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54 Commits

Author SHA1 Message Date
Peter J. A. Cock
37f6c5f81d Test on Python 3.10 ~ 3.14 2025-10-10 12:26:54 +01:00
dependabot[bot]
a32c56e1a1 Bump tj-actions/changed-files from 46 to 47 
Bumps [tj-actions/changed-files](https://github.com/tj-actions/changed-files) from 46 to 47.
- [Release notes](https://github.com/tj-actions/changed-files/releases)
- [Changelog](https://github.com/tj-actions/changed-files/blob/main/HISTORY.md)
- [Commits](https://github.com/tj-actions/changed-files/compare/v46...v47)

---
updated-dependencies:
- dependency-name: tj-actions/changed-files
  dependency-version: '47'
  dependency-type: direct:production
  update-type: version-update:semver-major
...

Signed-off-by: dependabot[bot] <support@github.com>
 2025-09-21 10:06:42 +01:00
dependabot[bot]
b4d7c115d2 Bump actions/setup-python from 5 to 6 
Bumps [actions/setup-python](https://github.com/actions/setup-python) from 5 to 6.
- [Release notes](https://github.com/actions/setup-python/releases)
- [Commits](https://github.com/actions/setup-python/compare/v5...v6)

---
updated-dependencies:
- dependency-name: actions/setup-python
  dependency-version: '6'
  dependency-type: direct:production
  update-type: version-update:semver-major
...

Signed-off-by: dependabot[bot] <support@github.com>
 2025-09-11 19:57:40 +01:00
dependabot[bot]
a4f7ca03bb Bump actions/checkout from 4 to 5 
Bumps [actions/checkout](https://github.com/actions/checkout) from 4 to 5.
- [Release notes](https://github.com/actions/checkout/releases)
- [Changelog](https://github.com/actions/checkout/blob/main/CHANGELOG.md)
- [Commits](https://github.com/actions/checkout/compare/v4...v5)

---
updated-dependencies:
- dependency-name: actions/checkout
  dependency-version: '5'
  dependency-type: direct:production
  update-type: version-update:semver-major
...

Signed-off-by: dependabot[bot] <support@github.com>
 2025-08-17 12:18:23 +01:00
João Rodrigues
fb837c6c3b Update ci.yml and change windows-2019 to windows-2022 (#5024) 
Closes #5023
 2025-07-03 08:53:04 -07:00
mdehoon
7ada95b6c5 Reset to 3.13 
3.13.5 is now cached on the runners, so specifying 3.13 will resolve to that version, and we don't need to hardcode it here any more.
 2025-06-30 13:21:37 +09:00
mdehoon
f340157030 Also use 3.13.5 when testing on Windows 2025-06-20 19:17:20 +09:00
mdehoon
2875c9d91d Use 3.13.5 instead of 3.13 2025-06-20 19:08:03 +09:00
dependabot[bot]
332c800b4d Bump tj-actions/changed-files from 45 to 46 
Bumps [tj-actions/changed-files](https://github.com/tj-actions/changed-files) from 45 to 46.
- [Release notes](https://github.com/tj-actions/changed-files/releases)
- [Changelog](https://github.com/tj-actions/changed-files/blob/main/HISTORY.md)
- [Commits](https://github.com/tj-actions/changed-files/compare/v45...v46)

---
updated-dependencies:
- dependency-name: tj-actions/changed-files
  dependency-type: direct:production
  update-type: version-update:semver-major
...

Signed-off-by: dependabot[bot] <support@github.com>
 2025-03-17 18:21:52 +00:00
Peter Cock
0a19feed25 Drop Python 3.9; focus tests on 3.10 and 3.13 (#4912) 
Note the last 32bit Windows MiniConda was for Python 3.9, this means
we will be dropping testing on 32bit Windows with these changes.
 2025-01-15 21:26:18 +00:00
Peter Cock
16596530dd Increase Linux GitHub actions timout to 20mins 
Python 3.13 was hitting the 15min limit with coverage
 2025-01-06 11:18:52 +00:00
Peter Cock
36e82eb537 GitHub actions CodeCov (#4904) 
* coverage capture on GitHub Actions (not PyPy), Linux may be too slow?
* collect coverage for Bio and BioSQL (although later not working)
* drop restriction on numpy (no longer an issue)

