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Release/0.5.1 #163

Merged
merged 96 commits into from
Dec 8, 2023
Merged

Release/0.5.1 #163

merged 96 commits into from
Dec 8, 2023

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picciama
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@picciama picciama commented Dec 8, 2023 •
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PR Checklist

  • This comment contains a description of changes (with reason)
  • Referenced issue is linked
  • If you've fixed a bug or added code that should be tested, add tests!
  • Documentation in docs is updated

Description of changes

see release notes

Technical details

see descriptions of PRs in release notes

dependabot bot and others added 30 commits July 10, 2023 04:21
@dependabot
[DEPENDABOT]: Bump mshick/add-pr-comment from 1 to 2
8977b8a 
Bumps [mshick/add-pr-comment](https://github.com/mshick/add-pr-comment) from 1 to 2.
- [Release notes](https://github.com/mshick/add-pr-comment/releases)
- [Commits](mshick/add-pr-comment@v1...v2)

---
updated-dependencies:
- dependency-name: mshick/add-pr-comment
  dependency-type: direct:production
  update-type: version-update:semver-major
...

Signed-off-by: dependabot[bot] <[email protected]>
@dependabot
[DEPENDABOT]: Bump codecov/codecov-action from 2.1.0 to 3.1.4
5ec5bbf 
Bumps [codecov/codecov-action](https://github.com/codecov/codecov-action) from 2.1.0 to 3.1.4.
- [Release notes](https://github.com/codecov/codecov-action/releases)
- [Changelog](https://github.com/codecov/codecov-action/blob/main/CHANGELOG.md)
- [Commits](codecov/codecov-action@v2.1.0...v3.1.4)

---
updated-dependencies:
- dependency-name: codecov/codecov-action
  dependency-type: direct:production
  update-type: version-update:semver-major
...

Signed-off-by: dependabot[bot] <[email protected]>
@dependabot
[DEPENDABOT]: Bump pypa/gh-action-pypi-publish from 1.4.2 to 1.8.10
58750e6 
Bumps [pypa/gh-action-pypi-publish](https://github.com/pypa/gh-action-pypi-publish) from 1.4.2 to 1.8.10.
- [Release notes](https://github.com/pypa/gh-action-pypi-publish/releases)
- [Commits](pypa/gh-action-pypi-publish@v1.4.2...v1.8.10)

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

Signed-off-by: dependabot[bot] <[email protected]>
@picciama
added filter for model method
57c4924
@picciama
new svg with paths instead of font
7388d2f
@picciama
fixed line number to end
fb46a62
@picciama
fixed wrong key in config
9fc0ea2
@picciama
corrected missedCleavages key
bfce8db
@picciama
filter for files not in search results
74adaa1
@picciama
return list of filenames after splitting search
50613b5
@picciama
added log filehandler and cleaned up init scripts
c9d781d
@picciama
Merge pull request #112 from wilhelm-lab/dependabot/github_actions/de…
e4b5f43 
…velopment/pypa/gh-action-pypi-publish-1.8.10

[DEPENDABOT]: Bump pypa/gh-action-pypi-publish from 1.4.2 to 1.8.10
@picciama
Merge pull request #92 from wilhelm-lab/dependabot/github_actions/dev…
e031c41 
…elopment/codecov/codecov-action-3.1.4

[DEPENDABOT]: Bump codecov/codecov-action from 2.1.0 to 3.1.4
@picciama
Merge pull request #90 from wilhelm-lab/dependabot/github_actions/dev…
9205354 
…elopment/mshick/add-pr-comment-2

[DEPENDABOT]: Bump mshick/add-pr-comment from 1 to 2
@picciama
added missing annotation function
8a6ad69
@picciama
corrected speclib example config
302b7bf
@picciama
corrected header
0a94598
@picciama
added code examples for import of config
472f990
@picciama
better description on loading and viewing config
88c2679
@picciama
export example configs and make them available
058f5a1
@picciama
added example configs
be9036f
@picciama
updated info about example configs
7724172
@dependabot
[DEPENDABOT]: Bump actions/cache from 3.3.1 to 3.3.2
2e42401 
Bumps [actions/cache](https://github.com/actions/cache) from 3.3.1 to 3.3.2.
- [Release notes](https://github.com/actions/cache/releases)
- [Changelog](https://github.com/actions/cache/blob/main/RELEASES.md)
- [Commits](actions/cache@v3.3.1...v3.3.2)

---
updated-dependencies:
- dependency-name: actions/cache
  dependency-type: direct:production
  update-type: version-update:semver-patch
...

