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

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geneticsjesse wants to merge 104 commits intomainDNAstack/wdl-ci:mainfrom feature/task-and-output-test-coverageDNAstack/wdl-ci:feature/task-and-output-test-coverageCopy head branch name to clipboard

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Commits

Commits on Mar 5, 2024

• Merge branch 'bugfix/avoid-detecting-changes-for-tasks-with-no-tests' of https://github.com/DNAstack/wdl-ci into feature/task-and-output-test-coverage

  

  geneticsjesse

  committed
  7333647

• Add command to calculate coverage for each task and output

  

  geneticsjesse

  committed
  3727b17

Commits on Mar 6, 2024

• Add initial version of script/CLI command to output task and output coverage

  

  geneticsjesse

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  ceeb069

• Make minor formatting adjustments

  

  geneticsjesse

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  0b940ef

• Make more minor formatting adjustments

  

  geneticsjesse

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  4abf55a

• Remove check and append to list for tests with no tasks

  

  geneticsjesse

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  2425e70

• Adjust formatting of print statements

  

  geneticsjesse

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  cf8a6ed

Commits on Mar 7, 2024

• Remove creation of unused list

  

  geneticsjesse

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  45f99e8

• Adjust style of warnings to match internal format

  

  geneticsjesse

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  013cdec

• Initial commit for handling output key errors

  

  geneticsjesse

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  0eea505

Commits on Mar 8, 2024

• Add error message for when an output key is not found

  

  geneticsjesse

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  bf59f2d

• Add error message for when an output key is not found

  

  geneticsjesse

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  89e896c

Commits on Mar 11, 2024

• Reorganize and simplify handling of missing outputs key error

  

  geneticsjesse

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  bdd8e82

• Further reorganize and simplify handling of missing outputs key error

  Show description for 4ba4380
  

  geneticsjesse

  committed
  4ba4380

Commits on Mar 12, 2024

• Fix creation of list of outputs

  

  geneticsjesse

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  76dda77

Commits on Mar 13, 2024

• Adjust style of warnings to match internal format

  

  geneticsjesse

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  6171a33

• Merge branch 'develop' into feature/task-and-output-test-coverage

  hkeward

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  ebd8a3d

Commits on Mar 14, 2024

• Test handling of output key error in submit script instead of write_workflow

  

  geneticsjesse

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  0639e9a

• Add comments for clarity

  

  geneticsjesse

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  bd269ed

• Merge branch 'feature/task-and-output-test-coverage' into feature/handle-output-key-error

  geneticsjesse

  authored
  331d6e8

• Revert all commits that handled output key errors in write_workflow

  

  geneticsjesse

  committed
  2efa231

Commits on Mar 27, 2024

• Merge pull request #49 from DNAstack/feature/handle-output-key-error

  Show description for 5334c53
  geneticsjesse

  authored
  5334c53

• Add documentation surrounding wdl-ci coverage command

  

  geneticsjesse

  committed
  09d4094

Commits on Apr 4, 2024

• Rename subcommand; remove old subcommand script

  

  geneticsjesse

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  b46ffae

• Add coverage subcommand to calculate and display test coverage

  Show description for f611b09
  

  geneticsjesse

  committed
  f611b09

Commits on Apr 5, 2024

• Adjust subcommand to handle compound outputs; clean up calculations

  

  geneticsjesse

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  8d9d5ce

• Adjust formatting/organization of task coverage output

  

  geneticsjesse

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  d8c0ad7

Commits on Nov 15, 2024

• Wrap task name properly

  geneticsjesse

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  5bb45db

Commits on Nov 18, 2024

• Clarify parameter precedence

  hkeward

  committed
  2f0e8cc

Commits on Nov 21, 2024

• Improve coverage calculation login; add specific warning for optional outputs

  Show description for 3ac87fc
  geneticsjesse

  committed
  3ac87fc

• Merge branch 'feature/task-and-output-test-coverage' of https://github.com/DNAstack/wdl-ci into feature/task-and-output-test-coverage

  geneticsjesse

  committed
  0a762f0

• Add threshold and workflow name arguments to coverage command

  geneticsjesse

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  8498965

• Implement usage of threshold and workflow name within coverage command

  geneticsjesse

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  8e88ad1

• Add context to new features of wdl-ci coverage

  geneticsjesse

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  a29df08

Commits on Nov 22, 2024

• Clean up documentation

  geneticsjesse

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  a998e8f

• Merge branch 'main' of https://github.com/DNAstack/wdl-ci into feature/task-and-output-test-coverage

  geneticsjesse

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  eec18b2

• Make formatting changes

  geneticsjesse

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  624b22a

• Report to user any optional input not covered as part of wdl-ci tests

  geneticsjesse

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  b6a665e

• Comment out print statement re: optional inputs; add relevant TODO

  geneticsjesse

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  c4da040

Commits on Nov 25, 2024

• Remove unused input checking code; adjust TODO

  geneticsjesse

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  fb07f30

Commits on Nov 29, 2024

• Merge branch 'main' into feature/task-and-output-test-coverage

  hkeward

  committed
  09057ef

• Rename coverage_threshold to target_coverage to make it a bit clearer

  hkeward

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  2f3248c

• Update docs for changed arg name

  hkeward

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  149eb63

Commits on Dec 5, 2024

• Remove comment and creation of set; add check for length to avoid false-y

  geneticsjesse

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  8b8b032

• Clarify workflow file name is required

  geneticsjesse

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  b24c357

• Avoid more false-y traps; remove redundant checks if threshold is not None

  geneticsjesse

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  5052744

• Fix check for threshold > task_coverage or threshold not specified

  geneticsjesse

  committed
  3ec8f62

Commits on Dec 6, 2024

• Avoid more false-ys; add TODOs

  geneticsjesse

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  ac61953

• Begin working through PR revisions; making holistic changes to test namespaced outputs that are linked to their respective workflows

