Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

[docs][python] Add autosummary #1392

Merged
merged 7 commits into from
May 23, 2023
Merged

[docs][python] Add autosummary #1392

merged 7 commits into from
May 23, 2023

Conversation

ebezzi
Copy link
Member

@ebezzi ebezzi commented May 18, 2023

Issue and/or context:
Fixes #1326

Changes:

  • Adds autosummary to the docs. This creates auto-generated pages for each doc entry (functions, classes etc) and groups them using a hierarchical toctree that shows up in the sidebar

Notes for Reviewer:

@ebezzi ebezzi requested a review from johnkerl May 18, 2023 15:48
@@ -6,7 +6,7 @@
Python package is an implementation of SOMA using the
`TileDB Embedded <https://github.com/TileDB-Inc/TileDB>`_ engine.

Provides:
Provides
Copy link
Member Author

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Colons should be removed as these end up into toctree entities.

:members:

.. toctree::
:maxdepth: 2
Copy link
Member Author

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Can be set to 1 if we don't want this toctree to include the subsections.

@codecov-commenter
Copy link

codecov-commenter commented May 18, 2023

Codecov Report

Patch coverage has no change and project coverage change: +25.72 🎉

Comparison is base (e22e1d4) 65.36% compared to head (d9b975f) 91.08%.

❗ Current head d9b975f differs from pull request most recent head 3cc91a9. Consider uploading reports for the commit 3cc91a9 to get more accurate results

❗ Your organization is not using the GitHub App Integration. As a result you may experience degraded service beginning May 15th. Please install the Github App Integration for your organization. Read more.

Additional details and impacted files
@@             Coverage Diff             @@
##             main    #1392       +/-   ##
===========================================
+ Coverage   65.36%   91.08%   +25.72%     
===========================================
  Files          96       30       -66     
  Lines        7720     2400     -5320     
===========================================
- Hits         5046     2186     -2860     
+ Misses       2674      214     -2460     
Flag Coverage Δ
python 91.08% <ø> (ø)
r ?

Flags with carried forward coverage won't be shown. Click here to find out more.

Impacted Files Coverage Δ
apis/python/src/tiledbsoma/__init__.py 100.00% <ø> (ø)

... and 66 files with indirect coverage changes

☔ View full report in Codecov by Sentry.
📢 Do you have feedback about the report comment? Let us know in this issue.

Comment on lines 16 to 22
tiledbsoma.io.add_X_layer
tiledbsoma.io.add_matrix_to_collection
tiledbsoma.io.create_from_matrix
tiledbsoma.io.from_anndata
tiledbsoma.io.from_h5ad
tiledbsoma.io.to_anndata
tiledbsoma.io.to_h5ad
Copy link
Member

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Let's go "top down"

Copy link
Member

@johnkerl johnkerl left a comment

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

LGTM, except I think alphabetical ordering isn't ever the intuitive thing to do -- I left concrete suggestions

doc/source/python-tiledbsoma-io.rst Outdated Show resolved Hide resolved
doc/source/python-tiledbsoma-logging.rst Outdated Show resolved Hide resolved
doc/source/python-tiledbsoma.rst Outdated Show resolved Hide resolved
doc/source/python-tiledbsoma.rst Outdated Show resolved Hide resolved
@ebezzi ebezzi merged commit 1169798 into main May 23, 2023
@ebezzi ebezzi deleted the ebezzi/autosummary branch May 23, 2023 13:31
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

Successfully merging this pull request may close these issues.

[Feature request] Table of contents for Python API
3 participants