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test nar PR #175

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wants to merge 320 commits into from
Closed

test nar PR #175

wants to merge 320 commits into from
This pull request is big! We’re only showing the most recent 250 commits.

Commits on Nov 18, 2022

  1. Merge branch 'ligo' of https://github.com/uio-bmi/immuneML into ligo_dev

    @pavlovicmilena
    pavlovicmilena committed Nov 18, 2022
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Commits on Nov 22, 2022

  1. - Added AminoAcidFrequencyDistribution report: plots a barplot of eac… 

    …h amino acid in each position of all sequences in a dataset (any dataset type)

- small fix in SequenceLengthDistribution (set output_written=False to ensure correct error message, since this report writes no data file)
    @LonnekeScheffer
    LonnekeScheffer committed Nov 22, 2022
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  2. Updated color palette

    @LonnekeScheffer
    LonnekeScheffer committed Nov 22, 2022
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  3. updated AminoAcidFrequencyDistribution to include splitting by label … 

    …values
    @LonnekeScheffer
    LonnekeScheffer committed Nov 22, 2022
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  4. Updated docs

    @LonnekeScheffer
    LonnekeScheffer committed Nov 22, 2022
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  5. hacking around bnp for implanting

    @pavlovicmilena
    pavlovicmilena committed Nov 22, 2022
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Commits on Nov 25, 2022

  1. update bnp util stuff

    @pavlovicmilena
    pavlovicmilena committed Nov 25, 2022
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  2. Merge branch 'master' of https://github.com/uio-bmi/immuneML into lig… 

    …o_dev

� Conflicts:
�	immuneML/IO/dataset_import/OLGAImport.py
�	immuneML/encodings/abundance_encoding/CompAIRRSequenceAbundanceEncoder.py
�	immuneML/encodings/reference_encoding/MatchedRegexRepertoireEncoder.py
�	immuneML/simulation/signal_implanting/FullSequenceImplanting.py
�	setup.py
�	test/IO/dataset_import/test_genericImport.py
�	test/simulation/signal_implanting/test_FullSequenceImplanting.py
    @pavlovicmilena
    pavlovicmilena committed Nov 25, 2022
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  3. Merge branch 'master' of https://github.com/uio-bmi/immuneML into lig… 

    …o_dev
    @pavlovicmilena
    pavlovicmilena committed Nov 25, 2022
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Commits on Nov 27, 2022

  1. fix olga gene naming and update to new bnp version

    @pavlovicmilena
    pavlovicmilena committed Nov 27, 2022
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Commits on Dec 5, 2022

  1. fix: np match arguments

    @pavlovicmilena
    pavlovicmilena committed Dec 5, 2022
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Commits on Dec 14, 2022

  1. add positional options for rejection sampling

    @pavlovicmilena
    pavlovicmilena committed Dec 14, 2022
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  2. fix parsing for signal

    @pavlovicmilena
    pavlovicmilena committed Dec 14, 2022
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Commits on Dec 15, 2022

  1. add filtering based on pgens

    @pavlovicmilena
    pavlovicmilena committed Dec 15, 2022
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Commits on Dec 16, 2022

  1. update implanter

    @pavlovicmilena
    pavlovicmilena committed Dec 16, 2022
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Commits on Jan 4, 2023

  1. bugfix matches report: get subject ids

    @LonnekeScheffer
    LonnekeScheffer committed Jan 4, 2023
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  2. Merge branch 'master' into amino_acid_frequency_distribution_report

    @LonnekeScheffer
    LonnekeScheffer committed Jan 4, 2023
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  3. Merge branch 'bugfixes' into development

    @LonnekeScheffer
    LonnekeScheffer committed Jan 4, 2023
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Commits on Jan 9, 2023

  1. update implanting

    @pavlovicmilena
    pavlovicmilena committed Jan 9, 2023
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Commits on Jan 10, 2023

  1. make implanting run from yaml

    @pavlovicmilena
    pavlovicmilena committed Jan 10, 2023
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Commits on Jan 13, 2023

  1. refactor ligo

    @pavlovicmilena
    pavlovicmilena committed Jan 13, 2023
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Commits on Jan 15, 2023

  1. refactor ligo - finalize update

    @pavlovicmilena
    pavlovicmilena committed Jan 15, 2023
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Commits on Jan 17, 2023

  1. update weights check in GappedKmerInstantiation

    @pavlovicmilena
    pavlovicmilena committed Jan 17, 2023
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  2. fix weights to sum to 0 or 1 in GappedKmerInstantiation

    @pavlovicmilena
    pavlovicmilena committed Jan 17, 2023
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Commits on Jan 21, 2023

  1. fix gene read in from Olga

    @pavlovicmilena
    pavlovicmilena committed Jan 21, 2023
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  2. fix default weights and add ligo main class

    @pavlovicmilena
    pavlovicmilena committed Jan 21, 2023
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Commits on Jan 22, 2023

  1. bug fixes

    @pavlovicmilena
    pavlovicmilena committed Jan 22, 2023
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Commits on Jan 23, 2023

  1. fix: work also when no signals given

    @pavlovicmilena
    pavlovicmilena committed Jan 23, 2023
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Commits on Jan 27, 2023

  1. fix: position and string matching

    @pavlovicmilena
    pavlovicmilena committed Jan 27, 2023
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Commits on Jan 30, 2023

  1. fix: load olga model also for skewed seqs

    @pavlovicmilena
    pavlovicmilena committed Jan 30, 2023
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  2. add top/bottom n and filtering to FeatureValueBarplot

    @pavlovicmilena
    pavlovicmilena committed Jan 30, 2023
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Commits on Feb 3, 2023