Signed-off-by: dependabot[bot] <[email protected]>
@dependabot
[DEPENDABOT]: Bump actions/checkout from 2 to 4
f2d7c1f 
Bumps [actions/checkout](https://github.com/actions/checkout) from 2 to 4.
- [Release notes](https://github.com/actions/checkout/releases)
- [Changelog](https://github.com/actions/checkout/blob/main/CHANGELOG.md)
- [Commits](actions/checkout@v2...v4)

---
updated-dependencies:
- dependency-name: actions/checkout
  dependency-type: direct:production
  update-type: version-update:semver-major
...

Signed-off-by: dependabot[bot] <[email protected]>
@picciama
cleaned up READMEs, added citations / quickstart
296a523
@picciama
updated imports and dependencies
f541dd6
@picciama
added missing sphinx_autodoc_typehints
e597f2e
@picciama
added headings
e5a0d8c
@picciama
lower limit to numpy + updated deps
251512b
@picciama
updated requirements.txt for build docs
dafe07a
picciama and others added 23 commits November 12, 2023 17:38
@picciama
pickle issue resolved by wrapping exceptions
87a1adc
@picciama
optimize/fix _get_best_ce:
af01790 
1. don't return best_ce but handle individually in the function, depending on ransac
2. don't write best_ce files if using ransac
@picciama
temporary dirty fix for mismatched RT column name
6dabca9
@picciama
correct the wrong job type
92e1eba
@picciama
fix ce_calib with one process not in pool
62cc782
@picciama
remove files when done
6d46383
@picciama
added test for ce_calib with runner and ransac
6f7bddc
@picciama
fixed typeguard issues
37d094d
@picciama
properly remove created folders after unit tests
5b3406b
@picciama
added time delay for windows
835f653
@picciama
Merge pull request #148 from wilhelm-lab/feature/timsTOF
ca1b2ec 
timsTOF support
@LLautenbacher
Improve Koina client error handling.
ba4458e
@LLautenbacher
Add explicit stacklevel
59a71ca
@LLautenbacher
Fix typing
6ac00c0
@MatthewThe
Allow bootstrapping of make pipeline
4288457
@MatthewThe
end-of-file fix for .gitignore
a998d54
@picciama
Merge pull request #158 from wilhelm-lab/bootstrap
f4eebb7 
Allow bootstrapping of make pipeline
@picciama
Merge branch 'development' into chore/improve_koina_error_handling
e9073e7
@picciama
retry if requests failed and set timeout to 60s
1764d7c
@picciama
fixed mypy: store debug instead of returning it
959e5d3
@picciama
fixed overwriting exception with none
9d7491b
@picciama
fix typeguard: del failed request, not None
f3407a8
@picciama
Merge pull request #155 from wilhelm-lab/chore/improve_koina_error_ha…
c6c45f3 
…ndling

Improve Koina client error handling.
@picciama picciama self-assigned this Dec 8, 2023
@picciama picciama merged commit c9bfc1b into main Dec 8, 2023
39 checks passed
@picciama picciama linked an issue Dec 8, 2023 that may be closed by this pull request
Percolator returns error in Rescoring "CalledProcessError: Command 'percolator --weights..." #151
Closed
@picciama picciama deleted the release/0.5.1 branch December 15, 2023 17:31
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@mostafakalhor mostafakalhor mostafakalhor approved these changes

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Percolator returns error in Rescoring "CalledProcessError: Command 'percolator --weights..."
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@picciama @mostafakalhor @LLautenbacher @MatthewThe