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⬆️ Combined updates #1458

Merged
merged 12 commits into from
Jun 1, 2024
Merged

⬆️ Combined updates #1458

merged 12 commits into from
Jun 1, 2024

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s-weigand
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@s-weigand s-weigand commented May 30, 2024

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

Checklist

  • ✔️ 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

dependabot bot and others added 8 commits May 30, 2024 20:02
Bumps [pre-commit/action](https://github.com/pre-commit/action) from 3.0.0 to 3.0.1.
- [Release notes](https://github.com/pre-commit/action/releases)
- [Commits](pre-commit/action@v3.0.0...v3.0.1)

---
updated-dependencies:
- dependency-name: pre-commit/action
  dependency-type: direct:production
  update-type: version-update:semver-patch
...

Signed-off-by: dependabot[bot] <support@github.com>
Bumps [pypa/gh-action-pypi-publish](https://github.com/pypa/gh-action-pypi-publish) from 1.8.11 to 1.8.14.
- [Release notes](https://github.com/pypa/gh-action-pypi-publish/releases)
- [Commits](pypa/gh-action-pypi-publish@v1.8.11...v1.8.14)

---
updated-dependencies:
- dependency-name: pypa/gh-action-pypi-publish
  dependency-type: direct:production
  update-type: version-update:semver-patch
...

Signed-off-by: dependabot[bot] <support@github.com>
Bumps [asteval](https://github.com/lmfit/asteval) from 0.9.32 to 0.9.33.
- [Release notes](https://github.com/lmfit/asteval/releases)
- [Commits](lmfit/asteval@0.9.32...0.9.33)

---
updated-dependencies:
- dependency-name: asteval
  dependency-type: direct:development
  update-type: version-update:semver-patch
...

Signed-off-by: dependabot[bot] <support@github.com>
Bumps [openpyxl](https://openpyxl.readthedocs.io) from 3.1.2 to 3.1.3.

---
updated-dependencies:
- dependency-name: openpyxl
  dependency-type: direct:development
  update-type: version-update:semver-patch
...

Signed-off-by: dependabot[bot] <support@github.com>
Bumps [pandas](https://github.com/pandas-dev/pandas) from 2.2.1 to 2.2.2.
- [Release notes](https://github.com/pandas-dev/pandas/releases)
- [Commits](pandas-dev/pandas@v2.2.1...v2.2.2)

---
updated-dependencies:
- dependency-name: pandas
  dependency-type: direct:production
  update-type: version-update:semver-patch
...

Signed-off-by: dependabot[bot] <support@github.com>
Bumps [scipy](https://github.com/scipy/scipy) from 1.12.0 to 1.13.1.
- [Release notes](https://github.com/scipy/scipy/releases)
- [Commits](scipy/scipy@v1.12.0...v1.13.1)

---
updated-dependencies:
- dependency-name: scipy
  dependency-type: direct:development
  update-type: version-update:semver-minor
...

Signed-off-by: dependabot[bot] <support@github.com>
Bumps [sdtfile](https://github.com/cgohlke/sdtfile) from 2023.9.28 to 2024.5.24.
- [Release notes](https://github.com/cgohlke/sdtfile/releases)
- [Changelog](https://github.com/cgohlke/sdtfile/blob/master/CHANGES.rst)
- [Commits](cgohlke/sdtfile@v2023.9.28...v2024.5.24)

---
updated-dependencies:
- dependency-name: sdtfile
  dependency-type: direct:development
  update-type: version-update:semver-major
...

Signed-off-by: dependabot[bot] <support@github.com>
Bumps [xarray](https://github.com/pydata/xarray) from 2024.2.0 to 2024.5.0.
- [Release notes](https://github.com/pydata/xarray/releases)
- [Changelog](https://github.com/pydata/xarray/blob/main/HOW_TO_RELEASE.md)
- [Commits](pydata/xarray@v2024.02.0...v2024.05.0)

---
updated-dependencies:
- dependency-name: xarray
  dependency-type: direct:production
  update-type: version-update:semver-minor
...

Signed-off-by: dependabot[bot] <support@github.com>
@s-weigand s-weigand requested review from jsnel and a team as code owners May 30, 2024 18:54
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We've reviewed this pull request using the Sourcery rules engine. If you would also like our AI-powered code review then let us know.

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Binder 👈 Launch a binder notebook on branch s-weigand/pyglotaran/combined-updates

glotaran/optimization/data_provider.py:615: UserWarning: The `squeeze` kwarg to GroupBy is being removed.Pass .groupby(..., squeeze=False) to disable squeezing, which is the new default, and to silence this warning.
    ["".join(sub_arr.values) for _, sub_arr in aligned_groups.groupby("global")]
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github-actions bot commented May 30, 2024

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] <v0.7.2>   | 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    |

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codecov bot commented May 30, 2024

Codecov Report

All modified and coverable lines are covered by tests ✅

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

Additional details and impacted files
@@          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           

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

s-weigand and others added 2 commits May 31, 2024 10:27
The old link still works if accessed via browser but the CI link check is blocked (HTTP 403) and link check fails
Bumps [devops-actions/action-get-tag](https://github.com/devops-actions/action-get-tag) from 1.0.2 to 1.0.3.
- [Release notes](https://github.com/devops-actions/action-get-tag/releases)
- [Commits](devops-actions/action-get-tag@v1.0.2...v1.0.3)

---
updated-dependencies:
- dependency-name: devops-actions/action-get-tag
  dependency-type: direct:production
  update-type: version-update:semver-patch
...

Signed-off-by: dependabot[bot] <support@github.com>
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sonarcloud bot commented May 31, 2024

Quality Gate Passed 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

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Note pydantic being updated from v1 to v2!

@jsnel jsnel merged commit 751502d into glotaran:main Jun 1, 2024
40 checks passed
@jsnel jsnel deleted the combined-updates branch June 1, 2024 20:21
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