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CPG flow division #962

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Commits on Oct 28, 2024

  1. docs(metamist.py): classification complete 

    Added region tags for the two unused methods and a modify for one method that has unused variables
    @violetbrina
    violetbrina committed Oct 28, 2024
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  2. docs(cpg_workflows/targets.py): Tag regions for unused code, as well … 

    …as some modifications for the Cohort.create_dataset that has an open ticket.
    @violetbrina
    violetbrina committed Oct 28, 2024
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  3. docs(cpg_workflows/inputs.py): remove the deprecated functions when m… 

    …oving across, fix the function call appropriately
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    violetbrina committed Oct 28, 2024
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  4. docs(cpg_workflows/batch.py): Move the function across, however renam… 

    …e or relocate to a utils.py file
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  5. docs(cpg_workflows/resources.py): move file with a small deletion

    @violetbrina
    violetbrina committed Oct 28, 2024
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  6. docs(cpg_workflows/workflow.py): move the whole file but split betwee… 

    …n workflow and stage code
    @violetbrina
    violetbrina committed Oct 28, 2024
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Commits on Oct 29, 2024

  1. docs(test/test_cohort.py): Added regions to modify unused imports

    @nevoodoo
    nevoodoo committed Oct 29, 2024
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  2. docs(test/test_metamist.py): Added regions to modify for unused imports

    @nevoodoo
    nevoodoo committed Oct 29, 2024
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  3. docs(test/test_multicohort.py): Added regions to modify for unused im… 

    …ports
    @nevoodoo
    nevoodoo committed Oct 29, 2024
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  4. docs(cpg_workflows/__init__.py): Added regions to modify for unused i… 

    …mports
    @nevoodoo
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  5. docs(test.yaml): keep the whole workflow

    @violetbrina
    violetbrina committed Oct 29, 2024
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  6. docs(cpg_workflows/utils.py): keep the whole utility file

    @violetbrina
    violetbrina committed Oct 29, 2024
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  7. Merge branch 'cpg-flow-division' of github.com:populationgenomics/pro… 

    …duction-pipelines into cpg-flow-division
    @violetbrina
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  8. docs(misc/attach_disk_test.py): keep the whole test file, move it int… 

    …o tests/ directory
    @violetbrina
    violetbrina committed Oct 29, 2024
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  9. docs(test/__init__.py): helper code for our testing functions

    @violetbrina
    violetbrina committed Oct 29, 2024
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  10. docs(test/conftest.py): legacy pytest fixture, not used anywhere, lea… 

    …ve behind
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  11. docs(test/README.md): writing tests documentation, keep

    @violetbrina
    violetbrina committed Oct 29, 2024
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Commits on Oct 30, 2024

  1. docs(test/stages/__init__.py): helper code for tests of the stages, k… 

    …eep it all
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  2. docs(test/stages/test_first_last_stages_misconfigured.py): tests api,… 

    … keep it
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  3. docs(test/stages/test_first_last_stages.py): test, keep it all

    @violetbrina
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  4. docs(cpg_workflows/targets.py): formatter fix

    @violetbrina
    violetbrina committed Oct 30, 2024
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  5. docs(test/stages/test_first_stages.py): test, keep

    @violetbrina
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  6. docs(test/stages/test_force_stages.py): test, keep

    @violetbrina
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  7. docs(test/stages/test_last_stages.py): test, keep

    @violetbrina
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  8. docs(test/stages/test_only_stages.py): test, keep

    @violetbrina
    violetbrina committed Oct 30, 2024
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  9. docs(test/stages/test_skip_stages_fail.py): test, keep

    @violetbrina
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  10. docs(test/stages/test_skip_stages.py): test, keep

    @violetbrina
    violetbrina committed Oct 30, 2024
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  11. docs(test/stages/test_stage_types.py): test, keep

    @violetbrina
    violetbrina committed Oct 30, 2024
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  12. docs(test/test_status.py): test, keep

    @violetbrina
    violetbrina committed Oct 30, 2024
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  13. docs(test/test_workflow.py): test, keep

    @violetbrina
    violetbrina committed Oct 30, 2024
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