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Fix tests that fail from new Xarray variable and attribute assignment updates #1433

Merged
merged 6 commits into from
Feb 2, 2025
Merged

Fix tests that fail from new Xarray variable and attribute assignment updates #1433

merged 6 commits into from
Feb 2, 2025

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ctuguinay
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@ctuguinay ctuguinay commented Jan 31, 2025 •
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Fixes a series of tests that fail due to recent Xarray package changes.

@ctuguinay ctuguinay changed the title Fix Tests Fix tests that fail from new Xarray updates Jan 31, 2025
@ctuguinay ctuguinay changed the title Fix tests that fail from new Xarray updates Fix tests that fail from new Xarray variable and attribute assignment updates Jan 31, 2025
@ctuguinay ctuguinay requested a review from leewujung January 31, 2025 20:58
@ctuguinay ctuguinay self-assigned this Jan 31, 2025
@ctuguinay ctuguinay added the bug Something isn't working label Jan 31, 2025
@ctuguinay ctuguinay added this to the v0.9.2 milestone Jan 31, 2025
@ctuguinay ctuguinay marked this pull request as ready for review January 31, 2025 20:59
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@leewujung This should be ready for review

leewujung
leewujung reviewed Feb 1, 2025
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echopype/tests/consolidate/test_add_depth.py Outdated
@@ -232,6 +232,7 @@ def test_ek_depth_utils_group_variable_NaNs_logger_warnings(caplog):
"NaNs. This will result in NaNs in the final `depth` array. Consider filling the "
"NaNs and calling `.add_depth(...)` again."
)
print(expected_warning)
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Since this is in test, do you still want to print this out?

leewujung
leewujung previously approved these changes Feb 1, 2025
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@ctuguinay : Looks good! Just have a small comment and otherwise feel free to merge.

@leewujung leewujung self-requested a review February 2, 2025 00:29
@ctuguinay ctuguinay merged commit f64e8c3 into OSOceanAcoustics:main Feb 2, 2025
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leewujung added a commit that referenced this pull request Feb 2, 2025
@leewujung @ctuguinay @pre-commit-ci
add exception for "anc" (#1437)
d6965c1 
* 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>

* add exception for "anc"

---------

Co-authored-by: Caesar Tuguinay <87830138+ctuguinay@users.noreply.github.com>
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
oftfrfbf pushed a commit to oftfrfbf/echopype that referenced this pull request Feb 5, 2025
@ctuguinay @oftfrfbf
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
@leewujung leewujung mentioned this pull request Feb 5, 2025
Merged
@leewujung leewujung modified the milestones: v0.9.2, v0.10.0 Feb 18, 2025
leewujung added a commit that referenced this pull request Feb 20, 2025
@oftfrfbf @ctuguinay
@leewujung @pre-commit-ci @dependabot
Backward compatibility of raw-converted dataset with xr.DataTree [a…
616f4c7 
…ll 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] <support@github.com>
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] <support@github.com>
Co-authored-by: Caesar Tuguinay <87830138+ctuguinay@users.noreply.github.com>
Co-authored-by: Wu-Jung Lee <leewujung@gmail.com>
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>
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@leewujung leewujung leewujung approved these changes

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@ctuguinay ctuguinay

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bug Something isn't working
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Echopype
Status: Done
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v0.10.0
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@ctuguinay @leewujung