Skip to content

Commit 9830dc5

Browse files
IAlibayIAlibay
committed
Merge branch 'main' into add_PoreAnalyser_to_MDKits
2 parents 5ade7c8 + c8f8a2b commit 9830dc5

29 files changed

+1452
-845
lines changed

‎.github/workflows/gh-ci-cron.yaml

+2-2
Original file line numberDiff line numberDiff line change
@@ -79,13 +79,13 @@ jobs:
7979
8080
- id: install-conda-env
8181
name: install-conda-env
82-
uses: conda-incubator/setup-miniconda@v2
82+
uses: conda-incubator/setup-miniconda@v3
8383
with:
8484
python-version: ${{ env.PYVER }}
8585
add-pip-as-python-dependency: true
8686
architecture: x64
8787
use-mamba: true
88-
miniforge-variant: Mambaforge
88+
miniforge-version: latest
8989
channels: conda-forge, defaults
9090
channel-priority: flexible
9191
auto-update-conda: true

‎.github/workflows/gh-ci.yaml

+2-2
Original file line numberDiff line numberDiff line change
@@ -82,13 +82,13 @@ jobs:
8282
8383
- id: install-conda-env
8484
name: install-conda-env
85-
uses: conda-incubator/setup-miniconda@v2
85+
uses: conda-incubator/setup-miniconda@v3
8686
with:
8787
python-version: ${{ env.PYVER }}
8888
add-pip-as-python-dependency: true
8989
architecture: x64
9090
use-mamba: true
91-
miniforge-variant: Mambaforge
91+
miniforge-version: latest
9292
channels: conda-forge, defaults
9393
channel-priority: flexible
9494
auto-update-conda: true

‎docs/requirements.yaml

+1
Original file line numberDiff line numberDiff line change
@@ -9,6 +9,7 @@ dependencies:
99

1010
- sphinx
1111
- mdanalysis-sphinx-theme
12+
- sphinxcontrib-youtube
1213

1314
- pyyaml
1415
- pydantic

‎docs/source/about.rst

+3-1
Original file line numberDiff line numberDiff line change
@@ -1,5 +1,7 @@
11
.. -*- coding: utf-8 -*-
22
3+
.. _about-mdakits:
4+
35
*************
46
About MDAKits
57
*************
@@ -27,7 +29,7 @@ requirements**:
2729
#. Minimal documentation is provided (what your code does, how to install it,
2830
and how to use it)
2931
#. At least minimal regression tests are present; continuous integration is encouraged
30-
#. The code is installable as a standard package
32+
#. The source code is installable as a standard package
3133

3234
It is also highly encouraged that the MDAKit also satisfies:
3335

‎docs/source/add.rst

-160
This file was deleted.

‎docs/source/addingakit.rst

+34
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,34 @@
1+
.. _add-mdakit:
2+
3+
********************************
4+
Adding an MDAKit to the Registry
5+
********************************
6+
7+
Do you have an MDAKit? Consider adding it to the
8+
:ref:`MDAKits Registry! <mdakits>`.
9+
10+
.. note::
11+
The `MDAKit registry`_ is still in its initial stages. We expect that the way
12+
in which MDAKits are added, and the type of information required, may change
13+
over time. Please reach out via the `issue tracker`_ if you have any
14+
questions.
15+
16+
Registering an MDAKit requires you to create a single file with meta information
17+
(called ``metadata.yaml``) describing the Kit, and add this to the
18+
`MDAnalysis/mdakits repository`_ on GitHub. The links below provide information
19+
about this process and more detail about the ``metadata.yaml`` file.
20+
21+
.. toctree::
22+
:maxdepth: 2
23+
24+
registering-a-kit/step-by-step
25+
registering-a-kit/metadata-yaml
26+
27+
28+
.. _`MDAKit registry`: https://mdakits.mdanalysis.org/mdakits.html
29+
30+
.. _`issue tracker`:
31+
https://github.com/MDAnalysis/MDAKits/issues
32+
33+
.. _`MDAnalysis/mdakits repository`:
34+
https://github.com/MDAnalysis/mdakits

