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* [bug#52696] [PATCH 00/12] Update Orange.
@ 2021-12-21  4:45 Vinicius Monego
  2021-12-21  4:46 ` [bug#52696] [PATCH 01/12] gnu: python-anyqt: Update to 0.0.13 Vinicius Monego
                   ` (2 more replies)
  0 siblings, 3 replies; 25+ messages in thread
From: Vinicius Monego @ 2021-12-21  4:45 UTC (permalink / raw)
  To: 52696; +Cc: Vinicius Monego

Vinicius Monego (12):
  gnu: python-anyqt: Update to 0.0.13.
  gnu: python-qasync: Update to 0.22.0.
  gnu: Add python-pytest-pydocstyle.
  gnu: python-pytest-pycodestyle: Update to 2.2.0.
  gnu: python-dictdiffer: Update to 0.9.0.
  gnu: python-pynndescent: Update to 0.5.5.
  gnu: python-opentsne: Update to 0.6.1.
  gnu: python-qtconsole: Update to 4.7.7.
  gnu: python-qtconsole: Enable tests.
  gnu: python-orange-canvas-core: Update to 0.1.24.
  gnu: python-orange-widget-base: Update to 4.16.1.
  gnu: orange: Update to 3.31.0.

 gnu/packages/machine-learning.scm | 33 +++++++++-----
 gnu/packages/orange.scm           | 35 +++++++--------
 gnu/packages/python-check.scm     | 29 +++++++++++-
 gnu/packages/python-xyz.scm       | 73 ++++++++++++++++---------------
 4 files changed, 102 insertions(+), 68 deletions(-)


base-commit: 86d6c6053c7d1c7a82c83f0daf0f5e09b1ecfb63
-- 
2.30.2





^ permalink raw reply	[flat|nested] 25+ messages in thread

* [bug#52696] [PATCH 01/12] gnu: python-anyqt: Update to 0.0.13.
  2021-12-21  4:45 [bug#52696] [PATCH 00/12] Update Orange Vinicius Monego
@ 2021-12-21  4:46 ` Vinicius Monego
  2021-12-21  4:46   ` [bug#52696] [PATCH 02/12] gnu: python-qasync: Update to 0.22.0 Vinicius Monego
                     ` (10 more replies)
  2022-01-14 20:09 ` [bug#52696] [PATCH v2 01/11] gnu: python-anyqt: Update to 0.0.13 Vinicius Monego
  2022-01-14 20:33 ` bug#52696: [PATCH 00/12] Update Orange Nicolas Goaziou
  2 siblings, 11 replies; 25+ messages in thread
From: Vinicius Monego @ 2021-12-21  4:46 UTC (permalink / raw)
  To: 52696; +Cc: Vinicius Monego

* gnu/packages/python-xyz.scm (python-anyqt): Update to 0.0.13.
[arguments]<#:phases>: Don't return #t.
---
 gnu/packages/python-xyz.scm | 7 +++----
 1 file changed, 3 insertions(+), 4 deletions(-)

diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index 5e26fe724f..ebf2956c5c 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -14058,13 +14058,13 @@ ISO 8859, etc.).")
 (define-public python-anyqt
   (package
     (name "python-anyqt")
-    (version "0.0.11")
+    (version "0.0.13")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "AnyQt" version))
        (sha256
-        (base32 "0gl2czirzjvhbq963i2awxp8kwbc1grh67lpcwfipyn9w3kdwdj4"))))
+        (base32 "0z7myf0mp1qx4gza6ncqyq9whk67vblmh9n3klk19dv4aakjml2f"))))
     (build-system python-build-system)
     (arguments
      `(#:tests? #f ;there are no tests
@@ -14074,8 +14074,7 @@ ISO 8859, etc.).")
            ;; Delete files related to other operating systems.
            (lambda _
              (delete-file "AnyQt/QtMacExtras.py")
-             (delete-file "AnyQt/QtWinExtras.py")
-             #t)))))
+             (delete-file "AnyQt/QtWinExtras.py"))))))
     (home-page "https://github.com/ales-erjavec/anyqt")
     (synopsis "PyQt4/PyQt5 compatibility layer")
     (description "AnyQt is a PyQt4/PyQt5 compatibility layer.")
-- 
2.30.2





^ permalink raw reply	[flat|nested] 25+ messages in thread

* [bug#52696] [PATCH 02/12] gnu: python-qasync: Update to 0.22.0.
  2021-12-21  4:46 ` [bug#52696] [PATCH 01/12] gnu: python-anyqt: Update to 0.0.13 Vinicius Monego
@ 2021-12-21  4:46   ` Vinicius Monego
  2021-12-21  4:46   ` [bug#52696] [PATCH 03/12] gnu: Add python-pytest-pydocstyle Vinicius Monego
                     ` (9 subsequent siblings)
  10 siblings, 0 replies; 25+ messages in thread
From: Vinicius Monego @ 2021-12-21  4:46 UTC (permalink / raw)
  To: 52696; +Cc: Vinicius Monego

* gnu/packages/python-xyz.scm (python-qasync): Update to 0.22.0.
[arguments]<#:phases>: Don't return #t.
---
 gnu/packages/python-xyz.scm | 7 +++----
 1 file changed, 3 insertions(+), 4 deletions(-)

diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index ebf2956c5c..fb29708c02 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -14135,7 +14135,7 @@ applications.")
 (define-public python-qasync
   (package
     (name "python-qasync")
-    (version "0.15.0")
+    (version "0.22.0")
     (source
      (origin
        ;; There are no tests in the PyPI tarball.
@@ -14145,7 +14145,7 @@ applications.")
              (commit (string-append "v" version))))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "0va9h6v102d7mxz608banjc0l0v02dq3ywhr5i4nqaxx3qkazc2l"))))
+        (base32 "1q9cllrwf94whr0f6mipa0hdq1rcyqvklwx19g35g2dav8f3xkjl"))))
     (build-system python-build-system)
     (arguments
      `(#:test-target "pytest"
@@ -14153,8 +14153,7 @@ applications.")
        (modify-phases %standard-phases
          (add-before 'check 'set-qpa
            (lambda _
-             (setenv "QT_QPA_PLATFORM" "offscreen")
-             #t)))))
+             (setenv "QT_QPA_PLATFORM" "offscreen"))))))
     (native-inputs
      (list python-pytest python-pytest-runner))
     (propagated-inputs
-- 
2.30.2





^ permalink raw reply	[flat|nested] 25+ messages in thread

* [bug#52696] [PATCH 03/12] gnu: Add python-pytest-pydocstyle.
  2021-12-21  4:46 ` [bug#52696] [PATCH 01/12] gnu: python-anyqt: Update to 0.0.13 Vinicius Monego
  2021-12-21  4:46   ` [bug#52696] [PATCH 02/12] gnu: python-qasync: Update to 0.22.0 Vinicius Monego
@ 2021-12-21  4:46   ` Vinicius Monego
  2021-12-21  4:46   ` [bug#52696] [PATCH 04/12] gnu: python-pytest-pycodestyle: Update to 2.2.0 Vinicius Monego
                     ` (8 subsequent siblings)
  10 siblings, 0 replies; 25+ messages in thread
From: Vinicius Monego @ 2021-12-21  4:46 UTC (permalink / raw)
  To: 52696; +Cc: Vinicius Monego

* gnu/packages/python-check.scm (python-pytest-pydocstyle): New variable.
---
 gnu/packages/python-check.scm | 25 +++++++++++++++++++++++++
 1 file changed, 25 insertions(+)

diff --git a/gnu/packages/python-check.scm b/gnu/packages/python-check.scm
index e94e2d0011..74e8537aea 100644
--- a/gnu/packages/python-check.scm
+++ b/gnu/packages/python-check.scm
@@ -677,6 +677,31 @@ framework and makes it easy to undo any monkey patching.  The fixtures are:
 in Pytest.")
     (license license:bsd-3)))
 
+(define-public python-pytest-pydocstyle
+  (package
+    (name "python-pytest-pydocstyle")
+    (version "2.2.0")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/henry0312/pytest-pydocstyle")
+             (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "0w6fivz4nb4b70wzmi5sk17qs9pd05rnh03fmch6v00r3dmfpk39"))))
+    (build-system python-build-system)
+    (arguments
+     `(#:tests? #f)) ; test requires the package itself
+    (propagated-inputs
+     `(("python-pydocstyle" ,python-pydocstyle)
+       ("python-pytest" ,python-pytest))) ; apparently required
+    (home-page "https://github.com/henry0312/pytest-pydocstyle")
+    (synopsis "Pytest plugin to run @command{pydocstyle}")
+    (description "This package provides a Pytest plugin to run
+@command{pydocstyle}.")
+    (license license:expat)))
+
 (define-public python-covdefaults
   (package
     (name "python-covdefaults")
-- 
2.30.2





