Add codecov token to test_and_deploy.yml #129
Conversation
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not sure why the coverage reports are not found despite being successfully generated on macos-14 py3.10 and on windows-latest py3.10 |
Maybe because I'm using actions v2, and that still doesn't have the optional argument for the codecov token? Let me try with main. |
I've tried this but it hasn't fixed the issue. I also refreshed (regenerated) the token and updated it in the secrets, but no luck also there. Is it possible that there is no code report because we there are no relevant code lines in the diff? |
not sure that's the reason as uploading works in ubuntu and macOS-latest. I didn't encounter any issues with the toy example used to test the codecov PR in actions. |
You are absolutely right. This is strange indeed. Tagging @adamltyson as he has more experience with codecov. |
Codecov ReportAll modified and coverable lines are covered by tests ✅
Additional details and impacted files@@ Coverage Diff @@
## main #129 +/- ##
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+ Coverage 99.13% 99.21% +0.08%
==========================================
Files 8 8
Lines 461 509 +48
==========================================
+ Hits 457 505 +48
Misses 4 4 ☔ View full report in Codecov by Sentry. |
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I think it's working now? Based on this comment I generated a new org-level token and added that to the repo. Assuming this works, I think this token should be added at the GitHub org level (and also for @brainglobe, cc @alessandrofelder). |
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Is that related to codecov though, the error says |
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Yes, it may be unrelated to codecov. It seems to me that the tests are not even being run on these two operating systems?
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Aha, now finding a trail: quantumjot/btrack#119 |
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We might have to replicate the solution implemented here: quantumjot/btrack#130 |
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Now that we think the problem is not due to codecov, I plan to:
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* Add codecov token to test_and_deploy.yml * use test action from main branch * switch back to using v2 of the test action
* Added `filtering.py` module, w/ draft `interp_pose()` & `filter_confidence()` fxns * Fix logging for operations in place * Renamed fxns to `interpolate_over_time()` and `filter_by_confidence` * Cleaned up code + corrected docstrings * Refactored `filtering.py` to movement base folder * Improved logging logic, fixed diagnostic report, removed in-place * Removed printing of diagnostic report * Updated dependency from `xarray` to `xarray[accel]` * Added testing for `filtering.py` * Minor fixes and clean-up * Reorganise Accessor (#122) * Check for expected `dims` and `data_vars` in dataset * Fix `missing_dim_dataset` fixture * Rename `poses` accessor to `move` * Rename `PoseAccessor` class to `MoveAccessor` * Rename `poses_accessor.py` to `move_accessor.py` * Move `move_accessor.py` to the top level * Fix accessor docstring formatting * Compute locomotion features (#106) * Draft compute velocity * Add test for displacement * Fix confidence values in `valid_pose_dataset` fixture * Refactor kinematics test and functions * Vectorise kinematic functions * Refactor repeated calls to compute magnitude + direction * Displacement to return 0 instead of NaN * Return x y components in kinematic functions * Refactor kinematics tests * Remove unnecessary instantiations * Improve time diff calculation * Prefix kinematics methods with `compute_` * Add kinematic properties to `PosesAccessor` * Update `test_property` docstring * Refactor `_vector` methods and kinematics tests * Update `expected_dataset` docstring * Rename `poses` to `move` in `PosesAccessor` * Refactor properties in `PosesAccessor` * Remove vector util functions and tests * Update `not_a_dataset` fixture description * Validate dataset upon accessor property access * Update `poses_accessor` test description * Validate input data in kinematic functions * Remove unused fixture * Parametrise kinematics tests * Set `compute_derivative` as internal function * Update `kinematics.py` docstrings * Add new modules to API docs * Update `move_accessor` docstrings * Rename `test_move_accessor` filename * Include M1 runners in CI and update install instructions (#125) * also test on macOS 14 M1 runner * conda install hdf5 * Add dependabot config (#128) * Bump actions/cache from 3 to 4 (#130) 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](actions/cache@v3...v4) --- updated-dependencies: - dependency-name: actions/cache dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * [pre-commit.ci] pre-commit autoupdate (#131) updates: - [github.com/astral-sh/ruff-pre-commit: v0.2.0 → v0.3.0](astral-sh/ruff-pre-commit@v0.2.0...v0.3.0) - [github.com/psf/black: 24.1.1 → 24.2.0](psf/black@24.1.1...24.2.0) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> * Add codecov token to test_and_deploy.yml (#129) * Add codecov token to test_and_deploy.yml * use test action from main branch * switch back to using v2 of the test action * tweaked phrasing in docstrings * added filtering functions to API index * add note about default confidence threshold * rename and reorganise filter_diagnostics as report_nan_values * use xarray's copy method * max_gaps is in seconds and also works at edges * use xarray's built-in isnull method * added sphinx-gallery example for filtering and interpolation --------- Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: Chang Huan Lo <[email protected]> Co-authored-by: Niko Sirmpilatze <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
This will have to wait until @lochhh has tested the updated action in PR 128, and a new v2 release of NIU actions is made.
neuroinformatics-unit/actions/test@mainneuroinformatics-unit/actions