mkdocs.yml

site_name: "BEDbase: a unified platform for genomic regions"

theme:
  logo: img/bedbase_logo.svg
  favicon: img/bb_docs.svg
  name: material
  custom_dir: overrides

  features:
    - header.autohide
    - navigation.sections
    # - navigation.expand
    - navigation.footer
    - navigation.indexes 
    - toc.follow
    - content.action.edit
    - content.action.view
    - navigation.tabs
    - navigation.top

markdown_extensions:
  - attr_list
  - md_in_html
  - admonition
  - pymdownx.details
  - pymdownx.highlight:
      use_pygments: true
  - pymdownx.superfences:
      custom_fences:
        - name: mermaid
          class: mermaid
          format: !!python/name:pymdownx.superfences.fence_div_format
  - pymdownx.tabbed:
      alternate_style: true
extra_css:
  - stylesheets/extra.css
  - https://unpkg.com/mermaid@10/dist/mermaid.min.css
extra_javascript:
  - https://unpkg.com/mermaid@10/dist/mermaid.min.js
  - javascripts/mermaid-init.js
extra:
  generator: false  # turn off theme link
copyright: >
    <a class="" href="http://databio.org/">
      <img src="https://databio.org/images/logo/logo_databio_long.svg"
        style="height:60px;"
        alt="Databio logo">
    </a>