  1. fix printing log

    @pavlovicmilena
    pavlovicmilena committed Feb 3, 2023
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  2. start adding PWM

    @pavlovicmilena
    pavlovicmilena committed Feb 3, 2023
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  3. Merge branch 'ligo_dev' of https://github.com/uio-bmi/immuneML into ligo 

    � Conflicts:
�	immuneML/simulation/motif_instantiation_strategy/GappedKmerInstantiation.py
    @pavlovicmilena
    pavlovicmilena committed Feb 3, 2023
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  4. fix: add missing params and background sequence simulation when no ge… 

    …nes set
    @pavlovicmilena
    pavlovicmilena committed Feb 3, 2023
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Commits on Feb 7, 2023

  1. fix: default weights is None

    @pavlovicmilena
    pavlovicmilena committed Feb 7, 2023
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  2. fix: logging

    @pavlovicmilena
    pavlovicmilena committed Feb 7, 2023
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Commits on Feb 8, 2023

  1. add proportion per signal for repertoire simulation

    @pavlovicmilena
    pavlovicmilena committed Feb 8, 2023
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  2. fix: add all params to new seqs after implanting

    @pavlovicmilena
    pavlovicmilena committed Feb 8, 2023
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Commits on Feb 16, 2023

  1. Merge branch 'master' into development

    @LonnekeScheffer
    LonnekeScheffer committed Feb 16, 2023
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  2. Allow metrics to be computed during MLApplication if the same label i… 

    …s provided
    @LonnekeScheffer
    LonnekeScheffer committed Feb 16, 2023
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  3. small fix to make tests pass

    @LonnekeScheffer
    LonnekeScheffer committed Feb 16, 2023
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  4. fix: html was overwritten

    @LonnekeScheffer
    LonnekeScheffer committed Feb 16, 2023
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  5. bugfixes

    @LonnekeScheffer
    LonnekeScheffer committed Feb 16, 2023
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Commits on Feb 17, 2023

  1. bugfix: dont access _proba columns when not defined

    @LonnekeScheffer
    LonnekeScheffer committed Feb 17, 2023
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  2. bugfix: convert everything to string

    @LonnekeScheffer
    LonnekeScheffer committed Feb 17, 2023
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Commits on Feb 19, 2023

  1. bugfixes

    @LonnekeScheffer
    LonnekeScheffer committed Feb 19, 2023
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Commits on Feb 22, 2023

  1. fix: allow empty signal list for sim item

    @pavlovicmilena
    pavlovicmilena committed Feb 22, 2023
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Commits on Feb 28, 2023

  1. add RepertoireClonotypeSummary report

    @pavlovicmilena
    pavlovicmilena committed Feb 28, 2023
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Commits on Mar 1, 2023

  1. add default params to RepertoireClonotypeSummary

    @pavlovicmilena
    pavlovicmilena committed Mar 1, 2023
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Commits on Mar 2, 2023

  1. Merge branch 'ligo' of https://github.com/uio-bmi/immuneML into ligo_dev

    @pavlovicmilena
    pavlovicmilena committed Mar 2, 2023
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  2. update structure for Motif -> SeedMotif and PWM

    @pavlovicmilena
    pavlovicmilena committed Mar 2, 2023
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Commits on Mar 3, 2023

  1. add support for two motifs per signal to co-occur in the same sequence

    @pavlovicmilena
    pavlovicmilena committed Mar 3, 2023
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Commits on Mar 5, 2023

  1. add support for 2 signals per receptor

    @pavlovicmilena
    pavlovicmilena committed Mar 5, 2023
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  2. add name check for signal

    @pavlovicmilena
    pavlovicmilena committed Mar 5, 2023
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Commits on Mar 6, 2023

  1. Merge branch 'master' of https://github.com/uio-bmi/immuneML into lig… 

    …o_dev

� Conflicts:
�	immuneML/IO/dataset_export/AIRRExporter.py
�	immuneML/data_model/receptor/Receptor.py
�	immuneML/data_model/receptor/receptor_sequence/SequenceAnnotation.py
�	immuneML/data_model/repertoire/Repertoire.py
�	immuneML/encodings/reference_encoding/MatchedReceptorsEncoder.py
�	immuneML/encodings/reference_encoding/MatchedReceptorsRepertoireEncoder.py
�	immuneML/encodings/reference_encoding/MatchedSequencesEncoder.py
�	immuneML/encodings/reference_encoding/MatchedSequencesRepertoireEncoder.py
�	immuneML/simulation/sequence_implanting/GappedMotifImplanting.py
�	test/IO/dataset_export/test_AIRRExporter.py
�	test/simulation/signal_implanting/test_healthySequenceImplanting.py
    @pavlovicmilena
    pavlovicmilena committed Mar 6, 2023
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  2. allow only dict for signals (no list anymore)

    @pavlovicmilena
    pavlovicmilena committed Mar 6, 2023
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  3. add default for is_noise

    @pavlovicmilena
    pavlovicmilena committed Mar 6, 2023
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  4. support PWM

    @pavlovicmilena
    pavlovicmilena committed Mar 6, 2023
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Commits on Mar 7, 2023

  1. add exp import draft

    @pavlovicmilena
    pavlovicmilena committed Mar 7, 2023
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  2. add ExperimentalImport as option for generative models

    @pavlovicmilena
    pavlovicmilena committed Mar 7, 2023
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Commits on Mar 10, 2023

  1. add ReferenceSequenceAnnotator preprocessor

    @pavlovicmilena
    pavlovicmilena committed Mar 10, 2023
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  2. fix: ReferenceSequenceAnnotator build_object validation

