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Tags in the format `v.*-source` will build docs for the given version.
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@@ -37,6 +41,7 @@ Steps to build a release:
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5. (Force) push to the remote tag (`git push origin v`version`-source`).
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6. CircleCI should deploy the versioned documentation. If the version tag is the newest, it should also overwrite `latest` with these documents.
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<aid="markdown-guidelines"name="guidelines"></a>
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## Guidelines
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- Only write a document once, and liberally use the [reStructured Text `.. include::` directive](https://docutils.sourceforge.io/docs/ref/rst/directives.html#include) to include that document where appropriate.
#### Let CircleCI build your drafts / works-in-progress
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* Build environment will match actual docs build environment
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* CircleCI takes ~2 minutes to build
@@ -66,7 +73,8 @@ Steps to build a release:
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1. Merge your draft / work-in-progress into your fork's `source` branch. Make sure you push to your fork and not the main repository's `source` branch.
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1. Your fork will publish at `https://[your_GitHub_username].github.io/fcp-indi.github.com/`.
This documentation aspires to rely on a [single source of truth](https://en.wikipedia.org/wiki/Single_source_of_truth) where possible. To this end, building this documentation requires an installation of the version of [C-PAC](https://github.com/FCP-INDI/C-PAC) that is being documented.
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Steps to build this documentation locally:
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1. Locally install [C-PAC](https://github.com/FCP-INDI/C-PAC) from source.
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1. Run `./bin/build $VERSION` where `$VERSION` is the version to build (`nightly`, `latest`, or [<span title='Semantic Versioning'>semver</span>](https://semver.org/) for production, but this string can be anything you want locally). 
- SVGs exported from Lucidchart have scaling coded inin`width` and `height` XML attributes. Add the XML attributes `preserveAspectRatio="xMinYMin meet"` and `viewBox` to the SVG element in the actual SVG files:
@@ -110,6 +119,7 @@ where `{width}` and `{height}` are the values already present in the existing `w
[sphinxcontrib-bibtex](https://sphinxcontrib-bibtex.readthedocs.io/) is installed and configured. This extension creates links between the citations and the reference in the reference list and formats citations in referenced BibTeX files using built-in or [custom styles](https://github.com/FCP-INDI/fcp-indi.github.com/blob/source/docs/_sources/references/style.py). To use this Sphinx extension,
@@ -160,6 +170,7 @@ The rendered file should look something like
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>
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><a name="ref1" href="#backref1">[1]</a> Craddock, C., Sikka, S., Cheung, B., Khanuja, R., Ghosh, S. S., Yan, C., Li, Q., Lurie, D., Vogelstein, J., Burns, R., Colcombe, S., Mennes, M., Kelly, C., Di Martino, A., Castellanos, F. X., and Milham, M. 2013. [Towards automated analysis of connectomes: the Configurable Pipeline forthe Analysis of Connectomes (C-PAC).](http://www.frontiersin.org/neuroinformatics/10.3389/conf.fninf.2013.09.00042/full) *Frontiersin neuroinformatics* 42. doi:[10.3389/conf.fninf.2013.09.00042](https://dx.doi.org/10.3389/conf.fninf.2013.09.00042)
* Because [C-PAC](https://github.com/FCP-INDI/C-PAC.git) and [cpac](https://github.com/FCP-INDI/cpac.git) have conflicting commandline commands, we first run any `cpac` commands in a virtual environment and spoof the `command-output` directive with `code-block` like
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