site_name: BPNet

# ------- readthedocs ---------

theme:

 name: readthedocs

 custom_dir: theme_dir

extra_css: [css/extra.css]

# --------------------------

repo_url: http://github.com/kundajelab/bpnet

site_url: https://kundajelab.github.io/bpnet

edit_uri: edit/master/docs/templates/

site_description: 'Documentation of BPNet.'

dev_addr: '0.0.0.0:8000'

# google_analytics: ["UA-115025493-1", "kipoi.org"]

# --------------------------------------------

# This tells pydocmd which pages to generate from which Python modules,

# functions and classes. At the first level is the page name, below that

# is a tree of Python member names (modules, classes, etc.) that should be

# documented. Higher indentation leads to smaller header size.

generate:

  - extractors.md:

    - bpnet.extractors+

  - transforms/functional.md:

    - bpnet.transforms.functional+

  - transforms/transforms.md:

    - bpnet.transforms.transforms+

  - dataloaders.md:

    - bpnet.dataloaders.sequence+

    - bpnet.dataloaders.splicing.MMSpliceDl

# - baz/cool-stuff.md:

#   - foobar.baz:

#     - foobar.baz.CoolClass+     # (+ to include members)

#     - foobar.baz.some_function

# - baz/more-stuff.md:

#   - foobar.more++               # (++ to include members, and their members)

# MkDocs pages configuration. The `<<` operator is sugar added by pydocmd

# that allows you to use an external Markdown file (eg. your project's README)

# in the documentation. The path must be relative to current working directory.

# pages:

# - Home: index.md << ../README.md

# - foobar.baz:

#   - Cool Stuff: baz/cool-stuff.md

pages:

- Home: index.md << ../README.md

- Dataloaders: dataloaders.md

- Transforms:

  - Functional: transforms/functional.md

  - Class-based: transforms/transforms.md

- Extractors: extractors.md

# These options all show off their default values. You don't have to add

# them to your configuration if you're fine with the default.

docs_dir: templates

gens_dir: sources

site_dir: site

loader:   pydocmd.loader.PythonLoader

# preprocessor: kiposeq.utils.YamlPreprocessor

preprocessor: pydocmd.preprocessor.DataLoaderYamlPreprocessor

# preprocessor: pydocmd.preprocessor.Preprocessor

# TODO - modify parsing of the yaml doc-strings?

# Additional search path for your Python module. If you use Pydocmd from a

# subdirectory of your project (eg. docs/), you may want to add the parent

# directory here.

additional_search_paths:

- ..