    @pavlovicmilena
    pavlovicmilena committed Mar 10, 2023
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  3. fix: add missing param to ReferenceSequenceAnnotator

    @pavlovicmilena
    pavlovicmilena committed Mar 10, 2023
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  4. fix: make ClonesPerRepertoireFilter limits inclusive (as per docs)

    @pavlovicmilena
    pavlovicmilena committed Mar 10, 2023
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  5. imports: check explicitly if to import stop codon

    @pavlovicmilena
    pavlovicmilena committed Mar 10, 2023
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  6. imports: add log on removed seqs

    @pavlovicmilena
    pavlovicmilena committed Mar 10, 2023
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  7. update version

    @pavlovicmilena
    pavlovicmilena committed Mar 10, 2023
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  8. add more logging for DatasetExportInstruction

    @pavlovicmilena
    pavlovicmilena committed Mar 10, 2023
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Commits on Mar 12, 2023

  1. support diff region type when calling CompAIRR

    @pavlovicmilena
    pavlovicmilena committed Mar 12, 2023
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  2. fix: DatasetExport result path

    @pavlovicmilena
    pavlovicmilena committed Mar 12, 2023
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  3. remove export formats as option (always export AIRR format)

    @pavlovicmilena
    pavlovicmilena committed Mar 12, 2023
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  4. bugfix: make dataset from new repertoires in ClonesPerRepertoireFilter

    @pavlovicmilena
    pavlovicmilena committed Mar 12, 2023
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  5. fix: don't export field_list to metadata

    @pavlovicmilena
    pavlovicmilena committed Mar 12, 2023
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Commits on Mar 16, 2023

  1. add SequenceLengthFilter

    @pavlovicmilena
    pavlovicmilena committed Mar 16, 2023
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  2. fix filenames in AIRRExporter

    @pavlovicmilena
    pavlovicmilena committed Mar 16, 2023
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Commits on Mar 20, 2023

  1. add clonal frequency support

    @pavlovicmilena
    pavlovicmilena committed Mar 20, 2023
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  2. add sequence_len_limits to SimConfigItem

    @pavlovicmilena
    pavlovicmilena committed Mar 20, 2023
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  3. remove unused files

    @pavlovicmilena
    pavlovicmilena committed Mar 20, 2023
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Commits on Mar 23, 2023

  1. add subject ids as a column to Matches output

    @pavlovicmilena
    pavlovicmilena committed Mar 23, 2023
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  2. add nicer feature names to MatchedSequencesEncoder

    @pavlovicmilena
    pavlovicmilena committed Mar 23, 2023
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  3. minor updates 'Report' class 

    - allow different plot callables (useful for reports with multiple plots)
- generic function for writing output tables, as this type of code is repeated in many reports
    @LonnekeScheffer
    LonnekeScheffer committed Mar 23, 2023
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  4. ParameterValidator: 

    - add min_exclusive and max_exclusive (in addition to inclusive)
- add assert_valid_tabular_file to check if a file exists and contains the expected columns
    @LonnekeScheffer
    LonnekeScheffer committed Mar 23, 2023
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Commits on Mar 27, 2023

  1. add duplicate_count defaults to OLGA

    @pavlovicmilena
    pavlovicmilena committed Mar 27, 2023
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Commits on Mar 29, 2023

  1. Merge branch 'development' of https://github.com/uio-bmi/immuneML int… 

    …o ligo

� Conflicts:
�	immuneML/IO/dataset_import/AIRRImport.py
�	immuneML/IO/dataset_import/MiXCRImport.py
�	immuneML/IO/dataset_import/TenxGenomicsImport.py
�	immuneML/IO/dataset_import/VDJdbImport.py
�	immuneML/encodings/reference_encoding/MatchedSequencesEncoder.py
�	immuneML/util/ImportHelper.py
�	test/reports/encoding_reports/test_Matches.py
    @pavlovicmilena
    pavlovicmilena committed Mar 29, 2023
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  2. remove obsolete files

    @pavlovicmilena
    pavlovicmilena committed Mar 29, 2023
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Commits on Mar 30, 2023

  1. start adding feasibility instruction

    @pavlovicmilena
    pavlovicmilena committed Mar 30, 2023
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  2. make FeasibilitySummary instruction run with minimal features

    @pavlovicmilena
    pavlovicmilena committed Mar 30, 2023
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  3. add is_same implementation to ExperimentalImport

    @pavlovicmilena
    pavlovicmilena committed Mar 30, 2023
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  4. Merge branch 'master' of https://github.com/uio-bmi/immuneML into dev… 

    …elopment
    @pavlovicmilena
    pavlovicmilena committed Mar 30, 2023
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  5. support seq len dist for sequence datasets

    @pavlovicmilena
    pavlovicmilena committed Mar 30, 2023
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  6. add signals_aggregated field in sequences

    @pavlovicmilena
    pavlovicmilena committed Mar 30, 2023
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Commits on Apr 1, 2023

  1. added pathbuilder to SequenceLengthDistribution.py

    Theodor Bergersen committed Apr 1, 2023
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Commits on Apr 3, 2023

  1. remove internal cv in outer assessment loop for sklearn

    @pavlovicmilena
    pavlovicmilena committed Apr 3, 2023
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Commits on Apr 4, 2023

  1. Merge branch 'sklearn_internal_cv_fix' of https://github.com/uio-bmi/… 

    …immuneML into development
    @pavlovicmilena
    pavlovicmilena committed Apr 4, 2023
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  2. update ref seq annotator

    @pavlovicmilena
    pavlovicmilena committed Apr 4, 2023
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  3. explicitly order columns when exporting repertoires for CompAIRR

