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mkdocs.yml
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131 lines (118 loc) · 3.78 KB
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site_name: flowpaths
repo_url: https://github.com/algbio/flowpaths
nav:
- Home:
- About: index.md
- FAQ: faq.md
- References: references.md
- Contributing: contributing.md
- Acyclic Decomposition Models:
- Minimum Flow Decomposition: minimum-flow-decomposition.md
- $k$-Flow Decomposition: k-flow-decomposition.md
- $k$-Least Absolute Errors: k-least-absolute-errors.md
- $k$-Minimum Path Error: k-min-path-error.md
- Minimum Path Cover: minimum-path-cover.md
- Optimizing $k$: numpathsoptimization.md
- Decomposition Models with Cycles:
- Minimum Flow Decomposition: minimum-flow-decomposition-cycles.md
- $k$-Flow Decomposition: k-flow-decomposition-cycles.md
- $k$-Least Absolute Errors: k-least-absolute-errors-cycles.md
- $k$-Minimum Path Error: k-min-path-error-cycles.md
- Minimum Path Cover: minimum-path-cover-cycles.md
- Advanced Options:
- Flows/weights on nodes: node-expanded-digraph.md
- Subpath constraints: subpath-constraints.md
- Subset constraints: subset-constraints.md
- Ignoring edges: ignoring-edges.md
- Additional start/end nodes: additional-start-end-nodes.md
- Correcting weights: minimum-error-flow.md
- Solver options and optimizations: solver-options-optimizations.md
- Various utils: utils.md
- Developing New Models:
- Solver Wrapper: solver-wrapper.md
- Abstract Path Model: abstract-path-model.md
- stDAG: stdag.md
- Abstract Walk Model: abstract-walk-model.md
- stDiGraph: stdigraph.md
- Abstract Source Sink Graph: abstractsourcesinkgraph.md
- Minimum Generating Set: minimum-generating-set.md
- Minimum Set Cover: minimum-set-cover.md
use_directory_urls: false
theme:
name: material
theme:
palette:
# Palette toggle for automatic mode
- media: "(prefers-color-scheme)"
primary: black
toggle:
icon: material/lightbulb-auto
name: Switch to light mode
# Palette toggle for light mode
- media: "(prefers-color-scheme: light)"
primary: black
scheme: default
toggle:
icon: material/lightbulb
name: Switch to dark mode
# Palette toggle for dark mode
- media: "(prefers-color-scheme: dark)"
primary: black
scheme: slate
toggle:
icon: material/lightbulb-outline
name: Switch to system preference
features:
- content.code.copy
- navigation.tabs
- navigation.tabs.sticky
- navigation.expand
- navigation.path
- search.highlight
logo: flowpaths-logo.svg
favicon: flowpaths-logo.svg
icon:
repo: fontawesome/brands/github
extra_javascript:
- javascripts/katex.js
- https://unpkg.com/katex@0/dist/katex.min.js
- https://unpkg.com/katex@0/dist/contrib/auto-render.min.js
extra_css:
- https://unpkg.com/katex@0/dist/katex.min.css
markdown_extensions:
- pymdownx.highlight:
use_pygments: true
anchor_linenums: true
line_spans: __span
pygments_lang_class: true
- pymdownx.inlinehilite
- pymdownx.snippets
- pymdownx.superfences:
custom_fences:
- name: mermaid
class: mermaid
format: !!python/name:pymdownx.superfences.fence_code_format
- attr_list
- md_in_html
- smarty
- admonition
- pymdownx.arithmatex:
generic: true
- pymdownx.details
plugins:
- search
- mkdocstrings:
default_handler: python
handlers:
python:
options:
show_root_toc_entry: false
# docstring_options:
merge_init_into_class: true
# docstring_section_style: spacy
separate_signature: true
show_signature_annotations: true
modernize_annotations: true
signature_crossrefs: false
line_length: 30
load_external_modules: true