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Merging all changes to the IMBG-refactoring to the main branch #4

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Merging all changes to the IMBG-refactoring to the main branch #4

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Commits on Jun 28, 2024

  1. add test data config and TODOs for steps 1.1-2.3

    @d-goryslavets
    d-goryslavets committed Jun 28, 2024
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  2. add test suite skeleton

    @d-goryslavets
    d-goryslavets committed Jun 28, 2024
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Commits on Jul 2, 2024

  1. add TODOs for steps 2.1-2.5 and update paths to point to test data

    @d-goryslavets
    d-goryslavets committed Jul 2, 2024
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Commits on Jul 4, 2024

  1. minimal refactoring. add tmp_dir config. add mk43_ prefix to shared i… 

    …ntermediate files and output files.
    @mkrooted256
    mkrooted256 committed Jul 4, 2024
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  2. draft of a get_path util

    @mkrooted256
    mkrooted256 committed Jul 4, 2024
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  3. successful 2.1. replace + with os.path.join. annotate hardcoded paths… 

    …. add WES_CONFIG env var to specify config file programmatically. make header file optional.
    @mkrooted256
    mkrooted256 committed Jul 4, 2024
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Commits on Jul 15, 2024

  1. add test suite skeleton and test data

    @d-goryslavets
    d-goryslavets committed Jul 15, 2024
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  2. Merge branch 'mk43/first-run' into imbg-refactoring. Refactor steps 1… 

    ….1 and 2.1
    @d-goryslavets
    d-goryslavets committed Jul 15, 2024
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  3. add tmp_dir to test data configs

    @d-goryslavets
    d-goryslavets committed Jul 15, 2024
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  4. cleanup 1.1

    @mkrooted256
    mkrooted256 committed Jul 15, 2024
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Commits on Jul 16, 2024

  1. first attempts

    @mkrooted256
    mkrooted256 committed Jul 16, 2024
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Commits on Jul 18, 2024

  1. steps 1.1-2.1: refactor config and move hardcoded values

    @mkrooted256
    mkrooted256 committed Jul 18, 2024
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Commits on Jul 23, 2024

  1. add todo

    @mkrooted256
    mkrooted256 committed Jul 23, 2024
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Commits on Jul 25, 2024

  1. upload documentation

    @lbombini
    lbombini committed Jul 25, 2024
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  2. change smoke test design and add unit test template

    @d-goryslavets
    d-goryslavets committed Jul 25, 2024
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  3. change string concat to os.path.join in steps 1-2, make some function… 

    …s in step 2 return mts and change spark init way
    @d-goryslavets
    d-goryslavets committed Jul 25, 2024
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  4. add integration tests that run main() function of each step

    @d-goryslavets
    d-goryslavets committed Jul 25, 2024
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  5. add unit tests for steps 1.1-2.2

    @d-goryslavets
    d-goryslavets committed Jul 25, 2024
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  6. add a snippet for new config system. research possible ways to refact… 

    …or config.
    @mkrooted256
    mkrooted256 committed Jul 25, 2024
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  7. add config utils and config ipynb playground

    @mkrooted256
    mkrooted256 committed Jul 25, 2024
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  8. refactor path config for 1.1

    @mkrooted256
    mkrooted256 committed Jul 25, 2024
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Commits on Jul 26, 2024

  1. Finish config refactoring for 2.1. 

    Adopt path_spark. remove file:// paths from config. Add example cvar usage.
    @mkrooted256
    mkrooted256 committed Jul 26, 2024
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Commits on Jul 31, 2024

  1. update the docs

    @lbombini
    lbombini committed Jul 31, 2024
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  2. Merge branch 'imbg-refactoring' of https://github.com/wtsi-hgi/wes-qc … 

    …into imbg-refactoring
    @lbombini
    lbombini committed Jul 31, 2024
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Commits on Aug 1, 2024

  1. fix the code blocks

    @lbombini
    lbombini committed Aug 1, 2024
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  2. refactor path concatenation in steps 2.3-2.5

    @d-goryslavets
    d-goryslavets committed Aug 1, 2024
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  3. add unit and integration tests for steps 2.3-2.5

    @d-goryslavets
    d-goryslavets committed Aug 1, 2024
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Commits on Aug 4, 2024

  1. Merge branch 'imbg-refactoring' into mk43/refactor-hardcoded-config/2.1

    @mkrooted256
    mkrooted256 committed Aug 4, 2024
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  2. add config tests. move config utils to a separate file.

