Skip to content

Install petab on rtd - #676

Merged
arrjon merged 11 commits into
ICB-DCM:developfrom
kilianvolmer:install_petab_on_rtd
Oct 26, 2026
Merged

arrjon merged 11 commits into
ICB-DCM:developfrom
kilianvolmer:install_petab_on_rtd

Conversation

@kilianvolmer

Copy link
Copy Markdown
Collaborator

I try to resolve #675 by including petab to the dependencies that readthedocs needs to install.

@codecov-commenter

codecov-commenter commented Jul 31, 2026 •

Copy link
Copy Markdown

⚠️ Please install the 'codecov app svg image' to ensure uploads and comments are reliably processed by Codecov.

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 79.48%. Comparing base (5600423) to head (bed9f48).
❗ Your organization needs to install the Codecov GitHub app to enable full functionality.

Additional details and impacted files
@@             Coverage Diff             @@
##           develop     #676      +/-   ##
===========================================
+ Coverage    79.47%   79.48%   +0.01%     
===========================================
  Files          142      142              
  Lines         8415     8415              
  Branches      1122     1122              
===========================================
+ Hits          6688     6689       +1     
+ Misses        1358     1357       -1     
  Partials       369      369              
Flag Coverage Δ
base 59.39% <ø> (+0.01%) ⬆️
external-R 36.86% <ø> (-0.02%) ⬇️
external-other-simulators 31.50% <ø> (ø)
migrate 27.10% <ø> (ø)
petab 35.57% <ø> (ø)
visualization 52.57% <ø> (-0.14%) ⬇️

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

☔ View full report in Codecov by Harness.
📢 Have feedback on the report? Share it here.

🚀 New features to boost your workflow:
  • ❄️ Test Analytics: Detect flaky tests, report on failures, and find test suite problems.

@arrjon
arrjon self-requested a review August 21, 2026 15:53
@kilianvolmer

Copy link
Copy Markdown
Collaborator Author

This is not functional yet, but I need a PR in order to test the build on rtd.

@arrjon

arrjon commented Oct 26, 2026

Copy link
Copy Markdown
Member

Are you still working on it @kilianvolmer?

@kilianvolmer

Copy link
Copy Markdown
Collaborator Author

The documentation build for the PR includes https://pyabc--676.org.readthedocs.build/en/676/api/pyabc.petab.html#module-pyabc.petab which is missing from the main docs. This documents all public PEtab functionality, so #675 is resolved. I am not sure why the tests are failing now.

@arrjon

arrjon commented Oct 26, 2026

Copy link
Copy Markdown
Member

Tests were failing due to some dependencies related to petab.

@arrjon
arrjon merged commit 72d64ee into ICB-DCM:develop Oct 26, 2026
16 checks passed
@kilianvolmer
kilianvolmer deleted the install_petab_on_rtd branch October 26, 2026 14:12
@kilianvolmer kilianvolmer linked an issue Oct 26, 2026 that may be closed by this pull request
arrjon added a commit that referenced this pull request Oct 28, 2026
* fix petab dependencies

* Update Bernton et al citation to published paper instead of arxiv (#677)

* Install petab on rtd (#676)

* Update docstring
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.

pyabc.petab documentation is not built

3 participants