Pending - coverage upload from AppVeyor too
 2025-01-05 20:27:25 +00:00
Peter Cock
c4ff6403a6 Shift GitHub actions to test on Python 3.13 2024-12-06 15:00:52 +00:00
dependabot[bot]
572ce93023 Bump tj-actions/changed-files from 44 to 45 
Bumps [tj-actions/changed-files](https://github.com/tj-actions/changed-files) from 44 to 45.
- [Release notes](https://github.com/tj-actions/changed-files/releases)
- [Changelog](https://github.com/tj-actions/changed-files/blob/main/HISTORY.md)
- [Commits](https://github.com/tj-actions/changed-files/compare/v44...v45)

---
updated-dependencies:
- dependency-name: tj-actions/changed-files
  dependency-type: direct:production
  update-type: version-update:semver-major
...

Signed-off-by: dependabot[bot] <support@github.com>
 2024-08-26 18:59:39 +01:00
Michael M.
80743c4e9d Run tests with sanitizers and the debug allocator, use PyMem_Raw instead of malloc-family (#4791) 
* run github ci tests with ASAN and UBSAN
* Use PyMem raw domain instead of malloc/calloc in Cluster
* Use PyMem_Raw over malloc-family in ccealignmodule.c
* Revert changes to cluster.c and use copy trees from system to python memory
* Turn off leak sanitizer
* Use PyMem_* in cluster.c (define CLUSTER_USE_PYTHON_MEMORY macro)
* Add libstdc++.so to LD_PRELOAD when testing with ASAN

See https://github.com/google/sanitizers/issues/934
 2024-08-26 09:48:00 +01:00
Peter Cock
c0b029af66 Avoid Numpy 2.1.0 (#4798) 
Avoid numpy 2.1.0 due to np.set_printoptions() regression

See numpy bug 27254
 2024-08-21 10:37:23 +01:00
Peter Cock
abf5a3b077 Drop CodeCov from CI (wasn't working) (#4723) 
Currently this sometimes causes a CI failure, and isn't doing anything useful due to changes on the CodeCov side.

Closes #3752.
 2024-05-13 14:02:54 -04:00
Peter Cock
99eea9bf1c Drop Python 3.8 in GitHub actions; add more 3.12 
This overall drops one OS/version combination.
Could be leaner and mainly use older and newest
rather than three version?
 2024-05-13 09:29:54 +01:00
dependabot[bot]
742576a7c2 Bump tj-actions/changed-files from 43 to 44 
Bumps [tj-actions/changed-files](https://github.com/tj-actions/changed-files) from 43 to 44.
- [Release notes](https://github.com/tj-actions/changed-files/releases)
- [Changelog](https://github.com/tj-actions/changed-files/blob/main/HISTORY.md)
- [Commits](https://github.com/tj-actions/changed-files/compare/v43...v44)

---
updated-dependencies:
- dependency-name: tj-actions/changed-files
  dependency-type: direct:production
  update-type: version-update:semver-major
...

Signed-off-by: dependabot[bot] <support@github.com>
 2024-04-01 20:04:33 +01:00
dependabot[bot]
368d07cd67 Bump geekyeggo/delete-artifact from 4 to 5 
Bumps [geekyeggo/delete-artifact](https://github.com/geekyeggo/delete-artifact) from 4 to 5.
- [Release notes](https://github.com/geekyeggo/delete-artifact/releases)
- [Changelog](https://github.com/GeekyEggo/delete-artifact/blob/main/CHANGELOG.md)
- [Commits](https://github.com/geekyeggo/delete-artifact/compare/v4...v5)

---
updated-dependencies:
- dependency-name: geekyeggo/delete-artifact
  dependency-type: direct:production
  update-type: version-update:semver-major
...

Signed-off-by: dependabot[bot] <support@github.com>
 2024-03-25 14:56:19 +00:00
dependabot[bot]
9f0507d4cd Bump tj-actions/changed-files from 42 to 43 
Bumps [tj-actions/changed-files](https://github.com/tj-actions/changed-files) from 42 to 43.
- [Release notes](https://github.com/tj-actions/changed-files/releases)
- [Changelog](https://github.com/tj-actions/changed-files/blob/main/HISTORY.md)
- [Commits](https://github.com/tj-actions/changed-files/compare/v42...v43)

---
updated-dependencies:
- dependency-name: tj-actions/changed-files
  dependency-type: direct:production
  update-type: version-update:semver-major
...

