⬆️ Combined python updates

[s-weigand]

Combined update of python dependencies

Change summary

• Bump pandas from 2.1.4 to 2.2.1
• 🩹🗑️ Fix pandas deprecations
• Bump numba from 0.58.1 to 0.59.0
• Bump numpy from 1.26.2 to 1.26.4
• Bump asteval from 0.9.31 to 0.9.32
• Bump attrs from 23.1.0 to 23.2.0
• Bump pydantic from 1.10.13 to 1.10.14
• Bump ruamel-yaml from 0.18.5 to 0.18.6
• Bump scipy from 1.11.4 to 1.12.0
• Bump xarray from 2023.11.0 to 2024.2.0

Checklist

• [x] ✔️ Passing the tests (mandatory for all PR's)
• [x] 👌 Closes issue (mandatory for ✨ feature and 🩹 bug fix PR's)

Closes issues

closes #1413 closes #1416 closes #1421 closes #1428 closes #1430 closes #1431 closes #1432 closes #1433 closes #1434

[github-actions[bot]]

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

[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

[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 [c00e1ee7] | Ratio | Benchmark (Parameter) | |----------|------------------------------|---------------------|---------|-----------------------------------------| | | 239M | 239M | 1 | IntegrationTwoDatasets.peakmem_optimize | | | 1.42±0.07s | 1.40±0.08s | 0.98 | IntegrationTwoDatasets.time_optimize | ```

Benchmark diff main vs. PR

``` All benchmarks: | Change | Before [c00e1ee7] | After [06edc16f] | Ratio | Benchmark (Parameter) | |----------|----------------------|---------------------|---------|-----------------------------------------| | | 239M | 239M | 1 | IntegrationTwoDatasets.peakmem_optimize | | | 1.40±0.08s | 1.40±0.05s | 1 | 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 (c00e1ee) to head (06edc16).

Additional details and impacted files

```diff @@ Coverage Diff @@ ## main #1435 +/- ## ===================================== Coverage 88.6% 88.6% ===================================== Files 107 107 Lines 5128 5128 Branches 962 962 ===================================== Hits 4544 4544 Misses 468 468 Partials 116 116 ```

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