    @pavlovicmilena
    pavlovicmilena committed Apr 4, 2023
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Commits on Apr 7, 2023

  1. fix: multiple motifs in same sequence

    @pavlovicmilena
    pavlovicmilena committed Apr 7, 2023
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Commits on Apr 25, 2023

  1. fix: receptor superclass call

    @pavlovicmilena
    pavlovicmilena committed Apr 25, 2023
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Commits on May 10, 2023

  1. fix: add missing params to CompAIRRParams in CompAIRRSequenceAbundanc… 

    …eEncoder
    @pavlovicmilena
    pavlovicmilena committed May 10, 2023
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Commits on May 15, 2023

  1. fix: column names for matching in CompAIRRSequenceAbundanceEncoder

    @pavlovicmilena
    pavlovicmilena committed May 15, 2023
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Commits on May 22, 2023

  1. fix: path for importing repertoire files

    @pavlovicmilena
    pavlovicmilena committed May 22, 2023
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Commits on May 25, 2023

  1. fix tests

    @pavlovicmilena
    pavlovicmilena committed May 25, 2023
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  2. fix tests and dependencies, update version

    @pavlovicmilena
    pavlovicmilena committed May 25, 2023
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  3. fix region type in test data

    @pavlovicmilena
    pavlovicmilena committed May 25, 2023
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  4. fix AIRRImport with region type

    @pavlovicmilena
    pavlovicmilena committed May 25, 2023
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Commits on Jun 15, 2023

  1. add bnpdataclass to rep

    @pavlovicmilena
    pavlovicmilena committed Jun 15, 2023
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  2. bionumpy integration

    @knutdrand
    knutdrand committed Jun 15, 2023
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  3. working test

    @knutdrand
    knutdrand committed Jun 15, 2023
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  4. working 2

    @knutdrand
    knutdrand committed Jun 15, 2023
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  5. minor test update

    @pavlovicmilena
    pavlovicmilena committed Jun 15, 2023
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Commits on Jun 16, 2023

  1. Merge branch 'master' of https://github.com/uio-bmi/immuneML into nar 

    # Conflicts:
#	immuneML/IO/dataset_import/AIRRImport.py
#	immuneML/IO/dataset_import/MiXCRImport.py
#	immuneML/IO/dataset_import/TenxGenomicsImport.py
#	immuneML/IO/dataset_import/VDJdbImport.py
#	immuneML/data_model/dataset/RepertoireDataset.py
#	immuneML/data_model/receptor/receptor_sequence/ReceptorSequence.py
#	immuneML/data_model/repertoire/Repertoire.py
#	immuneML/encodings/reference_encoding/MatchedSequencesEncoder.py
#	immuneML/environment/Constants.py
#	immuneML/preprocessing/ReferenceSequenceAnnotator.py
#	immuneML/reports/data_reports/SequenceLengthDistribution.py
#	immuneML/util/ImportHelper.py
#	immuneML/util/PathBuilder.py
#	setup.py
#	test/IO/dataset_import/test_VDJdbImport.py
#	test/encodings/reference_encoding/test_matchedSequencesEncoder.py
#	test/preprocessing/test_ReferenceSequenceAnnotator.py
#	test/reports/data_reports/test_sequenceLengthDistribution.py
#	test/reports/encoding_reports/test_Matches.py
#	test/reports/encoding_reports/test_featureValueBarplot.py
    @pavlovicmilena
    pavlovicmilena committed Jun 16, 2023
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Commits on Jun 19, 2023

  1. update Repertoire and tests

    @pavlovicmilena
    pavlovicmilena committed Jun 19, 2023
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Commits on Jun 20, 2023

  1. Merge branch 'master' into nar 

    # Conflicts:
#	requirements.txt
    Milena Pavlovic committed Jun 20, 2023
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Commits on Jul 12, 2023

  1. fix some of the tests after data model refactor

    @pavlovicmilena
    pavlovicmilena committed Jul 12, 2023
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Commits on Jul 31, 2023

  1. fix ElementGenerator and Repertoire; remove cells from Repertoire

    @pavlovicmilena
    pavlovicmilena committed Jul 31, 2023
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Commits on Aug 28, 2023

  1. update DeepRC to new package version

    @pavlovicmilena
    pavlovicmilena committed Aug 28, 2023
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Commits on Sep 1, 2023

  1. update to work with new package versions with python 3.11

    @pavlovicmilena
    pavlovicmilena committed Sep 1, 2023
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  2. DeepRC update - not working yet

    @pavlovicmilena
    pavlovicmilena committed Sep 1, 2023
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Commits on Sep 10, 2023

  1. Merge branch 'development' into nar 

    # Conflicts:
#	immuneML/IO/dataset_import/AIRRImport.py
#	immuneML/data_model/receptor/BCKReceptor.py
#	immuneML/data_model/receptor/BCReceptor.py
#	immuneML/data_model/receptor/TCABReceptor.py
#	immuneML/data_model/receptor/TCGDReceptor.py
#	immuneML/data_model/receptor/receptor_sequence/ReceptorSequence.py
#	immuneML/data_model/repertoire/Repertoire.py
#	immuneML/preprocessing/ReferenceSequenceAnnotator.py
#	immuneML/util/CompAIRRHelper.py
#	requirements.txt
#	setup.py
#	test/IO/dataset_import/test_VDJdbImport.py
#	test/app/test_immuneMLApp.py
#	test/encodings/deeprc/test_deepRCEncoder.py
#	test/encodings/distance_encoding/test_compAIRRDistanceEncoder.py
#	test/reports/data_reports/test_RecoveredSignificantFeatures.py
#	test/reports/data_reports/test_SignificantFeatures.py
    @pavlovicmilena
    pavlovicmilena committed Sep 10, 2023
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Commits on Sep 11, 2023