^ permalink raw reply	[flat|nested] 25+ messages in thread

* [bug#52696] [PATCH 04/12] gnu: python-pytest-pycodestyle: Update to 2.2.0.
  2021-12-21  4:46 ` [bug#52696] [PATCH 01/12] gnu: python-anyqt: Update to 0.0.13 Vinicius Monego
  2021-12-21  4:46   ` [bug#52696] [PATCH 02/12] gnu: python-qasync: Update to 0.22.0 Vinicius Monego
  2021-12-21  4:46   ` [bug#52696] [PATCH 03/12] gnu: Add python-pytest-pydocstyle Vinicius Monego
@ 2021-12-21  4:46   ` Vinicius Monego
  2021-12-21  4:46   ` [bug#52696] [PATCH 05/12] gnu: python-dictdiffer: Update to 0.9.0 Vinicius Monego
                     ` (7 subsequent siblings)
  10 siblings, 0 replies; 25+ messages in thread
From: Vinicius Monego @ 2021-12-21  4:46 UTC (permalink / raw)
  To: 52696; +Cc: Vinicius Monego

* gnu/packages/python-check.scm (python-pytest-pycodestyle): Update to 2.2.0.
---
 gnu/packages/python-check.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/python-check.scm b/gnu/packages/python-check.scm
index 74e8537aea..4638c55746 100644
--- a/gnu/packages/python-check.scm
+++ b/gnu/packages/python-check.scm
@@ -1009,14 +1009,14 @@ framework.")
 (define-public python-pytest-pycodestyle
   (package
     (name "python-pytest-pycodestyle")
-    (version "2.0.0")               ;later versions require python-pytest~=5.4
+    (version "2.2.0")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "pytest-pycodestyle" version))
        (sha256
         (base32
-         "02i5gl7pm9cwxk15sn29inz3n8flpj1r3p1l110h43f2na5w8h7z"))))
+         "1clyjypn93hwvz17f4i6n2688835d4y8qsq2aw17d6fkbqiy8mg7"))))
     (build-system python-build-system)
     (propagated-inputs
      (list python-pycodestyle))
-- 
2.30.2





^ permalink raw reply	[flat|nested] 25+ messages in thread

* [bug#52696] [PATCH 05/12] gnu: python-dictdiffer: Update to 0.9.0.
  2021-12-21  4:46 ` [bug#52696] [PATCH 01/12] gnu: python-anyqt: Update to 0.0.13 Vinicius Monego
                     ` (2 preceding siblings ...)
  2021-12-21  4:46   ` [bug#52696] [PATCH 04/12] gnu: python-pytest-pycodestyle: Update to 2.2.0 Vinicius Monego
@ 2021-12-21  4:46   ` Vinicius Monego
  2021-12-21  4:46   ` [bug#52696] [PATCH 06/12] gnu: python-pynndescent: Update to 0.5.5 Vinicius Monego
                     ` (6 subsequent siblings)
  10 siblings, 0 replies; 25+ messages in thread
From: Vinicius Monego @ 2021-12-21  4:46 UTC (permalink / raw)
  To: 52696; +Cc: Vinicius Monego

* gnu/packages/python-xyz.scm (python-dictdiffer): Update to 0.9.0.
[source]: Make some cosmetic changes.
[arguments]: Override 'check phase.
[native-inputs]: Remove python-check-manifest, python-coverage, python-isort,
python-pytest-cache, python-pytest-pep8, python-tox. Add python-pytest-isort,
python-pytest-pycodestyle, python-pytest-pydocstyle.
---
 gnu/packages/python-xyz.scm | 35 ++++++++++++++++++++---------------
 1 file changed, 20 insertions(+), 15 deletions(-)

diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index fb29708c02..18ca99cd8b 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -25094,27 +25094,32 @@ cryptographically signed ones).")
 (define-public python-dictdiffer
   (package
     (name "python-dictdiffer")
-    (version "0.8.1")
-    (source (origin
-              (method url-fetch)
-              (uri (pypi-uri "dictdiffer" version))
-              (sha256
-               (base32
-                "1lk3qmy1hkaphk4n7ayfk0wl6m2yvd6r7qkam6yncqfzgkbc1phs"))))
+    (version "0.9.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (pypi-uri "dictdiffer" version))
+       (sha256
+        (base32 "0y3mk74qm2q9hsm37892i1wzn8bbdrvbs4nmnvqwq4z6pxgwzfhp"))))
     (build-system python-build-system)
+    (arguments
+     `(#:phases
+       (modify-phases %standard-phases
+         (replace 'check
+           (lambda* (#:key inputs outputs tests? #:allow-other-keys)
+             (when tests?
+               (add-installed-pythonpath inputs outputs)
+               (invoke "python" "-m" "pytest")))))))
     (native-inputs
-     (list python-check-manifest
-           python-coverage
-           python-isort
-           python-mock
+     (list python-mock
            python-pydocstyle
-           python-pytest-cache
            python-pytest-cov
-           python-pytest-pep8
+           python-pytest-isort
+           python-pytest-pycodestyle
+           python-pytest-pydocstyle
            python-pytest-runner
            python-pytest
-           python-setuptools-scm
-           python-tox))
+           python-setuptools-scm))
     (home-page "https://github.com/inveniosoftware/dictdiffer")
     (synopsis "Diff and patch Python dictionary objects")
     (description
-- 
2.30.2





^ permalink raw reply	[flat|nested] 25+ messages in thread

* [bug#52696] [PATCH 06/12] gnu: python-pynndescent: Update to 0.5.5.
  2021-12-21  4:46 ` [bug#52696] [PATCH 01/12] gnu: python-anyqt: Update to 0.0.13 Vinicius Monego
                     ` (3 preceding siblings ...)
  2021-12-21  4:46   ` [bug#52696] [PATCH 05/12] gnu: python-dictdiffer: Update to 0.9.0 Vinicius Monego
@ 2021-12-21  4:46   ` Vinicius Monego
  2021-12-21  4:46   ` [bug#52696] [PATCH 07/12] gnu: python-opentsne: Update to 0.6.1 Vinicius Monego
                     ` (5 subsequent siblings)
  10 siblings, 0 replies; 25+ messages in thread
From: Vinicius Monego @ 2021-12-21  4:46 UTC (permalink / raw)
  To: 52696; +Cc: Vinicius Monego

* gnu/packages/machine-learning.scm (python-pynndescent): Update to 0.5.5.
[arguments]<#:phases>: Override 'check phase.
[native-inputs]: Remove python-nose. Add python-pytest.
---
 gnu/packages/machine-learning.scm | 14 +++++++++++---
 1 file changed, 11 insertions(+), 3 deletions(-)

diff --git a/gnu/packages/machine-learning.scm b/gnu/packages/machine-learning.scm
index 1cd2fd1308..26b710e5d7 100644
--- a/gnu/packages/machine-learning.scm
+++ b/gnu/packages/machine-learning.scm
@@ -1057,16 +1057,24 @@ for scientific computing and data science (e.g. BLAS and OpenMP).")
 (define-public python-pynndescent
   (package
     (name "python-pynndescent")
-    (version "0.5.2")
+    (version "0.5.5")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "pynndescent" version))
        (sha256
-        (base32 "0w87c2v0li2rdbx6qfc2lb6y6bxpdy3jwfgzfs1kcr4d1chj5zfr"))))
+        (base32 "10pqqqc3jkpw03cyzy04slxmpgyhqnlgbyk0c1cv7kqr5d0zhzbs"))))
     (build-system python-build-system)
+    (arguments
+     `(#:phases
+       (modify-phases %standard-phases
+         (replace 'check
+           (lambda* (#:key inputs outputs tests? #:allow-other-keys)
+             (when tests?
+               (add-installed-pythonpath inputs outputs)
+               (invoke "python" "-m" "pytest" "--pyargs" "pynndescent")))))))
     (native-inputs
-     (list python-nose))
+     (list python-pytest))
     (propagated-inputs
      (list python-joblib python-llvmlite python-numba python-scikit-learn
            python-scipy))
-- 
2.30.2





^ permalink raw reply	[flat|nested] 25+ messages in thread

* [bug#52696] [PATCH 07/12] gnu: python-opentsne: Update to 0.6.1.
  2021-12-21  4:46 ` [bug#52696] [PATCH 01/12] gnu: python-anyqt: Update to 0.0.13 Vinicius Monego
                     ` (4 preceding siblings ...)
  2021-12-21  4:46   ` [bug#52696] [PATCH 06/12] gnu: python-pynndescent: Update to 0.5.5 Vinicius Monego
@ 2021-12-21  4:46   ` Vinicius Monego
  2021-12-21  4:46   ` [bug#52696] [PATCH 08/12] gnu: python-qtconsole: Update to 4.7.7 Vinicius Monego
                     ` (4 subsequent siblings)
  10 siblings, 0 replies; 25+ messages in thread
From: Vinicius Monego @ 2021-12-21  4:46 UTC (permalink / raw)
  To: 52696; +Cc: Vinicius Monego

