (substitute* "test/unit/module/formatters/test_formatters.py"
+               (("def test_sarif_formatter") "def _test_sarif_formatter"))))
          (replace 'check
            (lambda* (#:key inputs outputs tests? #:allow-other-keys)
              (when tests?
@@ -744,11 +749,14 @@ (define-public python-cfn-lint
      (list python-pydot python-mock))
     (propagated-inputs
      (list python-aws-sam-translator
+           python-importlib-resources
+           python-jschema-to-python
            python-jsonpatch
            python-jsonschema
            python-junit-xml
            python-networkx
            python-pyyaml
+           python-sarif-om
            python-six))
     (synopsis "Validate CloudFormation templates")
     (description
-- 
2.37.3

Message #23 received at 58012 <at> debbugs.gnu.org (full text, mbox):

From: Greg Hogan <code <at> greghogan.com>
To: 58012 <at> debbugs.gnu.org
Cc: Greg Hogan <code <at> greghogan.com>
Subject: [core-updates PATCH 6/7] gnu: python-setools: Update to 4.4.0.
Date: Thu, 22 Sep 2022 19:44:09 +0000

* gnu/packages/selinux.scm (python-setools): Update to 4.4.0.
[source, home-page]: Update url.
[inputs]: Add python-pyqt.
[native-inputs]: Add python-cython.
---
 gnu/packages/selinux.scm | 13 +++++++------
 1 file changed, 7 insertions(+), 6 deletions(-)

diff --git a/gnu/packages/selinux.scm b/gnu/packages/selinux.scm
index b4f074b695..d898b55129 100644
--- a/gnu/packages/selinux.scm
+++ b/gnu/packages/selinux.scm
@@ -42,6 +42,7 @@ (define-module (gnu packages selinux)
   #:use-module (gnu packages pkg-config)
   #:use-module (gnu packages python)
   #:use-module (gnu packages python-xyz)
+  #:use-module (gnu packages qt)
   #:use-module (gnu packages swig)
   #:use-module (gnu packages xml))
 
@@ -305,16 +306,16 @@ (define-public python-sepolgen
 (define-public python-setools
   (package
     (name "python-setools")
-    (version "4.1.1")
+    (version "4.4.0")
     (source (origin
               (method git-fetch)
               (uri (git-reference
-                    (url "https://github.com/TresysTechnology/setools")
+                    (url "https://github.com/SELinuxProject/setools")
                     (commit version)))
               (file-name (string-append name "-" version "-checkout"))
               (sha256
                (base32
-                "0459xxly6zzqc5azcwk3rbbcxvj60dq08f8z6xr05y7dsbb16cg6"))))
+                "1qvd5j6zwq4fmlahg45swjplhif2z89x7s6pnp07gvcp2fbqdsh5"))))
     (build-system python-build-system)
     (arguments
      `(#:tests? #f ; the test target causes a rebuild
@@ -339,10 +340,10 @@ (define-public python-setools
     (propagated-inputs
      (list python-networkx))
     (inputs
-     (list libsepol libselinux))
+     (list libsepol libselinux python-pyqt))
     (native-inputs
-     (list bison flex swig))
-    (home-page "https://github.com/TresysTechnology/setools")
+     (list bison flex python-cython swig))
+    (home-page "https://github.com/SELinuxProject/setools")
     (synopsis "Tools for SELinux policy analysis")
     (description "SETools is a collection of graphical tools, command-line
 tools, and libraries designed to facilitate SELinux policy analysis.")
-- 
2.37.3

Message #26 received at 58012 <at> debbugs.gnu.org (full text, mbox):

From: Greg Hogan <code <at> greghogan.com>
To: 58012 <at> debbugs.gnu.org
Cc: Greg Hogan <code <at> greghogan.com>
Subject: [core-updates PATCH 7/7] gnu: python-louvain: Fix test.
Date: Thu, 22 Sep 2022 19:44:10 +0000

