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Release/0.4.3 #100

Merged
merged 61 commits into from
Apr 27, 2024
Merged

Release/0.4.3 #100

merged 61 commits into from
Apr 27, 2024

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picciama
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@picciama picciama commented Apr 27, 2024 •
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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

mostafakalhor and others added 30 commits June 2, 2023 19:44
@mostafakalhor
cover plink2 result - need to check
c0280c8
@mostafakalhor
fixed plink2.py
a88ead0
@mostafakalhor
import plink2 and fix reverse col to boolean
07b73d8
fixed some bugs
bfb7cf7
@mostafakalhor
a
41edd8a
@mostafakalhor
Merge branch 'development' into feature/xl_search_engine
413a97e
@mostafakalhor
updatae msraw.py from development branch
fa7fd21
@mostafakalhor
changed plink2
08e3334
@mostafakalhor
updated plink2.py
3df8997
added xlinkx for cce (cce is working based on pep 1)
7a00019
cover xisearch result
e1942ff
cover xisearch result
c045e25
try to merge development to mine
102dc51
@arne-vdb
divided rt by 60 to get minutes instead of seconds
2a975b1
@arne-vdb
blake file format modifications
105283d
focusing on xisearch - remove xlink and plink2 - everything is workin…
608c4e1 
…g - test code is needed for xisearch
xisearch test was added - pytest is working
7edebff
working on nox-based errors
00e2f8a
working on nox-related errors - only Xisearch.add_mod_sequence is nee…
e7a7dd5 
…ded to be fixd
fixed typeguard error. only pre-commit need to be fixed
8c36f75
everything is working -ready for pull request
52fc13d
still working on errors - fixed typrguard error
fe89064
ready for pull request
cdd6a08
@picciama
readd darglint to flake8 tests
8f7a236
@picciama
fix pre-commit hooks and cleanup self/static
ca3c20d
@picciama
fix line endings CRLF -> LF
bbbc87b
@picciama
fixed gitattributes
97c0887
@picciama
deleted unnecessary files
4a1f735
@picciama
custom init with xl arg and raise on tmt label
4147606
@mostafakalhor
removed def in
698ceaa
mostafakalhor and others added 28 commits April 12, 2024 11:24
@mostafakalhor
clean up
f659213
@picciama
Merge branch 'feature/xl_search_engine' of github.com:wilhelm-lab/spe…
ac86440 
…ctrum_io into feature/xl_search_engine
@picciama
ensure deletion of output files
b7df496
@picciama
remove print statements
d10b921
@picciama
fixed reading with dtypes correctly
4c854e3
@picciama
updated fundamentals to 0.51
03b547c
@picciama
Merge pull request #91 from wilhelm-lab/feature/xl_search_engine
c932841 
Feature/xl search engine
@dependabot
[DEPENDABOT]: Bump pypa/gh-action-pypi-publish from 1.6.4 to 1.8.14
45313a3 
Bumps [pypa/gh-action-pypi-publish](https://github.com/pypa/gh-action-pypi-publish) from 1.6.4 to 1.8.14.
- [Release notes](https://github.com/pypa/gh-action-pypi-publish/releases)
- [Commits](pypa/gh-action-pypi-publish@v1.6.4...v1.8.14)

---
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
Merge pull request #90 from wilhelm-lab/fix/alphatims_rt
100afb2 
alphatims RT in minutes instead of seconds
@dependabot
[DEPENDABOT]: Bump actions/cache from 3.2.4 to 4.0.2
28bef6b 
Bumps [actions/cache](https://github.com/actions/cache) from 3.2.4 to 4.0.2.
- [Release notes](https://github.com/actions/cache/releases)
- [Changelog](https://github.com/actions/cache/blob/main/RELEASES.md)
- [Commits](actions/cache@v3.2.4...v4.0.2)

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

Signed-off-by: dependabot[bot] <[email protected]>
@dependabot
[DEPENDABOT]: Bump actions/checkout from 2 to 4
476697e 
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
fix read decoy info from label column
318008c
@picciama
fixed dlib for new oktoberfest logic
e7372d8
@picciama
Merge branch 'development' into feature/dlib_support
21a03b4
@picciama
fix removing n-terminal dash for TMT sequences
80484f6
@picciama
cleanup reading / storing to internal format
e14f86e
@picciama
fix carbamidomethylation weight
cfdf207
@picciama
Merge branch 'main' into development
efb28f8
@picciama
Merge branch 'development' into feature/dlib_support
4855cde
@picciama
fixed dep to fundamentals changed unimod:4 mass)
436109f
@picciama
close connection after writing is done
f684731
@picciama
update deps, removing tables
4a0c100
@picciama
Merge pull request #99 from wilhelm-lab/feature/dlib_support
275ef32 
Feature/dlib support
@picciama
Merge pull request #98 from wilhelm-lab/fix/sage_read_tmt_and_decoys
080a28a 
Fix/sage read tmt and decoys
@picciama
Merge pull request #93 from wilhelm-lab/dependabot/github_actions/dev…
e55dab1 
…elopment/actions/cache-4.0.2

[DEPENDABOT]: Bump actions/cache from 3.2.4 to 4.0.2
@picciama
Merge pull request #92 from wilhelm-lab/dependabot/github_actions/dev…
1d8e49c 
…elopment/pypa/gh-action-pypi-publish-1.8.14

[DEPENDABOT]: Bump pypa/gh-action-pypi-publish from 1.6.4 to 1.8.14
@picciama
Merge pull request #94 from wilhelm-lab/dependabot/github_actions/dev…
071657f 
…elopment/actions/checkout-4

[DEPENDABOT]: Bump actions/checkout from 2 to 4
@picciama
Bump version from 0.4.2 to 0.4.3
c6f6a42
@picciama picciama merged commit 25dc1fd into main Apr 27, 2024
56 checks passed
@picciama picciama deleted the release/0.4.3 branch April 27, 2024 15:09
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3 participants
@picciama @mostafakalhor @arne-vdb