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MDAnalysis documentation style #1
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7795d4e
TODO for fast-math
ianmkenney ec740c1
Applied the MDAnalysis docs theme
ianmkenney 8f305e9
Added workflow for building docs
ianmkenney 0c24502
Updated env name based on logs
ianmkenney f4d35d1
Added page artifact upload
ianmkenney 03b9fa0
Used path specified in the gh pages action
ianmkenney 814c34e
Merge branch 'main' into docsformatting
ianmkenney 0f25a92
Use the mdanalysis-sphinx-theme
ianmkenney 228b962
Include mdanalysis_sphinx_theme in pyproject.toml
ianmkenney 5baedbc
Updated the module paths and removed versionadded
ianmkenney c4cded7
Removed ToC from index body
ianmkenney a775626
Ignore tests module in docs
ianmkenney 784cb16
Missed some versionadded directives
ianmkenney 3b268d9
trimmed references
ianmkenney 97dff50
Move the references to the bottom of the docstring
ianmkenney f047216
Included sphinxcontrib-bibtex in conf.py
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Original file line number | Diff line number | Diff line change |
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@@ -0,0 +1,62 @@ | ||
name: docs | ||
on: | ||
push: | ||
branches: | ||
- main | ||
pull_request: | ||
branches: | ||
- main | ||
|
||
concurrency: | ||
group: "${{ github.ref }}-${{ github.head_ref }}" | ||
cancel-in-progress: true | ||
|
||
defaults: | ||
run: | ||
shell: bash -l {0} | ||
|
||
jobs: | ||
docs: | ||
if: "github.repository == 'MDAnalysis/mdaencore'" | ||
runs-on: ubuntu-latest | ||
|
||
steps: | ||
- uses: actions/checkout@v3 | ||
with: | ||
fetch-depth: 0 | ||
|
||
- name: setup_miniconda | ||
uses: conda-incubator/setup-miniconda@v2 | ||
with: | ||
python-version: 3.11 | ||
environment-file: docs/requirements.yaml | ||
auto-update-conda: true | ||
channel-priority: flexible | ||
channels: conda-forge | ||
miniforge-variant: Mambaforge | ||
use-mamba: true | ||
|
||
- name: Build and install package | ||
run: | | ||
mamba env update -n test -f devtools/conda-envs/test_env.yaml | ||
python setup.py build_ext -i | ||
python -m pip install -e . | ||
|
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- name: build docs | ||
run: | | ||
cd docs && sphinx-build -b html source build | ||
|
||
- name: deploy docs | ||
uses: peaceiris/actions-gh-pages@v3 | ||
if: github.event_name != 'pull_request' | ||
with: | ||
github_token: ${{ secrets.GITHUB_TOKEN }} | ||
publish_dir: ./docs/build | ||
user_name: 'github-actions' | ||
user_email: 'github-action@users.noreply.github.com' | ||
|
||
- uses: actions/upload-artifact@v3 | ||
if: github.event_name == 'pull_request' | ||
with: | ||
name: pr_docs | ||
path: ./docs/build/ |
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Original file line number | Diff line number | Diff line change |
---|---|---|
@@ -1,14 +1,19 @@ | ||
name: mdaencore-docs | ||
channels: | ||
- default | ||
- conda-forge | ||
dependencies: | ||
# Base depends | ||
- python | ||
- pip | ||
- python | ||
- pip | ||
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- sphinx<7.0 | ||
- sphinxcontrib-bibtex | ||
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- sphinx_rtd_theme | ||
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# Pip-only installs | ||
#- pip: | ||
- numpy | ||
- scipy | ||
- MDAnalysis | ||
- MDAnalysisTests | ||
- pytest | ||
|
||
- pip: | ||
- mdanalysis-sphinx-theme |
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Original file line number | Diff line number | Diff line change |
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@@ -0,0 +1,25 @@ | ||
@article{LindorffLarsen2009, | ||
doi = {10.1371/journal.pone.0004203}, | ||
author = {Lindorff-Larsen, Kresten AND Ferkinghoff-Borg, Jesper}, | ||
journal = {PLOS ONE}, | ||
publisher = {Public Library of Science}, | ||
title = {Similarity Measures for Protein Ensembles}, | ||
year = {2009}, | ||
month = {01}, | ||
volume = {4}, | ||
pages = {1-13}, | ||
number = {1} | ||
} | ||
|
||
@article{Tiberti2015, | ||
doi = {10.1371/journal.pcbi.1004415}, | ||
author = {Tiberti, Matteo AND Papaleo, Elena AND Bengtsen, Tone AND Boomsma, Wouter AND Lindorff-Larsen, Kresten}, | ||
journal = {PLOS Computational Biology}, | ||
publisher = {Public Library of Science}, | ||
title = {ENCORE: Software for Quantitative Ensemble Comparison}, | ||
year = {2015}, | ||
month = {10}, | ||
volume = {11}, | ||
pages = {1-16}, | ||
number = {10} | ||
} |
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not shipping the MDA bib style?
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This wasn't done in the hole2 kit docs either, trying to keep it consistent between the two packages for when we create a proper extension
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ok, references in the hole kit look reasonable (although not as nice in the MDA docs) so I am fine with keeping it simple for right now. Maybe something for a docs extension.