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:
- ..