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mkdocs.yml
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site_name: Cylindra
site_description: Cryo-ET image analysis tool for cylindric periodic structures such as microtubules.
repo_name: cylindra
repo_url: https://github.com/hanjinliu/cylindra
copyright: Copyright (c) 2023 - 2024 Hanjin Liu
theme:
name: material
palette:
- scheme: slate
primary: lime
accent: light-green
toggle:
icon: material/brightness-4
name: Switch to light mode
- scheme: default
primary: lime
toggle:
icon: material/brightness-7
name: Switch to dark mode
features:
- content.code.annotate
- content.code.copy
- navigation.sections
- navigation.indexes
- navigation.footer
- toc.follow
- search.suggest
- search.share
font:
text: Roboto
code: Roboto Mono
nav:
- Overview: index.md
- Installation: installation.md
- Basics: basics.md
- Usage:
- open_image.md
- fit_splines.md
- lattice_params.md
- inspect_results.md
- project_io.md
- workflows.md
- plugins.md
- Spline:
- Spline: spline/index.md
- spline/clip.md
- spline/config.md
- Molecules:
- Molecules: molecules/index.md
- molecules/spline_to_molecules.md
- molecules/features.md
- molecules/expressions.md
- molecules/split_and_combine.md
- molecules/filter_molecules.md
- molecules/transform.md
- molecules/headers.md
- Alignment:
- Subtomogram Alignment and Averaging: alignment/index.md
- alignment/conventional.md
- alignment/landscape.md
- alignment/viterbi.md
- alignment/rma.md
- Working with Many Projects:
- Working with Many Projects: batch/index.md
- batch/collect_projects.md
- batch/construct.md
- batch/average.md
- Working with External Softwares:
- Working with External Softwares: extern/index.md
- extern/imod.md
- extern/relion.md
- process_images.md
- simulate.md
- cli.md
- Case Studies:
- Case Studies: case_studies/index.md
- case_studies/seam_search.md
- case_studies/ssta.md
- case_studies/make_figure.md
- API References:
- api/index.md
- api/components.md
- api/core.md
- api/project.md
- api/cylmeasure.md
- api/cylfilters.md
- api/plugin.md
- Widgets:
- api/widgets/main.md
- api/widgets/sta.md
- api/widgets/subwidgets.md
- api/widgets/batch.md
- Builtin Plugins:
- api/builtins/imod.md
- api/builtins/relion.md
hooks:
- docs/scripts/_dynamic_doc.py
plugins:
- search
- autorefs
- mkdocstrings:
handlers:
python:
import:
- https://docs.python.org/3/objects.inv
options:
docstring_style: numpy
show_source: true
show_bases: false
show_signature_annotations: true
- gen-files:
scripts:
- docs/scripts/_screenshots.py
markdown_extensions:
- admonition
- pymdownx.details
- pymdownx.superfences
- pymdownx.tabbed:
alternate_style: true
- pymdownx.keys
- pymdownx.arithmatex:
generic: true
- attr_list
- md_in_html
- pymdownx.emoji:
emoji_index: !!python/name:material.extensions.emoji.twemoji
emoji_generator: !!python/name:material.extensions.emoji.to_svg
extra_javascript:
- https://polyfill.io/v3/polyfill.min.js?features=es6
- https://cdn.jsdelivr.net/npm/mathjax@3/es5/tex-mml-chtml.js
watch:
- cylindra