zensical.toml

# Zensical configuration for the leech documentation site.
# Migrated from mkdocs.yml. See https://zensical.org/docs/setup/basics/

[project]
site_name = "Leech Documentation"
site_description = "Learning Enhanced Electrical Classifiers from Hanopore signals"
site_url = "https://rnabioco.github.io/leech"
repo_url = "https://github.com/rnabioco/leech"
repo_name = "rnabioco/leech"
edit_uri = "edit/main/docs/"
copyright = "Copyright © 2025 RNA Bioscience Initiative"

nav = [
  { "Home" = "index.md" },
  { "Getting Started" = [
    { "Installation" = "getting-started/installation.md" },
    { "Quick Start" = "getting-started/quick-start.md" },
  ] },
  { "Guides" = [
    { "Data Preparation" = "data_preparation.md" },
    { "Understanding Move Tables" = "guides/move-tables.md" },
    { "Dwell Time Features" = "guides/dwell-features.md" },
    { "Classification Tasks" = "guides/classification-tasks.md" },
    { "Grid Search" = "grid-search/grid-search-usage.md" },
  ] },
  { "Reference" = [
    { "CLI" = "reference/cli.md" },
  ] },
  { "Pipeline" = [
    { "Overview" = "pipeline.md" },
  ] },
  { "Troubleshooting" = "troubleshooting.md" },
  { "API Reference" = [
    { "Overview" = "api/index.md" },
    { "Data Preparation" = "api/data_prep.md" },
    { "Features" = "api/features.md" },
    { "Dataset" = "api/dataset.md" },
    { "Models" = "api/models.md" },
    { "CRF" = "api/crf.md" },
    { "Training" = "api/training.md" },
    { "Evaluation" = "api/evaluation.md" },
    { "Inference" = "api/inference.md" },
    { "Grid Search" = "api/gridsearch.md" },
    { "Utilities" = "api/util.md" },
  ] },
]

# ----------------------------------------------------------------------------
# Theme
# ----------------------------------------------------------------------------
[project.theme]
features = [
  "content.code.annotate",
  "content.code.copy",
  "content.tabs.link",
  "content.tooltips",
  "content.action.edit",
  "navigation.instant",
  "navigation.instant.prefetch",
  "navigation.tracking",
  "navigation.sections",
  "navigation.expand",
  "navigation.path",
  "navigation.indexes",
  "navigation.top",
  "navigation.footer",
  "toc.follow",
  "search.highlight",
]

[project.theme.icon]
logo = "material/dna"
repo = "fontawesome/brands/github"

[[project.theme.palette]]
media = "(prefers-color-scheme: light)"
scheme = "default"
primary = "teal"
accent = "deep orange"
toggle.icon = "material/brightness-7"
toggle.name = "Switch to dark mode"

[[project.theme.palette]]
media = "(prefers-color-scheme: dark)"
scheme = "slate"
primary = "teal"
accent = "deep orange"
toggle.icon = "material/brightness-4"
toggle.name = "Switch to light mode"

[[project.extra.social]]
icon = "fontawesome/brands/github"
link = "https://github.com/rnabioco/leech"

[[project.extra.social]]
icon = "fontawesome/brands/python"
link = "https://pypi.org/project/leech/"

# ----------------------------------------------------------------------------
# Plugins
# ----------------------------------------------------------------------------
[project.plugins.mkdocstrings.handlers.python]
paths = ["src"]
inventories = ["https://docs.python.org/3/objects.inv"]

[project.plugins.mkdocstrings.handlers.python.options]
docstring_style = "google"
docstring_section_style = "table"
show_source = true
show_root_heading = true
show_root_full_path = false
show_symbol_type_heading = true
show_symbol_type_toc = true
members_order = "source"
group_by_category = true
show_signature = true
show_signature_annotations = true
separate_signature = true
line_length = 100
merge_init_into_class = true
filters = ["!^_"]

[project.plugins.mkdocstrings.handlers.python.options.docstring_options]
ignore_init_summary = true

# ----------------------------------------------------------------------------
# Markdown extensions
# ----------------------------------------------------------------------------
[project.markdown_extensions.abbr]
[project.markdown_extensions.admonition]
[project.markdown_extensions.attr_list]
[project.markdown_extensions.def_list]
[project.markdown_extensions.footnotes]
[project.markdown_extensions.md_in_html]

[project.markdown_extensions.toc]
permalink = true
permalink_title = "Anchor link to this section"
toc_depth = 3

[project.markdown_extensions.pymdownx.arithmatex]
generic = true

[project.markdown_extensions.pymdownx.betterem]
smart_enable = "all"

[project.markdown_extensions.pymdownx.caret]
[project.markdown_extensions.pymdownx.details]

[project.markdown_extensions.pymdownx.emoji]
emoji_index = "zensical.extensions.emoji.twemoji"
emoji_generator = "zensical.extensions.emoji.to_svg"

[project.markdown_extensions.pymdownx.highlight]
anchor_linenums = true
line_spans = "__span"
pygments_lang_class = true

[project.markdown_extensions.pymdownx.inlinehilite]
[project.markdown_extensions.pymdownx.keys]
[project.markdown_extensions.pymdownx.mark]
[project.markdown_extensions.pymdownx.smartsymbols]

[project.markdown_extensions.pymdownx.superfences]
custom_fences = [
  { name = "mermaid", class = "mermaid", format = "pymdownx.superfences.fence_code_format" },
]

[project.markdown_extensions.pymdownx.tabbed]
alternate_style = true

[project.markdown_extensions.pymdownx.tasklist]
custom_checkbox = true

[project.markdown_extensions.pymdownx.tilde]