* gnu/packages/machine-learning.scm (python-opentsne): Update to 0.6.1.
[source]<file-name>: Use git-file-name.
[arguments]<#:phases>: Don't return #t. Add 'skip-test phase after 'unpack to
skip a failing test.
---
 gnu/packages/machine-learning.scm | 19 ++++++++++---------
 1 file changed, 10 insertions(+), 9 deletions(-)

diff --git a/gnu/packages/machine-learning.scm b/gnu/packages/machine-learning.scm
index 26b710e5d7..ec5adab09c 100644
--- a/gnu/packages/machine-learning.scm
+++ b/gnu/packages/machine-learning.scm
@@ -1088,17 +1088,16 @@ for k-neighbor-graph construction and approximate nearest neighbor search.")
 (define-public python-opentsne
   (package
     (name "python-opentsne")
-    (version "0.5.2")
+    (version "0.6.1")
     (source
      (origin
-       ;; No tests in the PyPI tarball.
-       (method git-fetch)
+       (method git-fetch) ; no tests in PyPI release
        (uri (git-reference
              (url "https://github.com/pavlin-policar/openTSNE")
              (commit (string-append "v" version))))
-       (file-name (string-append name "-" version "-checkout"))
+       (file-name (git-file-name name version))
        (sha256
-        (base32 "1hl42wmafydk4fxdx05l180k3canmqw8h9r20fsqq2aq440b09gh"))))
+        (base32 "124nid27lfq1ipfjd2gkynqcmb4khisjb4r05jv42ckfkk4dbsxs"))))
     (build-system python-build-system)
     (arguments
      `(#:phases
@@ -1106,13 +1105,15 @@ for k-neighbor-graph construction and approximate nearest neighbor search.")
          ;; Benchmarks require the 'macosko2015' data files.
          (add-after 'unpack 'delete-benchmark
            (lambda _
-             (delete-file-recursively "benchmarks")
-             #t))
+             (delete-file-recursively "benchmarks")))
+         (add-after 'unpack 'skip-test
+           (lambda _ ;; TODO: figure out why this test fails.
+             (substitute* "tests/test_correctness.py"
+               (("def test_iris\\(self\\)") "def _test_iris(self)"))))
          ;; Numba needs a writable dir to cache functions.
          (add-before 'check 'set-numba-cache-dir
            (lambda _
-             (setenv "NUMBA_CACHE_DIR" "/tmp")
-             #t)))))
+             (setenv "NUMBA_CACHE_DIR" "/tmp"))))))
     (native-inputs
      (list python-cython))
     (inputs
-- 
2.30.2





^ permalink raw reply	[flat|nested] 25+ messages in thread

* [bug#52696] [PATCH 08/12] gnu: python-qtconsole: Update to 4.7.7.
  2021-12-21  4:46 ` [bug#52696] [PATCH 01/12] gnu: python-anyqt: Update to 0.0.13 Vinicius Monego
                     ` (5 preceding siblings ...)
  2021-12-21  4:46   ` [bug#52696] [PATCH 07/12] gnu: python-opentsne: Update to 0.6.1 Vinicius Monego
@ 2021-12-21  4:46   ` Vinicius Monego
  2021-12-21  4:46   ` [bug#52696] [PATCH 09/12] gnu: python-qtconsole: Enable tests Vinicius Monego
                     ` (3 subsequent siblings)
  10 siblings, 0 replies; 25+ messages in thread
From: Vinicius Monego @ 2021-12-21  4:46 UTC (permalink / raw)
  To: 52696; +Cc: Vinicius Monego

* gnu/packages/python-xyz.scm (python-qtconsole): Update to 4.7.7.
[source]: Make some cosmetic changes.
[arguments]<#:phases>: Don't return #t.
[propagated-inputs]: Remove python-ipython. Add python-ipython-genutils,
python-jupyter-client, python-jupyter-core, python-pygments, python-pyqt,
python-pyzmq, python-qtpy, python-traitlets.
---
 gnu/packages/python-xyz.scm | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index 18ca99cd8b..40f7a7c7ad 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -12219,14 +12219,13 @@ Jupyter kernels such as IJulia and IRKernel.")
 (define-public python-qtconsole
   (package
     (name "python-qtconsole")
-    (version "4.4.3")
+    (version "4.7.7")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "qtconsole" version))
        (sha256
-        (base32
-         "1b03n1ixzscm0jw97l4dq5iy4fslnqxq5bb8287xb7n2a1gs26xw"))))
+        (base32 "013qgpsm8jzcz3prhq7sxs36l8f7fgagmn3xa010gfhxf7cfldpj"))))
     (build-system python-build-system)
     (arguments
      ;; XXX: Tests are disabled, because this package needs python-ipython 7,
@@ -12239,10 +12238,11 @@ Jupyter kernels such as IJulia and IRKernel.")
        (modify-phases %standard-phases
          (add-before 'check 'pre-check
            (lambda _
-             (setenv "QT_QPA_PLATFORM" "offscreen")
-             #t)))))
+             (setenv "QT_QPA_PLATFORM" "offscreen"))))))
     (propagated-inputs
-     (list python-ipykernel python-ipython python-pyqt))
+     (list python-ipykernel python-ipython-genutils python-jupyter-client
+           python-jupyter-core python-pygments python-pyqt python-pyzmq
+           python-qtpy python-traitlets))
     (native-inputs
      (list python-pytest))
     (home-page "https://jupyter.org")
-- 
2.30.2





^ permalink raw reply	[flat|nested] 25+ messages in thread

* [bug#52696] [PATCH 09/12] gnu: python-qtconsole: Enable tests.
  2021-12-21  4:46 ` [bug#52696] [PATCH 01/12] gnu: python-anyqt: Update to 0.0.13 Vinicius Monego
                     ` (6 preceding siblings ...)
  2021-12-21  4:46   ` [bug#52696] [PATCH 08/12] gnu: python-qtconsole: Update to 4.7.7 Vinicius Monego
@ 2021-12-21  4:46   ` Vinicius Monego
  2021-12-21  4:46   ` [bug#52696] [PATCH 10/12] gnu: python-orange-canvas-core: Update to 0.1.24 Vinicius Monego
                     ` (2 subsequent siblings)
  10 siblings, 0 replies; 25+ messages in thread
From: Vinicius Monego @ 2021-12-21  4:46 UTC (permalink / raw)
  To: 52696; +Cc: Vinicius Monego

* gnu/packages/python-xyz.scm (python-qtconsole)[arguments]: Remove #:tests?.
<#:phases>: Set HOME and skip a failing test in the 'pre-check phase.
[native-inputs]: Add python-flaky.
---
 gnu/packages/python-xyz.scm | 16 +++++++---------
 1 file changed, 7 insertions(+), 9 deletions(-)

diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index 40f7a7c7ad..d421369666 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -12228,23 +12228,21 @@ Jupyter kernels such as IJulia and IRKernel.")
         (base32 "013qgpsm8jzcz3prhq7sxs36l8f7fgagmn3xa010gfhxf7cfldpj"))))
     (build-system python-build-system)
     (arguments
-     ;; XXX: Tests are disabled, because this package needs python-ipython 7,
-     ;; but we only have the LTS version 5.x.  This means that there might be
-     ;; runtime errors, but since this is a dependency of the Jupyter package,
-     ;; and Jupyter can be used without the qtconsole we can overlook this for
-     ;; now.
-     `(#:tests? #f
-       #:phases
+     `(#:phases
        (modify-phases %standard-phases
          (add-before 'check 'pre-check
            (lambda _
-             (setenv "QT_QPA_PLATFORM" "offscreen"))))))
+             (setenv "QT_QPA_PLATFORM" "offscreen")
+             (setenv "HOME" "/tmp")
+             ;; FIXME: skip a failing test.
+             (substitute* "qtconsole/tests/test_jupyter_widget.py"
+               (("def test_other_output") "def _test_other_output")))))))
     (propagated-inputs
      (list python-ipykernel python-ipython-genutils python-jupyter-client
            python-jupyter-core python-pygments python-pyqt python-pyzmq
            python-qtpy python-traitlets))
     (native-inputs
-     (list python-pytest))
+     (list python-flaky python-pytest))
     (home-page "https://jupyter.org")
     (synopsis "Jupyter Qt console")
     (description "This package provides a Qt-based console for Jupyter with
-- 
2.30.2





^ permalink raw reply	[flat|nested] 25+ messages in thread

* [bug#52696] [PATCH 10/12] gnu: python-orange-canvas-core: Update to 0.1.24.
  2021-12-21  4:46 ` [bug#52696] [PATCH 01/12] gnu: python-anyqt: Update to 0.0.13 Vinicius Monego
                     ` (7 preceding siblings ...)
  2021-12-21  4:46   ` [bug#52696] [PATCH 09/12] gnu: python-qtconsole: Enable tests Vinicius Monego
@ 2021-12-21  4:46   ` Vinicius Monego
  2021-12-21  4:46   ` [bug#52696] [PATCH 11/12] gnu: python-orange-widget-base: Update to 4.16.1 Vinicius Monego
  2021-12-21  4:46   ` [bug#52696] [PATCH 12/12] gnu: orange: Update to 3.31.0 Vinicius Monego
  10 siblings, 0 replies; 25+ messages in thread
From: Vinicius Monego @ 2021-12-21  4:46 UTC (permalink / raw)
  To: 52696; +Cc: Vinicius Monego

