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Release/0.4.3#100

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picciama merged 61 commits intomainwilhelm-lab/spectrum_io:mainfrom release/0.4.3wilhelm-lab/spectrum_io:release/0.4.3Copy head branch name to clipboardApr 27, 2024

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Commits

Commits on Jun 2, 2023

• cover plink2 result - need to check

  mostafakalhor

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Commits on Jun 4, 2023

• fixed plink2.py

  mostafakalhor

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Commits on Jun 9, 2023

• import plink2 and fix reverse col to boolean

  mostafakalhor

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Commits on Jun 12, 2023

• fixed some bugs

  

  Mostafa Kalhor

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• a

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• Merge branch 'development' into feature/xl_search_engine

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Commits on Jul 3, 2023

• updatae msraw.py from development branch

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Commits on Jul 6, 2023

• changed plink2

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Commits on Jul 9, 2023

• updated plink2.py

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Commits on Jul 26, 2023

• added xlinkx for cce (cce is working based on pep 1)

  

  Mostafa Kalhor

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Commits on Nov 15, 2023

• cover xisearch result

  

  Mostafa Kalhor

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• cover xisearch result

  

  Mostafa Kalhor

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Commits on Apr 9, 2024

• try to merge development to mine

  

  Mostafa Kalhor

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• divided rt by 60 to get minutes instead of seconds

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• blake file format modifications

  arne-vdb

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• focusing on xisearch - remove xlink and plink2 - everything is working - test code is needed for xisearch

  

  Mostafa Kalhor

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• xisearch test was added - pytest is working

  

  Mostafa Kalhor

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Commits on Apr 10, 2024

• working on nox-based errors

  

  Mostafa Kalhor

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• working on nox-related errors - only Xisearch.add_mod_sequence is needed to be fixd

  

  Mostafa Kalhor

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• fixed typeguard error. only pre-commit need to be fixed

  

  Mostafa Kalhor

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• everything is working -ready for pull request

  

  Mostafa Kalhor

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• still working on errors - fixed typrguard error

  

  Mostafa Kalhor

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• ready for pull request

  

  Mostafa Kalhor

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• readd darglint to flake8 tests

  picciama

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• fix pre-commit hooks and cleanup self/static

  picciama

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• fix line endings CRLF -> LF

  picciama

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• fixed gitattributes

  picciama

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• deleted unnecessary files

  picciama

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• custom init with xl arg and raise on tmt label

  picciama

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Commits on Apr 11, 2024

• removed def in

  mostafakalhor

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• updated requirements.txt according to poetry

  picciama

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• Merge branch 'feature/xl_search_engine' of github.com:wilhelm-lab/spectrum_io into feature/xl_search_engine

  picciama

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• removed def internal to xisearch and import it from mod_string spectrum fundamental

  mostafakalhor

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Commits on Apr 12, 2024

• clean up

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• Merge branch 'feature/xl_search_engine' of github.com:wilhelm-lab/spectrum_io into feature/xl_search_engine

  picciama

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• ensure deletion of output files

  picciama

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• remove print statements

  picciama

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• fixed reading with dtypes correctly

  picciama

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• updated fundamentals to 0.51

  picciama

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• Merge pull request #91 from wilhelm-lab/feature/xl_search_engine

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• [DEPENDABOT]: Bump pypa/gh-action-pypi-publish from 1.6.4 to 1.8.14

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• Merge pull request #90 from wilhelm-lab/fix/alphatims_rt

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Commits on Apr 15, 2024

• [DEPENDABOT]: Bump actions/cache from 3.2.4 to 4.0.2

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• [DEPENDABOT]: Bump actions/checkout from 2 to 4

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Commits on Apr 27, 2024

• fix read decoy info from label column

  picciama

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• fixed dlib for new oktoberfest logic

  picciama

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• Merge branch 'development' into feature/dlib_support

  picciama

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• fix removing n-terminal dash for TMT sequences

  picciama

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• cleanup reading / storing to internal format

  picciama

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• fix carbamidomethylation weight

  picciama

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• Merge branch 'main' into development

  picciama

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• Merge branch 'development' into feature/dlib_support

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• fixed dep to fundamentals changed unimod:4 mass)

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• close connection after writing is done

  picciama

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• update deps, removing tables

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• Merge pull request #99 from wilhelm-lab/feature/dlib_support

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• Merge pull request #98 from wilhelm-lab/fix/sage_read_tmt_and_decoys

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• Merge pull request #93 from wilhelm-lab/dependabot/github_actions/development/actions/cache-4.0.2

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• Merge pull request #92 from wilhelm-lab/dependabot/github_actions/development/pypa/gh-action-pypi-publish-1.8.14

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• Merge pull request #94 from wilhelm-lab/dependabot/github_actions/development/actions/checkout-4

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• Bump version from 0.4.2 to 0.4.3

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