Merge dev branch to main

.all-contributorsrc

@@ -0,0 +1,81 @@
+{
+  "projectName": "BaSiCPy",
+  "projectOwner": "peng-lab",
+  "repoType": "github",
+  "repoHost": "https://github.com",
+  "files": [
+    "README.md"
+  ],
+  "imageSize": 100,
+  "commit": true,
+  "commitConvention": "gitmoji",
+  "contributors": [
+    {
+      "login": "Nicholas-Schaub",
+      "name": "Nicholas-Schaub",
+      "avatar_url": "https://avatars.githubusercontent.com/u/15925882?v=4",
+      "profile": "https://github.com/Nicholas-Schaub",
+      "contributions": [
+        "projectManagement",
+        "review",
+        "infra",
+        "test",
+        "code",
+        "ideas"
+      ]
+    },
+    {
+      "login": "tdmorello",
+      "name": "Tim Morello",
+      "avatar_url": "https://avatars.githubusercontent.com/u/34800427?v=4",
+      "profile": "https://github.com/tdmorello",
+      "contributions": [
+        "code",
+        "doc",
+        "review",
+        "test",
+        "ideas",
+        "infra"
+      ]
+    },
+    {
+      "login": "tying84",
+      "name": "Tingying Peng",
+      "avatar_url": "https://avatars.githubusercontent.com/u/11461947?v=4",
+      "profile": "https://github.com/tying84",
+      "contributions": [
+        "data",
+        "financial",
+        "projectManagement",
+        "talk",
+        "code"
+      ]
+    },
+    {
+      "login": "yfukai",
+      "name": "Yohsuke T. Fukai",
+      "avatar_url": "https://avatars.githubusercontent.com/u/5919272?v=4",
+      "profile": "https://github.com/yfukai",
+      "contributions": [
+        "research",
+        "code",
+        "ideas",
+        "review",
+        "test",
+        "question",
+        "infra"
+      ]
+    },
+    {
+      "login": "YuLiu-web",
+      "name": "YuLiu-web",
+      "avatar_url": "https://avatars.githubusercontent.com/u/70626217?v=4",
+      "profile": "https://github.com/YuLiu-web",
+      "contributions": [
+        "doc",
+        "userTesting"
+      ]
+    }
+  ],
+  "contributorsPerLine": 7
+}

.bumpversion.cfg

@@ -0,0 +1,21 @@
+[bumpversion]
+current_version = 1.0.1
+commit = True
+tag = True
+parse = (?P<major>\d+)\.(?P<minor>\d+)\.(?P<patch>\d+)(\-(?P<release>[a-z]+)(?P<build>\d+))?
+serialize = 
+	{major}.{minor}.{patch}-{release}{build}
+	{major}.{minor}.{patch}
+
+[bumpversion:part:release]
+optional_value = _
+first_value = dev
+values = 
+	dev
+	_
+
+[bumpversion:part:build]
+
+[bumpversion:file:VERSION]
+
+[bumpversion:file:docs/conf.py]

.flake8

@@ -0,0 +1,6 @@
+[flake8]
+docstring-convention=google
+max-line-length=88
+exclude=noxfile.py,docs/*,tests/*,scripts/*
+ignore=D105, W503
+extend-ignore = E203

.github/workflows/ci.yml

@@ -0,0 +1,80 @@
+name: CI
+
+on: [push, pull_request]
+
+jobs:
+  test:
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ["3.7", "3.8", "3.9", "3.10"]
+        os: ["ubuntu-latest", "macos-latest", "windows-latest"]
+    steps:
+      - uses: actions/checkout@v2
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v2
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          python -m pip install nox
+
+      - name: Test with nox
+        run: |
+          nox --sessions=tests --python=${{ matrix.python-version }}
+
+  docs:
+    runs-on: "ubuntu-latest"
+    steps:
+      - uses: actions/checkout@v2
+      - name: Set up packages
+        run: sudo apt-get install pandoc
+      - name: Set up Python
+        uses: actions/setup-python@v2
+        with:
+          python-version: "3.10"
+
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          python -m pip install nox
+
+      - name: Test with nox
+        run: |
+          nox --sessions=docs-build
+
+
+  #     - name: Coverage
+  #       uses: codecov/codecov-action@v2
+
+  # deploy:
+  #   needs: [test]
+  #   runs-on: ubuntu-latest
+  #   steps:
+  #     - uses: actions/checkout@v2
+  #     - name: Set up Python 3.10
+  #       uses: actions/setup-python@v2
+  #       with:
+  #         python-version: "3.10"
+
+  #     - name: Install dependencies
+  #       run: |
+  #         python -m pip install --upgrade pip
+  #         python -m pip install poetry
+
+  #     - name: Bump version and build
+  #       run: |
+  #         poetry version patch &&
+  #         version=$(poetry version | awk '{ print $2 }') &&
+  #         poetry version $version.dev.$(date +%s) &&
+  #         poetry build
+
+  #     - name: Release on TestPyPI
+  #       uses: pypa/[email protected]
+  #       with:
+  #         user: __token__
+  #         password: ${{ secrets.TEST_PYPI_TOKEN }}
+  #         repository_url: https://test.pypi.org/legacy/

.github/workflows/release.yml

@@ -0,0 +1,30 @@
+name: PyPi
+
+on:
+  push:
+    tags:
+      - v[0-9]+.[0-9]+.[0-9]+
+      - v[0-9]+.[0-9]+.[0-9]+-dev[0-9]+
+
+jobs:
+  package:
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout 🛎️
+        uses: actions/checkout@v2
+
+      - name: Set up Python 3.9
+        uses: actions/setup-python@v2
+        with:
+          python-version: 3.9
+
+      - name: Build basicpy
+        run: |
+          python -m pip install wheel twine setuptools build
+          python -m build
+      - name: Publish a Python distribution to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1
+        with:
+          user: __token__
+          password: ${{ secrets.PYPI_API_TOKEN }}

.gitignore

@@ -1,22 +1,158 @@
-# test data
-/.pytest_cache/
-
-# Python files:
+# Byte-compiled / optimized / DLL files
 __pycache__/
-*.pyc
-*.egg-info
+*.py[cod]
+*$py.class
 
-#tests
-/.pytest_cache/
-pybasic/test/units/*
+# C extensions
+*.so
 
-# OS files
-.DS_Store
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+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/
+cover/
+
+# 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
+.pybuilder/
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+#   For a library or package, you might want to ignore these files since the code is
+#   intended to run in multiple environments; otherwise, check them in:
+.python-version
 
-# IDE
-.spyproject/
+# 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
 
-# venv
-.venv_pybasic/
+# poetry
+#   Similar to Pipfile.lock, it is generally recommended to include poetry.lock in version control.
+#   This is especially recommended for binary packages to ensure reproducibility, and is more
+#   commonly ignored for libraries.
+#   https://python-poetry.org/docs/basic-usage/#commit-your-poetrylock-file-to-version-control
+#poetry.lock
 
-.ipynb_checkpoints
+# 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/
+
+# pytype static type analyzer
+.pytype/
+
+# Cython debug symbols
+cython_debug/
+
+# PyCharm
+#  JetBrains specific template is maintainted in a separate JetBrains.gitignore that can
+#  be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore
+#  and can be added to the global gitignore or merged into this file.  For a more nuclear
+#  option (not recommended) you can uncomment the following to ignore the entire idea folder.
+#.idea/
+
+.vscode/
+.DS_Store
+scratch/
+node_modules/
+package-lock.json