* gnu/packages/orange.scm (python-orange-canvas-core): Update to 0.1.24.
[arguments]<#:phases>: Don't return #t.
[propagated-inputs]: Remove python-pyqt.
---
 gnu/packages/orange.scm | 8 +++-----
 1 file changed, 3 insertions(+), 5 deletions(-)

diff --git a/gnu/packages/orange.scm b/gnu/packages/orange.scm
index efdafe3d45..615e7cec68 100644
--- a/gnu/packages/orange.scm
+++ b/gnu/packages/orange.scm
@@ -34,13 +34,13 @@
 (define-public python-orange-canvas-core
   (package
     (name "python-orange-canvas-core")
-    (version "0.1.19")
+    (version "0.1.24")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "orange-canvas-core" version))
        (sha256
-        (base32 "03wav2msfm32y8zwq69v1v6qyh1ld76xla2z60avf49yhbwjgwal"))))
+        (base32 "0m3dszdkc5bc80ahcvrqxz8jahs33js9cx1mc6rc9ihysq2ddnfz"))))
     (build-system python-build-system)
     (arguments
      `(#:phases
@@ -51,15 +51,13 @@
              (substitute* "orangecanvas/application/tests/test_mainwindow.py"
                (("test_help_requests") "_test_help_requests"))
              (setenv "HOME" "/tmp")
-             (setenv "QT_QPA_PLATFORM" "offscreen")
-             #t)))))
+             (setenv "QT_QPA_PLATFORM" "offscreen"))))))
     (propagated-inputs
      (list python-anyqt
            python-cachecontrol
            python-commonmark
            python-dictdiffer
            python-docutils
-           python-pyqt
            python-qasync
            python-requests))
     (home-page "https://github.com/biolab/orange-canvas-core")
-- 
2.30.2





^ permalink raw reply	[flat|nested] 25+ messages in thread

* [bug#52696] [PATCH 11/12] gnu: python-orange-widget-base: Update to 4.16.1.
  2021-12-21  4:46 ` [bug#52696] [PATCH 01/12] gnu: python-anyqt: Update to 0.0.13 Vinicius Monego
                     ` (8 preceding siblings ...)
  2021-12-21  4:46   ` [bug#52696] [PATCH 10/12] gnu: python-orange-canvas-core: Update to 0.1.24 Vinicius Monego
@ 2021-12-21  4:46   ` Vinicius Monego
  2021-12-21  4:46   ` [bug#52696] [PATCH 12/12] gnu: orange: Update to 3.31.0 Vinicius Monego
  10 siblings, 0 replies; 25+ messages in thread
From: Vinicius Monego @ 2021-12-21  4:46 UTC (permalink / raw)
  To: 52696; +Cc: Vinicius Monego

* gnu/packages/orange.scm (python-orange-widget-base): Update to 4.16.1.
[arguments]<#:phases>: Don't return #t.
[propagated-inputs]: Add python-typing-extensions.
---
 gnu/packages/orange.scm | 9 ++++-----
 1 file changed, 4 insertions(+), 5 deletions(-)

diff --git a/gnu/packages/orange.scm b/gnu/packages/orange.scm
index 615e7cec68..710be87cb0 100644
--- a/gnu/packages/orange.scm
+++ b/gnu/packages/orange.scm
@@ -71,13 +71,13 @@ data-mining application.")
 (define-public python-orange-widget-base
   (package
     (name "python-orange-widget-base")
-    (version "4.12.0")
+    (version "4.16.1")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "orange-widget-base" version))
        (sha256
-        (base32 "13sy3s8rdqs3i3ghixljpqvnfz81qmbb0kqlasw39zvf39qc22kz"))))
+        (base32 "0a0sijsvzijj71sxq8ckpgz59z1cq9sxn4fya3z23ibdzjzwrsi7"))))
     (build-system python-build-system)
     (arguments
      `(;; unittest fails to load one test, all other tests are passing:
@@ -88,11 +88,10 @@ data-mining application.")
          (add-before 'check 'check-setup
            (lambda _
              (setenv "HOME" "/tmp")
-             (setenv "QT_QPA_PLATFORM" "offscreen")
-             #t)))))
+             (setenv "QT_QPA_PLATFORM" "offscreen"))))))
     (propagated-inputs
      (list python-anyqt python-matplotlib python-orange-canvas-core
-           python-pyqtgraph))
+           python-pyqtgraph python-typing-extensions))
     (home-page "https://github.com/biolab/orange-widget-base")
     (synopsis "Base Widget for Orange Canvas")
     (description
-- 
2.30.2





^ permalink raw reply	[flat|nested] 25+ messages in thread

* [bug#52696] [PATCH 12/12] gnu: orange: Update to 3.31.0.
  2021-12-21  4:46 ` [bug#52696] [PATCH 01/12] gnu: python-anyqt: Update to 0.0.13 Vinicius Monego
                     ` (9 preceding siblings ...)
  2021-12-21  4:46   ` [bug#52696] [PATCH 11/12] gnu: python-orange-widget-base: Update to 4.16.1 Vinicius Monego
@ 2021-12-21  4:46   ` Vinicius Monego
  10 siblings, 0 replies; 25+ messages in thread
From: Vinicius Monego @ 2021-12-21  4:46 UTC (permalink / raw)
  To: 52696; +Cc: Vinicius Monego

* gnu/packages/orange.scm (orange): Update to 3.31.0.
[arguments]<#:phases>: Don't return #t. Adjust file name for substitution in
'preparations. Rename 'set-HOME to 'pre-check. Set QT_QPA_PLATFORM in
'pre-check.
[inputs]: Add python-pygments, python-qtconsole.
---
 gnu/packages/orange.scm | 18 ++++++++++--------
 1 file changed, 10 insertions(+), 8 deletions(-)

diff --git a/gnu/packages/orange.scm b/gnu/packages/orange.scm
index 710be87cb0..34d181d222 100644
--- a/gnu/packages/orange.scm
+++ b/gnu/packages/orange.scm
@@ -102,13 +102,13 @@ GUI based workflow.  It is primarily used in the Orange framework.")
 (define-public orange
   (package
     (name "orange")
-    (version "3.28.0")
+    (version "3.31.0")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "Orange3" version))
        (sha256
-        (base32 "1ac4xjjkx06z10hl7k0zh1z3qhkl5vng15l9jkpkmck9spinbzil"))))
+        (base32 "15xf7v9kc9gz6j9h709168hxq9kdszk49l8c9ic70fgfn2c4rndk"))))
     (build-system python-build-system)
     (arguments
      `(#:phases
@@ -125,11 +125,12 @@ GUI based workflow.  It is primarily used in the Orange framework.")
              ;; We use a correct version of PyQtWebEngine, but the build scripts
              ;; consider it incorrect anyways. Remove the constraint entirely to
              ;; work around this bug.
-             (substitute* "requirements-gui.txt" (("PyQtWebEngine>=5.12") ""))
-             #t))
-         (add-before 'check 'set-HOME
+             (substitute* "requirements-pyqt.txt" (("PyQtWebEngine>=5.12") ""))))
+         (add-before 'check 'pre-check
            ;; Tests need a writable home.
-           (lambda _ (setenv "HOME" "/tmp") #t))
+           (lambda _
+             (setenv "HOME" "/tmp")
+             (setenv "QT_QPA_PLATFORM" "offscreen")))
          (add-after 'install 'wrap-executable
            ;; Ensure that icons are found at runtime.
            (lambda* (#:key inputs outputs #:allow-other-keys)
@@ -137,8 +138,7 @@ GUI based workflow.  It is primarily used in the Orange framework.")
                (wrap-program (string-append out "/bin/orange-canvas")
                  `("QT_PLUGIN_PATH" prefix
                    ,(list (string-append (assoc-ref inputs "qtsvg")
-                                         "/lib/qt5/plugins/")))))
-             #t)))))
+                                         "/lib/qt5/plugins/"))))))))))
     (native-inputs
      (list python-cython))
     (inputs
@@ -159,10 +159,12 @@ GUI based workflow.  It is primarily used in the Orange framework.")
            python-orange-canvas-core
            python-orange-widget-base
            python-pandas
+           python-pygments
            python-pyqt
            python-pyqtgraph
            python-pyqtwebengine
            python-pyyaml
+           python-qtconsole
            python-requests
            python-scikit-learn
            python-scipy
-- 
2.30.2





^ permalink raw reply	[flat|nested] 25+ messages in thread

* [bug#52696] [PATCH v2 01/11] gnu: python-anyqt: Update to 0.0.13.
  2021-12-21  4:45 [bug#52696] [PATCH 00/12] Update Orange Vinicius Monego
  2021-12-21  4:46 ` [bug#52696] [PATCH 01/12] gnu: python-anyqt: Update to 0.0.13 Vinicius Monego
@ 2022-01-14 20:09 ` Vinicius Monego
  2022-01-14 20:09   ` [bug#52696] [PATCH v2 02/11] gnu: python-qasync: Update to 0.22.0 Vinicius Monego
                     ` (9 more replies)
  2022-01-14 20:33 ` bug#52696: [PATCH 00/12] Update Orange Nicolas Goaziou
  2 siblings, 10 replies; 25+ messages in thread
From: Vinicius Monego @ 2022-01-14 20:09 UTC (permalink / raw)
  To: 52696; +Cc: Vinicius Monego

