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Develop #1243

Merged
merged 101 commits into from
Aug 29, 2023
Merged

Develop #1243

merged 101 commits into from
Aug 29, 2023

Commits on May 23, 2023

  1. Bump requests from 2.27.1 to 2.31.0 

    Bumps [requests](https://github.com/psf/requests) from 2.27.1 to 2.31.0.
- [Release notes](https://github.com/psf/requests/releases)
- [Changelog](https://github.com/psf/requests/blob/main/HISTORY.md)
- [Commits](psf/requests@v2.27.1...v2.31.0)

---
updated-dependencies:
- dependency-name: requests
  dependency-type: direct:production
...

Signed-off-by: dependabot[bot] <[email protected]>
    @dependabot
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Commits on Jun 16, 2023

  1. stricter label checks

    @bgruening
    bgruening authored Jun 16, 2023
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Commits on Jun 17, 2023

  1. add validator

    @bgruening
    bgruening authored Jun 17, 2023
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  2. add validator

    @bgruening
    bgruening authored Jun 17, 2023
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Commits on Jun 21, 2023

  1. Merge pull request #1230 from deeptools/master 

    Keeping branches in sync
    @adRn-s
    adRn-s authored Jun 21, 2023
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Commits on Jul 6, 2023

  1. Bump scipy from 1.8.0 to 1.10.0 

    Bumps [scipy](https://github.com/scipy/scipy) from 1.8.0 to 1.10.0.
- [Release notes](https://github.com/scipy/scipy/releases)
- [Commits](scipy/scipy@v1.8.0...v1.10.0)

---
updated-dependencies:
- dependency-name: scipy
  dependency-type: direct:production
...

Signed-off-by: dependabot[bot] <[email protected]>
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Commits on Jul 20, 2023

  1. Bump pygments from 2.12.0 to 2.15.0 

    Bumps [pygments](https://github.com/pygments/pygments) from 2.12.0 to 2.15.0.
- [Release notes](https://github.com/pygments/pygments/releases)
- [Changelog](https://github.com/pygments/pygments/blob/master/CHANGES)
- [Commits](pygments/pygments@2.12.0...2.15.0)

---
updated-dependencies:
- dependency-name: pygments
  dependency-type: direct:production
...

Signed-off-by: dependabot[bot] <[email protected]>
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Commits on Jul 21, 2023

  1. np.{type} to {type}

    @ggraham
    ggraham committed Jul 21, 2023
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Commits on Jul 25, 2023

  1. Bump certifi from 2022.12.7 to 2023.7.22 

    Bumps [certifi](https://github.com/certifi/python-certifi) from 2022.12.7 to 2023.7.22.
- [Commits](certifi/python-certifi@2022.12.07...2023.07.22)

---
updated-dependencies:
- dependency-name: certifi
  dependency-type: direct:production
...

Signed-off-by: dependabot[bot] <[email protected]>
    @dependabot
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Commits on Aug 10, 2023

  1. Merge pull request #1237 from deeptools/dependabot/pip/certifi-2023.7.22 

    Bump certifi from 2022.12.7 to 2023.7.22
    @WardDeb
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  2. Merge pull request #1234 from deeptools/dependabot/pip/pygments-2.15.0 

    Bump pygments from 2.12.0 to 2.15.0
    @WardDeb
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  3. Merge pull request #1232 from deeptools/dependabot/pip/scipy-1.10.0 

    Bump scipy from 1.8.0 to 1.10.0
    @WardDeb
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  4. Merge pull request #1227 from deeptools/label_check 

    stricter label checks
    @WardDeb
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  5. Merge pull request #1216 from deeptools/dependabot/pip/requests-2.31.0 

    Bump requests from 2.27.1 to 2.31.0
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  6. float64 to float

    @WardDeb
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  7. Merge pull request #1235 from ggraham/np_types 

    np.{type} to {type}
    @WardDeb
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Commits on Aug 16, 2023

  1. bin execs replaced by toml scripts

    @WardDeb
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  2. replace version check for tests with toml version definition

    @WardDeb
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  3. remove _version file

    @WardDeb
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  4. version checks with importlib

    @WardDeb
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  5. version check docs update to importlib

    @WardDeb
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  6. purge reqs & setup.py