    @mkrooted256
    mkrooted256 committed Aug 4, 2024
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  3. fix a probable config bug

    @mkrooted256
    mkrooted256 committed Aug 4, 2024
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Commits on Aug 7, 2024

  1. refactor unittests for 1.1-2.1

    @mkrooted256
    mkrooted256 committed Aug 7, 2024
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Commits on Aug 8, 2024

  1. minor changes to run 1.1 and 2.1

    @lbombini
    lbombini committed Aug 8, 2024
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Commits on Aug 15, 2024

  1. revert stratified_sample_qc to be general 

    do identical sample QC for all population (no difference between AFR and others)
    @y-popov
    y-popov committed Aug 15, 2024
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Commits on Aug 20, 2024

  1. fix circular import and name mangling in utils

    @d-goryslavets
    d-goryslavets committed Aug 20, 2024
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  2. fix step that required its own output files to run

    @d-goryslavets
    d-goryslavets committed Aug 20, 2024
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  3. upd unit tests to match refactored steps 1.1-2.1

    @d-goryslavets
    d-goryslavets committed Aug 20, 2024
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Commits on Aug 21, 2024

  1. Merge pull request #1 from wtsi-hgi/fix-2.4 

    Change `stratified_sample_qc`
    @d-goryslavets
    d-goryslavets authored Aug 21, 2024
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Commits on Aug 22, 2024

  1. upd unit test after stratified sample qc change

    @d-goryslavets
    d-goryslavets committed Aug 22, 2024
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  2. Refactor 2.2. Minor change in config naming. Change config fields ann… 

    …otation style. Add new dict utils
    @mkrooted256
    mkrooted256 committed Aug 22, 2024
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  3. Remove sanity checks in direct kwargs config groups. Fix ld_prune con… 

    …fig.
    @mkrooted256
    mkrooted256 committed Aug 22, 2024
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  4. integrate tesr data download

    @lbombini
    lbombini committed Aug 22, 2024
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Commits on Aug 27, 2024

  1. Merge branch 'mk43/refactor-hardcoded-config/2.2' into dh24/refactor-… 

    …hardcoded-config/2.3
    @d-goryslavets
    d-goryslavets committed Aug 27, 2024
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Commits on Aug 29, 2024

  1. Extract hardcoded values from step 2.4; add stub 2.3 config

    @mkrooted256
    mkrooted256 committed Aug 29, 2024
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  2. Add path type adapters in step 2.4

    @mkrooted256
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  3. Complete function annotations with indirect config fields in 2.4

    @mkrooted256
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  4. refactor step 2.3

    @d-goryslavets
    d-goryslavets committed Aug 29, 2024
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  5. upd integration test config structure

    @d-goryslavets
    d-goryslavets committed Aug 29, 2024
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  6. Extract hardcoded values from 2.5; add path type adapters

    @mkrooted256
    mkrooted256 committed Aug 29, 2024
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  7. update unit tests to reflect refactored steps 2.2

    @lbombini
    lbombini committed Aug 29, 2024
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Commits on Aug 30, 2024

  1. download data for integration tests from s3 bucket

    @d-goryslavets
    d-goryslavets committed Aug 30, 2024
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  2. Merge branch 'vk11/refactor-unit-test/2.2' into vk11/refactor-unit-te… 

    …st/2.3
    @lbombini
    lbombini committed Aug 30, 2024
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  3. download only required data from the bucket and fix back stratified s… 

    …ample qc
    @d-goryslavets
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  4. update the unit test to reflect changes in step 2.3

    @lbombini
    lbombini committed Aug 30, 2024
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  5. fix config and add ref_mtdir

    @lbombini
    lbombini committed Aug 30, 2024
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Commits on Sep 2, 2024

