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toml install / requirements version boost #1242

Merged
merged 77 commits into from
Aug 28, 2023
Merged

toml install / requirements version boost #1242

merged 77 commits into from
Aug 28, 2023

Commits on Aug 16, 2023

  1. bin execs replaced by toml scripts

    @WardDeb
    WardDeb committed Aug 16, 2023
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  2. replace version check for tests with toml version definition

    @WardDeb
    WardDeb committed Aug 16, 2023
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  3. remove _version file

    @WardDeb
    WardDeb committed Aug 16, 2023
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  4. version checks with importlib

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    WardDeb committed Aug 16, 2023
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  5. version check docs update to importlib

    @WardDeb
    WardDeb committed Aug 16, 2023
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  6. purge reqs & setup.py

    @WardDeb
    WardDeb committed Aug 16, 2023
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  7. init toml

    @WardDeb
    WardDeb committed Aug 16, 2023
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  8. update cm for mpl > 3.7

    @WardDeb
    WardDeb committed Aug 16, 2023
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  9. port nosetests to pytest

    @WardDeb
    WardDeb committed Aug 16, 2023
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  10. escape sysargv check in case of pytests

    @WardDeb
    WardDeb committed Aug 16, 2023
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  11. deprecate nosetest in favor of pytest

    @WardDeb
    WardDeb committed Aug 16, 2023
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  12. rollback heatmapperr imgs test until later

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    WardDeb committed Aug 16, 2023
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  13. flake8

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    WardDeb committed Aug 16, 2023
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Commits on Aug 17, 2023

  1. add conda env for workflows

    @WardDeb
    WardDeb committed Aug 17, 2023
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  2. switch test to micromamba

    @WardDeb
    WardDeb committed Aug 17, 2023
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  3. planemo tests to python 3.11, include samtools in test env

    @WardDeb
    WardDeb committed Aug 17, 2023
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  4. shell defaults planemo test

    @WardDeb
    WardDeb committed Aug 17, 2023
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  5. pin allure version for planemo tests

    @WardDeb
    WardDeb committed Aug 17, 2023
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  6. pin python to 3.10 in test env

    @WardDeb
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  7. pin 3.10 in planemo wf as well

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  8. test env channel priority into condarc

    @WardDeb
    WardDeb committed Aug 17, 2023
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  9. planemo on 3.9, test on 3.11

    @WardDeb
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  10. complete rollback to 3.7 planemo with same deps as previous action

    @WardDeb
    WardDeb committed Aug 17, 2023
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  11. pybw typo

    @WardDeb
    WardDeb committed Aug 17, 2023
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  12. include pip install in planemo..

    @WardDeb
    WardDeb committed Aug 17, 2023
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  13. test with planemo test run python 3.10

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  14. planemo tests with python 3.11 under galaxy

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  15. py2bit as pip dep

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    WardDeb committed Aug 17, 2023
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Commits on Aug 18, 2023

  1. python 3.10 for tests & planemo galaxy version

    @WardDeb
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  2. plotcorr - parsed labels changed slightly due to mpl versions (assumed)

    @WardDeb
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  3. typo in pltfingerprint comment, typo in bin script, include 1 extra s… 

    …ignificant digit in synthetic JS distance test (np default changed?)
    @WardDeb
    WardDeb committed Aug 18, 2023
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  4. replace both expected heatmaps in planemo tests (mpl version boost ==… 

    … size difference)
    @WardDeb
    WardDeb committed Aug 18, 2023
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  5. replace plotprofile png in planemo test

    @WardDeb
    WardDeb committed Aug 18, 2023
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  6. test with NA in fp qualmets

    @WardDeb
    WardDeb committed Aug 18, 2023
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  7. remove extra float + switch back to lower case nan qual metrics

    @WardDeb
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  8. include dist creation + test wheel install

    @WardDeb
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  9. add name to test wheel wf

    @WardDeb
    WardDeb committed Aug 18, 2023
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  10. name in diff place

    @WardDeb
    WardDeb committed Aug 18, 2023
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  11. include build in building env

