Compute dask array before np array equal [all tests ci] #1452
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ctuguinay
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Codecov ReportAll modified and coverable lines are covered by tests ✅
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## main #1452 +/- ##
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+ Coverage 83.52% 85.22% +1.69%
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Files 64 72 +8
Lines 5686 6590 +904
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+ Hits 4749 5616 +867
- Misses 937 974 +37
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leewujung
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Feb 18, 2025
ctuguinay
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Apr 3, 2025
* use align vectors instead of from matrix for a channel-wise rotation * use normalization logic, add warnings, and add tests * simplify test * small word change * Update echopype/consolidate/ek_depth_utils.py Co-authored-by: Wu-Jung Lee <[email protected]> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * replace previous APA7 citation with recent ICES APA7 citation (#1455) * pin scipy to temporarily ensure that rotation matrix calculation does not fail (#1460) * [pre-commit.ci] pre-commit autoupdate (#1461) updates: - [github.com/PyCQA/flake8: 7.1.1 → 7.1.2](PyCQA/flake8@7.1.1...7.1.2) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> * Check if there exist any swap files before cleaning them up [all tests ci] (#1451) * check if zarr stores > 0 * add a test for echodata delete * fix path * add comments for readability --------- Co-authored-by: Wu-Jung Lee <[email protected]> * remove __setattr__ from EchoData (#1457) * compute dask array before np array equal (#1452) * Dataset.dims to Dataset.sizes [all tests ci] (#1453) * dims to sizes * dims to sizes when using ds.dims * dims to sizes for test echodata combine * Chunks as dictionaries in `_get_auto_chunk` [all tests ci] (#1454) * chunks as dictionaries in _get_auto_chunk * when zarr encoding get chunks as list-like and rename _get_auto_chunk to _get_dask_auto_chunk to show that there is a difference between Dask and Zarr chunking * set decode timedelta to False since it will default to this in later xarray versions (#1462) * Fix deprecation warning for truth value of an empty array [all tests ci] (#1450) * fix deprecation warning for truth value of an empty array * change test outcome from True to False when param is missing * found logic error in checking parameter validity before loading XML --------- Co-authored-by: Wu-Jung Lee <[email protected]> * Fill in NaN for missing EK80 coefficients [all tests ci] (#1458) * fill in nan for missing filter coeffs from all channels * update test_convert_ek80_no_fil_coeff * remove commented out section * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * cast numpy float array to int * add compute Sv test * remove test mark --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: ctuguinay <[email protected]> * Backward compatibility of raw-converted dataset with `xr.DataTree` [all tests ci] (#1447) * EP-1420 resolved path issue with ek60_missing_channel_power * EP-1420 fixed path to use string concatenation * formatting * adding conditionals for checking platform nmea and exchange from time1 to time_nmea * working datatree for v0.9.0 w o calibration * Drop Ping Time Duplicates (#1382) * init commit * revert change to fix merge conflict * test only one file * use other file * move test duplicate to test convert ek * add extra line * move test back to ek80 convert * pin zarr and add check unique ping time duplicates and tests * fix test message * test remove zarr pin * add back zarr pin * Fix tests that fail from new Xarray variable and attribute assignment updates (#1433) * add .values to change water level scalar value * add .values to fillna * fix assign attributes * remove test1 * update echodata properly * remove print statement * Assemble AD2CP timestamp with nanosecond precision (#1436) * assemble ad2cp timestamp at ns instead of us * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * add noqa --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> * Use `import_resources.files` instead of the legacy `open_text` (#1434) * use import_resources.files to open yaml files * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * import from importlib.resources * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> * bump codespell version, add exceptions (#1438) * Pin `zarr` and `netcdf4` temporarily [all tests ci] (#1429) * pin zarr and netcdf4 in requirements.txt * change np.alltrue to np.all * use np.argmin(da.data) instead of da.argmin() * use S instead s for MVBS ping_time_bin * extract single element in computing nsamples and L in tapered_chirp * change from S to s in testing.py * Add `type-extensions` to requirements.txt (#1440) * add type-extensions * sort requirements.txt * add manual trigger to pypi workflow (#1442) * update cff with ices paper data (#1443) * add assign actual range utility function (#1435) * chore(deps): bump actions/setup-python from 5.3.0 to 5.4.0 (#1445) Bumps [actions/setup-python](https://github.com/actions/setup-python) from 5.3.0 to 5.4.0. - [Release notes](https://github.com/actions/setup-python/releases) - [Commits](actions/setup-python@v5.3.0...v5.4.0) --- updated-dependencies: - dependency-name: actions/setup-python dependency-type: direct:production update-type: version-update:semver-minor ... 