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Modernize ClubCpG dependencies and dev environment #24

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merged 34 commits into from
Jul 8, 2023
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@canthonyscott canthonyscott commented Jul 7, 2023

This pull request includes the following:

  • A major overhaul and modernization of the ClubCpG dependencies.
  • setup.py removed in favor of a pyproject.toml
  • All project dependencies updated to modern versions
  • Support of python 3.5, 3.6, 3.7, and 3.8 dropped as these versions are End of Life or near so
  • Minimum version of python is now 3.9
  • Added GitHub Actions workflows to automate testing of python 3.9 and 3.10
  • Updated readthedocs build configuration ahead of deprecation of old method
  • Added a workflow to automatically build and publish new versions of the package to PyPi when new tags are created
  • Additions of some new error handling when working on small datasets
  • Removal of one unit test that was dependent on pre-trained PReLIM models on an ancient version of scikit-learn

No logic has been changed with ClubCpG itself.

A Minor version bump from v.0.2.x to v0.3.0 has been included mostly to indicate that these updates will no longer work with older versions of Python

canthonyscott and others added 30 commits July 6, 2023 16:31
* added poetry env

* disabled testing of imputation as this model was trained on an outdates version of scikit-learn

* travis ci no longer online

* min supported python 3.9

* updated tests to use poetry

* refactor code for use with poetry

* refactored for poetry install of scripts and added additional error handling

* Don't write model if not successfully trained

* poetry handle scripts

* reuse setup workflow

* attempt to fix workflow syntax

* removed these files, not ready for them yet

* undo workflow changes

* fixed indent for sphinx

* adapted to poetry

* update doc groups

* latest docs build

* update workflows, attempt to build docs

* Added classifiers

* run sphinx without make

* make docs deps optional

* updated workflow steps
@canthonyscott canthonyscott added the dependencies Pull requests that update a dependency file label Jul 7, 2023
@canthonyscott canthonyscott added this to the v0.3.0 milestone Jul 7, 2023
@canthonyscott canthonyscott self-assigned this Jul 7, 2023
@canthonyscott canthonyscott requested a review from cjgunase July 7, 2023 22:34
@canthonyscott canthonyscott changed the title Misc updates Modernize ClubCpG dependencies and dev environment Jul 7, 2023
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@cjgunase I added you as a reviewer so you could put your eyes on this before I merge it to master and deploy

@cjgunase cjgunase merged commit f1042b4 into master Jul 8, 2023
@canthonyscott canthonyscott deleted the misc-updates branch July 18, 2023 20:55
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2 participants