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feat: support for python 3.11 #207

Merged
merged 95 commits into from
Jan 12, 2024
Merged

feat: support for python 3.11 #207

merged 95 commits into from
Jan 12, 2024

Commits on Apr 12, 2023

  1. support py3.11 now that pysam does (in v0.21.0) 

    https://github.com/pysam-developers/pysam/releases/tag/v0.21.0
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    aryarm committed Apr 12, 2023
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  2. update lock file for py3.11

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    aryarm committed Apr 12, 2023
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  3. use newer version of nox-poetry for py3.11

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  4. update nox-poetry in pyproject too

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  5. downgrade py version in which poetry and nox are installed

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  6. upgrade nox pin for github action

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  7. downgrade coverage

    @aryarm
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  8. completely regenerate lock file

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Commits on Apr 13, 2023

  1. add pysam dependencies to install command

    @aryarm
    aryarm committed Apr 13, 2023
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  2. update necessary noxfile version

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    aryarm committed Apr 13, 2023
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Commits on Apr 19, 2023

  1. revert poetry lock file to python 3.7

    @aryarm
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  2. upgrade numpy version used in tests 

    to ensure that a version compatible with python 3.11 is installed
    @aryarm
    aryarm committed Apr 19, 2023
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  3. refmt for newer black

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  4. add pysam build dependencies to noxfile in case wheels aren't available

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  5. downgrade numpy version in noxfile

    @aryarm
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  6. remove pysam build dependencies

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Commits on Jul 11, 2023

  1. update docs to install correct gcc

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  2. try to install custom numpy despite nox_poetry constraint

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  3. Merge branch 'main' into feat/py311

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  4. refmt with black

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Commits on Oct 1, 2023

  1. delete comment bot action

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Commits on Dec 22, 2023

  1. resolve conflicts with main

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  2. oops try again

    @aryarm
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  3. Merge branch 'main' into feat/py311

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  4. use poetry-conda in dev setup

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  5. lock with min versions at py3.8

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  6. update lock hash with current pyproject.toml

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  7. move extras into groups

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    aryarm authored Dec 22, 2023
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  8. allow py versions 3.7 <= x < 4.0

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  9. adjust readthedocs for use with dependency groups

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  10. add poetry shell command to install instructions

    @aryarm
    aryarm authored Dec 22, 2023
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  11. use nox-poetry workaround 

    from cjolowicz/nox-poetry#1116 (comment)
since py3.11 is the most recent version we support anyway, so it's ok
if it uses the most recent versions of all our dependencies
    @aryarm
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  12. bump all constraints

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    aryarm authored Dec 22, 2023
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  13. try to use pip instead of pipx in github actions

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  14. try using system python with pipx

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    aryarm authored Dec 22, 2023
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  15. try to use executable name

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  16. note that poetry shell will need to be rerun

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  17. account for poetry + python 3.7 incompatibility

    @aryarm
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  18. update numpy to support 3.10

    @aryarm
    aryarm authored Dec 22, 2023
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  19. upgrade pip version

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  20. revert macos test to py3.10 

    since it was failing for py3.11
    @aryarm
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  21. try more recent cyvcf2

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  22. fix lock file after bumping cyvcf2

    @aryarm
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  23. update to cyvcf2 0.30.18 since that seemed to work on main

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  24. bumpy cyvcf2 to 0.30.25 to try to resolve failing tests

    @aryarm
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  25. try cyvcf2 0.30.17

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  26. try cyvcf2 0.30.16 instead

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  27. revert to cyvcf2 0.30.17 b/c < 0.30.16 leads to a binary incompatibil… 

    …ity with numpy
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  28. remove direct mention of 255 or 254 since they might be platform spec… 

    …ific
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  29. refmt for black

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Commits on Dec 23, 2023

  1. try to lock numpy version at 1.21.6

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  2. try to lock at numpy==1.21.6 again

    @aryarm
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  3. try to trick poetry by editing lock file manually

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  4. revert to locking at numpy 1.21.1 but switch macos to 3.9

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  5. make numpy version conditional on py version

    @aryarm
    aryarm authored Dec 23, 2023
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  6. try to lock dev-env.yml

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  7. try python 3.10 on macos again

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  8. revert to 746555d 

    at least until python-poetry/poetry-plugin-export#183 is resolved
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Commits on Dec 24, 2023

  1. match constraints and locks for test dependencies

    @aryarm
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  2. move nox and nox-poetry into global env, actually

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Commits on Dec 27, 2023

  1. Merge branch 'main' into feat/py311

    @aryarm
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  2. revise devcontainer with new dev env setup

    @aryarm
    aryarm authored Dec 27, 2023
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  3. try to use mamba instead of pipx in github actions

    @aryarm
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  4. dont try using mamba

    @aryarm
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  5. try again to remove mamba

    @aryarm
    aryarm authored Dec 27, 2023
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  6. try to set channels in action

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    aryarm authored Dec 27, 2023
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  7. try removing miniforge

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  8. try caching env instead of packages

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  9. move lint test into separate github action step

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    aryarm authored Dec 27, 2023
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  10. try to retrigger github actions

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    aryarm authored Dec 27, 2023
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  11. fix yml error oops

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  12. add verbose option to nox

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Commits on Dec 28, 2023

  1. try building package internally

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  2. oops fix yml syntax error

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  3. remove build step to see if it works now

    @aryarm
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Commits on Dec 29, 2023

  1. Revert "remove build step to see if it works now" 

    This reverts commit bb9edab.
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  2. ensure other nox sessions are run with locked py version

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  3. remove old lint step in testing workflow

    @aryarm
    aryarm authored Dec 29, 2023
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  4. remove constraints.txt, superseded by dev-env.yml

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  5. Merge branch 'feat/py311' of github.com:CAST-genomics/haptools into f… 

    …eat/py311
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  6. rfmt to fix spacing issue

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Commits on Dec 30, 2023

  1. try to use --only in readthedocs build

    @aryarm
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  2. try again but with main

    @aryarm
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  3. remove --with params from install instructions

    @aryarm
    aryarm authored Dec 30, 2023
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  4. add check for size of dist/ folder

    @aryarm
    aryarm authored Dec 30, 2023
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  5. try to break dist check

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  6. restore dist check

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  7. downgrade to a 0.3 MB check for dist/

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Commits on Jan 8, 2024

  1. rename dist-size check to size and remove strict channel priority

    @aryarm
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  2. copy trtools pr checklist

    @aryarm
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  3. Merge branch 'main' into feat/py311

    @aryarm
    aryarm authored Jan 8, 2024
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Commits on Jan 12, 2024

  1. copy example from docs

    @aryarm
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  2. adjust example to work as automated test

    @aryarm
    aryarm authored Jan 12, 2024
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  3. fix buggy example in api docs

    @aryarm
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  4. revert commits 84fde9d..0d914e0 agh

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