Signed-off-by: dependabot[bot] <support@github.com>
 2024-03-18 13:26:40 +00:00
dependabot[bot]
798b0acf20 Bump tj-actions/changed-files from 41 to 42 
Bumps [tj-actions/changed-files](https://github.com/tj-actions/changed-files) from 41 to 42.
- [Release notes](https://github.com/tj-actions/changed-files/releases)
- [Changelog](https://github.com/tj-actions/changed-files/blob/main/HISTORY.md)
- [Commits](https://github.com/tj-actions/changed-files/compare/v41...v42)

---
updated-dependencies:
- dependency-name: tj-actions/changed-files
  dependency-type: direct:production
  update-type: version-update:semver-major
...

Signed-off-by: dependabot[bot] <support@github.com>
 2024-01-22 13:45:34 +00:00
dependabot[bot]
9e06d9a5df Bump actions/cache from 3 to 4 
Bumps [actions/cache](https://github.com/actions/cache) from 3 to 4.
- [Release notes](https://github.com/actions/cache/releases)
- [Changelog](https://github.com/actions/cache/blob/main/RELEASES.md)
- [Commits](https://github.com/actions/cache/compare/v3...v4)

---
updated-dependencies:
- dependency-name: actions/cache
  dependency-type: direct:production
  update-type: version-update:semver-major
...

Signed-off-by: dependabot[bot] <support@github.com>
 2024-01-22 13:44:48 +00:00
Peter Cock
7df51f072d Single set of Sphinx CI requirements 
Note Sphinx 7.2.0 dropped Python 3.8 support, so didn't
work to include that in all the GitHub Actions

See #4583
 2024-01-17 14:21:03 +00:00
Peter Cock
3f4885c622 Adjust CI for Doc/Makefile not Doc/api/Makefile 2024-01-04 09:10:45 +00:00
Peter Cock
146f9f4ba9 Test on pypy-3.9 rather than 3.8 2024-01-01 19:32:40 +00:00
dependabot[bot]
cf3dbadb9b Bump geekyeggo/delete-artifact from 2 to 4 
Bumps [geekyeggo/delete-artifact](https://github.com/geekyeggo/delete-artifact) from 2 to 4.
- [Release notes](https://github.com/geekyeggo/delete-artifact/releases)
- [Changelog](https://github.com/GeekyEggo/delete-artifact/blob/main/CHANGELOG.md)
- [Commits](https://github.com/geekyeggo/delete-artifact/compare/v2...v4)

---
updated-dependencies:
- dependency-name: geekyeggo/delete-artifact
  dependency-type: direct:production
  update-type: version-update:semver-major
...

Signed-off-by: dependabot[bot] <support@github.com>
 2023-12-25 15:31:37 +00:00
dependabot[bot]
6582edbef5 Bump tj-actions/changed-files from 40 to 41 
Bumps [tj-actions/changed-files](https://github.com/tj-actions/changed-files) from 40 to 41.
- [Release notes](https://github.com/tj-actions/changed-files/releases)
- [Changelog](https://github.com/tj-actions/changed-files/blob/main/HISTORY.md)
- [Commits](https://github.com/tj-actions/changed-files/compare/v40...v41)

---
updated-dependencies:
- dependency-name: tj-actions/changed-files
  dependency-type: direct:production
  update-type: version-update:semver-major
...

Signed-off-by: dependabot[bot] <support@github.com>
 2023-12-25 15:31:21 +00:00
Alex
60c6ae6f25 Update ci.yml 
Signed-off-by: sashashura <93376818+sashashura@users.noreply.github.com>
 2023-12-21 20:14:33 +00:00
dependabot[bot]
dc632858e5 Bump actions/setup-python from 4 to 5 
Bumps [actions/setup-python](https://github.com/actions/setup-python) from 4 to 5.
- [Release notes](https://github.com/actions/setup-python/releases)
- [Commits](https://github.com/actions/setup-python/compare/v4...v5)

---
updated-dependencies:
- dependency-name: actions/setup-python
  dependency-type: direct:production
  update-type: version-update:semver-major
...