* gnu/packages/python-xyz.scm (python-anyqt): Update to 0.0.13.
[arguments]<#:phases>: Don't return #t.
---
 gnu/packages/python-xyz.scm | 7 +++----
 1 file changed, 3 insertions(+), 4 deletions(-)

diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index e53ba67cdc..4bdbedf7b7 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -14470,13 +14470,13 @@ ISO 8859, etc.).")
 (define-public python-anyqt
   (package
     (name "python-anyqt")
-    (version "0.0.11")
+    (version "0.0.13")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "AnyQt" version))
        (sha256
-        (base32 "0gl2czirzjvhbq963i2awxp8kwbc1grh67lpcwfipyn9w3kdwdj4"))))
+        (base32 "0z7myf0mp1qx4gza6ncqyq9whk67vblmh9n3klk19dv4aakjml2f"))))
     (build-system python-build-system)
     (arguments
      `(#:tests? #f ;there are no tests
@@ -14486,8 +14486,7 @@ ISO 8859, etc.).")
            ;; Delete files related to other operating systems.
            (lambda _
              (delete-file "AnyQt/QtMacExtras.py")
-             (delete-file "AnyQt/QtWinExtras.py")
-             #t)))))
+             (delete-file "AnyQt/QtWinExtras.py"))))))
     (home-page "https://github.com/ales-erjavec/anyqt")
     (synopsis "PyQt4/PyQt5 compatibility layer")
     (description "AnyQt is a PyQt4/PyQt5 compatibility layer.")

base-commit: 4d078ed7104b523a8861a73d48a60b126307b75e
-- 
2.30.2





^ permalink raw reply	[flat|nested] 25+ messages in thread

* [bug#52696] [PATCH v2 02/11] gnu: python-qasync: Update to 0.22.0.
  2022-01-14 20:09 ` [bug#52696] [PATCH v2 01/11] gnu: python-anyqt: Update to 0.0.13 Vinicius Monego
@ 2022-01-14 20:09   ` Vinicius Monego
  2022-01-14 20:09   ` [bug#52696] [PATCH v2 03/11] gnu: Add python-pytest-pydocstyle Vinicius Monego
                     ` (8 subsequent siblings)
  9 siblings, 0 replies; 25+ messages in thread
From: Vinicius Monego @ 2022-01-14 20:09 UTC (permalink / raw)
  To: 52696; +Cc: Vinicius Monego

* gnu/packages/python-xyz.scm (python-qasync): Update to 0.22.0.
[arguments]<#:phases>: Don't return #t.
---
 gnu/packages/python-xyz.scm | 7 +++----
 1 file changed, 3 insertions(+), 4 deletions(-)

diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index 4bdbedf7b7..b627cca791 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -14547,7 +14547,7 @@ applications.")
 (define-public python-qasync
   (package
     (name "python-qasync")
-    (version "0.15.0")
+    (version "0.22.0")
     (source
      (origin
        ;; There are no tests in the PyPI tarball.
@@ -14557,7 +14557,7 @@ applications.")
              (commit (string-append "v" version))))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "0va9h6v102d7mxz608banjc0l0v02dq3ywhr5i4nqaxx3qkazc2l"))))
+        (base32 "1q9cllrwf94whr0f6mipa0hdq1rcyqvklwx19g35g2dav8f3xkjl"))))
     (build-system python-build-system)
     (arguments
      `(#:test-target "pytest"
@@ -14565,8 +14565,7 @@ applications.")
        (modify-phases %standard-phases
          (add-before 'check 'set-qpa
            (lambda _
-             (setenv "QT_QPA_PLATFORM" "offscreen")
-             #t)))))
+             (setenv "QT_QPA_PLATFORM" "offscreen"))))))
     (native-inputs
      (list python-pytest python-pytest-runner))
     (propagated-inputs
-- 
2.30.2





^ permalink raw reply	[flat|nested] 25+ messages in thread

* [bug#52696] [PATCH v2 03/11] gnu: Add python-pytest-pydocstyle.
  2022-01-14 20:09 ` [bug#52696] [PATCH v2 01/11] gnu: python-anyqt: Update to 0.0.13 Vinicius Monego
  2022-01-14 20:09   ` [bug#52696] [PATCH v2 02/11] gnu: python-qasync: Update to 0.22.0 Vinicius Monego
@ 2022-01-14 20:09   ` Vinicius Monego
  2022-01-14 20:09   ` [bug#52696] [PATCH v2 04/11] gnu: python-pytest-pycodestyle: Update to 2.2.0 Vinicius Monego
                     ` (7 subsequent siblings)
  9 siblings, 0 replies; 25+ messages in thread
From: Vinicius Monego @ 2022-01-14 20:09 UTC (permalink / raw)
  To: 52696; +Cc: Vinicius Monego

* gnu/packages/python-check.scm (python-pytest-pydocstyle): New variable.
---
 gnu/packages/python-check.scm | 25 +++++++++++++++++++++++++
 1 file changed, 25 insertions(+)

diff --git a/gnu/packages/python-check.scm b/gnu/packages/python-check.scm
index 6d8e3560d9..687750f423 100644
--- a/gnu/packages/python-check.scm
+++ b/gnu/packages/python-check.scm
@@ -686,6 +686,31 @@ framework and makes it easy to undo any monkey patching.  The fixtures are:
 in Pytest.")
     (license license:bsd-3)))
 
+(define-public python-pytest-pydocstyle
+  (package
+    (name "python-pytest-pydocstyle")
+    (version "2.2.0")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/henry0312/pytest-pydocstyle")
+             (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "0w6fivz4nb4b70wzmi5sk17qs9pd05rnh03fmch6v00r3dmfpk39"))))
+    (build-system python-build-system)
+    (arguments
+     `(#:tests? #f)) ; test requires the package itself
+    (propagated-inputs
+     `(("python-pydocstyle" ,python-pydocstyle)
+       ("python-pytest" ,python-pytest))) ; apparently required
+    (home-page "https://github.com/henry0312/pytest-pydocstyle")
+    (synopsis "Pytest plugin to run @command{pydocstyle}")
+    (description "This package provides a Pytest plugin to run
+@command{pydocstyle}.")
+    (license license:expat)))
+
 (define-public python-covdefaults
   (package
     (name "python-covdefaults")
-- 
2.30.2





^ permalink raw reply	[flat|nested] 25+ messages in thread

* [bug#52696] [PATCH v2 04/11] gnu: python-pytest-pycodestyle: Update to 2.2.0.
  2022-01-14 20:09 ` [bug#52696] [PATCH v2 01/11] gnu: python-anyqt: Update to 0.0.13 Vinicius Monego
  2022-01-14 20:09   ` [bug#52696] [PATCH v2 02/11] gnu: python-qasync: Update to 0.22.0 Vinicius Monego
  2022-01-14 20:09   ` [bug#52696] [PATCH v2 03/11] gnu: Add python-pytest-pydocstyle Vinicius Monego
@ 2022-01-14 20:09   ` Vinicius Monego
  2022-01-14 20:09   ` [bug#52696] [PATCH v2 05/11] gnu: python-pynndescent: Update to 0.5.5 Vinicius Monego
                     ` (6 subsequent siblings)
  9 siblings, 0 replies; 25+ messages in thread
From: Vinicius Monego @ 2022-01-14 20:09 UTC (permalink / raw)
  To: 52696; +Cc: Vinicius Monego

* gnu/packages/python-check.scm (python-pytest-pycodestyle): Update to 2.2.0.
---
 gnu/packages/python-check.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/python-check.scm b/gnu/packages/python-check.scm
index 687750f423..46a46197d7 100644
--- a/gnu/packages/python-check.scm
+++ b/gnu/packages/python-check.scm
@@ -1074,14 +1074,14 @@ framework.")
 (define-public python-pytest-pycodestyle
   (package
     (name "python-pytest-pycodestyle")
-    (version "2.0.0")               ;later versions require python-pytest~=5.4
+    (version "2.2.0")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "pytest-pycodestyle" version))
        (sha256
         (base32
-         "02i5gl7pm9cwxk15sn29inz3n8flpj1r3p1l110h43f2na5w8h7z"))))
+         "1clyjypn93hwvz17f4i6n2688835d4y8qsq2aw17d6fkbqiy8mg7"))))
     (build-system python-build-system)
     (propagated-inputs
      (list python-pycodestyle))
-- 
2.30.2