  geneticsjesse

  committed
  5538a07

Commits on Dec 9, 2024

• Add function for repeated code and import/implement

  geneticsjesse

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  262f0ea

Commits on Dec 10, 2024

• Clarify how to provide workflow name based on changes to coverage command

  geneticsjesse

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  fbf2645

• Get command in a functional state based on PR revisions; UX changes and testing to follow

  geneticsjesse

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  7c8bc76

• Remove some dev code and a TODO

  geneticsjesse

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  f180629

Commits on Dec 12, 2024

• Add TODOs for more flags for the coverage command

  geneticsjesse

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  3647f99

• Add working version but still in dev

  geneticsjesse

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  2b88c42

• Remove redundant code that was refactored with helper functions

  geneticsjesse

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  12edb32

Commits on Dec 13, 2024

• Remove unnecessary print

  geneticsjesse

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  a66bde7

• Handle case where test_tasks is an empty list; would have considered tested before this check

  geneticsjesse

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  e79a4ad

• Adjust comment wording

  geneticsjesse

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  4ed57c1

• Add .DS_STORE

  geneticsjesse

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  f1c3ee0

• Adjust TODO

  geneticsjesse

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  4237fd4

• Add tests for coverage handler -- in dev

  geneticsjesse

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  e243224

• Improve naming conventions of coverage_summary keys; set boolean flags dynamically as part of code; adjust TODOs

  geneticsjesse

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  8187b2b

• Add additional handling of boolean checks

  geneticsjesse

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  086c75a

• Added extra test; rename coverage summary keys

  geneticsjesse

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  3cebce8

• Improve prints; return tested outputs for each {workflow.task}

  geneticsjesse

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  c6e774c

• Suppress ResourceWarning; add additional tests to add; comment out second test to avoid config load error

  Show description for 36b712b
  geneticsjesse

  committed
  36b712b

• Move tests dir

  geneticsjesse

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  7ff888e

• Fix typo

  geneticsjesse

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  9f83394

• Remove unused file with single test

  geneticsjesse

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  32c214d

• Add more tests to add

  geneticsjesse

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  f7166e0

• Comment our warning suppression so I can handle it later

  geneticsjesse

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  3a2100e

• Adjust name of coverage_summary dict keys

  geneticsjesse

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  9156cdc

• Add threshold to test

  geneticsjesse

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  ba14693

• rename test

  geneticsjesse

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  4c589e2

• Rename key

  geneticsjesse

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  a8833d4

• Improve naming conventions

  geneticsjesse

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  660f8be

• Add explicit tests for any remaining instances of if <varname>

  geneticsjesse

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  987a03c

• Add clarity in some comments; add single TODO

  geneticsjesse

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  074bde5

Commits on Dec 14, 2024

• Avoid adding to untested_outputs_dict if there are no missing outputs

  geneticsjesse

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  0a0ec33

• Avoid adding to tested_outputs_dict if there are no tested outputs

  geneticsjesse

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  d6c82f4

• 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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  351a3ad

• Redirect stdout to hide coverage output; suppress warning as part of setUp; add more TODO tests

  geneticsjesse

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  9e5a19b

• Set tasks below threshold to false if there is the workflow is skipped based on workflow_name filter

  geneticsjesse

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  586ce4d

• Add more tests; still in dev

  geneticsjesse

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  98e2c31

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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  b271da1

• Set workflow_found via else explicitly

  geneticsjesse

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  2a59feb

• Remove TODO

  geneticsjesse

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  47c97df

• Add three threshold tests; add test for optional inputs

  geneticsjesse

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  9a667b9

• Clarify TODO

  geneticsjesse

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  db6c3fd

• Remove TODO; improve naming of all tests list; handle case where no outputs to compute coverage for

  geneticsjesse

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  a727fbf

• Remove another TODO

  geneticsjesse

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  1645d98

• Rename for clarity

  geneticsjesse

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  59e65cc

• Simplify workflow_name_filter returned to user; remove check for filter that resulted in confusing output

  Show description for b1f68b9
  geneticsjesse

  committed
  b1f68b9

Commits on Dec 17, 2024

• Add test todo

  geneticsjesse

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  b2e46a9

• Remove comment; explicitly check workflow name; rename function for clarity

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  3385477

Commits on Dec 18, 2024

• Move reset of config into a finally block

  geneticsjesse

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  b21590a

• Adjust if to elif

  geneticsjesse

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  87b6ae9

• Add todo

  geneticsjesse

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  7396c86

• Simplify checking for missing outputs

  hkeward

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  b391d6e

• Allow multiple workflow filters to be passed

  hkeward

  committed
  ac98336

• Move coverage summary inside function; change strategy for detecting

  Show description for 7def2da
  hkeward

  committed
  7def2da

• Moved final output messages around

  hkeward

  committed
  db8950c

Commits on Dec 20, 2024

• Add skipped workflows to check prior to printing warnings

  geneticsjesse

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  6d49270