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Docs update (more extensions, new theme) #100

Merged
merged 34 commits into from
Oct 11, 2022
Merged

Docs update (more extensions, new theme) #100

merged 34 commits into from
Oct 11, 2022

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adamgayoso
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@adamgayoso adamgayoso commented Oct 10, 2022 •
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  • Use sphinx_book_theme instead of furo as it requires no custom css to look good for our purposes (and dark mode is coming soon)
  • Remove scanpydoc dependency
  • Remove nbsphinx in favor of myst-nb
  • Add typed returns custom extension like in scanpy
  • Use same autosummary class template as in scvi-tools (single page for classes with methods/attr tables)

See here for a live example.

Fixes #74 by using a different theme.

@adamgayoso adamgayoso changed the title Docs Docs update Oct 10, 2022
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A PR has been generated to the instance repo:
scverse/cookiecutter-scverse-instance#18

You can check out the PR to preview your changes
in an instance of the cookiecutter template. The PR will be kept in sync with
this PR automatically.

@adamgayoso adamgayoso requested a review from grst October 10, 2022 02:10
@adamgayoso adamgayoso changed the base branch from main to project_name October 10, 2022 02:38
@adamgayoso adamgayoso changed the base branch from project_name to main October 10, 2022 02:39
@adamgayoso adamgayoso changed the title Docs update Docs update (more extensions, new theme) Oct 10, 2022
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adamgayoso commented Oct 10, 2022 •
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@grst it should pass but I can't figure out how to make cookiecutter ignore rendering the class.rst file I added

Update: I figured it out, there are two json files.

@adamgayoso adamgayoso enabled auto-merge (squash) October 10, 2022 03:43
@adamgayoso adamgayoso disabled auto-merge October 10, 2022 03:44
@grst grst requested a review from flying-sheep October 10, 2022 06:56
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To make this PR simpler I removed linkcode

@adamgayoso adamgayoso requested review from grst and ivirshup October 10, 2022 17:21
ivirshup
ivirshup reviewed Oct 10, 2022
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{{cookiecutter.project_name}}/docs/conf.py Outdated
html_static_path = ["_static"]
html_title = project_name

github_repo = "https://github.com/" + html_context["github_user"] + "/" + project_name
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html_context["github_user"]

Should github_user get it's own variable? Similar fields e.g. project_name, package_name do.

OTOH, the repo url is probably available in the metadata info derived from the pyproject.toml (e.g. the info url in this scope)

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It's actually not, only the docs url is there

grst
grst approved these changes Oct 11, 2022
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Suggested the modifications suggested by @ivirshup -- Once these are resolved, feel free to merge.

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@adamgayoso, question about the theme:

Weren't a number of the cases that we needed CSS for related to the dark theme?

@ivirshup ivirshup mentioned this pull request Oct 11, 2022
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@adamgayoso adamgayoso merged commit c27563d into main Oct 11, 2022
@adamgayoso adamgayoso deleted the docs branch October 11, 2022 16:00
This was referenced Oct 24, 2022
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@grst grst grst approved these changes

@flying-sheep flying-sheep Awaiting requested review from flying-sheep

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Furo theme special CSS (from scvi-tools)
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@adamgayoso @ivirshup @grst