init

.github/workflows/deploy.yaml

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+name: Deploy to GitHub Pages
+
+permissions:
+  contents: write
+  pages: write
+
+on:
+  push:
+    branches: [ "main", "master" ]
+  workflow_dispatch:
+jobs:
+  deploy:
+    runs-on: ubuntu-latest
+    steps: [uses: fastai/workflows/quarto-ghp@master]

.gitignore

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+_docs/
+_proc/
+
+*.bak
+.gitattributes
+.last_checked
+.gitconfig
+*.bak
+*.log
+*~
+~*
+_tmp*
+tmp*
+tags
+*.pkg
+
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+env/
+build/
+conda/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+.hypothesis/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# pyenv
+.python-version
+
+# celery beat schedule file
+celerybeat-schedule
+
+# SageMath parsed files
+*.sage.py
+
+# dotenv
+.env
+
+# virtualenv
+.venv
+venv/
+ENV/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+
+.vscode
+*.swp
+
+# osx generated files
+.DS_Store
+.DS_Store?
+.Trashes
+ehthumbs.db
+Thumbs.db
+.idea
+
+# pytest
+.pytest_cache
+
+# tools/trust-doc-nbs
+docs_src/.last_checked
+
+# symlinks to fastai
+docs_src/fastai
+tools/fastai
+
+# link checker
+checklink/cookies.txt
+
+# .gitconfig is now autogenerated
+.gitconfig
+
+# Quarto installer
+.deb
+.pkg
+
+# Quarto
+.quarto

MANIFEST.in

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+include settings.ini
+include LICENSE
+include CONTRIBUTING.md
+include README.md
+recursive-exclude * __pycache__

README.md

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+# bio-nbs
+
+
+<!-- WARNING: THIS FILE WAS AUTOGENERATED! DO NOT EDIT! -->
+
+## Documentation
+
+Documentation can be found hosted on this GitHub
+[repository](https://github.com/sky1ove/bio-nbs)’s
+[pages](https://sky1ove.github.io/bio-nbs/).
+
+## How to use
+
+Go to `nbs` folder to check notebooks.

nbs/_quarto.yml

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+project:
+  type: website
+
+format:
+  html:
+    theme: cosmo
+    css: styles.css
+    toc: true
+    keep-md: true
+  commonmark: default
+
+website:
+  twitter-card: true
+  open-graph: true
+  repo-actions: [issue]
+  navbar:
+    background: primary
+    search: true
+  sidebar:
+    style: floating
+
+metadata-files: [nbdev.yml, sidebar.yml]

nbs/index.ipynb

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+{
+ "cells": [
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "# bio-nbs\n",
+    "\n",
+    "> A collection of notebooks for bio-related data analysis"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "## Documentation"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "Documentation can be found hosted on this GitHub [repository][repo]'s [pages][docs].\n",
+    "\n",
+    "[repo]: https://github.com/sky1ove/bio-nbs\n",
+    "[docs]: https://sky1ove.github.io/bio-nbs/"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "## How to use"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "Go to `nbs` folder to check notebooks."
+   ]
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "Python 3",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.10.10"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 4
+}

nbs/nbdev.yml

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+project:
+  output-dir: _docs
+
+website:
+  title: "bio-nbs"
+  site-url: "https://sky1ove.github.io/bio-nbs"
+  description: "A collection of notebooks for bio-related data analysis"
+  repo-branch: main
+  repo-url: "https://github.com/sky1ove/bio-nbs"

nbs/styles.css

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+.cell {
+  margin-bottom: 1rem;
+}
+
+.cell > .sourceCode {
+  margin-bottom: 0;
+}
+
+.cell-output > pre {
+  margin-bottom: 0;
+}
+
+.cell-output > pre, .cell-output > .sourceCode > pre, .cell-output-stdout > pre {
+  margin-left: 0.8rem;
+  margin-top: 0;
+  background: none;
+  border-left: 2px solid lightsalmon;
+  border-top-left-radius: 0;
+  border-top-right-radius: 0;
+}
+
+.cell-output > .sourceCode {
+  border: none;
+}
+
+.cell-output > .sourceCode {
+  background: none;
+  margin-top: 0;
+}
+
+div.description {
+  padding-left: 2px;
+  padding-top: 5px;
+  font-style: italic;
+  font-size: 135%;
+  opacity: 70%;
+}

pyproject.toml

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+[build-system]
+requires = ["setuptools>=64.0"]
+build-backend = "setuptools.build_meta"

settings.ini

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+[DEFAULT]
+# All sections below are required unless otherwise specified.
+# See https://github.com/fastai/nbdev/blob/master/settings.ini for examples.
+
+### Python library ###
+repo = bio-nbs
+lib_name = %(repo)s
+version = 0.0.1
+min_python = 3.7
+license = apache2
+black_formatting = False
+
+### nbdev ###
+doc_path = _docs
+lib_path = bio_nbs
+nbs_path = nbs
+recursive = True
+tst_flags = notest
+put_version_in_init = True
+
+### Docs ###
+branch = main
+custom_sidebar = False
+doc_host = https://%(user)s.github.io
+doc_baseurl = /%(repo)s
+git_url = https://github.com/%(user)s/%(repo)s
+title = %(lib_name)s
+
+### PyPI ###
+audience = Developers
+author = keke
+author_email = [email protected]
+copyright = 2024 onwards, %(author)s
+description = A collection of notebooks for bio-related data analysis
+keywords = nbdev jupyter notebook python
+language = English
+status = 3
+user = sky1ove
+
+### Optional ###
+# requirements = fastcore pandas
+# dev_requirements = 
+# console_scripts =
+# conda_user = 
+# package_data =