nav:
#  - Home: README.md
  - BEDbase:
    - BEDbase: bedbase/README.md
    - User guides:
      - 📖 Public BEDbase UI user guide: bedbase/user/bedbase-ui-user-guide.md
      - 📖 Public BEDbase API user guide: bedbase/user/bedbase-api-user-guide.md
      - ✅ Reference Genome Compatibility: bedbase/user/reference-genome-compatibility.md
      - 📝 BED Classification:  bedbase/user/bed_classification.md
      - 💻 BBClient & caching: bedbase/user/bbclient.md
      - 🔍 BEDbase Search: bedbase/user/bedbase-search.md
      - 🪩 Embedding Visualization: bedbase/user/umap-visualizer.md
      - ⚙️ BED analyzer: bedbase/user/bed-analyzer.md
    - Developer guides:
      - 📇 BEDhost API server:
        - BEDhost overview: bedhost/README.md
        - Building docker image: bedhost/build_image.md
        - Deploy API: bedhost/deployment.md
        - Changelog: bedhost/changelog.md
      - 🔌 BBConf configuration:
        - BBConf: bbconf/README.md
        - Overview: bbconf/overview.md
        - Guide: bbconf/bbc_api.md
        - Changelog: bbconf/changelog.md
      - 🧰 BEDBoss processing pipeline: bedboss/README.md
      - 🔄 Data Loading: bedbase/bedbase-data-loading.md
      - 📜 Configuration file: bedbase/how-to-configure.md
    - Reference:
      - How to cite: citations.md
      - Support: https://github.com/databio/bedhost/issues
      - Contributing: contributing.md
      - Changelog: changelog.md
  - BEDboss:
    - BEDboss: bedboss/README.md
    - Tutorials:
        - Python modules:
          - BEDboss run-pep: bedboss/tutorials/python/tutorial_run_pep.md
          - BEDboss-all pipeline: bedboss/tutorials/python/tutorial_all.md
          - BEDmaker: bedboss/tutorials/python/bedmaker_tutorial.md
          - BEDstat: bedboss/tutorials/python/bedstat_tutorial.md
          - BEDbuncher: bedboss/tutorials/python/bedbuncher_tutorial.md
          - BEDindex: bedboss/tutorials/python/bedindex_tutorial.md
          - BEDclassifier: bedboss/tutorials/python/bedclassifier_tutorial.md
          - Ref_genome validator: bedboss/tutorials/python/ref_genome_tutorial.md
        - Command line interface: bedboss/usage.md
        - BEDMS tutorial: bedboss/tutorials/bedms_tutorial.md
    - How to guides:
      - Plot GEO BED files number: bedboss/how-to/bedfiles-geo-count.md
      - Upload GEO data: bedboss/how-to/upload-geo-data.md
      - Upload BED from PEP: bedboss/how-to/how-to-run-pep.md
      - Reindex vector store: bedboss/how-to/how-to-reindex-db.md
      - Generate UMAP: bedboss/how-to/how-to-create-umap.md
      - Create BEDbase database: bedboss/how-to/how-to-create-database.md
      - Run BEDboss in Docker: bedboss/how-to/how-to-run-in-docker.md
      - Create config file: bedbase/how-to-configure.md
      - Install dependencies: bedboss/how-to/how-to-install-requirements.md
    - Reference:
      - How to cite: citations.md
      - Changelog: bedboss/changelog.md
  - Geniml:
    - Geniml: geniml/README.md
    - Getting Started: 
      - Module overviews: geniml/modules.md
    - BBclient:
      - Cache BED files with BBClient: geniml/bbclient/bbclient.md
      - BBClient tutorial: geniml/tutorials/bbclient-workflow.md
      - Use BED cache in R: geniml/bbclient/pyBiocFileCache.md
    - Atacformer:
      - Atacformer: atacformer/README.md
      - Getting started:
        - Core concepts: atacformer/core-concepts.md
        - Quickstart: atacformer/quickstart.md
      - Tutorials:
        - Generating a UMAP from fragments files: atacformer/tutorials/umap_from_fragments.md
        - Example Brain3k Processing: atacformer/tutorials/example-brain3k-processing.md
        - Visualizing new embeddings in the latent space of a reference: atacformer/tutorials/ev-projection.md
        - Training:
          - Pre-tokenize data for training: atacformer/tutorials/training/pretokenize-for-training.md
          - Train a model from scratch: atacformer/tutorials/training/train-from-scratch.md
          - Fine-tune a model: atacformer/tutorials/training/fine-tune.md
      - Local compute guides:
        - Compute requirements: atacformer/local_compute/compute_requirements.md
        - Using atacformer locally: atacformer/local_compute/local_compute.md
        - Using atacformer with Apple Silicon: atacformer/local_compute/apple_silicon.md
    - How-to guides:
      - Train region2vec embeddings: geniml/tutorials/region2vec.md
      - Train BEDspace model:
        - Train BEDSpace embeddings: geniml/tutorials/bedspace.md
        - BEDspace results notebook: geniml/notebooks/bedspace-analysis.ipynb
      - Use scEmbed model:
        - Train single-cell embeddings: geniml/tutorials/train-scembed-model.md
        - Populate a vector store: geniml/tutorials/load-qdrant-with-cell-embeddings.md
        - Predict cell-types using KNN: geniml/tutorials/cell-type-annotation-with-knn.md
      - Evaluate embeddings: geniml/tutorials/evaluation.md
      - Create consensus peaks with CLI: geniml/tutorials/create-consensus-peaks.md
      - Create consensus peaks with Python: geniml/notebooks/create-consensus-peaks-python.ipynb
      - Assess universe fit: geniml/notebooks/assess-universe.ipynb
      - Fine-tune embeddings: geniml/tutorials/fine-tune-region2vec-model.md
      - Randomize bed files: geniml/tutorials/bedshift.md
      - Create evaluation dataset with bedshift: geniml/tutorials/bedshift-evaluation-guide.md
      - Create search backend: geniml/tutorials/text2bednn-search-interface.md
    - Reference:
      - How to cite: citations.md
      - Python API documentation:
        - Assess: geniml/api-reference/assess.md
        - Atacformer: geniml/api-reference/atacformer.md
        - BBClient: geniml/api-reference/bbclient.md
        - BEDshift: geniml/api-reference/bedshift.md
        - BEDspace: geniml/api-reference/bedspace.md
        - Craft: geniml/api-reference/craft.md
        - Evaluation: geniml/api-reference/eval.md
        - Geneformer: geniml/api-reference/geneformer.md
        - I/O: geniml/api-reference/io.md
        - Likelihood: geniml/api-reference/likelihood.md
        - Models: geniml/api-reference/models.md
        - Region2Vec: geniml/api-reference/region2vec.md
        - scEmbed: geniml/api-reference/scembed.md
        - Search: geniml/api-reference/search.md
        - Text2BedNN: geniml/api-reference/text2bednn.md
        - Tokenization: geniml/api-reference/tokenization.md
        - Universe: geniml/api-reference/universe.md
        - Utilities: geniml/api-reference/utils.md
      - Support: geniml/support.md
      - Contributing: geniml/contributing.md
      - Changelog: geniml/changelog.md
  - Gtars:
    - Gtars: gtars/README.md
    - 💿 Install: gtars/install.md
    - Modules:
      - Overview: gtars/modules.md
      - gtars-core: gtars/core.md
      # - gtars-io: gtars/io.md
      - gtars-models: gtars/regionSet.md
      - gtars-overlaprs: gtars/overlaprs.md
      - gtars-uniwig: gtars/uniwig.md
      - gtars-igd: gtars/igd.md
      - gtars-scoring: gtars/scoring.md
      - gtars-fragsplit: gtars/fragsplit.md
      - gtars-tokenizers: gtars/tokenizers.md
      - gtars-scatrs: gtars/scatrs.md
      - gtars-refget: gtars/refget.md
      - gtars-bbcache: gtars/bbcache.md
    - Bindings:
      - Python:
        - Overview: gtars/python-overview.md
        - Digests: gtars/python/digests.md
        - RefgetStore Tutorial: gtars/python/refgetstore.ipynb
        - RefgetStore Python Reference: gtars/python/refget-store.md
        - Refget API Reference: gtars/python/refget-api.md
      - Wasm:
        - Overview: gtars/wasm.md
        - Overlappers: gtars/wasm/overlappers.md
      - CLI: gtars/cli.md
      - R:
        - R: gtars/r.md
        - RefgetStore: gtars/r/refgetstore.md
    - Reference:
      - Changelog: gtars/changelog.md
      - Rust source API docs: https://docs.rs/gtars/latest/gtars/
      - Versioning policy: gtars/versioning.md
  - Manuscripts: 
    - How to cite: citations.md
    - Published manuscripts:
      - Gharavi et al. 2021: manuscripts/gharavi2021.md
      - Gu et al. 2021: manuscripts/gu2021.md
      - Rymuza et al. 2024: manuscripts/rymuza2024.md
      - Gharavi et al. 2024: manuscripts/gharavi2024.md
      - LeRoy et al.  2024: manuscripts/leroy2024.md
      - Zheng et al. 2024: manuscripts/zheng2024.md

plugins:
- search
- mkdocs-jupyter:
    include:
      - geniml/notebooks/assess-universe.ipynb
      - geniml/notebooks/bedspace-analysis.ipynb
      - geniml/notebooks/create-consensus-peaks-python.ipynb
      - gtars/python/refgetstore.ipynb
    ignore_h1_titles: True
- mkdocstrings:
    default_handler: python
    handlers:
      python:
        options:
          docstring_style: google  # Default to Google style
          show_symbol_type_heading: true
          show_symbol_type_toc: true
          show_root_heading: true
          show_root_full_path: false
          show_source: true  # Optional: Show source code links
          show_signature: true  # Show method signatures
          show_if_no_docstring: false
          docstring_section_style: table  # Optional: Format style
          separate_signature: true  # Ensure __init__ appears clearly
          merge_init_into_class: true  # This ensures __init__ is documented