Documentation Infrastructure¶
The documentation of SeqAn has two parts: (1) the API documentation and (2) the manual that you are reading right now.
SeqAn API Documentation¶
The SeqAn API documentation is created using a customly-written system called dox. You can find out more about the syntax in Dox API Docs.
You can build the documentation in the dox folder:
dox # ./dox_only.sh
SeqAn Manual¶
The SeqAn manual is created using the Sphinx documentation system.
Follow these instructions to setup a local sphinx environment and build the manual:
$ virtualenv ~/seqan-manual-env
$ source ~/seqan-manual-env/bin/activate
(seqan-manual-env) $ cd ~/seqan/manual
(seqan-manual-env) $ pip install -r requirements.txt
(seqan-manual-env) $ make html
Note that you have to first build the dox documentation since plugins for generating the :dox: links rely on the generated search index for checks.
In order to get correct dox-links within the generated manuals, you have to specify the correct branch version.
If you are working on the develop branch there is nothing to do, since 'develop' is set by default.
But if you are working on another branch, for example master, you can set the correct branch by calling
(seqan-manual-env) $ export READTHEDOCS_VERSION='master'
before you call make html as described in the previous step.
This will generate the correct links to the master’s version of the dox, i.e., http://docs.seqan.de/seqan/master/