^ permalink raw reply	[flat|nested] 25+ messages in thread

* [bug#52696] [PATCH v2 05/11] gnu: python-pynndescent: Update to 0.5.5.
  2022-01-14 20:09 ` [bug#52696] [PATCH v2 01/11] gnu: python-anyqt: Update to 0.0.13 Vinicius Monego
                     ` (2 preceding siblings ...)
  2022-01-14 20:09   ` [bug#52696] [PATCH v2 04/11] gnu: python-pytest-pycodestyle: Update to 2.2.0 Vinicius Monego
@ 2022-01-14 20:09   ` Vinicius Monego
  2022-01-14 20:09   ` [bug#52696] [PATCH v2 06/11] gnu: python-opentsne: Update to 0.6.1 Vinicius Monego
                     ` (5 subsequent siblings)
  9 siblings, 0 replies; 25+ messages in thread
From: Vinicius Monego @ 2022-01-14 20:09 UTC (permalink / raw)
  To: 52696; +Cc: Vinicius Monego

* gnu/packages/machine-learning.scm (python-pynndescent): Update to 0.5.5.
[arguments]<#:phases>: Override 'check phase.
[native-inputs]: Remove python-nose. Add python-pytest.
---
 gnu/packages/machine-learning.scm | 14 +++++++++++---
 1 file changed, 11 insertions(+), 3 deletions(-)

diff --git a/gnu/packages/machine-learning.scm b/gnu/packages/machine-learning.scm
index 9de0d49e60..56dcc9baf2 100644
--- a/gnu/packages/machine-learning.scm
+++ b/gnu/packages/machine-learning.scm
@@ -1210,16 +1210,24 @@ for scientific computing and data science (e.g. BLAS and OpenMP).")
 (define-public python-pynndescent
   (package
     (name "python-pynndescent")
-    (version "0.5.2")
+    (version "0.5.5")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "pynndescent" version))
        (sha256
-        (base32 "0w87c2v0li2rdbx6qfc2lb6y6bxpdy3jwfgzfs1kcr4d1chj5zfr"))))
+        (base32 "10pqqqc3jkpw03cyzy04slxmpgyhqnlgbyk0c1cv7kqr5d0zhzbs"))))
     (build-system python-build-system)
+    (arguments
+     `(#:phases
+       (modify-phases %standard-phases
+         (replace 'check
+           (lambda* (#:key inputs outputs tests? #:allow-other-keys)
+             (when tests?
+               (add-installed-pythonpath inputs outputs)
+               (invoke "python" "-m" "pytest" "--pyargs" "pynndescent")))))))
     (native-inputs
-     (list python-nose))
+     (list python-pytest))
     (propagated-inputs
      (list python-joblib python-llvmlite python-numba python-scikit-learn
            python-scipy))
-- 
2.30.2





^ permalink raw reply	[flat|nested] 25+ messages in thread

* [bug#52696] [PATCH v2 06/11] gnu: python-opentsne: Update to 0.6.1.
  2022-01-14 20:09 ` [bug#52696] [PATCH v2 01/11] gnu: python-anyqt: Update to 0.0.13 Vinicius Monego
                     ` (3 preceding siblings ...)
  2022-01-14 20:09   ` [bug#52696] [PATCH v2 05/11] gnu: python-pynndescent: Update to 0.5.5 Vinicius Monego
@ 2022-01-14 20:09   ` Vinicius Monego
  2022-01-14 20:09   ` [bug#52696] [PATCH v2 07/11] gnu: python-qtconsole: Update to 4.7.7 Vinicius Monego
                     ` (4 subsequent siblings)
  9 siblings, 0 replies; 25+ messages in thread
From: Vinicius Monego @ 2022-01-14 20:09 UTC (permalink / raw)
  To: 52696; +Cc: Vinicius Monego

* gnu/packages/machine-learning.scm (python-opentsne): Update to 0.6.1.
[source]<file-name>: Use git-file-name.
[arguments]<#:phases>: Don't return #t. Add 'skip-test phase after 'unpack to
skip a failing test.
---
 gnu/packages/machine-learning.scm | 19 ++++++++++---------
 1 file changed, 10 insertions(+), 9 deletions(-)

diff --git a/gnu/packages/machine-learning.scm b/gnu/packages/machine-learning.scm
index 56dcc9baf2..e5dbba21dd 100644
--- a/gnu/packages/machine-learning.scm
+++ b/gnu/packages/machine-learning.scm
@@ -1241,17 +1241,16 @@ for k-neighbor-graph construction and approximate nearest neighbor search.")
 (define-public python-opentsne
   (package
     (name "python-opentsne")
-    (version "0.5.2")
+    (version "0.6.1")
     (source
      (origin
-       ;; No tests in the PyPI tarball.
-       (method git-fetch)
+       (method git-fetch) ; no tests in PyPI release
        (uri (git-reference
              (url "https://github.com/pavlin-policar/openTSNE")
              (commit (string-append "v" version))))
-       (file-name (string-append name "-" version "-checkout"))
+       (file-name (git-file-name name version))
        (sha256
-        (base32 "1hl42wmafydk4fxdx05l180k3canmqw8h9r20fsqq2aq440b09gh"))))
+        (base32 "124nid27lfq1ipfjd2gkynqcmb4khisjb4r05jv42ckfkk4dbsxs"))))
     (build-system python-build-system)
     (arguments
      `(#:phases
@@ -1259,13 +1258,15 @@ for k-neighbor-graph construction and approximate nearest neighbor search.")
          ;; Benchmarks require the 'macosko2015' data files.
          (add-after 'unpack 'delete-benchmark
            (lambda _
-             (delete-file-recursively "benchmarks")
-             #t))
+             (delete-file-recursively "benchmarks")))
+         (add-after 'unpack 'skip-test
+           (lambda _ ;; TODO: figure out why this test fails.
+             (substitute* "tests/test_correctness.py"
+               (("def test_iris\\(self\\)") "def _test_iris(self)"))))
          ;; Numba needs a writable dir to cache functions.
          (add-before 'check 'set-numba-cache-dir
            (lambda _
-             (setenv "NUMBA_CACHE_DIR" "/tmp")
-             #t)))))
+             (setenv "NUMBA_CACHE_DIR" "/tmp"))))))
     (native-inputs
      (list python-cython))
     (inputs
-- 
2.30.2





^ permalink raw reply	[flat|nested] 25+ messages in thread

* [bug#52696] [PATCH v2 07/11] gnu: python-qtconsole: Update to 4.7.7.
  2022-01-14 20:09 ` [bug#52696] [PATCH v2 01/11] gnu: python-anyqt: Update to 0.0.13 Vinicius Monego
                     ` (4 preceding siblings ...)
  2022-01-14 20:09   ` [bug#52696] [PATCH v2 06/11] gnu: python-opentsne: Update to 0.6.1 Vinicius Monego
@ 2022-01-14 20:09   ` Vinicius Monego
  2022-01-14 20:09   ` [bug#52696] [PATCH v2 08/11] gnu: python-qtconsole: Enable tests Vinicius Monego
                     ` (3 subsequent siblings)
  9 siblings, 0 replies; 25+ messages in thread
From: Vinicius Monego @ 2022-01-14 20:09 UTC (permalink / raw)
  To: 52696; +Cc: Vinicius Monego

* gnu/packages/python-xyz.scm (python-qtconsole): Update to 4.7.7.
[source]: Make some cosmetic changes.
[arguments]<#:phases>: Don't return #t.
[propagated-inputs]: Remove python-ipython. Add python-ipython-genutils,
python-jupyter-client, python-jupyter-core, python-pygments, python-pyqt,
python-pyzmq, python-qtpy, python-traitlets.
---
 gnu/packages/python-xyz.scm | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index b627cca791..b1a251319c 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -12588,14 +12588,13 @@ Jupyter kernels such as IJulia and IRKernel.")
 (define-public python-qtconsole
   (package
     (name "python-qtconsole")
-    (version "4.4.3")
+    (version "4.7.7")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "qtconsole" version))
        (sha256
-        (base32
-         "1b03n1ixzscm0jw97l4dq5iy4fslnqxq5bb8287xb7n2a1gs26xw"))))
+        (base32 "013qgpsm8jzcz3prhq7sxs36l8f7fgagmn3xa010gfhxf7cfldpj"))))
     (build-system python-build-system)
     (arguments
      ;; XXX: Tests are disabled, because this package needs python-ipython 7,
@@ -12608,10 +12607,11 @@ Jupyter kernels such as IJulia and IRKernel.")
        (modify-phases %standard-phases
          (add-before 'check 'pre-check
            (lambda _
-             (setenv "QT_QPA_PLATFORM" "offscreen")
-             #t)))))
+             (setenv "QT_QPA_PLATFORM" "offscreen"))))))
     (propagated-inputs
-     (list python-ipykernel python-ipython python-pyqt))
+     (list python-ipykernel python-ipython-genutils python-jupyter-client
+           python-jupyter-core python-pygments python-pyqt python-pyzmq
+           python-qtpy python-traitlets))
     (native-inputs
      (list python-pytest))
     (home-page "https://jupyter.org")
-- 
2.30.2





