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Implement CI testing and increase testing coverage #413

Merged
merged 44 commits into from
Feb 9, 2024
Merged

Implement CI testing and increase testing coverage #413

merged 44 commits into from
Feb 9, 2024

Commits on Jan 31, 2024

  1. bump dev reqs

    @kedhammar
    kedhammar committed Jan 31, 2024
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  2. move functional tests into subdir

    @kedhammar
    kedhammar committed Jan 31, 2024
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  3. move configuration of pytest to pyproject.toml and replace coverage e… 

    …xclusion method
    @kedhammar
    kedhammar committed Jan 31, 2024
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  4. start building testing framework

    @kedhammar
    kedhammar committed Jan 31, 2024
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  5. remove unused var

    @kedhammar
    kedhammar committed Jan 31, 2024
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Commits on Feb 2, 2024

  1. update hint for checking manual coverage

    @kedhammar
    kedhammar committed Feb 2, 2024
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  2. wip

    @kedhammar
    kedhammar committed Feb 2, 2024
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  3. good progress

    @kedhammar
    kedhammar committed Feb 2, 2024
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  4. bump file being tested to dev version

    @kedhammar
    kedhammar committed Feb 2, 2024
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  5. successfully instantiate run object for testing

    @kedhammar
    kedhammar committed Feb 2, 2024
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  6. update docs

    @kedhammar
    kedhammar committed Feb 2, 2024
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  7. fix error, 28% coverage!

    @kedhammar
    kedhammar committed Feb 2, 2024
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Commits on Feb 5, 2024

  1. Merge remote-tracking branch 'upstream/master' into pytest-ci

    @kedhammar
    kedhammar committed Feb 5, 2024
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  2. update config to ignore deprecationwarnings from external packages

    @kedhammar
    kedhammar committed Feb 5, 2024
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  3. docstring

    @kedhammar
    kedhammar committed Feb 5, 2024
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Commits on Feb 6, 2024

  1. move fixture to conftest file

    @kedhammar
    kedhammar committed Feb 6, 2024
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  2. wip

    @kedhammar
    kedhammar committed Feb 6, 2024
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  3. remove redundancy

    @kedhammar
    kedhammar committed Feb 6, 2024
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  4. update test

    @kedhammar
    kedhammar committed Feb 6, 2024
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  5. add conditional files to created run dir

    @kedhammar
    kedhammar committed Feb 6, 2024
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  6. remove irrelevant rows from test data

    @kedhammar
    kedhammar committed Feb 6, 2024
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Commits on Feb 7, 2024

  1. Don't fail ONT run class instantiation w. missing analysis server config

    @kedhammar
    kedhammar committed Feb 7, 2024
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  2. ATTN! Fix what I interpret as a bug

    @kedhammar
    kedhammar committed Feb 7, 2024
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  3. remove analysis server from test config and add mail mock entry

    @kedhammar
    kedhammar committed Feb 7, 2024
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  4. functional user run processing, continuing with qc run

    @kedhammar
    kedhammar committed Feb 7, 2024
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  5. add comment headers

    @kedhammar
    kedhammar committed Feb 7, 2024
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  6. formatting

    @kedhammar
    kedhammar committed Feb 7, 2024
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  7. add anglerfish samplesheets dir to fixture

    @kedhammar
    kedhammar committed Feb 7, 2024
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  8. make samplesheet glob agnostic to current year and fix bug

    @kedhammar
    kedhammar committed Feb 7, 2024
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  9. - add anglerfish dir to config and add more options for creating test… 

    … run
    @kedhammar
    kedhammar committed Feb 7, 2024
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  10. implement BRILLIANT way to conditionally circumvent anglerfish call

    @kedhammar
    kedhammar committed Feb 7, 2024
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  11. remove ipdb

    @kedhammar
    kedhammar committed Feb 7, 2024
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  12. Adress pytest warnings by using r strings

    @kedhammar
    kedhammar committed Feb 7, 2024
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  13. Update old test

    @kedhammar
    kedhammar committed Feb 7, 2024
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  14. add config of coverage.py to pyproject.toml, exclude __init__.py files

    @kedhammar
    kedhammar committed Feb 7, 2024
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  15. vlog bump

    @kedhammar
    kedhammar committed Feb 7, 2024
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  16. update gitignore

    @kedhammar
    kedhammar committed Feb 7, 2024
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  17. Clean up comments

    @kedhammar
    kedhammar committed Feb 7, 2024
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Commits on Feb 8, 2024

  1. fix ci

    @kedhammar
    kedhammar committed Feb 8, 2024
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  2. prettier

    @kedhammar
    kedhammar committed Feb 8, 2024
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  3. try editable install of taca in gha

    @kedhammar
    kedhammar committed Feb 8, 2024
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  4. Merge branch 'master' into pytest-ci

    @kedhammar
    kedhammar authored Feb 8, 2024
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  5. adress pytest warnings by adding r strings

    @kedhammar
    kedhammar committed Feb 8, 2024
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  6. fix bug in instrument transfer script

    @kedhammar
    kedhammar committed Feb 8, 2024
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