    @WardDeb
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  7. init toml

    @WardDeb
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  8. update cm for mpl > 3.7

    @WardDeb
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  9. port nosetests to pytest

    @WardDeb
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  10. escape sysargv check in case of pytests

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  11. deprecate nosetest in favor of pytest

    @WardDeb
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  12. rollback heatmapperr imgs test until later

    @WardDeb
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  13. flake8

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Commits on Aug 17, 2023

  1. add conda env for workflows

    @WardDeb
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  2. switch test to micromamba

    @WardDeb
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  3. planemo tests to python 3.11, include samtools in test env

    @WardDeb
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  4. shell defaults planemo test

    @WardDeb
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  5. pin allure version for planemo tests

    @WardDeb
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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

    @WardDeb
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  8. test env channel priority into condarc

    @WardDeb
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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
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  11. pybw typo

    @WardDeb
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  12. include pip install in planemo..

    @WardDeb
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  13. test with planemo test run python 3.10

    @WardDeb
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  14. planemo tests with python 3.11 under galaxy

    @WardDeb
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  15. py2bit as pip dep

    @WardDeb
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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
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  4. replace both expected heatmaps in planemo tests (mpl version boost ==… 

    … size difference)
    @WardDeb
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  5. replace plotprofile png in planemo test

    @WardDeb
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  6. test with NA in fp qualmets

    @WardDeb
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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
    WardDeb committed Aug 18, 2023
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  13. ship test wheels inside build-linux job

    @WardDeb
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  14. testwheels as separate job with artifact download

    @WardDeb
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  15. add depends on

    @WardDeb
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  16. ls to see if download works

    @WardDeb
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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
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  20. tilde in pip install

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Commits on Aug 19, 2023

  1. importlib toml req for python 3.7

    @WardDeb
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  2. importlib escapes for python 3.7

    @WardDeb
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  3. flake fix try except

    @WardDeb
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  4. test pypi build with micromamba

    @WardDeb
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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
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  2. rounding qual metrics fingerprint galaxy test

    @WardDeb
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  3. set version to 3.5.3

    @WardDeb
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  4. revert back to fingerprint qual metrics

    @WardDeb
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  5. rollback galaxy again

    @WardDeb
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  6. update installation instructions doc

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  7. qual metrics 14

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Commits on Aug 22, 2023

  1. usage and -h for all executables

    @WardDeb
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  2. flakes

    @WardDeb
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  3. switch pytest to -v

    @WardDeb
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  4. switch pytest to -v in init build as well

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Commits on Aug 24, 2023

  1. Update .github/workflows/planemo.yml 

    Co-authored-by: Björn Grüning <[email protected]>
    @WardDeb @bgruening
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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

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  4. include pytests for 3.11

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  5. bring back no dependency resolution planemo

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Commits on Aug 25, 2023

  1. parse toml for tool tests + verify version

    @WardDeb
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  2. fstring tests

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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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  4. setup-miniconda runner instead of micromamba for planemo test

    @WardDeb
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  5. print planemo version in shell runner

    @WardDeb
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  6. flake fixes tests

    @WardDeb
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  7. drop channelprio / planemo fingerprint back to 13 (again)

    @WardDeb
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  8. update changelog

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Commits on Aug 28, 2023

  1. Merge pull request #1242 from WardDeb/pyproject 

    toml install / requirements version boost
    @WardDeb
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  2. update galaxy version & tool version in galaxy xml

    @WardDeb
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  3. Merge pull request #1245 from WardDeb/galaxy_wrapper_version 

    update galaxy version & tool version in galaxy xml
    @WardDeb
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  4. round getJSDcommon to 16 decimals, attempt to fix planemo test

    @WardDeb
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  5. Merge pull request #1246 from WardDeb/plotFP_nd 

    round getJSDcommon to 16 decimals
    @WardDeb
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  6. JSD round to 15 decimals

    @WardDeb
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  7. Merge pull request #1247 from WardDeb/plotFP_nd 

    JSD round to 15 decimals
    @WardDeb
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  8. decrease galaxy profile version 

    The profile version does not need to be the latest Galaxy version. It specifies the latest version in which those tools will work. So it would be better to keep it a bit lower. Otherwise, older Galaxy instances can not install this tool.
    @bgruening
    bgruening authored Aug 28, 2023
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