Comments (6)
Okay, I've converted readme.md
to a single readme.rst
file directly using pandoc. Based on the structure I'm seeing for the docs in dcodex
, I imagine that this might end up being divided into smaller files or that we'll add other docs later, but again, I'm not familiar with how the process of documentation generation works.
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Thanks, Rob! I've generated the build files and built the HTML page locally via
poetry run sphinx-build -b html docs docs/_build/html
and the result looked as expected. I probably need to do some additional steps to publish the page online, so I'll leave this issue open for now.
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Hey @rbturnbull! I just pulled the latest changes, and the updated documentation looks great! And thanks for the paper stub; I hope to get started on that soon! 😄
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I've seen and edited some of the docs for dcodex
before, and I should be able to convert the readme in Markdown to RST using pandoc, but I might need some help with the next step of "building" the docs and automating this process with GitHub actions per #11.
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great work Joey. Here are some instructions:
- Install sphinx as a dev dependency with: poetry add --dev Sphinx
- Then use sphinx to create the docs project: sphinx-quickstart
- more info here: https://www.sphinx-doc.org/en/master/usage/quickstart.html
- install a sphinx theme. I usually use readthedocs. To install that you can do this: poetry add --dev sphinx-rtd-theme
- then you add the theme to your conf.py with the line: html_theme = "sphinx_rtd_theme"
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Hi @jjmccollum - I've refactored the docs and the readme a bit. I've merged the pull request myself because I wanted the docs to deploy to GH pages. You can see the update here: https://jjmccollum.github.io/teiphy/
I've also added a stub for the paper. it is converted to a PDF each push and it is deployed here: https://jjmccollum.github.io/teiphy/joss-draft.pdf
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Related Issues (20)
- Update documentation HOT 2
- Revise paper HOT 6
- Make `--states-present` default option for NEXUS output
- Add support for `--ascertainment` option HOT 4
- Incorporate latest feedback on paper
- Add `--long-table` option for tabular output
- Fix github actions workflow for iqtree HOT 1
- Failure with no user-oriented error message HOT 10
- Should teiphy convert all variation units, including trivial ones?
- Add support for BEAST XML output HOT 73
- add tip date sampling for beast HOT 5
- Create directory for output if needed HOT 1
- Relative path to chron file for stemma output HOT 2
- Assignment of random starting rate parameter values, new prior distributions, and support for `--seed` option
- Add support for NEXUS-style CSV/Excel output HOT 1
- Change CSV outputs to include BOM HOT 1
- Use fixed origin for BEAST BDSKY model if tradition has a fixed composition date
- Change AncestralStateLogger to AncestralSequenceLogger in BEAST output
- Add option for choice of AncestralSequenceLogger or AncestralStateLogger for BEAST outputs
- Add support for time-dependent substitution models with EpochSubstitutionModel in BEAST outputs HOT 2
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