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Add documentation #123

Merged
merged 23 commits into from
Jul 24, 2024
Merged

Add documentation #123

merged 23 commits into from
Jul 24, 2024

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jenniferjiangkells
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@jenniferjiangkells jenniferjiangkells commented Jul 18, 2024

CHANGES:

  • Added mkdocs documentation site
  • Tidied up README.md
  • Tidied up pyproject.md
  • Added contributing guidelines
  • Added workflows for building, deploying documentation
  • Added workflow for publishing
  • Added PR template
  • Added docstring to all functions

I did make some changes to Annotator that should technically be in another branch:

  • Moved some methods around and reduced the number of abstract classes needed
  • Moved lookup back as packaged data - this is because without the lookup tables configured, users would not be able to run MiADE at all and it's a bit of a pain to download the lookup data separately from a different source (given we already need to download med7 and spacy this might not add to the user experience).
  • However the option to configure lookup table source from a different source is still in the configs - so now it is more flexible.

@jenniferjiangkells jenniferjiangkells changed the title Initialise mkdocs Add documentation Jul 18, 2024
@jenniferjiangkells jenniferjiangkells added the documentation Improvements or additions to documentation label Jul 18, 2024
@jenniferjiangkells jenniferjiangkells marked this pull request as ready for review July 23, 2024 14:18
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jenniferjiangkells commented Jul 23, 2024

@jamesbrandreth FYI feel free to make changes / add things if I missed anything.

I've setup github actions that build and deploy the documentation page every time branch is merged to master (if i can get it working). We could make a MiADE slack or discord or something (I looked into discourse ala MedCAT and it's not as straightforward as I thought lol)

docs page is live here!

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Might want to consider restricting Python to >3.8, <3.12 because MiADE cannot install run on 3.12

@jenniferjiangkells jenniferjiangkells merged commit 99d5ee4 into master Jul 24, 2024
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@jenniferjiangkells jenniferjiangkells deleted the documentation branch July 24, 2024 14:21
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