diff --git a/.github/workflows/deploy.yaml b/.github/workflows/deploy.yaml new file mode 100644 index 0000000..29bfc57 --- /dev/null +++ b/.github/workflows/deploy.yaml @@ -0,0 +1,14 @@ +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] diff --git a/.gitignore b/.gitignore new file mode 100644 index 0000000..9233b81 --- /dev/null +++ b/.gitignore @@ -0,0 +1,152 @@ +_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 diff --git a/MANIFEST.in b/MANIFEST.in new file mode 100644 index 0000000..5c0e7ce --- /dev/null +++ b/MANIFEST.in @@ -0,0 +1,5 @@ +include settings.ini +include LICENSE +include CONTRIBUTING.md +include README.md +recursive-exclude * __pycache__ diff --git a/README.md b/README.md new file mode 100644 index 0000000..624134b --- /dev/null +++ b/README.md @@ -0,0 +1,14 @@ +# bio-nbs + + + + +## 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. diff --git a/nbs/_quarto.yml b/nbs/_quarto.yml new file mode 100644 index 0000000..59a1e49 --- /dev/null +++ b/nbs/_quarto.yml @@ -0,0 +1,22 @@ +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] \ No newline at end of file diff --git a/nbs/index.ipynb b/nbs/index.ipynb new file mode 100644 index 0000000..63c1d7b --- /dev/null +++ b/nbs/index.ipynb @@ -0,0 +1,65 @@ +{ + "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 +} diff --git a/nbs/nbdev.yml b/nbs/nbdev.yml new file mode 100644 index 0000000..bacfed4 --- /dev/null +++ b/nbs/nbdev.yml @@ -0,0 +1,9 @@ +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" diff --git a/nbs/styles.css b/nbs/styles.css new file mode 100644 index 0000000..66ccc49 --- /dev/null +++ b/nbs/styles.css @@ -0,0 +1,37 @@ +.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%; +} diff --git a/pyproject.toml b/pyproject.toml new file mode 100644 index 0000000..f2c07bf --- /dev/null +++ b/pyproject.toml @@ -0,0 +1,3 @@ +[build-system] +requires = ["setuptools>=64.0"] +build-backend = "setuptools.build_meta" diff --git a/settings.ini b/settings.ini new file mode 100644 index 0000000..1730a28 --- /dev/null +++ b/settings.ini @@ -0,0 +1,45 @@ +[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 = lcai888666@gmail.com +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 = \ No newline at end of file