Add _rtd folder for documentation to explain MIBI/ARK in more detail #221
Conversation
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I still need to figure out how to get the Home page automatically selected in Sphinx, but I'm sure it's pretty easy to do. For now, would appreciate comments on the directory structure as well as how everything appears on ReadTheDocs (click "Details" next to the readthedocs badge to view). For the record, Noah's |
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This looks great! It auto-generated sections based on the .md file headings. I notice that there's a hyperlink option for the sub-headings: is the best way to link from different docs to one another to embed the hardcoded absolute path to that heading, or is there some way we should use relative links or something within the docs? I remember you mentioning this before at one point |
…raneous comment from conf.py
I think for now, it's OK to use the absolute path. It looks like DeepCell uses the same thing. If by any chance you're talking about how index.rst's toctrees are formatted (Tab <path_to_md_file>), then that's because this is the .rst way to alias your file to a better-looking name. |
…221) * Push new documentation changes * Fix toctree error and duplicate link in contributing.md * Condense all sphinx parameters under the same heading, and remove extraneous comment from conf.py * Link homepage to toctree * Modify conf.py so it doesn't complain about lack of _rtd/landing.py in toctree * Further standardize the homepage and landing page * Change markdown tab to utils * Remove extraneous commented test in data_utils_test.py
…221) * Push new documentation changes * Fix toctree error and duplicate link in contributing.md * Condense all sphinx parameters under the same heading, and remove extraneous comment from conf.py * Link homepage to toctree * Modify conf.py so it doesn't complain about lack of _rtd/landing.py in toctree * Further standardize the homepage and landing page * Change markdown tab to utils * Remove extraneous commented test in data_utils_test.py
What is the purpose of this PR?
Addresses and closes #213. Currently, our ReadTheDocs page only supports a basic landing page and documentation. We want to have some more information to guide our users through how the actual pipeline works, how to set up their virtual environment, etc. We also want to make our ReadTheDocs site more sophisticated.
How did you implement your changes
We create a separate
_rtdfolder which will contain.mdfiles we can link to inindex.rst(specifically thetoctree) which each explain a certain aspect of our work. We will also be updating ourindex.rstfile to integrate these new files into the table of contents (aka thetoctree).Remaining issues
I have a set of template
.mdpages attached, but we may need to add/delete some of them. Please note that this PR only addresses the structure for our documentation moving forward. We will have another PR (or PRs) which will handle adding the meat to these.mdfiles.