  1. fix test

    @pavlovicmilena
    pavlovicmilena committed Sep 11, 2023
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Commits on Sep 22, 2023

  1. bugfix for DeepRC integration

    @pavlovicmilena
    pavlovicmilena committed Sep 22, 2023
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Commits on Sep 25, 2023

  1. start adding gen models

    @pavlovicmilena
    pavlovicmilena committed Sep 25, 2023
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  2. update deepRC test

    @pavlovicmilena
    pavlovicmilena committed Sep 25, 2023
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Commits on Sep 27, 2023

  1. integrate sonnia

    @pavlovicmilena
    pavlovicmilena committed Sep 27, 2023
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Commits on Sep 30, 2023

  1. bugfix: CountPerSequenceFilter

    @pavlovicmilena
    pavlovicmilena committed Sep 30, 2023
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  2. add more logging to CountPerSequenceFilter

    @pavlovicmilena
    pavlovicmilena committed Sep 30, 2023
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  3. add more logging to CountPerSequenceFilter

    @pavlovicmilena
    pavlovicmilena committed Sep 30, 2023
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Commits on Oct 1, 2023

  1. Merge branch 'development' into nar 

    # Conflicts:
#	requirements_DeepRC.txt
#	test/preprocessing/filters/test_countPerSequenceFilter.py
    @pavlovicmilena
    pavlovicmilena committed Oct 1, 2023
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  2. add galaxy tool for gen models

    @pavlovicmilena
    pavlovicmilena committed Oct 1, 2023
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Commits on Oct 3, 2023

  1. add init to package

    @pavlovicmilena
    pavlovicmilena committed Oct 3, 2023
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Commits on Oct 6, 2023

  1. update requirements.txt

    @pavlovicmilena
    pavlovicmilena committed Oct 6, 2023
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  2. update docs and standardize gen models a bit

    @pavlovicmilena
    pavlovicmilena committed Oct 6, 2023
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Commits on Oct 14, 2023

  1. add reports to TrainGenModel

    @pavlovicmilena
    pavlovicmilena committed Oct 14, 2023
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  2. fix IMGT position computation

    @pavlovicmilena
    pavlovicmilena committed Oct 14, 2023
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Commits on Oct 15, 2023

  1. temporary fix for SignificantKmerPositions test

    @pavlovicmilena
    pavlovicmilena committed Oct 15, 2023
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  2. Merge branch 'development' into nar 

    # Conflicts:
#	immuneML/simulation/sequence_implanting/GappedMotifImplanting.py
#	test/integration_tests/test_simulation.py
#	test/preprocessing/filters/test_clonesPerRepertoireFilter.py
#	test/preprocessing/filters/test_countPerSequenceFilter.py
#	test/reports/data_reports/test_SignificantKmerPositions.py
#	test/simulation/signal_implanting_strategy/sequence_implanting/test_gappedMotifImplanting.py
    @pavlovicmilena
    pavlovicmilena committed Oct 15, 2023
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Commits on Oct 19, 2023

  1. add LSTM draft

    @pavlovicmilena
    pavlovicmilena committed Oct 19, 2023
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  2. fix sklearn CV + selection loop bug

    @pavlovicmilena
    pavlovicmilena committed Oct 19, 2023
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  3. Merge remote-tracking branch 'origin/master' into development 

    # Conflicts:
#	immuneML/data_model/dataset/RepertoireDataset.py
#	immuneML/environment/Constants.py
#	immuneML/hyperparameter_optimization/core/HPAssessment.py
#	immuneML/preprocessing/ReferenceSequenceAnnotator.py
#	immuneML/util/CompAIRRHelper.py
#	immuneML/util/PathBuilder.py
#	requirements.txt
#	requirements_DeepRC.txt
#	setup.py
#	test/encodings/distance_encoding/test_compAIRRDistanceEncoder.py
#	test/preprocessing/filters/test_clonesPerRepertoireFilter.py
#	test/reports/data_reports/test_RecoveredSignificantFeatures.py
#	test/reports/data_reports/test_SignificantFeatures.py
    @pavlovicmilena
    pavlovicmilena committed Oct 19, 2023
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  4. Merge remote-tracking branch 'origin/master' into nar 

    # Conflicts:
#	immuneML/dsl/import_parsers/ImportParser.py
#	immuneML/preprocessing/ReferenceSequenceAnnotator.py
#	immuneML/simulation/sequence_implanting/GappedMotifImplanting.py
#	immuneML/util/CompAIRRHelper.py
#	requirements.txt
#	setup.py
#	test/analysis/similarities/test_repertoireSimilarityComputer.py
#	test/app/test_immuneMLApp.py
#	test/encodings/deeprc/test_deepRCEncoder.py
#	test/integration_tests/test_simulation.py
#	test/ml_methods/test_deepRC.py
#	test/preprocessing/filters/test_countPerSequenceFilter.py
#	test/simulation/signal_implanting_strategy/sequence_implanting/test_gappedMotifImplanting.py
    @pavlovicmilena
    pavlovicmilena committed Oct 19, 2023
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  5. Fix LSTM batches and add simple probabilities

    @pavlovicmilena
    pavlovicmilena committed Oct 19, 2023
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Commits on Oct 20, 2023

  1. add logging and docs to LSTM

    @pavlovicmilena
    pavlovicmilena committed Oct 20, 2023
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Commits on Oct 25, 2023

  1. update VAE (not working still)

