Feature/task-and-output-test-coverage#48

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geneticsjesse wants to merge 108 commits intomainfrom

feature/task-and-output-test-coverage

Commits on Mar 5, 2024

Commits on Mar 6, 2024

Add initial version of script/CLI command to output task and output coverage
geneticsjesse
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Make minor formatting adjustments
geneticsjesse
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Make more minor formatting adjustments
geneticsjesse
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Remove check and append to list for tests with no tasks
geneticsjesse
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Adjust formatting of print statements
geneticsjesse
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Commits on Mar 7, 2024

Remove creation of unused list
geneticsjesse
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Adjust style of warnings to match internal format
geneticsjesse
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Initial commit for handling output key errors
geneticsjesse
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Commits on Mar 8, 2024

Add error message for when an output key is not found
geneticsjesse
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Add error message for when an output key is not found
geneticsjesse
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Commits on Mar 11, 2024

Reorganize and simplify handling of missing outputs key error
geneticsjesse
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Further reorganize and simplify handling of missing outputs key error
geneticsjesse
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Commits on Mar 12, 2024

Fix creation of list of outputs
geneticsjesse
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Commits on Mar 13, 2024

Commits on Mar 14, 2024

Test handling of output key error in submit script instead of write_workflow
geneticsjesse
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Add comments for clarity
geneticsjesse
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Merge branch 'feature/task-and-output-test-coverage' into feature/handle-output-key-error
geneticsjesse
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Revert all commits that handled output key errors in write_workflow
geneticsjesse
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Commits on Mar 27, 2024

Commits on Apr 4, 2024

Rename subcommand; remove old subcommand script
geneticsjesse
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Add coverage subcommand to calculate and display test coverage
geneticsjesse
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Commits on Apr 5, 2024

Adjust subcommand to handle compound outputs; clean up calculations
geneticsjesse
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Adjust formatting/organization of task coverage output
geneticsjesse
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Commits on Nov 15, 2024

Wrap task name properly
geneticsjesse
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Commits on Nov 18, 2024

Clarify parameter precedence
hkeward
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Commits on Nov 21, 2024

Improve coverage calculation login; add specific warning for optional outputs
geneticsjesse
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Merge branch 'feature/task-and-output-test-coverage' of https://github.com/DNAstack/wdl-ci into feature/task-and-output-test-coverage
geneticsjesse
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Add threshold and workflow name arguments to coverage command
geneticsjesse
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Implement usage of threshold and workflow name within coverage command
geneticsjesse
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Add context to new features of wdl-ci coverage
geneticsjesse
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Commits on Nov 22, 2024

Clean up documentation
geneticsjesse
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Merge branch 'main' of https://github.com/DNAstack/wdl-ci into feature/task-and-output-test-coverage
geneticsjesse
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Make formatting changes
geneticsjesse
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Report to user any optional input not covered as part of wdl-ci tests
geneticsjesse
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Comment out print statement re: optional inputs; add relevant TODO
geneticsjesse
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Commits on Nov 25, 2024

Remove unused input checking code; adjust TODO
geneticsjesse
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Commits on Nov 29, 2024

Commits on Dec 5, 2024

Remove comment and creation of set; add check for length to avoid false-y
geneticsjesse
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Clarify workflow file name is required
geneticsjesse
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Avoid more false-y traps; remove redundant checks if threshold is not None
geneticsjesse
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Fix check for threshold > task_coverage or threshold not specified
geneticsjesse
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Commits on Dec 6, 2024

Avoid more false-ys; add TODOs
geneticsjesse
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Begin working through PR revisions; making holistic changes to test namespaced outputs that are linked to their respective workflows
geneticsjesse
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Commits on Dec 9, 2024

Add function for repeated code and import/implement
geneticsjesse
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Commits on Dec 10, 2024

Clarify how to provide workflow name based on changes to coverage command
geneticsjesse
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Get command in a functional state based on PR revisions; UX changes and testing to follow
geneticsjesse
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Remove some dev code and a TODO
geneticsjesse
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Commits on Dec 12, 2024

Add TODOs for more flags for the coverage command
geneticsjesse
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Add working version but still in dev
geneticsjesse
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Remove redundant code that was refactored with helper functions
geneticsjesse
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Commits on Dec 13, 2024

Remove unnecessary print
geneticsjesse
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Handle case where test_tasks is an empty list; would have considered tested before this check
geneticsjesse
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Adjust comment wording
geneticsjesse
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Add .DS_STORE
geneticsjesse
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Adjust TODO
geneticsjesse
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Add tests for coverage handler -- in dev
geneticsjesse
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Improve naming conventions of coverage_summary keys; set boolean flags dynamically as part of code; adjust TODOs
geneticsjesse
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Add additional handling of boolean checks
geneticsjesse
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Added extra test; rename coverage summary keys
geneticsjesse
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Improve prints; return tested outputs for each {workflow.task}
geneticsjesse
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Suppress ResourceWarning; add additional tests to add; comment out second test to avoid config load error
geneticsjesse
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Move tests dir
geneticsjesse
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Fix typo
geneticsjesse
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Remove unused file with single test
geneticsjesse
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Add more tests to add
geneticsjesse
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Comment our warning suppression so I can handle it later
geneticsjesse
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Adjust name of coverage_summary dict keys
geneticsjesse
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Add threshold to test
geneticsjesse
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rename test
geneticsjesse
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Rename key
geneticsjesse
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Improve naming conventions
geneticsjesse
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Add explicit tests for any remaining instances of if <varname>
geneticsjesse
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Add clarity in some comments; add single TODO
geneticsjesse
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Commits on Dec 14, 2024

Avoid adding to untested_outputs_dict if there are no missing outputs
geneticsjesse
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Avoid adding to tested_outputs_dict if there are no tested outputs
geneticsjesse
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Add a class method to reset the config and reset it at the end of the coverage script to facilitate testing
geneticsjesse
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Redirect stdout to hide coverage output; suppress warning as part of setUp; add more TODO tests
geneticsjesse
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Set tasks below threshold to false if there is the workflow is skipped based on workflow_name filter
geneticsjesse
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Add more tests; still in dev
geneticsjesse
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Commits on Dec 16, 2024

Set tasks_below_threshold to false if workflows are skipped based on name; calculate task coverage using dict instead of list; add TODO
geneticsjesse
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Set workflow_found via else explicitly
geneticsjesse
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Remove TODO
geneticsjesse
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Add three threshold tests; add test for optional inputs
geneticsjesse
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Clarify TODO
geneticsjesse
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Remove TODO; improve naming of all tests list; handle case where no outputs to compute coverage for
geneticsjesse
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Remove another TODO
geneticsjesse
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Rename for clarity
geneticsjesse
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Simplify workflow_name_filter returned to user; remove check for filter that resulted in confusing output
geneticsjesse
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Commits on Dec 17, 2024

Add test todo
geneticsjesse
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Remove comment; explicitly check workflow name; rename function for clarity
geneticsjesse
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Commits on Dec 18, 2024

Commits on Dec 20, 2024

Add skipped workflows to check prior to printing warnings
geneticsjesse
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Commits on Jan 8, 2025

Adjust total and workflow output counts to lists; write function to update coverage for imports and tasks
geneticsjesse
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Remove redundant code; begin trying to handle nested imports - in dev
geneticsjesse
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Revert "Remove redundant code; begin trying to handle nested imports - in dev"
geneticsjesse
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Revert "Adjust total and workflow output counts to lists; write function to update coverage for imports and tasks"
geneticsjesse
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