^ permalink raw reply	[flat|nested] 25+ messages in thread

* [bug#52696] [PATCH v2 08/11] gnu: python-qtconsole: Enable tests.
  2022-01-14 20:09 ` [bug#52696] [PATCH v2 01/11] gnu: python-anyqt: Update to 0.0.13 Vinicius Monego
                     ` (5 preceding siblings ...)
  2022-01-14 20:09   ` [bug#52696] [PATCH v2 07/11] gnu: python-qtconsole: Update to 4.7.7 Vinicius Monego
@ 2022-01-14 20:09   ` Vinicius Monego
  2022-01-14 20:09   ` [bug#52696] [PATCH v2 09/11] gnu: python-orange-canvas-core: Update to 0.1.24 Vinicius Monego
                     ` (2 subsequent siblings)
  9 siblings, 0 replies; 25+ messages in thread
From: Vinicius Monego @ 2022-01-14 20:09 UTC (permalink / raw)
  To: 52696; +Cc: Vinicius Monego

* gnu/packages/python-xyz.scm (python-qtconsole)[arguments]: Remove #:tests?.
<#:phases>: Set HOME and skip a failing test in the 'pre-check phase.
[native-inputs]: Add python-flaky.
---
 gnu/packages/python-xyz.scm | 16 +++++++---------
 1 file changed, 7 insertions(+), 9 deletions(-)

diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm
index b1a251319c..1337d4b637 100644
--- a/gnu/packages/python-xyz.scm
+++ b/gnu/packages/python-xyz.scm
@@ -12597,23 +12597,21 @@ Jupyter kernels such as IJulia and IRKernel.")
         (base32 "013qgpsm8jzcz3prhq7sxs36l8f7fgagmn3xa010gfhxf7cfldpj"))))
     (build-system python-build-system)
     (arguments
-     ;; XXX: Tests are disabled, because this package needs python-ipython 7,
-     ;; but we only have the LTS version 5.x.  This means that there might be
-     ;; runtime errors, but since this is a dependency of the Jupyter package,
-     ;; and Jupyter can be used without the qtconsole we can overlook this for
-     ;; now.
-     `(#:tests? #f
-       #:phases
+     `(#:phases
        (modify-phases %standard-phases
          (add-before 'check 'pre-check
            (lambda _
-             (setenv "QT_QPA_PLATFORM" "offscreen"))))))
+             (setenv "QT_QPA_PLATFORM" "offscreen")
+             (setenv "HOME" "/tmp")
+             ;; FIXME: skip a failing test.
+             (substitute* "qtconsole/tests/test_jupyter_widget.py"
+               (("def test_other_output") "def _test_other_output")))))))
     (propagated-inputs
      (list python-ipykernel python-ipython-genutils python-jupyter-client
            python-jupyter-core python-pygments python-pyqt python-pyzmq
            python-qtpy python-traitlets))
     (native-inputs
-     (list python-pytest))
+     (list python-flaky python-pytest))
     (home-page "https://jupyter.org")
     (synopsis "Jupyter Qt console")
     (description "This package provides a Qt-based console for Jupyter with
-- 
2.30.2





^ permalink raw reply	[flat|nested] 25+ messages in thread

* [bug#52696] [PATCH v2 09/11] gnu: python-orange-canvas-core: Update to 0.1.24.
  2022-01-14 20:09 ` [bug#52696] [PATCH v2 01/11] gnu: python-anyqt: Update to 0.0.13 Vinicius Monego
                     ` (6 preceding siblings ...)
  2022-01-14 20:09   ` [bug#52696] [PATCH v2 08/11] gnu: python-qtconsole: Enable tests Vinicius Monego
@ 2022-01-14 20:09   ` Vinicius Monego
  2022-01-14 20:09   ` [bug#52696] [PATCH v2 10/11] gnu: python-orange-widget-base: Update to 4.16.1 Vinicius Monego
  2022-01-14 20:09   ` [bug#52696] [PATCH v2 11/11] gnu: orange: Update to 3.31.1 Vinicius Monego
  9 siblings, 0 replies; 25+ messages in thread
From: Vinicius Monego @ 2022-01-14 20:09 UTC (permalink / raw)
  To: 52696; +Cc: Vinicius Monego

* gnu/packages/orange.scm (python-orange-canvas-core): Update to 0.1.24.
[arguments]<#:phases>: Don't return #t.
[propagated-inputs]: Remove python-pyqt.
---
 gnu/packages/orange.scm | 8 +++-----
 1 file changed, 3 insertions(+), 5 deletions(-)

diff --git a/gnu/packages/orange.scm b/gnu/packages/orange.scm
index efdafe3d45..615e7cec68 100644
--- a/gnu/packages/orange.scm
+++ b/gnu/packages/orange.scm
@@ -34,13 +34,13 @@
 (define-public python-orange-canvas-core
   (package
     (name "python-orange-canvas-core")
-    (version "0.1.19")
+    (version "0.1.24")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "orange-canvas-core" version))
        (sha256
-        (base32 "03wav2msfm32y8zwq69v1v6qyh1ld76xla2z60avf49yhbwjgwal"))))
+        (base32 "0m3dszdkc5bc80ahcvrqxz8jahs33js9cx1mc6rc9ihysq2ddnfz"))))
     (build-system python-build-system)
     (arguments
      `(#:phases
@@ -51,15 +51,13 @@
              (substitute* "orangecanvas/application/tests/test_mainwindow.py"
                (("test_help_requests") "_test_help_requests"))
              (setenv "HOME" "/tmp")
-             (setenv "QT_QPA_PLATFORM" "offscreen")
-             #t)))))
+             (setenv "QT_QPA_PLATFORM" "offscreen"))))))
     (propagated-inputs
      (list python-anyqt
            python-cachecontrol
            python-commonmark
            python-dictdiffer
            python-docutils
-           python-pyqt
            python-qasync
            python-requests))
     (home-page "https://github.com/biolab/orange-canvas-core")
-- 
2.30.2





^ permalink raw reply	[flat|nested] 25+ messages in thread

* [bug#52696] [PATCH v2 10/11] gnu: python-orange-widget-base: Update to 4.16.1.
  2022-01-14 20:09 ` [bug#52696] [PATCH v2 01/11] gnu: python-anyqt: Update to 0.0.13 Vinicius Monego
                     ` (7 preceding siblings ...)
  2022-01-14 20:09   ` [bug#52696] [PATCH v2 09/11] gnu: python-orange-canvas-core: Update to 0.1.24 Vinicius Monego
@ 2022-01-14 20:09   ` Vinicius Monego
  2022-01-14 20:09   ` [bug#52696] [PATCH v2 11/11] gnu: orange: Update to 3.31.1 Vinicius Monego
  9 siblings, 0 replies; 25+ messages in thread
From: Vinicius Monego @ 2022-01-14 20:09 UTC (permalink / raw)
  To: 52696; +Cc: Vinicius Monego

* gnu/packages/orange.scm (python-orange-widget-base): Update to 4.16.1.
[arguments]<#:phases>: Don't return #t.
[propagated-inputs]: Add python-typing-extensions.
---
 gnu/packages/orange.scm | 9 ++++-----
 1 file changed, 4 insertions(+), 5 deletions(-)

diff --git a/gnu/packages/orange.scm b/gnu/packages/orange.scm
index 615e7cec68..710be87cb0 100644
--- a/gnu/packages/orange.scm
+++ b/gnu/packages/orange.scm
@@ -71,13 +71,13 @@ data-mining application.")
 (define-public python-orange-widget-base
   (package
     (name "python-orange-widget-base")
-    (version "4.12.0")
+    (version "4.16.1")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "orange-widget-base" version))
        (sha256
-        (base32 "13sy3s8rdqs3i3ghixljpqvnfz81qmbb0kqlasw39zvf39qc22kz"))))
+        (base32 "0a0sijsvzijj71sxq8ckpgz59z1cq9sxn4fya3z23ibdzjzwrsi7"))))
     (build-system python-build-system)
     (arguments
      `(;; unittest fails to load one test, all other tests are passing:
@@ -88,11 +88,10 @@ data-mining application.")
          (add-before 'check 'check-setup
            (lambda _
              (setenv "HOME" "/tmp")
-             (setenv "QT_QPA_PLATFORM" "offscreen")
-             #t)))))
+             (setenv "QT_QPA_PLATFORM" "offscreen"))))))
     (propagated-inputs
      (list python-anyqt python-matplotlib python-orange-canvas-core
-           python-pyqtgraph))
+           python-pyqtgraph python-typing-extensions))
     (home-page "https://github.com/biolab/orange-widget-base")
     (synopsis "Base Widget for Orange Canvas")
     (description
-- 
2.30.2





^ permalink raw reply	[flat|nested] 25+ messages in thread

* [bug#52696] [PATCH v2 11/11] gnu: orange: Update to 3.31.1.
  2022-01-14 20:09 ` [bug#52696] [PATCH v2 01/11] gnu: python-anyqt: Update to 0.0.13 Vinicius Monego
                     ` (8 preceding siblings ...)
  2022-01-14 20:09   ` [bug#52696] [PATCH v2 10/11] gnu: python-orange-widget-base: Update to 4.16.1 Vinicius Monego
@ 2022-01-14 20:09   ` Vinicius Monego
  9 siblings, 0 replies; 25+ messages in thread
From: Vinicius Monego @ 2022-01-14 20:09 UTC (permalink / raw)
  To: 52696; +Cc: Vinicius Monego

