[med-svn] [Git][med-team/cyvcf2][master] 3 commits: New upstream version 0.31.1

[Étienne Mollier (@emollier)]

Étienne Mollier pushed to branch master at Debian Med / cyvcf2


Commits:
1504e340 by Étienne Mollier at 2024-07-20T20:04:06+02:00
New upstream version 0.31.1
- - - - -
bf1b89a7 by Étienne Mollier at 2024-07-20T20:04:06+02:00
Update upstream source from tag 'upstream/0.31.1'

Update to upstream version '0.31.1'
with Debian dir 88a33b23a05193dbc98dfbdbb6848638f6f5e031
- - - - -
0bad9e8a by Étienne Mollier at 2024-07-20T20:15:07+02:00
ready to upload to unstable.

- - - - -


7 changed files:

- .github/workflows/build.yml
- CHANGES.md
- cyvcf2/__init__.py
- debian/changelog
- pyproject.toml
- requirements.txt
- setup.py


Changes:

=====================================
.github/workflows/build.yml
=====================================
@@ -110,6 +110,18 @@ jobs:
         run: |
           pytest --cov cyvcf2 --cov-report term-missing
 
+      # make sure to keep this numpy version in sync with setup.py
+      - name: Test with oldest numpy that we support
+        if: contains(fromJson('["3.7"]'), matrix.python-version)
+        run: |
+          pip install --force-reinstall --no-cache-dir 'numpy==1.16.0'
+          pytest --cov cyvcf2 --cov-report term-missing
+
+      - name: Test with newest available numpy
+        run: |
+          pip install -U numpy
+          pytest --cov cyvcf2 --cov-report term-missing
+
   windows_build:
     name: Run tests on Python windows-2022 MSYS2 UCRT64
     runs-on: windows-2022
@@ -164,6 +176,11 @@ jobs:
         run: |
           pytest --cov cyvcf2 --cov-report term-missing
 
+      - name: Test with newest available numpy
+        run: |
+          pip install -U numpy
+          pytest --cov cyvcf2 --cov-report term-missing
+
   sdist:
     runs-on: ubuntu-22.04
     strategy:
@@ -207,6 +224,11 @@ jobs:
         run: |
           pytest --import-mode importlib --cov cyvcf2 --cov-report term-missing
 
+      - name: Test with newest available numpy
+        run: |
+          pip install -U numpy
+          pytest --import-mode importlib --cov cyvcf2 --cov-report term-missing
+
       - name: Upload sdist tarball
         if: runner.os == 'Linux'
         uses: actions/upload-artifact at v4


=====================================
CHANGES.md
=====================================
@@ -1,3 +1,6 @@
+# v0.31.1
++ build fix for numpy 2.0.0 (#307, #308 thanks @aryarm for fixing build)
+
 # v0.31.0
 + fix OSX ARM wheels (#305, #306 thanks @graphenn for fix)
 


=====================================
cyvcf2/__init__.py
=====================================
@@ -2,4 +2,4 @@ from .cyvcf2 import (VCF, Variant, Writer, r_ as r_unphased, par_relatedness,
                      par_het)
 Reader = VCFReader = VCF
 
-__version__ = "0.31.0"
+__version__ = "0.31.1"


=====================================
debian/changelog
=====================================
@@ -1,3 +1,9 @@
+cyvcf2 (0.31.1-1) unstable; urgency=medium
+
+  * New upstream version 0.31.1
+
+ -- Étienne Mollier <emollier at debian.org>  Sat, 20 Jul 2024 20:05:15 +0200
+
 cyvcf2 (0.31.0-1) unstable; urgency=medium
 
   * New upstream version 0.31.0


=====================================
pyproject.toml
=====================================
@@ -1,8 +1,9 @@
 [build-system]
 requires = [
-    "setuptools",
-    "wheel",
-    "cython>=0.23.3",
-    'oldest-supported-numpy; os_name != "nt"',
-    'numpy; os_name == "nt"'
+  "setuptools",
+  "wheel",
+  "cython>=0.23.3",
+  'oldest-supported-numpy; os_name != "nt" and python_version < "3.9"',
+  'numpy; os_name == "nt" and python_version < "3.9"',
+  'numpy>=2.0.0; python_version >= "3.9"',
 ]


=====================================
requirements.txt
=====================================
@@ -2,5 +2,6 @@ cython>=0.23.3
 coloredlogs
 click
 setuptools
-numpy; os_name == 'nt'  
-oldest-supported-numpy; os_name != 'nt'
+oldest-supported-numpy; os_name != "nt" and python_version < "3.9"
+numpy; os_name == "nt" and python_version < "3.9"
+numpy>=2.0.0; python_version >= "3.9"


=====================================
setup.py
=====================================
@@ -290,7 +290,8 @@ setup(
         ],
     ),
     python_requires=">=3.7",
-    install_requires=["numpy", "coloredlogs", "click"],
+    # make sure to keep this numpy version in sync with build.yml
+    install_requires=["numpy>=1.16.0", "coloredlogs", "click"],
     include_package_data=True,
     zip_safe=False,
     cmdclass={



View it on GitLab: https://salsa.debian.org/med-team/cyvcf2/-/compare/e915c373668585e314364bc9c9a2ea9a7c1f1c85...0bad9e8ad82291d91447ad0f5db878bd6514c893

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