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Cleanup docstrings, add notebook render #124

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merged 26 commits into from
Jan 19, 2023
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@CBroz1 CBroz1 commented Jan 12, 2023

Submission checklist

  • Reviewed all Files changed prior to selecting Create Pull Request.
  • Ran and passed all pytests, and ran the pipeline for features not covered by tests.
    • Caveat: there are pieces of the pytests needed adjustment to pass, including removing the 'ingest_lab' import
  • Ran pre-commit checks, including black, flake8, etc.
  • Updated the changelog and if making a new release, updated the version.py. no new release
  • Updated documentation, including concepts.md, tutorials.md, and relevant docstrings.
  • After merge, I will push a new tag to upstream (test* prefix if no new release).

Submission details

Please review commits individually. Linting edits have been separated from substantive edits by commit

In this pull request, I make the following changes:

  • Spellchecking
    • cspell.json - add permitted words for vscode spell extension
    • docs/mkdocs.yaml - spellcheck notes
    • docs/src/concepts - remove singular bullets, add spaces before/after headings
    • various ephys schemas - scehma -> schema
    • element_array_ephys/plotting/qc.py - various comment/docstring misspellings
  • Markdown linting
    • .markdownlint.yaml - config for markdown linting
    • docs/src/concepts.md - hard wrap, and change citation to footnote
    • code_of_conduct - ensure first line is heading 1
    • hard wrap: docs/src/index.md, docs/src/citation.md, contributing, changelog
  • Add tutorial notebooks
    • gitignore - add ignore of notebooks
    • tutorials.md -> tutorials/index.md - add summary of each notebook and links to other resources
    • docs/src/api/make_pages.py - migrate workflow download to docker compose
    • docs/mkdocs.yaml - add page for each notebook
    • docs/src/citation.md - change link to new tutorials index
    • docs/.docker/pip_requirements - add jupyter extension
  • NWB maintenance
    • nwb dependency update #123: nwb_conversion_tools -> neuroconv
    • migrate docstring style from sphynx to google for API docs
    • add extras_require installation options for nwb and dev work
  • Other maintenance
    • element_interface not in requirements #66
    • docs/docker-compose.yaml - add mkdocs log file (gitignored) - tee pulls copy to log without silencing stdout
    • docs/mkdocs.yaml - add mkdocstrings params so api renders in file order, not alphabetically
    • docs/mkdocs.yaml - add footnotes extension for concepts page
    • docs/src/changelog - refresh as soft link
    • various ephys schemas - blackify, add argument descriptions for API docs, add return type suggestion for API docs
    • update license for 2023, datajoint neuro -> datajoint

@CBroz1 CBroz1 self-assigned this Jan 12, 2023
@CBroz1 CBroz1 requested a review from kushalbakshi January 12, 2023 23:45
@CBroz1 CBroz1 marked this pull request as ready for review January 13, 2023 17:09
CBroz1 and others added 3 commits January 18, 2023 16:54
fix: 🐛 import from __future__ to support backward compatibility
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CBroz1 commented Jan 18, 2023

Thanks @JaerongA for looking into typing compatibility. Thanks for running the pytests with the previous list[dict] format. I've applied your suggestions

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nwb dependency update Documentation missing export requirements element_interface not in requirements
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