Backward compatibility of raw-converted dataset with `xr.DataTree` [all tests ci] #1447

oftfrfbf · 2025-02-05T20:24:11Z

This is for issue #1420 to reconcile backwards compatability.

Test files were added for legacy data from v0.8.4 up to v0.9.2 (technically up to version "0.9.1.dev30+gb328bf91.d20241223" since there is no tagged "0.9.2" yet). The test data was derived from an 'ek60' raw file and '.nc' and '.zarr' echodata backups were created using python 3.10.12.

I created a Pooch registry and wired the test files into the test path — if that is a problem I can rework the code and we can add the files to the google drive. In the interim that registry will eventually need to be pointed to test files living somewhere in echopype release assets and changes will need to be made to the conftest.py base_url and version values.

(Also sorry for some of the erroneous edits that got added. I am not sure why my pycharm environment was making so many changes, must be some problem with the way I configured the linter.)

…1 to time_nmea

* 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

… updates (OSOceanAcoustics#1433) * add .values to change water level scalar value * add .values to fillna * fix assign attributes * remove test1 * update echodata properly * remove print statement

…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>

…anAcoustics#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>

…#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 * sort requirements.txt

…oustics#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 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>

…ameterized test

codecov-commenter · 2025-02-05T20:36:15Z

Codecov Report

Attention: Patch coverage is 96.42857% with 1 line in your changes missing coverage. Please review.

Project coverage is 85.77%. Comparing base (9f56124) to head (ef015d9).
Report is 188 commits behind head on main.

Files with missing lines	Patch %	Lines
echopype/echodata/echodata.py	96.42%	1 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main    #1447      +/-   ##
==========================================
+ Coverage   83.52%   85.77%   +2.25%     
==========================================
  Files          64       72       +8     
  Lines        5686     6608     +922     
==========================================
+ Hits         4749     5668     +919     
- Misses        937      940       +3

Flag	Coverage Δ
unittests	`85.77% <96.42%> (+2.25%)`	⬆️

Flags with carried forward coverage won't be shown. Click here to find out more.

☔ View full report in Codecov by Sentry.
📢 Have feedback on the report? Share it here.

leewujung · 2025-02-10T13:07:41Z

@oftfrfbf : Ah ok, this is because the channel coordinate/dimension in the parent (Sonar) group has 5 channels, and one child group has 3 channels and the other has 2 channels (i.e., some channels collect power/angle data, some channels collect complex data, see here). I think the easiest is to change channel in the Sonar group to be channel_all, so that there is no conflicts here.

The ek80 legacy dataset is now in the docker image!

oftfrfbf · 2025-02-11T18:23:36Z

The ek80 legacy dataset is now in the docker image!

@leewujung thank you for adding that!

I think the easiest is to change channel in the Sonar group to be channel_all, so that there is no conflicts here.

Is this something I should follow up on? If so, where would it need to happen? I would assume in the "from_file" method to fix legacy versions I would need to do another rename operation, but it would also need to happen in the echodata object as well elsewhere?

(I will be offline from Feb 15th to the 23rd p.s.)

leewujung · 2025-02-13T22:20:12Z

I think the easiest is to change channel in the Sonar group to be channel_all, so that there is no conflicts here.

Is this something I should follow up on? If so, where would it need to happen? I would assume in the "from_file" method to fix legacy versions I would need to do another rename operation, but it would also need to happen in the echodata object as well elsewhere?

(I will be offline from Feb 15th to the 23rd p.s.)

Ah you're right, I somehow missed the part about the initial setting in the Echodata object.

Could you please make the change to fix legacy versions? and I'll pick up from there to update the part to set this variable when assembling the EchoData.

Also, thinking about the logic again, we can avoid opening the data twice by only reading the Sonar group using xr.open_dataset(FILENAME/Sonar, ...), and do open_datatree if it is the new data (containing channel_all) or do open_groups and the associated ops you have if it is the legacy data (containing channel). Do you think this would work?

oftfrfbf · 2025-02-14T23:44:04Z

Could you please make the change to fix legacy versions? and I'll pick up from there to update the part to set this variable when assembling the EchoData.

