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Update picked group fdr branch #254

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wants to merge 201 commits into from
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Update picked group fdr branch #254

wants to merge 201 commits into from

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arne-vdb
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@arne-vdb arne-vdb commented Aug 6, 2024 •
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  • If you've fixed a bug or added code that should be tested, add tests!
  • Documentation in docs is updated

Description of changes

Merging new commits from developement into outdated feature branch

dependabot bot and others added 30 commits December 4, 2023 04:07
@dependabot
[DEPENDABOT]: Bump pypa/gh-action-pypi-publish from 1.8.10 to 1.8.11
532d23e 
Bumps [pypa/gh-action-pypi-publish](https://github.com/pypa/gh-action-pypi-publish) from 1.8.10 to 1.8.11.
- [Release notes](https://github.com/pypa/gh-action-pypi-publish/releases)
- [Commits](pypa/gh-action-pypi-publish@v1.8.10...v1.8.11)

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

Signed-off-by: dependabot[bot] <[email protected]>
@dependabot
[DEPENDABOT]: Bump actions/setup-python from 4 to 5
6410e11 
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]>
@picciama
added preprocessing functions for bruker type data
9b398ef
@picciama
added read_timstof_metadata
b0f59ca
@picciama
added ignores for pickle
fa2cf5b
@picciama
read, pickle, query the tims metadata for raw file
22b5cb9
@picciama
properly split and handle timstof
67db2de
@picciama
added changed functions to documentation
b1fd9a6
@picciama
removed everything with pkl, including unit tests
1aa603d
@picciama
updated spectrum_io and fundamentals deps
e58a2cd
@picciama
Merge branch 'development' into feature/bruker_preprocessing
677034f
@picciama
fixed mypy and tests
827f14b
@picciama
updated requirements.txt based on poetry.lock
02cad8d
@picciama
Merge pull request #195 from wilhelm-lab/feature/bruker_preprocessing
ce42166 
Feature/bruker preprocessing
@picciama
use peptide column for merging
4cd4c67
@picciama
added 0.6.0 to news, fixed tables, added reference
6eb9ced
@picciama
Bump version from 0.5.3 to 0.6.0
13a47e8
@picciama
fix: don't write index when using mokapot
1c6cd76
@karimwh
Merge pull request #196 from wilhelm-lab/feature/improved_plotting
6503516 
use peptide column for merging
@picciama
Merge branch 'development' into release/0.6.0
8f98dfc
@picciama
Merge pull request #197 from wilhelm-lab/release/0.6.0
102c2b8 
Release/0.6.0
@picciama
added timsTOF model to supported models
a8dcd10
@arne-vdb
Added anndata to dependencies and changed python version to >=3.9
0718cbd
@arne-vdb
Added anndata to requirements
a565125
@arne-vdb
changed test to be suitable for AnnData
0eb488f
@arne-vdb
modified to be suitable for new AnnData based Spectra class
55c4474
@arne-vdb
modified Spectra class to use AnnData object instead of pd.DataFrame …
39577ac 
…to store data
@arne-vdb
modified to account for changes in Spectra object
9362afa
@arne-vdb
adjusted github workflows to test for version 3.9
b61b7c8
@arne-vdb
changed get_matrix to take a numpy array and optional annotation order
d7e4cae
victorgiurcoiu and others added 28 commits July 9, 2024 08:26
@victorgiurcoiu
Added documentation and example configs for nrOx parameter
79a333a
@picciama
Merge branch 'development' into feature/digest_nr_oxidations_arg
dd6146e
@picciama
fix safety and and requirements.txt
ef60de8
@picciama
Merge pull request #217 from wilhelm-lab/feature/digest_nr_oxidations…
86f6a34 
…_arg

Feature/digest nr oxidations arg
@picciama
Merge branch 'development' into release/0.7.0
7b73295
@dependabot
[DEPENDABOT]: Bump tritonclient from 2.44.0 to 2.47.0
29a2ebb 
Bumps [tritonclient](https://github.com/triton-inference-server/client) from 2.44.0 to 2.47.0.
- [Commits](https://github.com/triton-inference-server/client/commits)

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

Signed-off-by: dependabot[bot] <[email protected]>
@picciama
updated required fundmaentals and io versions
84d4f3a
@picciama
Merge pull request #232 from wilhelm-lab/dependabot/pip/development/x…
ad0b7a1 
…doctest-1.1.5

[DEPENDABOT]: Bump xdoctest from 1.1.3 to 1.1.5
@picciama
Merge pull request #234 from wilhelm-lab/dependabot/github_actions/de…
b4935fe 
…velopment/codecov/codecov-action-4.5.0

[DEPENDABOT]: Bump codecov/codecov-action from 4.4.1 to 4.5.0
@picciama
Merge pull request #235 from wilhelm-lab/dependabot/github_actions/de…
236ab92 
…velopment/pypa/gh-action-pypi-publish-1.9.0

[DEPENDABOT]: Bump pypa/gh-action-pypi-publish from 1.8.14 to 1.9.0
@picciama
Merge branch 'dependabot/pip/development/tritonclient-2.47.0' of gith…
422589d 
…ub.com:wilhelm-lab/oktoberfest into dependabot/pip/development/tritonclient-2.47.0
@picciama
updated to use tritonclient 2.47
4faa107
@picciama
Merge pull request #237 from wilhelm-lab/dependabot/pip/development/t…
47d9e3c 
…ritonclient-2.47.0

[DEPENDABOT]: Bump tritonclient from 2.44.0 to 2.47.0
@picciama
Merge branch 'development' into chore/documentation_anndata_multimodel
8e07a9c
@picciama
moved nr=x to speclib options
3519526
@picciama
Merge pull request #226 from wilhelm-lab/chore/documentation_anndata_…
ab99194 
…multimodel

updated config/prediction docs and added news
@picciama
Merge branch 'development' into release/0.7.0
724012c
@picciama
offer peptide list and internal format for speclib
9867ea3
@picciama
updated speclib with new options
a1fbf90
@picciama
updated docs with new speclib options
49eb97c
@picciama
updated requirements
00e6492
@picciama
Merge pull request #243 from wilhelm-lab/feature/peptide_list_for_spe…
aa5b903 
…clib

Feature/peptide list for speclib
@picciama
updated contributors, fixed table
922be6c
@picciama
change name of library file to "predicted_library"
3af36b1
@picciama
corrected singular/plural error in column names
8d63cd0
@picciama
Merge pull request #227 from wilhelm-lab/release/0.7.0
e1d4540 
Release/0.7.0
@picciama
fix docs
66e0f36
@picciama
fixed missing protein columns #253
6d66789
@arne-vdb arne-vdb closed this Aug 6, 2024
@arne-vdb arne-vdb changed the title update picked group fdr branch Update picked group fdr branch Aug 6, 2024
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5 participants
@arne-vdb @picciama @karimwh @arminsl @victorgiurcoiu