⬆️ Combined updates

[s-weigand]

Besides combining dependabot up PRs, this PR also changes pydantic from v1 to v2 and fixes a deprecation sharing when calling groupby on xarray data structures due to a changed default.

Change summary

• Bump pre-commit/action from 3.0.0 to 3.0.1
• Bump pypa/gh-action-pypi-publish from 1.8.11 to 1.8.14
• Bump asteval from 0.9.32 to 0.9.33
• Bump openpyxl from 3.1.2 to 3.1.3
• Bump pandas from 2.2.1 to 2.2.2
• Bump scipy from 1.12.0 to 1.13.1
• Bump sdtfile from 2023.9.28 to 2024.5.24
• Bump xarray from 2024.2.0 to 2024.5.0
• ⬆️ Use pydantic 2
• 🧹 Address squeeze deprecated in xarray groupby call
• 📚 Update link to tee command explanation in docstring
• Bump devops-actions/action-get-tag from 1.0.2 to 1.0.3

Checklist

• [x] ✔️ Passing the tests (mandatory for all PR's)

Closes issues

closes #1460 closes #1457 closes #1456 closes #1454 closes #1453 closes #1451 closes #1449 closes #1448 closes #1444 closes #1443 closes #1442

[github-actions[bot]]

:point_left: Launch a binder notebook on branch s-weigand/pyglotaran/combined-updates

[github-actions[bot]]

Benchmark is done. Checkout the benchmark result page. Benchmark differences below 5% might be due to CI noise.

Benchmark diff v0.7.2 vs. main

``` All benchmarks: | Change | Before [1fb14bbc] | After [d1cd0bc0] | Ratio | Benchmark (Parameter) | |----------|------------------------------|---------------------|---------|-----------------------------------------| | | 239M | 239M | 1 | IntegrationTwoDatasets.peakmem_optimize | | | 1.51±0.05s | 1.50±0.08s | 0.99 | IntegrationTwoDatasets.time_optimize | ```

Benchmark diff main vs. PR

``` All benchmarks: | Change | Before [d1cd0bc0] | After [9ea5f448] | Ratio | Benchmark (Parameter) | |----------|----------------------|---------------------|---------|-----------------------------------------| | | 239M | 239M | 1 | IntegrationTwoDatasets.peakmem_optimize | | | 1.50±0.08s | 1.44±0.06s | 0.96 | IntegrationTwoDatasets.time_optimize | ```

[codecov[bot]]

Codecov Report

All modified and coverable lines are covered by tests :white_check_mark:

Project coverage is 88.6%. Comparing base (2c88dce) to head (9ea5f44). Report is 27 commits behind head on main.

Additional details and impacted files

```diff @@ Coverage Diff @@ ## main #1458 +/- ## ===================================== Coverage 88.6% 88.6% ===================================== Files 107 107 Lines 5128 5133 +5 Branches 962 965 +3 ===================================== + Hits 4544 4549 +5 Misses 468 468 Partials 116 116 ```

:umbrella: View full report in Codecov by Sentry.
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[sonarcloud[bot]]

Quality Gate passed

Issues
0 New issues
0 Accepted issues

Measures
0 Security Hotspots
No data about Coverage
0.0% Duplication on New Code

See analysis details on SonarCloud