mkgendocs.yml

sources_dir: docs
templates_dir: docs/templates
repo: https://github.com/AndreaRubbi/Pear-EBI
version: master

pages:
  - page: "modules/gendoc.md"
    source: "gendoc.py"
    functions:
      - add_val
      - automate_mkdocs_from_docstring
      - automate_nav_structure
      - fix
      - indent

  - page: "modules/test/test.md"
    source: "test/test.py"
    classes:
      - TestPEAR

  - page: "modules/pear_ebi/tree_set.md"
    source: "pear_ebi/tree_set.py"
    classes:
      - tree_set
      - set_collection

  - page: "modules/pear_ebi/tree_emb_parser.md"
    source: "pear_ebi/tree_emb_parser.py"
    functions:
      - parser

  - page: "modules/pear_ebi/embeddings/LLE_e.md"
    source: "pear_ebi/embeddings/LLE_e.py"
    functions:
      - lle

  - page: "modules/pear_ebi/embeddings/PCoA_e.md"
    source: "pear_ebi/embeddings/PCoA_e.py"
    functions:
      - pcoa

  - page: "modules/pear_ebi/embeddings/tSNE_e.md"
    source: "pear_ebi/embeddings/tSNE_e.py"
    functions:
      - tsne

  - page: "modules/pear_ebi/embeddings/Isomap_e.md"
    source: "pear_ebi/embeddings/Isomap_e.py"
    functions:
      - isomap

  - page: "modules/pear_ebi/embeddings/emb_quality.md"
    source: "pear_ebi/embeddings/emb_quality.py"
    functions:
      - euclidean_distance
      - pear_correlation
      - DRM

  - page: "modules/pear_ebi/embeddings/graph/graph.md"
    source: "pear_ebi/embeddings/graph/graph.py"
    functions:
      - plot_embedding

  - page: "modules/pear_ebi/calculate_distances/tqdist.md"
    source: "pear_ebi/calculate_distances/tqdist.py"
    functions:
      - bash_command
      - quartet
      - triplet

  - page: "modules/pear_ebi/calculate_distances/hashrf.md"
    source: "pear_ebi/calculate_distances/hashrf.py"
    functions:
      - bash_command
      - hashrf
      - hashrf_weighted

  - page: "modules/pear_ebi/calculate_distances/maple_RF.md"
    source: "pear_ebi/calculate_distances/maple_RF.py"
    classes:
      - Tree
    functions:
      - readNewick
      - prepareTreeComparison
      - RobinsonFouldsWithDay1985
      - calculate_distance_matrix

  - page: "modules/pear_ebi/interactive_mode/interactive.md"
    source: "pear_ebi/interactive_mode/interactive.py"
    functions:
      - usage
      - exit_program
      - calculate_distances
      - embedding
      - plotting
      - add_set
      - get_subset
      - interact

  - page: "modules/pear_ebi/subsample/subsample.md"
    source: "pear_ebi/subsample/subsample.py"
    functions:
      - subsample

  - page: "modules/pear_ebi/subsample/subsample_multiprocess.md"
    source: "pear_ebi/subsample/subsample_multiprocess.py"
    functions:
      - subsample