  1. Merge branch 'mk43/refactor-hardcoded-config/2.5' of https://github.c… 

    …om/wtsi-hgi/wes-qc into mk43/refactor-hardcoded-config/2.5
    @lbombini
    lbombini committed Sep 2, 2024
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  2. rename path >> file and 2.2 functions in config

    @lbombini
    lbombini committed Sep 2, 2024
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Commits on Sep 3, 2024

  1. Merge branch 'dh24/refactor-hardcoded-config/2.3' into imbg-refactori… 

    …ng (includes refactored steps 2.2-2.3)
    @d-goryslavets
    d-goryslavets committed Sep 3, 2024
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  2. Merge branch 'vk11/refactor-unit-test/2.3' into imbg-refactoring, upd… 

    … download from s3 and refactor var names
    @d-goryslavets
    d-goryslavets committed Sep 3, 2024
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  3. minor fixes to run 2.4 test

    @lbombini
    lbombini committed Sep 3, 2024
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  4. Merge branch 'mk43/refactor-hardcoded-config/2.5' into imbg-refactori… 

    …ng (includes refactored steps 2.4-2.5)
    @d-goryslavets
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  5. Merge branch 'vk11/refactor-unit-test/2.4-2.5' into imbg-refactoring

    @d-goryslavets
    d-goryslavets committed Sep 3, 2024
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Commits on Sep 4, 2024

  1. Add stub config argument for consistency

    @mkrooted256
    mkrooted256 committed Sep 4, 2024
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Commits on Sep 5, 2024

  1. more config tests. first version of new config parser. config docs

    @mkrooted256
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Commits on Sep 6, 2024

  1. add test data downloading from s3 to integration tests, upd configs, … 

    …fix errors in main functions caused by wrong param names
    @d-goryslavets
    d-goryslavets committed Sep 6, 2024
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  2. refactor test data downloading into utils func, use it in unit tests

    @d-goryslavets
    d-goryslavets committed Sep 6, 2024
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  3. new config parser. add tests. add docs. enhance code structure.

    @mkrooted256
    mkrooted256 committed Sep 6, 2024
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Commits on Sep 9, 2024

  1. extract hardcoded params and add path type adapters for trios and non… 

    …-trios scripts separately
    @d-goryslavets
    d-goryslavets committed Sep 9, 2024
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  2. step 3.2: extract hardcoded params and add path type adapters for tri… 

    …os and non-trios scripts separately
    @d-goryslavets
    d-goryslavets committed Sep 9, 2024
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Commits on Sep 17, 2024

  1. step 3.3: extract hardcoded params and add path type adapters

    @d-goryslavets
    d-goryslavets committed Sep 17, 2024
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  2. rename config tests dir back to local_tests for a merge

    @mkrooted256
    mkrooted256 committed Sep 17, 2024
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  3. Merge branch 'mk43/new-config-parser' into mk43/parser/v2.0-pre 

    (and remove a flattened config parser)
    @mkrooted256
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  4. start fixing config tests. prepare a new config system

    @mkrooted256
    mkrooted256 committed Sep 17, 2024
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  5. rename local_tests to config_tests

    @mkrooted256
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  6. finish parser v2.0-pre. Ready for beta

    @mkrooted256
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Commits on Sep 19, 2024

  1. steps 3.4-3.9: extract hardcoded params, add path type adapters, fix … 

    …small bugs
    @d-goryslavets
    d-goryslavets committed Sep 19, 2024
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  2. download RF training data from the s3 bucket in tests

    @d-goryslavets
    d-goryslavets committed Sep 19, 2024
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  3. steps 3.4-3.9: add missing path adapters, fix incorrect paths, refact… 

    …or non-trios case, create variant qc random forest result folder in test suite
    @d-goryslavets
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Commits on Sep 20, 2024

  1. 3.4-3.9 add missing adapters, fix bokeh imports and other bugs

    @d-goryslavets
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  2. 3.9 add missing path adapter

    @d-goryslavets
    d-goryslavets committed Sep 20, 2024
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  3. fix and improve integration tests config

    @d-goryslavets
    d-goryslavets committed Sep 20, 2024
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  4. refactor step 4: move hardcoded params to config, add path type adapt… 

    …ers, fix bugs
    @d-goryslavets
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  5. add hail logs to gitignore

