Tools update

[eddiebergman]

Updates several aspects of the tools surrounding development on autosklearn as part of the "black and isort" major change. Most of the configuration for things can be found in pyproject.toml and are documented where non-obvious.

Reminder: Add attribution for @isaac-chung

These checks will fail but running make format will fix all files so that that it will pass these pre-commit checks. They have been left unformatted to keep the PR clean and reviewable.

TODO: Update Contribution Guide in light of these changes

• Formatting is now done with black and isort.
  • Line length was changed to 88 in accordance with usual black'nd libraries.
  • Black and isort now check for code formatting, flake8 does not.
  • Relevant updates were done to pre-commit
• Added the tool pydocstyle, however this is disabled for now as almost all modules fail this check.
  • Checks that most things we would like documented are indeed documented.
  • Disabled some things deemed not relevant (see pyproject.toml)
  • Checks for numpy style (the one we use)
• All mypy and pytest configurations were moved to the new pyproject.toml along with the black, pydocstyle and isort configurations.
• Removed testcommand.sh, seems like a stray file.
• Updated coverage.yml which controls our automatic code coverage checks through github actions.
  • Fixes how strict PR's can allow drop in overall code test percentage, from 50% -> 0.2%.
  • Updates overall strictness to 87% to match current test coverage
  • PR changed code now needs to be 90% tested
  • Branch coverage is now uploaded to code-cov, this will likely drop our coverage but indicate branches that were not taken.
• pre-commit now includes the aforementioned formatters and checkers. The packages were also updated to their latest versions.
• The root Makefile was remade to perform many of these commands and others. This should make it easier to perform the relevant commands as well as make it easier for new contributors to use our workflows. Notably:

  help:
  @echo "Makefile autosklearn"
  @echo "* install-dev      to install dev requirements and init pre-commit"
  @echo "* check            to check the source code for issues"
  @echo "* format           to format the code with black and isort"
  @echo "* pre-commit       to clean the dist and doc build files"
  @echo "* clean            to clean the dist and doc build files"
  @echo "* build            to build a dist"
  @echo "* doc              to generate and view the html files"
  @echo "* linkcheck        to check the documentation links"
  @echo "* examples         to run and generate the examples"
  @echo "* publish          to help publish the current branch to pypi"

  • Note the publish only publishes to the test servers but prints instructions for the real one after advising that the test distribution be pip installed and tested first.

[codecov]

Codecov Report

Merging #1358 (fed8668) into development (2bea930) will decrease coverage by 87.95%.
The diff coverage is n/a.

❗ Current head fed8668 differs from pull request most recent head b16d154. Consider uploading reports for the commit b16d154 to get more accurate results

@@               Coverage Diff               @@
##           development   #1358       +/-   ##
===============================================
- Coverage        87.95%       0   -87.96%     
===============================================
  Files              140       0      -140     
  Lines            10959       0    -10959     
===============================================
- Hits              9639       0     -9639     
+ Misses            1320       0     -1320