Made some changes to accommodate this. I noticed that the children were also changed from 'channel' to 'channel_all' when I renamed the variable, I am not entirely sure if that is what you were looking to happen.

I was having some sort of problem running the tests with versions 0.9.2 of the test files, I am not sure why that is so if you could please troubleshoot and resolve. Maybe it has to do with the test files being dev snapshot conversions that are out of date now (might have to recreate them with the latest dev 0.9.2 version of echopype).

Also, thinking about the logic again, we can avoid opening the data twice by only reading the Sonar group using xr.open_dataset(FILENAME/Sonar, ...), and do open_datatree if it is the new data (containing channel_all) or do open_groups and the associated ops you have if it is the legacy data (containing channel). Do you think this would work?

This makes sense to me. It would be nice to test it out to see what the performance differences are, I am out of time before leaving town though so this will have to wait for another day. I will be offline until the 22nd. Things are also getting very very grim with respect to university institute funding and my federal institution so I will have to see if we still exist a week from now. Good luck with continued development.

leewujung · 2025-02-15T00:06:11Z

Maybe it has to do with the test files being dev snapshot conversions that are out of date now (might have to recreate them with the latest dev 0.9.2 version of echopype)

By "the latest dev 0.9.2 version of echopype" do you mean what's in main?

I noticed that the children were also changed from 'channel' to 'channel_all' when I renamed the variable, I am not entirely sure if that is what you were looking to happen.

I think it may need to be a roundabout to make xarray recognizing the channels are not supposed to be inherited, something like:

changing channel in the child groups to channel_new
changing channel in the parent group to channel_all
changing channel_new back to channel

Things are also getting very very grim with respect to university institute funding and my federal institution so I will have to see if we still exist a week from now. Good luck with continued development.

Sigh, I hope things will go the right way... 🤞 Thanks for all of your help!

oftfrfbf · 2025-02-16T00:52:34Z

'By "the latest dev 0.9.2 version of echopype" do you mean what's in main?'

Yeah, I didn't have a lot of time to figure out what the problem was - or if there even was one. Maybe I just didn't have the latest updates synced properly.

leewujung · 2025-02-16T20:55:46Z

So the channel to channel_all actually was not the problem for the failed tests. The problem lies in assuming all echodata files one tries to open has time1 in the Platform/NMEA group, but that part may be different depending on the sonar_model and whether it's legacy.

I'll get this fixed using the approach I proposed above to open individual group instead of open_datatree or open_groups to avoid opening the dataset twice. Let's see if it works out!

for more information, see https://pre-commit.ci

leewujung · 2025-02-16T22:26:22Z

By "the latest dev 0.9.2 version of echopype" do you mean what's in main?

Yeah, I didn't have a lot of time to figure out what the problem was - or if there even was one. Maybe I just didn't have the latest updates synced properly.

Ok, I think we can do without this, since there isn't a v0.9.2 release!

… that removes EchoData.__setattr__

echopype/tests/echodata/test_echodata.py

ctuguinay · 2025-02-20T01:33:49Z

echopype/echodata/echodata.py

+            # Update Sonar for all sonar_model if channel exists as a coordinate
+            sonar = temp_tree["/Sonar"]
+            if "channel" in sonar.coords:
+                # TODO: do we actually want to rename the children as well?


Correct me if I'm wrong, but everything must be renamed to ensure that the datatree enforced parent-child inheritance holds if it's read in again right?

And from #1419, I think that the "channel_all" renaming should only be done to the EK80 files and not the EK60 files.

Or anything that goes through EK80 set groups, so EK80 and ES80.

Sorry I should've also highlighted line 224.

@ctuguinay : I think that we should keep the variable name the same across different sonar models, so that it is easier to code things up based on those downstream. In this case that would be channel_all in the Sonar group and channel in the Sonar/Beam_groupX groups.