‎docs/source/conf.py

+1
Original file line numberDiff line numberDiff line change
@@ -56,6 +56,7 @@
5656
'sphinx.ext.napoleon',
5757
'sphinx.ext.intersphinx',
5858
'sphinx.ext.extlinks',
59+
'sphinxcontrib.youtube',
5960
]
6061

6162
autosummary_generate = True

‎docs/source/index.rst

+20-4
Original file line numberDiff line numberDiff line change
@@ -11,8 +11,11 @@ Welcome to the MDAKit registry!
1111
Showcased here are a list of community generated packages which extend the
1212
functionality of the `MDAnalysis library`_.
1313

14-
Follow the links below to begin exploring the available MDAKits, or view
15-
additional resources about MDAKits and how to write and/or add your own.
14+
For more information about MDAKits and the motivation behind them, please see
15+
the :ref:`about-mdakits` page.
16+
17+
To begin exploring the :ref:`available MDAKits <mdakits>`, or view additional
18+
resources on MDAKits and how to write and/or add your own, follow the links below!
1619

1720

1821
.. toctree::
@@ -24,12 +27,25 @@ additional resources about MDAKits and how to write and/or add your own.
2427

2528
.. toctree::
2629
:maxdepth: 1
27-
:caption: Resources
30+
:caption: About
2831

2932
about
33+
34+
35+
.. toctree::
36+
:maxdepth: 1
37+
:caption: Resources for MDAKit Authors
38+
3039
makingakit
31-
add
40+
addingakit
41+
maintainingakit
3242
troubleshooting
43+
44+
45+
.. toctree::
46+
:maxdepth: 1
47+
:caption: Other Resources
48+
3349
reviewersguide
3450

3551

‎docs/source/maintainingakit.rst

+27
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,27 @@
1+
.. _maintaining:
2+
3+
*********************
4+
Maintaining an MDAKit
5+
*********************
6+
7+
.. note::
8+
This section is still under construction. If you have topics you would
9+
like to see covered here, please get in touch via
10+
`MDAnalysis Github Discussions`_.
11+
12+
There are a variety of reasons a kit may behave unexpectedly after being
13+
submitted to the registry. Apart from actively developing the kit, changes in
14+
kit dependencies, or even Python itself, can introduce/deprecate new/old functionality.
15+
For this reason, the kits' continuous integration is rerun weekly to
16+
confirm the kits expected behavior.
17+
18+
In the event that a kit no longer passes its tests, an issue in
19+
MDAnalysis/MDAKits is automatically raised while notifying the maintainers
20+
indicated in the `metadata.yaml` file.
21+
While the registry developers will be happy to help where possible, ultimately,
22+
the maintainers of the MDAKit are responsible for resolving such issues and
23+
ensuring that the tests pass.
24+
The issue will automatically close after the next CI run if the tests pass again.
25+
26+
.. _`MDAnalysis GitHub Discussions`:
27+
https://github.com/MDAnalysis/mdanalysis/discussions

‎docs/source/making-a-kit/documentation.rst

+24
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,24 @@
1+
.. _documentation:
2+
3+
*************
4+
Documentation
5+
*************
6+
7+
Basic documentation is **required** for MDAKit registration. The detail and
8+
depth of the documentation is ultimately up to you, but we require **at a
9+
minimum** that you provide README-style documentation explaining what the code
10+
is supposed to do, how to install it, and the basics of its use.
11+
12+
Although this is the minimum, we highly recommend that you consider generating
13+
your documentation with dedicated tools such as
14+
`Sphinx <https://www.sphinx-doc.org/en/master/>`_, which allows you to generate
15+
static documentation using
16+
`reStructuredText <https://www.sphinx-doc.org/en/master/usage/restructuredtext/index.html>`_
17+
-formatted plain text directly from your code. This makes it easier for your
18+
documentation to change alongside code changes.
19+
20+
Using a **documentation hosting service** such as
21+
`Read the Docs <https://readthedocs.org>`_ or
22+
`GitHub Pages <https://pages.github.com/>`_ allows easy public access to your
23+
automatically generated documentation.
24+

0 commit comments

Comments
 (0)