    @d-goryslavets
    d-goryslavets committed Sep 20, 2024
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Commits on Sep 21, 2024

  1. add step 3 integration tests

    @lbombini
    lbombini committed Sep 21, 2024
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Commits on Sep 23, 2024

  1. allow to manually set run id in 3-train_rf

    @d-goryslavets
    d-goryslavets committed Sep 23, 2024
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  2. add var_qc_rf_dir to config variables

    @d-goryslavets
    d-goryslavets committed Sep 23, 2024
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  3. switch to http-based test data downloading in unit tests; fix incorre… 

    …ct input in test_2_3_5_predict_pops
    @d-goryslavets
    d-goryslavets committed Sep 23, 2024
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  4. add updated integration tests template for step 3-variant_qc

    @d-goryslavets
    d-goryslavets committed Sep 23, 2024
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Commits on Sep 24, 2024

  1. Merge branch 'dh24/refactor-hardcoded-config/4' into imbg-refactoring

    @d-goryslavets
    d-goryslavets committed Sep 24, 2024
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  2. add missing path type adapters in 3.4

    @d-goryslavets
    d-goryslavets committed Sep 24, 2024
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  3. upd example config and add script running all steps of QC

    @d-goryslavets
    d-goryslavets committed Sep 24, 2024
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  4. improve helper script to run all steps

    @d-goryslavets
    d-goryslavets committed Sep 24, 2024
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  5. Merge branch 'mk43/parser/v2.0-pre' into imbg-refactoring

    @d-goryslavets
    d-goryslavets committed Sep 24, 2024
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  6. Make parse_config_file return nested config and not flat. Add corresp… 

    …onding test cases
    @mkrooted256
    mkrooted256 committed Sep 24, 2024
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  7. Merge branch 'mk43/parser/v2.0-pre' into imbg-refactoring; fix bugs

    @d-goryslavets
    d-goryslavets committed Sep 24, 2024
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  8. change dots to underscores in qc plot settings names

    @d-goryslavets
    d-goryslavets committed Sep 24, 2024
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  9. update config parsing function names in scripts

    @d-goryslavets
    d-goryslavets committed Sep 24, 2024
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Commits on Sep 27, 2024

  1. upd test suite to use new config system; add integration tests for 4-… 

    …genotype_qc
    @d-goryslavets
    d-goryslavets committed Sep 27, 2024
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  2. fix plot settings names in integration tests config template

    @d-goryslavets
    d-goryslavets committed Sep 27, 2024
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Commits on Oct 1, 2024

  1. adjust variant qc scripts

    @y-popov
    y-popov committed Oct 1, 2024
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Commits on Oct 3, 2024

  1. refactor evaluation script

    @y-popov
    y-popov committed Oct 3, 2024
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  2. fix indentation and partition calcs

    @y-popov
    y-popov committed Oct 3, 2024
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Commits on Oct 4, 2024

  1. make giab sample optional for compare combinations

    @y-popov
    y-popov committed Oct 4, 2024
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Commits on Oct 7, 2024

  1. add readme for the test suite

    @d-goryslavets
    d-goryslavets committed Oct 7, 2024
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  2. more robust path join

    @y-popov
    y-popov committed Oct 7, 2024
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Commits on Oct 11, 2024

  1. Merge pull request #2 from wtsi-hgi/ip13-1kg-trio-test 

    Changes to run manual tests on 1kg data with trios
    @d-goryslavets
    d-goryslavets authored Oct 11, 2024
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Commits on Oct 16, 2024

  1. add skeleton for the remaining regression tests

    @d-goryslavets
    d-goryslavets committed Oct 16, 2024
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  2. add draft for downloading test data using list of files instead of an… 

    … archive
    @d-goryslavets
    d-goryslavets committed Oct 16, 2024
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Commits on Oct 18, 2024

  1. create plots dir if doesn't exist; refactor path joining for RF outdir

    @d-goryslavets
    d-goryslavets committed Oct 18, 2024
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  2. switch to downloading unarchived test data; upd and refactor tests ac… 

    …cordingly
    @d-goryslavets
    d-goryslavets committed Oct 18, 2024
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