mkgendocs.yml

sources_dir: docs/docs/gendocs_docs
templates_dir: docs/docs/gendocs_templates
repo: https://github.com/cwieder/py-ssPA 
version: master

pages:

  # - page: "reference/download_pathways.md"
  #   source: "src/sspa/download_pathways.py"
  #   functions:
  #     - download_KEGG
  #     - download_reactome

  - page: "reference/identifier_conversion.md"
    source: "src/sspa/identifier_conversion.py"
    functions:
      - identifier_conversion
      - map_identifiers

  - page: "reference/load_pathways.md"
    source: "src/sspa/process_pathways.py"
    functions:
      - process_reactome
      - process_kegg
      - process_gmt
      - process_pathbank

  - page: "reference/utils.md"
    source: "src/sspa/utils.py"
    functions:
      - load_example_data
      - t_tests
      - pathwaydf_to_dict

  - page: "reference/ORA.md"
    source: "src/sspa/sspa_ora.py"
    classes:
      - sspa_ora

  - page: "reference/GSEA.md"
    source: "src/sspa/sspa_gsea.py"
    functions:
      - sspa_gsea

  - page: "reference/SVD.md"
    source: "src/sspa/sspa_svd.py"
    classes:
      - sspa_SVD

  - page: "reference/kPCA.md"
    source: "src/sspa/sspa_kpca.py"
    classes:
      - sspa_KPCA

  - page: "reference/ssClustPA.md"
    source: "src/sspa/sspa_cluster.py"
    classes:
      - sspa_ssClustPA

  # - page: "reference/GSVA.md"
  #   source: "src/sspa/sspa_gsva.py"
  #   functions:
  #     - sspa_gsva

  - page: "reference/ssGSEA.md"
    source: "src/sspa/sspa_ssGSEA.py"
    classes:
      - sspa_ssGSEA

  - page: "reference/zscore.md"
    source: "src/sspa/sspa_zscore.py"
    classes:
      - sspa_zscore