* gnu/packages/graph.scm (python-louvain)[source]: Add patch.
* gnu/packages/patches/python-louvain-fix-test.patch: New file.
* gnu/local.mk (dist_patch_DATA): Register patch.
---
 gnu/local.mk                                      |  1 +
 gnu/packages/graph.scm                            |  1 +
 .../patches/python-louvain-fix-test.patch         | 15 +++++++++++++++
 3 files changed, 17 insertions(+)
 create mode 100644 gnu/packages/patches/python-louvain-fix-test.patch

diff --git a/gnu/local.mk b/gnu/local.mk
index ef1bae5f3c..11213b2197 100644
--- a/gnu/local.mk
+++ b/gnu/local.mk
@@ -1614,6 +1614,7 @@ dist_patch_DATA =						\
   %D%/packages/patches/ppsspp-disable-upgrade-and-gold.patch		\
   %D%/packages/patches/pthreadpool-system-libraries.patch	\
   %D%/packages/patches/python-chai-drop-python2.patch		\
+  %D%/packages/patches/python-louvain-fix-test.patch		\
   %D%/packages/patches/python-random2-getrandbits-test.patch		\
   %D%/packages/patches/python-poppler-qt5-fix-build.patch	\
   %D%/packages/patches/python-w3lib-fix-test-failure.patch	\
diff --git a/gnu/packages/graph.scm b/gnu/packages/graph.scm
index 109ba68675..02c80f0682 100644
--- a/gnu/packages/graph.scm
+++ b/gnu/packages/graph.scm
@@ -290,6 +290,7 @@ (define-public python-louvain
      (origin
        (method url-fetch)
        (uri (pypi-uri "python-louvain" version))
+       (patches (search-patches "python-louvain-fix-test.patch"))
        (sha256
         (base32 "0sx53l555rwq0z7if8agirjgw4ddp8r9b949wwz8vlig03sjvfmp"))))
     (build-system python-build-system)
diff --git a/gnu/packages/patches/python-louvain-fix-test.patch b/gnu/packages/patches/python-louvain-fix-test.patch
new file mode 100644
index 0000000000..2127df681c
--- /dev/null
+++ b/gnu/packages/patches/python-louvain-fix-test.patch
@@ -0,0 +1,15 @@
+https://github.com/taynaud/python-louvain/commit/638804ae636dc65306900ef6518ca0a1c9202566.diff
+
+diff --git a/test_community.py b/test_community.py
+index 1ee1976..566a4b1 100644
+--- a/test_community.py
++++ b/test_community.py
+@@ -203,7 +203,7 @@ def test_karate(self):
+         self.assertAlmostEqual(co.modularity(part, graph),
+                                co.modularity(part_weight,
+                                              graph,
+-                                             "test_weight"), places=2)
++                                             "test_weight"), places=1)
+ 
+         part_res_low = co.best_partition(graph, resolution=0.1)
+         self.assertTrue(
-- 
2.37.3

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

From: Greg Hogan <code <at> greghogan.com>
To: guix-patches <at> gnu.org
Subject: Re: [PATCH 0/7] Update python-networkx.
Date: Thu, 22 Sep 2022 15:53:54 -0400

On Thu, Sep 22, 2022 at 3:39 PM Greg Hogan <code <at> greghogan.com> wrote:
>
> A version update to python-networkx and build fixes for several
> packages.

My apologies, this should be for the master branch. Not sure if this
can be retitled.

Greg

Message #34 received at 58012-done <at> debbugs.gnu.org (full text, mbox):

From: Ludovic Courtès <ludo <at> gnu.org>
To: Greg Hogan <code <at> greghogan.com>
Cc: 58012-done <at> debbugs.gnu.org
Subject: Re: bug#58012: [PATCH 0/7] Update python-networkx.
Date: Mon, 03 Oct 2022 00:10:24 +0200

Hi Greg,

Greg Hogan <code <at> greghogan.com> skribis:

>   gnu: python-networkx: Update to 2.8.6.
>   gnu: python-aws-sam-translator: Update to 1.51.0.
>   gnu: Add python-jschema-to-python.
>   gnu: Add python-sarif-om.
>   gnu: python-cfn-lint: Update to 0.65.0.
>   gnu: python-setools: Update to 4.4.0.
>   gnu: python-louvain: Fix test.

Applied on ‘master’, thanks!

Ludo’.

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