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 (#1446) * [pre-commit.ci] pre-commit autoupdate updates: - [github.com/PyCQA/isort: 5.13.2 → 6.0.0](PyCQA/isort@5.13.2...6.0.0) - [github.com/psf/black: 24.10.0 → 25.1.0](psf/black@24.10.0...25.1.0) - [github.com/codespell-project/codespell: v2.4.0 → v2.4.1](codespell-project/codespell@v2.4.0...v2.4.1) * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> * added pooch and bound the test registry to the echodata test * EP-1420 added legacy test files >=v0.8.4, created pooch registry, parameterized test * EP-1420 checked tests * EP-1420 debugging TestEchoData test failures, test_nbytes, test_setattr, & test_setitem * EP-1447 troubleshooting bug still * EP-1420 removed pooch and added normal test path resources * EP-1420 fixed test_nbytes, commented out test_setattr * EP-1420 changed "time_nmea" to "nmea_time", added ek80 legacy_datatree tests, fixed readme * EP-1420 removed import * trying to add sonar channel_all * EP-1420 checked sonar for channel and renamed to channel_all * check legacy data differently * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * remove v0.9.2 zarr test files * remove test_setattr that is no longer needed, see #1457 that removes EchoData.__setattr__ * Update echopype/tests/echodata/test_echodata.py --------- Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: Caesar Tuguinay <[email protected]> Co-authored-by: Wu-Jung Lee <[email protected]> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * Add v0.9.1 and v0.10.0 release notes to docs (#1465) * add v0.9.1 and v0.10.0 whats new * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> * Update workflows to use python 3.12 and ubuntu 22.04 [all tests ci] (#1466) * update to use python 3.12 and ubuntu 22.04 * update v0.10.0 release notes * Replace `pkg_resources.resource_string` with `importlib.resources.files` [all tests ci] (#1468) * replace pkg_resources with importlib.resources * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * remove unused pkg_resources import * update __name__ to __package__ and use read_text * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * remove unused pkg_resources again * update whats new --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> * chore(deps): bump pypa/gh-action-pypi-publish from 1.12.3 to 1.12.4 (#1430) Bumps [pypa/gh-action-pypi-publish](https://github.com/pypa/gh-action-pypi-publish) from 1.12.3 to 1.12.4. - [Release notes](https://github.com/pypa/gh-action-pypi-publish/releases) - [Commits](pypa/gh-action-pypi-publish@v1.12.3...v1.12.4) --- updated-dependencies: - dependency-name: pypa/gh-action-pypi-publish dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * chore(deps): bump actions/cache from 4.2.0 to 4.2.1 (#1469) Bumps [actions/cache](https://github.com/actions/cache) from 4.2.0 to 4.2.1. - [Release notes](https://github.com/actions/cache/releases) - [Changelog](https://github.com/actions/cache/blob/main/RELEASES.md) - [Commits](actions/cache@v4.2.0...v4.2.1) --- updated-dependencies: - dependency-name: actions/cache dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * not -> no (#1471) * [pre-commit.ci] pre-commit autoupdate (#1472) updates: - [github.com/PyCQA/isort: 6.0.0 → 6.0.1](PyCQA/isort@6.0.0...6.0.1) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> * chore(deps): bump actions/cache from 4.2.1 to 4.2.2 (#1473) Bumps [actions/cache](https://github.com/actions/cache) from 4.2.1 to 4.2.2. - [Release notes](https://github.com/actions/cache/releases) - [Changelog](https://github.com/actions/cache/blob/main/RELEASES.md) - [Commits](actions/cache@v4.2.1...v4.2.2) --- updated-dependencies: - dependency-name: actions/cache dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * chore(deps): bump actions/setup-python from 5.4.0 to 5.5.0 (#1481) Bumps [actions/setup-python](https://github.com/actions/setup-python) from 5.4.0 to 5.5.0. - [Release notes](https://github.com/actions/setup-python/releases) - [Commits](actions/setup-python@v5.4.0...v5.5.0) --- updated-dependencies: - dependency-name: actions/setup-python dependency-version: 5.5.0 dependency-type: direct:production update-type: version-update:semver-minor ... 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 (#1480) updates: - [github.com/PyCQA/flake8: 7.1.2 → 7.2.0](PyCQA/flake8@7.1.2...7.2.0) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> * chore(deps): bump actions/cache from 4.2.2 to 4.2.3 (#1479) Bumps [actions/cache](https://github.com/actions/cache) from 4.2.2 to 4.2.3. - [Release notes](https://github.com/actions/cache/releases) - [Changelog](https://github.com/actions/cache/blob/main/RELEASES.md) - [Commits](actions/cache@v4.2.2...v4.2.3) --- updated-dependencies: - dependency-name: actions/cache dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * expand ping time preemptively and add corresponding chunking tests (#1483) * Enhance `compute_MVBS` feasability (#1470) * add range var max and reindex to compute_MVBS parameters and drop flox maximum version * add tests for compute MVBS changes * add todo for compute NASC * add np.nan fill value * Update echopype/commongrid/api.py Co-authored-by: Wu-Jung Lee <[email protected]> --------- Co-authored-by: Wu-Jung Lee <[email protected]> * indent line of code --------- Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: Wu-Jung Lee <[email protected]> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: oftfrfbf <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Jan Meischner <[email protected]>
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Resolves:
which was discovered in #1444.