    @pavlovicmilena
    pavlovicmilena committed Oct 25, 2023
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  2. change AA layer type

    @pavlovicmilena
    pavlovicmilena committed Oct 25, 2023
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  3. add simple PWM

    @pavlovicmilena
    pavlovicmilena committed Oct 25, 2023
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  4. raise error for missing parts of implementation

    @pavlovicmilena
    pavlovicmilena committed Oct 25, 2023
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  5. Merge remote-tracking branch 'origin/nar' into vae

    @pavlovicmilena
    pavlovicmilena committed Oct 25, 2023
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  6. make full vae run without warmup

    @pavlovicmilena
    pavlovicmilena committed Oct 25, 2023
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Commits on Oct 29, 2023

  1. add beta warm up

    @pavlovicmilena
    pavlovicmilena committed Oct 29, 2023
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  2. reorganize ml methods folder

    @pavlovicmilena
    pavlovicmilena committed Oct 29, 2023
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  3. Merge remote-tracking branch 'origin/master' into nar 

    # Conflicts:
#	requirements.txt
    @pavlovicmilena
    pavlovicmilena committed Oct 29, 2023
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  4. add device to vae

    @pavlovicmilena
    pavlovicmilena committed Oct 29, 2023
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Commits on Oct 30, 2023

  1. add vae summary report

    @pavlovicmilena
    pavlovicmilena committed Oct 30, 2023
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  2. add pypi publish dev setup

    @pavlovicmilena
    pavlovicmilena committed Oct 30, 2023
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  3. update dev version

    @pavlovicmilena
    pavlovicmilena committed Oct 30, 2023
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  4. remove condition from pypi setup

    @pavlovicmilena
    pavlovicmilena committed Oct 30, 2023
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  5. update readme to reflect that this is dev version

    @pavlovicmilena
    pavlovicmilena committed Oct 30, 2023
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Commits on Oct 31, 2023

  1. add conda package workflow

    @pavlovicmilena
    pavlovicmilena committed Oct 31, 2023
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  2. update PyPI action

    @pavlovicmilena
    pavlovicmilena committed Oct 31, 2023
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  3. revert to trusted publisher for PyPI

    @pavlovicmilena
    pavlovicmilena committed Oct 31, 2023
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  4. add install conda-build

    @pavlovicmilena
    pavlovicmilena committed Oct 31, 2023
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  5. fix github action

    @pavlovicmilena
    pavlovicmilena committed Oct 31, 2023
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  6. add publish conda as separate action

    @pavlovicmilena
    pavlovicmilena committed Oct 31, 2023
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  7. fix paths in github action

    @pavlovicmilena
    pavlovicmilena committed Oct 31, 2023
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  8. update conda in github action

    @pavlovicmilena
    pavlovicmilena committed Oct 31, 2023
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  9. update conda in github action

    @pavlovicmilena
    pavlovicmilena committed Oct 31, 2023
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  10. tmp remove unused action

    @pavlovicmilena
    pavlovicmilena committed Oct 31, 2023
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  11. remove uses key in github action

    @pavlovicmilena
    pavlovicmilena committed Oct 31, 2023
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  12. update publish-dev-to-conda.yml

    @pavlovicmilena
    pavlovicmilena committed Oct 31, 2023
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  13. update publish-dev-to-conda.yml

    @pavlovicmilena
    pavlovicmilena committed Oct 31, 2023
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  14. update publish-dev-to-conda.yml

    @pavlovicmilena
    pavlovicmilena committed Oct 31, 2023
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  15. update publish-dev-to-conda.yml

    @pavlovicmilena
    pavlovicmilena committed Oct 31, 2023
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  16. update publish-dev-to-conda.yml

    @pavlovicmilena
    pavlovicmilena committed Oct 31, 2023
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  17. update publish-dev-to-conda.yml

    @pavlovicmilena
    pavlovicmilena committed Oct 31, 2023
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  18. update publish-dev-to-conda.yml

    @pavlovicmilena
    pavlovicmilena committed Oct 31, 2023
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Commits on Nov 1, 2023

  1. Updated AminoAcidFrequencyDistribution report: plot in addition 'freq… 

    …uency change'
    @LonnekeScheffer
    LonnekeScheffer committed Nov 1, 2023
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Commits on Nov 2, 2023

  1. keep only pypi-publish action

    @pavlovicmilena
    pavlovicmilena committed Nov 2, 2023
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  2. integrate ligo with immuneML

    @pavlovicmilena
    pavlovicmilena committed Nov 2, 2023
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  3. update README.md

    @pavlovicmilena
    pavlovicmilena committed Nov 2, 2023
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  4. add IMGT position fix

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    pavlovicmilena committed Nov 2, 2023
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  5. add dataset summary after import

    @pavlovicmilena
    pavlovicmilena committed Nov 2, 2023
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  6. run data reports on both simulated and original data in TrainGenModel

    @pavlovicmilena
    pavlovicmilena committed Nov 2, 2023
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Commits on Nov 3, 2023

  1. update docs in TrainGenModelInstruction

    @pavlovicmilena
    pavlovicmilena committed Nov 3, 2023
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  2. Dimensionality reduction using umap as part of exploratory analysis

    @ivargr
    ivargr committed Nov 3, 2023
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  3. Some minor fixes to dimensionality reduction

    @ivargr
    ivargr committed Nov 3, 2023
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  4. Merge branch 'nar' of github.com:uio-bmi/immuneML into nar

    @ivargr
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  5. Added umap-learn dependency

    @ivargr
    ivargr committed Nov 3, 2023
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Commits on Nov 4, 2023