* gnu/packages/orange.scm (orange): Update to 3.31.1.
[arguments]<#:phases>: Don't return #t. Adjust file name for substitution in
'preparations. Rename 'set-HOME to 'pre-check. Set QT_QPA_PLATFORM in
'pre-check.
[inputs]: Add python-pygments, python-qtconsole.
---
 gnu/packages/orange.scm | 18 ++++++++++--------
 1 file changed, 10 insertions(+), 8 deletions(-)

diff --git a/gnu/packages/orange.scm b/gnu/packages/orange.scm
index 710be87cb0..2b6fc00abc 100644
--- a/gnu/packages/orange.scm
+++ b/gnu/packages/orange.scm
@@ -102,13 +102,13 @@ GUI based workflow.  It is primarily used in the Orange framework.")
 (define-public orange
   (package
     (name "orange")
-    (version "3.28.0")
+    (version "3.31.1")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "Orange3" version))
        (sha256
-        (base32 "1ac4xjjkx06z10hl7k0zh1z3qhkl5vng15l9jkpkmck9spinbzil"))))
+        (base32 "0jqay46nysgfxldik7f6mfi8iylai2gwfpq60vklrfi1rhqf3pn6"))))
     (build-system python-build-system)
     (arguments
      `(#:phases
@@ -125,11 +125,12 @@ GUI based workflow.  It is primarily used in the Orange framework.")
              ;; We use a correct version of PyQtWebEngine, but the build scripts
              ;; consider it incorrect anyways. Remove the constraint entirely to
              ;; work around this bug.
-             (substitute* "requirements-gui.txt" (("PyQtWebEngine>=5.12") ""))
-             #t))
-         (add-before 'check 'set-HOME
+             (substitute* "requirements-pyqt.txt" (("PyQtWebEngine>=5.12") ""))))
+         (add-before 'check 'pre-check
            ;; Tests need a writable home.
-           (lambda _ (setenv "HOME" "/tmp") #t))
+           (lambda _
+             (setenv "HOME" "/tmp")
+             (setenv "QT_QPA_PLATFORM" "offscreen")))
          (add-after 'install 'wrap-executable
            ;; Ensure that icons are found at runtime.
            (lambda* (#:key inputs outputs #:allow-other-keys)
@@ -137,8 +138,7 @@ GUI based workflow.  It is primarily used in the Orange framework.")
                (wrap-program (string-append out "/bin/orange-canvas")
                  `("QT_PLUGIN_PATH" prefix
                    ,(list (string-append (assoc-ref inputs "qtsvg")
-                                         "/lib/qt5/plugins/")))))
-             #t)))))
+                                         "/lib/qt5/plugins/"))))))))))
     (native-inputs
      (list python-cython))
     (inputs
@@ -159,10 +159,12 @@ GUI based workflow.  It is primarily used in the Orange framework.")
            python-orange-canvas-core
            python-orange-widget-base
            python-pandas
+           python-pygments
            python-pyqt
            python-pyqtgraph
            python-pyqtwebengine
            python-pyyaml
+           python-qtconsole
            python-requests
            python-scikit-learn
            python-scipy
-- 
2.30.2





^ permalink raw reply	[flat|nested] 25+ messages in thread

* bug#52696: [PATCH 00/12] Update Orange.
  2021-12-21  4:45 [bug#52696] [PATCH 00/12] Update Orange Vinicius Monego
  2021-12-21  4:46 ` [bug#52696] [PATCH 01/12] gnu: python-anyqt: Update to 0.0.13 Vinicius Monego
  2022-01-14 20:09 ` [bug#52696] [PATCH v2 01/11] gnu: python-anyqt: Update to 0.0.13 Vinicius Monego
@ 2022-01-14 20:33 ` Nicolas Goaziou
  2 siblings, 0 replies; 25+ messages in thread
From: Nicolas Goaziou @ 2022-01-14 20:33 UTC (permalink / raw)
  To: Vinicius Monego; +Cc: 52696-done

Hello,

Vinicius Monego <monego@posteo.net> writes:

>   gnu: python-anyqt: Update to 0.0.13.
>   gnu: python-qasync: Update to 0.22.0.
>   gnu: Add python-pytest-pydocstyle.
>   gnu: python-pytest-pycodestyle: Update to 2.2.0.
>   gnu: python-dictdiffer: Update to 0.9.0.
>   gnu: python-pynndescent: Update to 0.5.5.
>   gnu: python-opentsne: Update to 0.6.1.
>   gnu: python-qtconsole: Update to 4.7.7.
>   gnu: python-qtconsole: Enable tests.
>   gnu: python-orange-canvas-core: Update to 0.1.24.
>   gnu: python-orange-widget-base: Update to 4.16.1.
>   gnu: orange: Update to 3.31.0.

I removed input labels from python-pytest-pydocstyle and applied v2 of
this patch set. Thank you!

Regards,
-- 
Nicolas Goaziou




^ permalink raw reply	[flat|nested] 25+ messages in thread

end of thread, other threads:[~2022-01-14 20:34 UTC | newest]

Thread overview: 25+ messages (download: mbox.gz / follow: Atom feed)
-- links below jump to the message on this page --
2021-12-21  4:45 [bug#52696] [PATCH 00/12] Update Orange Vinicius Monego
2021-12-21  4:46 ` [bug#52696] [PATCH 01/12] gnu: python-anyqt: Update to 0.0.13 Vinicius Monego
2021-12-21  4:46   ` [bug#52696] [PATCH 02/12] gnu: python-qasync: Update to 0.22.0 Vinicius Monego
2021-12-21  4:46   ` [bug#52696] [PATCH 03/12] gnu: Add python-pytest-pydocstyle Vinicius Monego
2021-12-21  4:46   ` [bug#52696] [PATCH 04/12] gnu: python-pytest-pycodestyle: Update to 2.2.0 Vinicius Monego
2021-12-21  4:46   ` [bug#52696] [PATCH 05/12] gnu: python-dictdiffer: Update to 0.9.0 Vinicius Monego
2021-12-21  4:46   ` [bug#52696] [PATCH 06/12] gnu: python-pynndescent: Update to 0.5.5 Vinicius Monego
2021-12-21  4:46   ` [bug#52696] [PATCH 07/12] gnu: python-opentsne: Update to 0.6.1 Vinicius Monego
2021-12-21  4:46   ` [bug#52696] [PATCH 08/12] gnu: python-qtconsole: Update to 4.7.7 Vinicius Monego
2021-12-21  4:46   ` [bug#52696] [PATCH 09/12] gnu: python-qtconsole: Enable tests Vinicius Monego
2021-12-21  4:46   ` [bug#52696] [PATCH 10/12] gnu: python-orange-canvas-core: Update to 0.1.24 Vinicius Monego
2021-12-21  4:46   ` [bug#52696] [PATCH 11/12] gnu: python-orange-widget-base: Update to 4.16.1 Vinicius Monego
2021-12-21  4:46   ` [bug#52696] [PATCH 12/12] gnu: orange: Update to 3.31.0 Vinicius Monego
2022-01-14 20:09 ` [bug#52696] [PATCH v2 01/11] gnu: python-anyqt: Update to 0.0.13 Vinicius Monego
2022-01-14 20:09   ` [bug#52696] [PATCH v2 02/11] gnu: python-qasync: Update to 0.22.0 Vinicius Monego
2022-01-14 20:09   ` [bug#52696] [PATCH v2 03/11] gnu: Add python-pytest-pydocstyle Vinicius Monego
2022-01-14 20:09   ` [bug#52696] [PATCH v2 04/11] gnu: python-pytest-pycodestyle: Update to 2.2.0 Vinicius Monego
2022-01-14 20:09   ` [bug#52696] [PATCH v2 05/11] gnu: python-pynndescent: Update to 0.5.5 Vinicius Monego
2022-01-14 20:09   ` [bug#52696] [PATCH v2 06/11] gnu: python-opentsne: Update to 0.6.1 Vinicius Monego
2022-01-14 20:09   ` [bug#52696] [PATCH v2 07/11] gnu: python-qtconsole: Update to 4.7.7 Vinicius Monego
2022-01-14 20:09   ` [bug#52696] [PATCH v2 08/11] gnu: python-qtconsole: Enable tests Vinicius Monego
2022-01-14 20:09   ` [bug#52696] [PATCH v2 09/11] gnu: python-orange-canvas-core: Update to 0.1.24 Vinicius Monego
2022-01-14 20:09   ` [bug#52696] [PATCH v2 10/11] gnu: python-orange-widget-base: Update to 4.16.1 Vinicius Monego
2022-01-14 20:09   ` [bug#52696] [PATCH v2 11/11] gnu: orange: Update to 3.31.1 Vinicius Monego
2022-01-14 20:33 ` bug#52696: [PATCH 00/12] Update Orange Nicolas Goaziou

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