    @WardDeb
    WardDeb committed Aug 18, 2023
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  12. purge checkout from testwheel

    @WardDeb
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  13. ship test wheels inside build-linux job

    @WardDeb
    WardDeb committed Aug 18, 2023
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  14. testwheels as separate job with artifact download

    @WardDeb
    WardDeb committed Aug 18, 2023
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  15. add depends on

    @WardDeb
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  16. ls to see if download works

    @WardDeb
    WardDeb committed Aug 18, 2023
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  17. list wdir after artifact dl

    @WardDeb
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  18. add checkout to test-wheels

    @WardDeb
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  19. whl in dist folder

    @WardDeb
    WardDeb committed Aug 18, 2023
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  20. tilde in pip install

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    WardDeb committed Aug 18, 2023
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Commits on Aug 19, 2023

  1. importlib toml req for python 3.7

    @WardDeb
    WardDeb committed Aug 19, 2023
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  2. importlib escapes for python 3.7

    @WardDeb
    WardDeb committed Aug 19, 2023
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  3. flake fix try except

    @WardDeb
    WardDeb committed Aug 19, 2023
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  4. test pypi build with micromamba

    @WardDeb
    WardDeb committed Aug 19, 2023
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  5. pypi push on tag

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Commits on Aug 21, 2023

  1. include pytest in test-wheels

    @WardDeb
    WardDeb committed Aug 21, 2023
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  2. rounding qual metrics fingerprint galaxy test

    @WardDeb
    WardDeb committed Aug 21, 2023
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  3. set version to 3.5.3

    @WardDeb
    WardDeb committed Aug 21, 2023
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  4. revert back to fingerprint qual metrics

    @WardDeb
    WardDeb committed Aug 21, 2023
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  5. rollback galaxy again

    @WardDeb
    WardDeb committed Aug 21, 2023
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  6. update installation instructions doc

    @WardDeb
    WardDeb committed Aug 21, 2023
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  7. qual metrics 14

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    WardDeb committed Aug 21, 2023
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Commits on Aug 22, 2023

  1. usage and -h for all executables

    @WardDeb
    WardDeb committed Aug 22, 2023
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  2. flakes

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    WardDeb committed Aug 22, 2023
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  3. switch pytest to -v

    @WardDeb
    WardDeb committed Aug 22, 2023
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  4. switch pytest to -v in init build as well

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    WardDeb committed Aug 22, 2023
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Commits on Aug 24, 2023

  1. Update .github/workflows/planemo.yml 

    Co-authored-by: Björn Grüning <[email protected]>
    @WardDeb @bgruening
    WardDeb and bgruening authored Aug 24, 2023
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  2. python >=3.7, combine env/planemo envs, planemo test galaxy 23.1

    @WardDeb
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  3. force conda prefix to micromamba env dir on runner

    @WardDeb
    WardDeb committed Aug 24, 2023
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  4. include pytests for 3.11

    @WardDeb
    WardDeb committed Aug 24, 2023
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  5. bring back no dependency resolution planemo

    @WardDeb
    WardDeb committed Aug 24, 2023
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Commits on Aug 25, 2023

  1. parse toml for tool tests + verify version

    @WardDeb
    WardDeb committed Aug 25, 2023
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  2. fstring tests

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    WardDeb committed Aug 25, 2023
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  3. 1 env for test/builds, pip planemo, python min version 3.7, drop allu… 

    …re restriction
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    WardDeb committed Aug 25, 2023
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  4. setup-miniconda runner instead of micromamba for planemo test

    @WardDeb
    WardDeb committed Aug 25, 2023
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  5. print planemo version in shell runner

    @WardDeb
    WardDeb committed Aug 25, 2023
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  6. flake fixes tests

    @WardDeb
    WardDeb committed Aug 25, 2023
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  7. drop channelprio / planemo fingerprint back to 13 (again)

    @WardDeb
    WardDeb committed Aug 25, 2023
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  8. update changelog

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    WardDeb committed Aug 25, 2023
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