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Release/0.5.0 #129

Merged
merged 43 commits into from
Jul 11, 2024
Merged

Release/0.5.0 #129

merged 43 commits into from
Jul 11, 2024

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picciama
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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

Additional context

victorgiurcoiu and others added 30 commits April 18, 2024 18:26
@victorgiurcoiu
Added protein ids for spectronaut and msp formats
14f1099
@victorgiurcoiu
Merge development into feature/digest_nr_oxidations_arg
89216d1
@victorgiurcoiu
Added protein ids for dlib format
5eeec06
@victorgiurcoiu
Added PROTEINS column for maxquant
c7e3cd6
@victorgiurcoiu
Filter peptides with *
2b441a8
@victorgiurcoiu
Fixed black
2a824f8
@victorgiurcoiu
Added protein ids for msfragger, sage, fixed tests and typeguard
0dbd1d6
@dependabot
[DEPENDABOT]: Bump crazy-max/ghaction-github-labeler from 4.1.0 to 5.0.0
624fc14 
Bumps [crazy-max/ghaction-github-labeler](https://github.com/crazy-max/ghaction-github-labeler) from 4.1.0 to 5.0.0.
- [Release notes](https://github.com/crazy-max/ghaction-github-labeler/releases)
- [Commits](crazy-max/ghaction-github-labeler@v4.1.0...v5.0.0)

---
updated-dependencies:
- dependency-name: crazy-max/ghaction-github-labeler
  dependency-type: direct:production
  update-type: version-update:semver-major
...

Signed-off-by: dependabot[bot] <[email protected]>
@dependabot
[DEPENDABOT]: Bump actions/download-artifact from 3 to 4
08d2462 
Bumps [actions/download-artifact](https://github.com/actions/download-artifact) from 3 to 4.
- [Release notes](https://github.com/actions/download-artifact/releases)
- [Commits](actions/download-artifact@v3...v4)

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

Signed-off-by: dependabot[bot] <[email protected]>
@JSchlensok
Add Parquet I/O similar to HDF5 support
98f4f30
@JSchlensok
Fix mypy and pre-commit tests failing
29f39c0
@JSchlensok
chore: upgrade Python version from 3.8 to 3.9
b883563
@JSchlensok
chore: Add exceptions for overly specific flake8 rules
ece1b57
@JSchlensok
chore: suppress typeguard checking on tests intentionally using incom…
9210c32 
…patible inputs
@JSchlensok
chore: fix pytest failing due to typeguard package import
51ebbb7 
Only import and use the suppress_type_checks context decorator if a
typeguard session is run by nox as it is not installed for other
sessions
@JSchlensok
chore: fix typeguard version
0582608
@JSchlensok
chore: formatting
53c65d0
@picciama
updated hash
d55c808
@picciama
ignored 70612 vulnerability in safety checks
2634852
@picciama
updated workflow python versions to 3.9
282f31c
@picciama
fix version number interpretation by quotation
702cf43
@JSchlensok
chore: Remove generic typing
c59dbfc
@JSchlensok
chore: fix flake8 rule B026
b306a8e
@JSchlensok
chore(parquet): delete output paths after writing
76819fb
@JSchlensok
Merge pull request #122 from wilhelm-lab/feature/parquet
1a9f28d 
Add Parquet I/O
@dependabot
[DEPENDABOT]: Bump actions/setup-python from 4 to 5
42a3ead 
Bumps [actions/setup-python](https://github.com/actions/setup-python) from 4 to 5.
- [Release notes](https://github.com/actions/setup-python/releases)
- [Commits](actions/setup-python@v4...v5)

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

Signed-off-by: dependabot[bot] <[email protected]>
@dependabot
[DEPENDABOT]: Bump coverage from 7.5.2 to 7.5.4
a8b8224 
Bumps [coverage](https://github.com/nedbat/coveragepy) from 7.5.2 to 7.5.4.
- [Release notes](https://github.com/nedbat/coveragepy/releases)
- [Changelog](https://github.com/nedbat/coveragepy/blob/master/CHANGES.rst)
- [Commits](nedbat/coveragepy@7.5.2...7.5.4)

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

Signed-off-by: dependabot[bot] <[email protected]>
@dependabot
[DEPENDABOT]: Bump types-requests
0d08bf1 
Bumps [types-requests](https://github.com/python/typeshed) from 2.32.0.20240602 to 2.32.0.20240622.
- [Commits](https://github.com/python/typeshed/commits)

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

Signed-off-by: dependabot[bot] <[email protected]>
@dependabot
[DEPENDABOT]: Bump mypy from 1.10.0 to 1.10.1
c6514db 
Bumps [mypy](https://github.com/python/mypy) from 1.10.0 to 1.10.1.
- [Changelog](https://github.com/python/mypy/blob/master/CHANGELOG.md)
- [Commits](python/mypy@v1.10.0...v1.10.1)

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

Signed-off-by: dependabot[bot] <[email protected]>
@JSchlensok
chore: delete erroneously included notebook
13606bd
picciama and others added 13 commits July 8, 2024 16:25
@picciama
Merge pull request #128 from wilhelm-lab/feature/parquet
cbe0c21 
chore: delete erroneously included notebook
@picciama
Merge pull request #127 from wilhelm-lab/dependabot/pip/development/m…
8da9691 
…ypy-1.10.1

[DEPENDABOT]: Bump mypy from 1.10.0 to 1.10.1
@picciama
Merge pull request #126 from wilhelm-lab/dependabot/pip/development/t…
431c702 
…ypes-requests-2.32.0.20240622

[DEPENDABOT]: Bump types-requests from 2.32.0.20240602 to 2.32.0.20240622
@picciama
Merge pull request #125 from wilhelm-lab/dependabot/pip/development/c…
ce38fe7 
…overage-7.5.4

[DEPENDABOT]: Bump coverage from 7.5.2 to 7.5.4
@picciama
Merge pull request #117 from wilhelm-lab/dependabot/github_actions/de…
d2041c5 
…velopment/actions/setup-python-5

[DEPENDABOT]: Bump actions/setup-python from 4 to 5
@picciama
Merge pull request #109 from wilhelm-lab/feature/digest_nr_oxidations…
f98e916 
…_arg

Feature/digest nr oxidations arg
@picciama
Merge pull request #118 from wilhelm-lab/dependabot/github_actions/de…
713db6b 
…velopment/actions/download-artifact-4

[DEPENDABOT]: Bump actions/download-artifact from 3 to 4
@picciama
Merge pull request #116 from wilhelm-lab/dependabot/github_actions/de…
c0251fb 
…velopment/crazy-max/ghaction-github-labeler-5.0.0

[DEPENDABOT]: Bump crazy-max/ghaction-github-labeler from 4.1.0 to 5.0.0
@picciama
Bump version from 0.4.4 to 0.5.0
3f4dd27
@picciama
updated required spectrum_fundamentals version
2d8ec2c
@picciama
rm unnecessary setup.py
15ed514
@picciama
fix poetry lock
2e3ff8e
@picciama
updated to use new coverage report up/download v4
8cb9098
@picciama picciama merged commit a34a547 into main Jul 11, 2024
37 checks passed
@picciama picciama deleted the release/0.5.0 branch August 5, 2024 17:19
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3 participants
@picciama @victorgiurcoiu @JSchlensok