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Feature #2985

Task #2045: API design and language bindings

Task #2698: gmxapi documentation integration

Python package documentation

Added by Eric Irrgang 6 months ago. Updated 30 days ago.

Status:
New
Priority:
Normal
Assignee:
-
Category:
documentation
Target version:
Difficulty:
uncategorized
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Description

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.


Subtasks

Task #3014: gmxapi example Python scriptsNew

Associated revisions

Revision f29a1758 (diff)
Added by Eric Irrgang 2 months ago

Build gmxapi documentation in main GROMACS documentation.

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

Refs #2698
Refs #2985

Change-Id: I6f1d6e6fe59e618144e4f14c0d2fe9f9b8c2c901

Revision 9124029b (diff)
Added by Eric Irrgang about 1 month 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 conf.py, 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 21 days 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

History

#1 Updated by Eric Irrgang 30 days ago

I believe this is blocked on deployment of GitLab Runner, but it appears that Python package documentation will ultimately live at http://manual.gromacs.org/current/gmxapi/

In the mean time, a single version is manually updated at http://gmxapi.org/ and at https://hub.docker.com/r/gmxapi/docs

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