  1. fix integration with ligo and bionumpy

    @pavlovicmilena
    pavlovicmilena committed Nov 4, 2023
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  2. Merge remote-tracking branch 'origin/nar' into nar 

    # Conflicts:
#	requirements.txt
    @pavlovicmilena
    pavlovicmilena committed Nov 4, 2023
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  3. remove unused code

    @pavlovicmilena
    pavlovicmilena committed Nov 4, 2023
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  4. Add pipeline for applying generative models (#162) 

    * WIP: skeleton for applying generative models  without logic

* feat: Add logic to applying generative models

* refactor: Merge fit and apply gen models integration tests

* refactor: Clean ApplyGenModelParser.py and ApplyGenModelInstruction.py

* test: Add unit test to ApplyGenModelParser.py

* test: Add unit test to ApplyGenModelInstruction.py

* test: Update test_ApplyGenModelInstruction.py with cleaning the folder tree

* refactor: Reduce redundancy for training and applying gen models in presentation layer and data classes

* refactor: Reduce redundancy by creating abstract gen instruction class for training and applying gen models
    @mmamica
    mmamica authored Nov 4, 2023
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  5. fix stochasticity in app test

    @pavlovicmilena
    pavlovicmilena committed Nov 4, 2023
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Commits on Nov 5, 2023

  1. update docs

    @pavlovicmilena
    pavlovicmilena committed Nov 5, 2023
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  2. fix TCRdist test

    @pavlovicmilena
    pavlovicmilena committed Nov 5, 2023
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Commits on Nov 6, 2023

  1. add clustering instruction draft

    @pavlovicmilena
    pavlovicmilena committed Nov 6, 2023
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  2. update ApplyGenModel for loading the method

    @pavlovicmilena
    pavlovicmilena committed Nov 6, 2023
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  3. Added VJ gene distribution report

    @LonnekeScheffer
    LonnekeScheffer committed Nov 6, 2023
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  4. small bugfix

    @LonnekeScheffer
    LonnekeScheffer committed Nov 6, 2023
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  5. fix IO for gen models

    @pavlovicmilena
    pavlovicmilena committed Nov 6, 2023
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  6. add more dim red methods

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    pavlovicmilena committed Nov 6, 2023
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Commits on Nov 7, 2023

  1. small update SimpleDatasetOverview

    @LonnekeScheffer
    LonnekeScheffer committed Nov 7, 2023
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  2. initial implementation of clustering instruction

    @pavlovicmilena
    pavlovicmilena committed Nov 7, 2023
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Commits on Nov 8, 2023

  1. refactoring

    @LonnekeScheffer
    LonnekeScheffer committed Nov 8, 2023
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  2. new build_dataset_overview script for updated create dataset tool

    @LonnekeScheffer
    LonnekeScheffer committed Nov 8, 2023
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  3. fix with new bionumpy, update docs, clustering updates

    @pavlovicmilena
    pavlovicmilena committed Nov 8, 2023
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  4. Added DatasetGenerationOverviewTool for Galaxy 

    Minor update ExploratoryAnalysis: report is allowed to be explicitly set to 'None' (though key cannot be missing)
RandomDatasetGenerator uses ImmuneMLExporter to ensure random datasets have 'dataset.yaml' files
    @LonnekeScheffer
    LonnekeScheffer committed Nov 8, 2023
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  5. fix docs

    @pavlovicmilena
    pavlovicmilena committed Nov 8, 2023
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  6. removed unused line, fix tests

    @LonnekeScheffer
    LonnekeScheffer committed Nov 8, 2023
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  7. updated HTML output of DatasetExport and ExploratoryAnalysis

    @LonnekeScheffer
    LonnekeScheffer committed Nov 8, 2023
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  8. updates and bugfixes build_dataset_overview_yaml.py

    @LonnekeScheffer
    LonnekeScheffer committed Nov 8, 2023
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  9. small update: only include 'empty' report when no other reports are s… 

    …pecified
    @LonnekeScheffer
    LonnekeScheffer committed Nov 8, 2023
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Commits on Nov 9, 2023

  1. fix docs

    @pavlovicmilena
    pavlovicmilena committed Nov 9, 2023
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  2. update exp analysis to work with any dim red

    @pavlovicmilena
    pavlovicmilena committed Nov 9, 2023
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  3. update docs

    @pavlovicmilena
    pavlovicmilena committed Nov 9, 2023
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  4. removed output typing "dict | None" as it is not compatible with Pyth… 

    …on 3.8
    @LonnekeScheffer
    LonnekeScheffer committed Nov 9, 2023
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  5. update in CompAIRR test to make test pass

    @LonnekeScheffer
    LonnekeScheffer committed Nov 9, 2023
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  6. Merge branch 'nar_summaryreports' into nar

    @LonnekeScheffer
    LonnekeScheffer committed Nov 9, 2023
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  7. bugfix: store training and test data at different paths so it does no… 

    …t get overwritten
    @LonnekeScheffer
    LonnekeScheffer committed Nov 9, 2023
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  8. bugfix: store training and test data at different paths so it does no… 

    …t get overwritten
    @LonnekeScheffer
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  9. preventative assertion statement i RepertoireBuilder, do not allow re… 

    …pertoires to be written in existing folder -> this can lead to halfway overwritten datasets with mismatching repertoires and metadata
    @LonnekeScheffer
    LonnekeScheffer committed Nov 9, 2023
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  10. minor fixes in tests and report titles

    @LonnekeScheffer
    LonnekeScheffer committed Nov 9, 2023
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Commits on Nov 10, 2023

