First Commit

.gitattributes

@@ -0,0 +1 @@
+*.ipynb linguist-documentation

.github/workflows/ci.yml

@@ -0,0 +1,42 @@
+name: CI
+on:
+  push:
+    branches: [main, develop]
+    paths: ["src/**", "tests/**", ".github/workflows/ci.yml"]
+  pull_request:
+    branches: [main, develop]
+    paths: ["src/**", "tests/**", ".github/workflows/ci.yml"]
+  workflow_dispatch:
+
+jobs:
+  CI_black-flake8-pytest:
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        os: [ubuntu-latest, macos-latest]
+        python-version: [3.8, 3.9, "3.10"]
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v3
+
+      - name: Setup Python ${{ matrix.python-version}}
+        uses: actions/setup-python@v4
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - name: Install Poetry
+        run: |
+          curl -sSL https://install.python-poetry.org | python3 -
+          echo "$HOME/.local/bin" >> $GITHUB_PATH
+
+      - name: Install Dependencies
+        run: poetry install -n
+
+      - name: Run black format check
+        run: poetry run black src tests --check --diff --verbose
+
+      - name: Run flake8 lint check
+        run: poetry run flake8 src tests --max-line-length=88 --ignore=E203,W503,W504
+
+      - name: Run pytest
+        run: poetry run pytest tests --tb=line --cov=src --cov-report=xml --cov-report=term

.github/workflows/publish_mkdocs.yml

@@ -0,0 +1,26 @@
+name: Publish MkDocs
+
+on:
+  release:
+    types: [released]
+  workflow_dispatch:
+
+jobs:
+  publish_mkdocs:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v3
+
+      - name: Setup Python 3.9
+        uses: actions/setup-python@v4
+        with:
+          python-version: 3.9
+
+      - name: Install MkDocs & Plugins
+        run: |
+          pip install .
+          pip install mkdocs mkdocs-material mkdocs-jupyter mkdocstrings[python] black
+
+      - name: Publish document
+        run: mkdocs gh-deploy --force

.github/workflows/publish_to_pypi.yml

@@ -0,0 +1,32 @@
+name: Publish to PyPI
+on:
+  release:
+    types: [released]
+  workflow_dispatch:
+
+jobs:
+  publish_to_pypi:
+    name: Publish to PyPI
+    runs-on: ubuntu-latest
+    env:
+      PYPI_USERNAME: ${{ secrets.PYPI_USERNAME }}
+      PYPI_PASSWORD: ${{ secrets.PYPI_PASSWORD }}
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v3
+
+      - name: Setup Python 3.9
+        uses: actions/setup-python@v4
+        with:
+          python-version: 3.9
+
+      - name: Install Poetry
+        run: |
+          curl -sSL https://install.python-poetry.org | python3 -
+          echo "$HOME/.local/bin" >> $GITHUB_PATH
+
+      - name: Build
+        run: poetry build
+
+      - name: Publish
+        run: poetry publish -u $PYPI_USERNAME -p $PYPI_PASSWORD

.gitignore

@@ -0,0 +1,133 @@
+examples
+.vscode/
+notebooks/
+
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+pip-wheel-metadata/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# 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/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py,cover
+.hypothesis/
+.pytest_cache/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+.python-version
+
+# pipenv
+#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
+#   However, in case of collaboration, if having platform-specific dependencies or dependencies
+#   having no cross-platform support, pipenv may install dependencies that don't work, or not
+#   install all needed dependencies.
+#Pipfile.lock
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/

CITATION.cff

@@ -0,0 +1,8 @@
+cff-version: 1.2.0
+message: If you use this software, please cite it as below.
+authors:
+  - family-names: Shimoyama
+    given-names: Yuki
+title: "pyCirclize: Circular visualization in Python"
+date-released: 2022-12-20
+url: https://github.com/moshi4/pyCirclize

LICENSE

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2022 moshi
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

README.md

@@ -1,2 +1,59 @@
-# pyCirclize
-Circular visualization in Python (Circos Plot, Chord Diagram)
+# pyCirclize: Circular visualization in Python
+
+![Python3](https://img.shields.io/badge/Language-Python3-steelblue)
+![OS](https://img.shields.io/badge/OS-_Windows_|_Mac_|_Linux-steelblue)
+![License](https://img.shields.io/badge/License-MIT-steelblue)
+[![Latest PyPI version](https://img.shields.io/pypi/v/pycirclize.svg)](https://pypi.python.org/pypi/pycirclize)
+[![conda-forge](https://img.shields.io/conda/vn/conda-forge/pycirclize.svg?color=green)](https://anaconda.org/conda-forge/pycirclize)
+[![CI](https://github.com/moshi4/pyCirclize/actions/workflows/ci.yml/badge.svg)](https://github.com/moshi4/pyCirclize/actions/workflows/ci.yml)
+
+## Table of contents
+
+- [Overview](#overview)
+- [Installation](#installation)
+- [API Usage](#api-usage)
+- [Not Implemented Features](#not-implemented-features)
+
+## Overview
+
+pyCirclize is a circular visualization python package implemented based on matplotlib.
+This package is developed for the purpose of easily and beautifully plotting circular figure such as Circos Plot and Chord Diagram in Python.
+In addition, useful genome and phylogenetic tree visualization methods for the bioinformatics field are also implemented.
+pyCirclize was inspired by [circlize](https://github.com/jokergoo/circlize) and [pyCircos](https://github.com/ponnhide/pyCircos).
+More detailed documentation is available [here](https://moshi4.github.io/pyCirclize/).
+
+![pyCirclize_gallery.png](https://raw.githubusercontent.com/moshi4/pyCirclize/main/docs/images/pyCirclize_gallery.png)  
+**Fig.1 pyCirclize example plot gallery**
+
+## Installation
+
+`Python 3.8 or later` is required for installation.
+
+**Install PyPI package:**
+
+    pip install pycirclize
+
+**Install conda-forge package:**
+
+    conda install -c conda-forge pycirclize
+
+## API Usage
+
+API usage is described in each of the following sections in the [document](https://moshi4.github.io/pyCirclize/).
+
+- [Getting Started](https://moshi4.github.io/pyCirclize/getting_started/)
+- [Plot API Example](https://moshi4.github.io/pyCirclize/plot_api_example/)
+- [Chord Diagram](https://moshi4.github.io/pyCirclize/chord_diagram/)
+- [Circos Plot (Genomics)](https://moshi4.github.io/pyCirclize/circos_plot/)
+- [Phylogenetic Tree](https://moshi4.github.io/pyCirclize/phylogenetic_tree/)
+
+## Not Implemented Features
+
+List of features implemented in other Circos plotting tools but not yet implemented in pyCirclize.
+I may implement them when I feel like it.
+
+- Plot histogram
+- Plot boxplot
+- Plot violin
+- Plot raster image
+- Label position auto adjustment

docs/api-docs/circos.md

@@ -0,0 +1,3 @@
+# Circos Class
+
+::: pycirclize.circos.Circos

docs/api-docs/sector.md

@@ -0,0 +1,3 @@
+# Sector Class
+
+::: pycirclize.sector.Sector

docs/api-docs/track.md

@@ -0,0 +1,3 @@
+# Track Class
+
+::: pycirclize.track.Track