This does mean that we have both channel_all and channel in the Sonar/Beam_groupX groups due to the inheritance, but no variables are aligned with the inherited channel_all coordinate.

@leewujung Ah I see, I think I agree with you on this. Right now, the set groups for EK60 doesn't have "channel_all" in Sonar/Beam_groupX. I can add that to ensure that we have uniform naming across both EK60 and EK80 set groups.

Good catch - I have overlooked that missing variable... yes please add it in!

Ok @ctuguinay and I just talked and decided to keep it as is to not introduce confusion. We'll take on a review of all variables at another time.

ctuguinay · 2025-02-20T01:50:25Z

@leewujung I just had a few comments on the legacy checker/fixing code. Let me know if they're correct and I can go in and modify if needed.

leewujung · 2025-02-20T04:11:35Z

@ctuguinay : Thanks for reviewing this, and making the change for .dims to .sizes. I responded to you comments above. Let me know what you think.

leewujung · 2025-02-20T22:54:44Z

Ok, we've resolved all points here now and I'll go ahead to merge. Thanks @oftfrfbf and @ctuguinay for your work on this!

…ll tests ci] (OSOceanAcoustics#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 (OSOceanAcoustics#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 (OSOceanAcoustics#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 (OSOceanAcoustics#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` (OSOceanAcoustics#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 (OSOceanAcoustics#1438) * Pin `zarr` and `netcdf4` temporarily [all tests ci] (OSOceanAcoustics#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 (OSOceanAcoustics#1440) * add type-extensions * sort requirements.txt * add manual trigger to pypi workflow (OSOceanAcoustics#1442) * update cff with ices paper data (OSOceanAcoustics#1443) * add assign actual range utility function (OSOceanAcoustics#1435) * chore(deps): bump actions/setup-python from 5.3.0 to 5.4.0 (OSOceanAcoustics#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 (OSOceanAcoustics#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 OSOceanAcoustics#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>

* 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]>

oftfrfbf and others added 20 commits January 19, 2025 05:46

EP-1420 resolved path issue with ek60_missing_channel_power

b9b6089

EP-1420 fixed path to use string concatenation

c0dcf24

formatting

7451792

adding conditionals for checking platform nmea and exchange from time…

21cdc22

…1 to time_nmea

working datatree for v0.9.0 w o calibration

9f8a406

Fix tests that fail from new Xarray variable and attribute assignment…

93d2d9a

… updates (OSOceanAcoustics#1433) * add .values to change water level scalar value * add .values to fillna * fix assign attributes * remove test1 * update echodata properly * remove print statement

bump codespell version, add exceptions (OSOceanAcoustics#1438)

820f4bf

Add type-extensions to requirements.txt (OSOceanAcoustics#1440)

f701820

* add type-extensions * sort requirements.txt

add manual trigger to pypi workflow (OSOceanAcoustics#1442)

d09be4e

update cff with ices paper data (OSOceanAcoustics#1443)

a66af37

add assign actual range utility function (OSOceanAcoustics#1435)

35310b7

added pooch and bound the test registry to the echodata test

9174b70

EP-1420 added legacy test files >=v0.8.4, created pooch registry, par…

e66bdf2

…ameterized test

EP-1420 checked tests

48f7118

oftfrfbf assigned oftfrfbf and leewujung and unassigned oftfrfbf Feb 5, 2025

oftfrfbf added bug Something isn't working AA SI labels Feb 5, 2025

oftfrfbf mentioned this pull request Feb 5, 2025

Backward compatibility of raw-converted dataset after xarray.DataTree migration #1420