  1. set version

    @pavlovicmilena
    pavlovicmilena committed Nov 10, 2023
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  2. Merge remote-tracking branch 'origin/development' into nar 

    # Conflicts:
#	immuneML/dsl/import_parsers/ImportParser.py
#	immuneML/environment/Constants.py
#	immuneML/preprocessing/ReferenceSequenceAnnotator.py
#	requirements.txt
#	setup.py
    @pavlovicmilena
    pavlovicmilena committed Nov 10, 2023
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  3. update github actions to run only on .py or .yaml file change

    @pavlovicmilena
    pavlovicmilena committed Nov 10, 2023
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  4. update python version

    @pavlovicmilena
    pavlovicmilena committed Nov 10, 2023
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Commits on Nov 13, 2023

  1. fix tests

    @pavlovicmilena
    pavlovicmilena committed Nov 13, 2023
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  2. fix tests

    @pavlovicmilena
    pavlovicmilena committed Nov 13, 2023
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Commits on Nov 17, 2023

  1. Merge remote-tracking branch 'origin/master' into nar 

    # Conflicts:
#	.github/workflows/publish-to-pypi.yml
#	Dockerfile
#	immuneML/__init__.py
    @pavlovicmilena
    pavlovicmilena committed Nov 17, 2023
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  2. add TrainGenModel reports and export combined dataset

    @pavlovicmilena
    pavlovicmilena committed Nov 17, 2023
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Commits on Nov 23, 2023

  1. Change storing of binary files for Sonnia model into storing weights … 

    …in json format (#165)
    @mmamica
    mmamica authored Nov 23, 2023
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  2. update clustering html output

    @pavlovicmilena
    pavlovicmilena committed Nov 23, 2023
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  3. add pwm summary report

    @pavlovicmilena
    pavlovicmilena committed Nov 23, 2023
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  4. add ApplyGenModelTool for Galaxy

    @pavlovicmilena
    pavlovicmilena committed Nov 23, 2023
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  5. fix paths in clustering html

    @pavlovicmilena
    pavlovicmilena committed Nov 23, 2023
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Commits on Nov 24, 2023

  1. add train/test split to TrainGenModelInstruction

    @pavlovicmilena
    pavlovicmilena committed Nov 24, 2023
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Commits on Nov 27, 2023

  1. KL report (#166) 

    * made test

* pre getting kl code from stash

* kl dist stuff from stash

* Writing kmer dist to file

* working test

* renamed files

* KL divergence report

* cleaning up

* actually print the kl divergence

* class doc for klgenmodel

* removed comment
    @knutdrand
    knutdrand authored Nov 27, 2023
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  2. add default params to KLGenModelReport

    @pavlovicmilena
    pavlovicmilena committed Nov 27, 2023
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Commits on Nov 28, 2023

  1. fix typo in build_apply_gen_model_specs

    @pavlovicmilena
    pavlovicmilena committed Nov 28, 2023
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Commits on Nov 30, 2023

  1. Updated docs for the feature reports. Improved test for featuredistri… 

    …bution report to make it clearer for us internally what it can be used for.
    @LonnekeScheffer
    LonnekeScheffer committed Nov 30, 2023
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  2. improved docs; added figure examples of some reports

    @LonnekeScheffer
    LonnekeScheffer committed Nov 30, 2023
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  3. Added support for ReceptorDataset in SequenceLengthDistribution

    @LonnekeScheffer
    LonnekeScheffer committed Nov 30, 2023
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Commits on Dec 2, 2023

  1. update galaxy sim tool to work with ligo

    @pavlovicmilena
    pavlovicmilena committed Dec 2, 2023
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Commits on Dec 5, 2023

  1. - updated overview figure 

    - Added SequenceLengthDistribution report, allow seq counts option to be accessible in galaxy tool
    @LonnekeScheffer
    LonnekeScheffer committed Dec 5, 2023
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  2. make airrexporter not depend on OLGA

    @LonnekeScheffer
    LonnekeScheffer committed Dec 5, 2023
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Commits on Dec 6, 2023

  1. added yamlbuilder for "train gen models" tool, + other galaxy tool up… 

    …dates
    @LonnekeScheffer
    LonnekeScheffer committed Dec 6, 2023
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  2. import sonia/sonnia internally so galaxy doesnt fail

    @LonnekeScheffer
    LonnekeScheffer committed Dec 6, 2023
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  3. added default params for galaxy generative models (except chain) 

    added chain option to galaxy tool
    @LonnekeScheffer
    LonnekeScheffer committed Dec 6, 2023
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  4. removed option (gen model overviews are always run)

    @LonnekeScheffer
    LonnekeScheffer committed Dec 6, 2023
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Commits on May 28, 2024

  1. Merge branch 'master' into nar 

    # Conflicts:
#	docs/source/_static/images/definitions_instructions_overview.png
#	immuneML/ml_methods/generative_models/SoNNia.py
#	immuneML/reports/data_reports/AminoAcidFrequencyDistribution.py
#	immuneML/reports/data_reports/DataReport.py
#	immuneML/reports/data_reports/SequenceLengthDistribution.py
#	immuneML/reports/data_reports/VJGeneDistribution.py
#	immuneML/reports/encoding_reports/FeatureDistribution.py
#	immuneML/reports/gen_model_reports/VAESummary.py
#	immuneML/reports/ml_reports/Coefficients.py
#	immuneML/reports/ml_reports/DeepRCMotifDiscovery.py
#	immuneML/reports/ml_reports/TCRdistMotifDiscovery.py
#	immuneML/workflows/instructions/train_gen_model/TrainGenModelInstruction.py
    @LonnekeScheffer
    LonnekeScheffer committed May 28, 2024
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