Feature #2985

Task #2045: API design and language bindings

Task #2698: gmxapi documentation integration

Python package documentation

Added by Eric Irrgang about 1 year ago. Updated 8 months ago.

Target version:


Some infrastructure and organizational details need to be worked out to build and publish documentation related to the gmxapi Python package.

For gmxapi <= 0.0.7, the Python package is in a separate repository on GitHub that is automatically downloaded and built by readthedocs. This is a little more complicated to do with the Python package in a subdirectory of the primary GROMACS repository, but we also probably want to integrate the Python package documentation with the rest of the GROMACS documentation.

The Python gmxapi package needs to be built and importable in order for Sphinx to automatically extract docstrings from the C++ bindings module.

This Redmine Issue is currently a stub to catch details of infrastructure, layout, contents, integration, publishing, and automation.

Associated revisions

Revision f29a1758 (diff)
Added by Eric Irrgang 12 months ago

Build gmxapi documentation in main GROMACS documentation.

  • Update gmxapi Python package installation instructions and remove
  • Minor updates to main installation guide document.

Refs #2698
Refs #2985

Change-Id: I6f1d6e6fe59e618144e4f14c0d2fe9f9b8c2c901

Revision 9124029b (diff)
Added by Eric Irrgang 11 months ago

Deduplicate gmxapi documentation.

`docs/gmxapi` seems to have settled down and does not have substantial
layout changes from the documentation in python_packaging/documentation.
Compartmentalized doc builds, e.g. with docs.dockerfile, still warrant
a separate simple, so that much is retained. Otherwise, it looks
like documentation for the standalone gmxapi package or development can
be maintained in a unified way with the GROMACS project documentation,
so this change removes the transitionally duplicated content.

  • Remove most of python_packaging/documentation
  • Update python_packaging/docker/docs.dockerfile

Refs #2698
Refs #2985

Change-Id: I0c23f6526894ec1eec4e910463c8c9d08a7315f6

Revision 37c5c0ae (diff)
Added by Eric Irrgang 10 months ago

Add transitional links for online gmxapi Python package reference.

  • Update and clarify pythonreference stub for when Python package was
    not available.
  • Note related Redmine reference.
  • Remove `python-procedural` label, which had lost meaning and which
    could cause awkward repositioning for the pythonreference stub with
    no section heading to follow the label.

Refs #2985

Change-Id: If81ba6500ce078fe4fc94bf37285324ec5702b1b

Revision fea93810 (diff)
Added by Eric Irrgang 9 months ago

Remove transitional links for online gmxapi Python package reference.

Provide link to current GROMACS gmxapi documentation,
built by GitLab Runner.

Fixes #2985

Change-Id: I1e56828aba4cc2568bbc9e6617863ca10197058d


#1 Updated by Eric Irrgang 10 months ago

I believe this is blocked on deployment of GitLab Runner, but it appears that Python package documentation will ultimately live at

In the mean time, a single version is manually updated at and at

#2 Updated by Eric Irrgang 9 months ago

If there is a tracked issue for the GitLab Runner infrastructure, we could make this issue dependent on it and update the target version to match. Otherwise, I need to defer to Paul on reasonable target version.

#3 Updated by Paul Bauer 9 months ago

  • Target version changed from 2020 to 2020.1

I created #3272 to act as an umbrella task

#4 Updated by Eric Irrgang 9 months ago

Paul Bauer wrote:

I created #3272 to act as an umbrella task

I see that the 2020 release docs include the full Python package docs, but I don't know if the automation is fully set up. Should we consider this issue complete?

#5 Updated by Eric Irrgang 9 months ago

  • Status changed from New to Resolved

#6 Updated by Paul Bauer 8 months ago

  • Status changed from Resolved to Closed

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