Closed

2 tasks

leewujung changed the title ~~Ep 1420~~ Backward compatibility of raw-converted dataset with xr.DataTree [all tests ci] Feb 5, 2025

leewujung closed this Feb 5, 2025

leewujung reopened this Feb 5, 2025

oftfrfbf added 2 commits February 14, 2025 16:31

trying to add sonar channel_all

a6acfcd

EP-1420 checked sonar for channel and renamed to channel_all

4da444e

ctuguinay mentioned this pull request Feb 16, 2025

Resolve critical warnings revealed in tests #1439

Open

7 tasks

leewujung and others added 2 commits February 16, 2025 14:08

check legacy data differently

4ee764e

[pre-commit.ci] auto fixes from pre-commit.com hooks

3599856

for more information, see https://pre-commit.ci

leewujung mentioned this pull request Feb 16, 2025

Inconsistency of if Platform/NMEA group exists #1456

Open

remove v0.9.2 zarr test files

b181b92

leewujung requested a review from ctuguinay February 16, 2025 22:29

leewujung mentioned this pull request Feb 17, 2025

Remove __setattr__ from EchoData [all tests ci] #1457

Merged

leewujung added 3 commits February 17, 2025 10:33

Merge branch 'main-upstream' into EP-1420

72d3d7a

Merge branch 'main-upstream' into EP-1420

e19c695

remove test_setattr that is no longer needed, see OSOceanAcoustics#1457…

a2eaacb

… that removes EchoData.__setattr__

ctuguinay reviewed Feb 20, 2025

View reviewed changes

echopype/tests/echodata/test_echodata.py Outdated Show resolved Hide resolved

ctuguinay reviewed Feb 20, 2025

View reviewed changes

Update echopype/tests/echodata/test_echodata.py

ef015d9

leewujung added this to the v0.10.0 milestone Feb 20, 2025

leewujung merged commit 616f4c7 into OSOceanAcoustics:main Feb 20, 2025
5 checks passed

Backward compatibility of raw-converted dataset with xr.DataTree [all tests ci] #1447

Backward compatibility of raw-converted dataset with xr.DataTree [all tests ci] #1447

Uh oh!

Conversation

oftfrfbf commented Feb 5, 2025 • edited Loading Uh oh! There was an error while loading. Please reload this page.

Uh oh!

Uh oh!

codecov-commenter commented Feb 5, 2025 • edited Loading Uh oh! There was an error while loading. Please reload this page.

Uh oh!

Codecov Report

Uh oh!

leewujung commented Feb 10, 2025

Uh oh!

oftfrfbf commented Feb 11, 2025 • edited Loading Uh oh! There was an error while loading. Please reload this page.

Uh oh!

Uh oh!

leewujung commented Feb 13, 2025

Uh oh!

oftfrfbf commented Feb 14, 2025 • edited Loading Uh oh! There was an error while loading. Please reload this page.

Uh oh!

Uh oh!

leewujung commented Feb 15, 2025

Uh oh!

oftfrfbf commented Feb 16, 2025

Uh oh!

leewujung commented Feb 16, 2025 • edited Loading Uh oh! There was an error while loading. Please reload this page.

Uh oh!

Uh oh!

leewujung commented Feb 16, 2025

Uh oh!

Uh oh!

Choose a reason for hiding this comment

Uh oh!

Choose a reason for hiding this comment

Uh oh!

Choose a reason for hiding this comment

Uh oh!

Choose a reason for hiding this comment

Uh oh!

Choose a reason for hiding this comment

Uh oh!

Choose a reason for hiding this comment

Uh oh!

Choose a reason for hiding this comment

Uh oh!

Choose a reason for hiding this comment

Uh oh!

ctuguinay commented Feb 20, 2025

Uh oh!

leewujung commented Feb 20, 2025

Uh oh!

leewujung commented Feb 20, 2025

Uh oh!

Uh oh!

Uh oh!

Backward compatibility of raw-converted dataset with `xr.DataTree` [all tests ci] #1447

Backward compatibility of raw-converted dataset with `xr.DataTree` [all tests ci] #1447

oftfrfbf commented Feb 5, 2025 •

edited

Loading

codecov-commenter commented Feb 5, 2025 •

edited

Loading

oftfrfbf commented Feb 11, 2025 •

edited

Loading

oftfrfbf commented Feb 14, 2025 •

edited

Loading

leewujung commented Feb 16, 2025 •

edited

Loading