Code

Fixes#180

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pavlovicmilena merged 50 commits intomasteruio-bmi/immuneML:masterfrom fixesuio-bmi/immuneML:fixesCopy head branch name to clipboardDec 18, 2024

+881-1,579

Commits

Commits on Nov 19, 2024

• docs fixes

  LonnekeScheffer

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  e063b7f

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• print dataset stats after preprocessing

  LonnekeScheffer

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• when makng random repertoire: add random counts (helpful for testing some reports)

  LonnekeScheffer

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• better display sequence count distribution: add locus facet for sequence datasets too

  LonnekeScheffer

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• remove distracting extra newlines in logging warning when importing data

  LonnekeScheffer

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• add region type to one hot encoder; cdr3 by default

  pavlovicmilena

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Commits on Nov 21, 2024

• convert boolean values to 'T'/'F' in import, default bool value is '' -> This way, custom bool columns are also converted to T/F strings (necessary for being AIRR compliant)

  LonnekeScheffer

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• Data import updates:

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  LonnekeScheffer

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• use default params loader in airr test

  LonnekeScheffer

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Commits on Nov 29, 2024

• bugfix separator tenxgenomics

  LonnekeScheffer

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  1d41e99

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• clearer error logging in Report

  LonnekeScheffer

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• Use logging.warning instead of warnings.warn; the latter does not show up in the log file

  LonnekeScheffer

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Commits on Dec 3, 2024

• VJ gene dist report updates:

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  LonnekeScheffer

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• minor fix in error VJGeneDistribution.py

  LonnekeScheffer

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• minor fix in VJGeneDistribution.py

  LonnekeScheffer

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• better logging/errors when importing repertoires + keep repertoire identifier from metadata

  LonnekeScheffer

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Commits on Dec 9, 2024

• add cdr3 as output to ligo

  pavlovicmilena

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• Merge remote-tracking branch 'origin/fixes' into fixes

  pavlovicmilena

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Commits on Dec 10, 2024

• add cdr3 from junction; standardize region type with gen models

  pavlovicmilena

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• minor bugfix

  LonnekeScheffer

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Commits on Dec 11, 2024

• fix tests

  pavlovicmilena

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• Merge remote-tracking branch 'origin/fixes' into fixes

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  pavlovicmilena

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Commits on Dec 15, 2024

• fix VAE region type

  pavlovicmilena

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Commits on Dec 16, 2024

• update requirements:

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  LonnekeScheffer

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• requirements: change < to <= as it sometimes does not recognize < correctly

  LonnekeScheffer

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• update dependency version restrictions in setup.py

  LonnekeScheffer

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• fix test_compAIRRDistanceEncoder.py: now, duplicate_counts are randomly set for repertoires, so "ignore_counts" must be set to True to get the same results

  LonnekeScheffer

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• Fix tests for matches report and related encoder:

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  LonnekeScheffer

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• bugfix in test_vae_summary.py (SimpleVAE must always be applied to junction data); added extra assert to SimpleVAE for clearer error in this casw

  LonnekeScheffer

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• fix in test_fit_apply_gen_model: always use IMGT_Junction

  LonnekeScheffer

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• undo comment shutil.rmtree

  LonnekeScheffer

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• import-related class documentation updates

  LonnekeScheffer

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• add failed html image for docs

  LonnekeScheffer

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• Merge remote-tracking branch 'origin/fixes' into fixes

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• docs updates: preferred python version

  LonnekeScheffer

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• Merge remote-tracking branch 'origin/fixes' into fixes

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Commits on Dec 17, 2024

• new metadata file showing identifier column

  LonnekeScheffer

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• Merge remote-tracking branch 'origin/fixes' into fixes

  LonnekeScheffer

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  19a51e3

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• update docs "how to import data in immuneml"

  LonnekeScheffer

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• update galaxy intro docs

  LonnekeScheffer

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• update clustering galaxy tool api

  pavlovicmilena

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• update clustering galaxy tool api

  pavlovicmilena

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• add galaxy_history_elements.png

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• Merge remote-tracking branch 'origin/fixes' into fixes

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• updated galaxy related docs

  LonnekeScheffer

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Commits on Dec 18, 2024

• made specification docs easier to navigate, removed clutter

  LonnekeScheffer

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• formatting reports/ml method subgroups in docs

  LonnekeScheffer

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• switch to 'avant' Galaxy url in docs + remove references to any history files which cannot be recreated with the same url

  LonnekeScheffer

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• fix reference to figures from reports and ML methods

  LonnekeScheffer

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• Update version

  pavlovicmilena

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