Signed-off-by: dependabot[bot] <support@github.com>
 2023-12-12 20:42:55 +00:00
Lenna
cee892df2c Switch to a maintained GitHub Action for changed files (#4470) 
This reduces GitHub Actions warnings from 6 to 0!
 2023-10-31 15:18:27 +00:00
Lenna Peterson
64ef618a08 Bump geekeggo/delete-artifact to v2 2023-10-30 12:25:37 +00:00
Lenna Peterson
2095768979 Bump cache to v3 2023-10-30 12:25:37 +00:00
Lenna Peterson
68b037c1d9 Bump setup-python to v4 2023-10-30 12:25:37 +00:00
Lenna Peterson
c233ca7433 Bump checkout to v4 2023-10-30 12:25:37 +00:00
Peter Cock
1087dffd62 Test on Python 3.12 (#4454) 
Only testing on Linux Python 3.11 instead of 3.12 as we
seem to hit some resource limit under Linux Python 3.12
(fine on macOS).

i.e. Exit Code 143: Graceful Termination (SIGTERM)
 2023-10-11 11:23:46 +01:00
Peter Cock
fc61f95db9 Reduce Python range for macOS and Windows testing 
Just our oldest and newest targetted Python should
suffice. Note still use the full range to build wheels
 2023-05-22 12:01:58 +01:00
Peter Cock
0a268947c6 Drop Python 3.7 in GitHub Actions 2023-05-22 12:01:58 +01:00
Peter Cock
0ab30333db Skip Windows Python 3.11 (for now) 
Multiple tests were failing when trying to delete
temporary SQLite databases.
 2022-11-18 13:28:39 +00:00
Peter Cock
d27c3a6afc Test on Python 3.11 
Would like to phase out Python 3.7 support, but
currently PyPy still targets that version of the
Python language - so not yet?

Also now recommending Python 3.10 (was Python 3.9),
not suggesting Python 3.11 at this point as it is
still quite new and not all third packages will have
been update for it yet (e.g. providing wheels).
 2022-11-18 13:28:39 +00:00
mdehoon
5f0d64bb2a Replace the other windows-latest by windows-2019 2022-08-24 18:19:08 +09:00
mdehoon
a1e1d70e54 Replace windows-latest by windows-2019 
to see if the Windows compilation problems also appear with the previous compiler.
 2022-08-24 18:09:11 +09:00
João Rodrigues
644f0416e3 Update testing to avoid issues with compiled code and increase robustness (#3912) 
- Remove sys.path hacking from `run_tests`
- Update CI workflow to use `pip` instead of `python setup.py install`
- Force-update build dependencies (setuptools, pip, wheel) across all 3 OSes.
 2022-04-25 15:51:19 -04:00
Peter Cock
cffae09b18 Support Python 3.10 (#3844) 
Must quote 3.10 to avoid getting Python 3.1
 2022-01-21 10:58:02 +00:00
Peter Cock
ea6711685e Put ci-dependencies.txt back at top level. 
I'd prefer this under .github/workflows/ next to ci.yml
but moving it was more trouble than I expected.

Cross reference original change attempted in #3837.
 2022-01-07 10:49:32 +00:00
Peter Cock
a87199ea3f Another path to fix 
I missed this in #3837.
 2022-01-07 10:12:03 +00:00
Peter Cock
5edb4c8b07 Disable MuSQL testing on GitHub Actions 
Workaround for #3834
 2022-01-07 09:33:09 +00:00
Peter Cock
2da89c7972 Move ci-dependencies.txt under .github next to ci.tml 2022-01-07 09:33:09 +00:00
Peter Cock
5f644bab19 Remove commented out RST linting [ci skip] 
This is done via pre-commit (under the style checks)
 2021-09-08 11:24:58 +01:00
Peter Cock
1e83d21ab0 Try explicitly asking for pypy-3.7 on GitHub Actions 
https://github.com/actions/setup-python
 2021-09-06 17:09:14 +01:00