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## MRtrix3 documentation generation
The [online documentation for *MRtrix3*](http://mrtrix.readthedocs.org/) is generated based on the contents of this `docs/` directory. It is additionally possible to generate a version of this documentation locally, which could theoretically then be produced in a different format (e.g. PDF) or with a different visual style. This document outlines the steps necessary to locally reproduce the documentation as it appears online.
1. If there have been local modifications made to *MRtrix3* executables (whether compiled C++ binaries or Python scripts / algorithm files), then the contents of specifically the `docs/reference/` directory may not match the contents of the commands' help pages / available config file options / environment variables as modified through those changes. In order to ensure that the documentation pages are concordant with the local code changes:
(from the *MRtrix3* root directory):
```
$ ./build
$ ./docs/generate_user_docs.sh
```
2. Install requisite packages via your distribution's package manager (exact package names may vary between different platforms) (may require `sudo`):
- `python-pip`
- `python-sphinx`
(may not be installable from package manager on all platforms)
3. Install requisite Python packages using `pip` (may require `sudo`):
- `pip install recommonmark sphinx sphinx-notfound-page sphinx_rtd_theme typing`
(should not need to include `sphinx` in this list if it was installed via the distribution package manager in step 2)
4. Compile the documentation:
```
$ python -m sphinx -n -N -w sphinx.log docs/ compiled_docs/
```
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