Create initial project infrastructure (#1)

* Create initial project infrastructure * Fix pylint warnings * Fix markdown heading
phasorpy · Aug 22, 2023 · beee234 · beee234
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diff --git a/.github/ISSUE_TEMPLATE/bug_report.md b/.github/ISSUE_TEMPLATE/bug_report.md
@@ -0,0 +1,37 @@
+---
+name: Bug report
+about: Create a report to help improve PhasorPy
+title: ''
+labels: ''
+assignees: ''
+
+---
+
+**Describe the bug**
+
+A clear and concise description of what the bug is and what was expected to happen.
+
+**To Reproduce**
+
+A minimal, self-contained Python code reproducing the problem. Format the code using markdown, for example:
+
+```Python
+import phasorpy
+phasorpy.do_something('my.file')
+```
+
+A Python traceback if available, for example:
+
+```Python traceback
+Traceback (most recent call last):
+File "<stdin>", line 1, in <module>
+AttributeError: module 'phasorpy' has no attribute 'do_something'
+```
+
+Any data files necessary to run the code can be attached to the issue or shared via cloud storage.
+
+Information how PhasorPy was installed (pip, conda, or other) and the console output of:
+
+```
+$ python -m phasorpy --versions
+```
diff --git a/.github/workflows/deploy-docs.yml b/.github/workflows/deploy-docs.yml
@@ -0,0 +1,51 @@
+name: Deploy documentation
+
+on:
+  push:
+    tags:
+      - '*'
+    branches:
+      - main
+  pull_request:
+    branches:
+      - main
+
+jobs:
+  build:
+
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ["3.11"]
+
+    steps:
+    - uses: actions/checkout@v3
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v4
+      with:
+        python-version: ${{ matrix.python-version }}
+    - name: Install package and dependencies
+      run: |
+        python -m pip install --upgrade pip
+        python -m pip install -r requirements_dev.txt
+        python -m pip install --no-build-isolation --no-deps --verbose --editable .
+    - name: Build docs
+      run: |
+        cd docs
+        make html
+    - name: Upload artifacts
+      uses: actions/upload-artifact@v3
+      with:
+        name: docs
+        path: docs/_build/html
+    - name: Deploy docs
+      if: github.event_name == 'push'
+      uses: peaceiris/actions-gh-pages@v3
+      with:
+        personal_token: ${{ secrets.PHASORPY_DOC_DEPLOY_KEY }}
+        external_repository: phasorpy/phasorpy.github.io
+        publish_dir: docs/_build/html
+        publish_branch: main
+        destination_dir: ${{github.ref_name}}
+        # cname: phasorpy.org
diff --git a/.github/workflows/release-pypi.yml b/.github/workflows/release-pypi.yml
@@ -0,0 +1,75 @@
+name: Publish to PyPI
+
+on:
+  push:
+    tags:
+      - '*'
+    branches:
+      - main
+  pull_request:
+    branches:
+      - main
+
+jobs:
+
+  build_artifacts:
+    name: Build sdist and wheel
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+
+    steps:
+      - uses: actions/checkout@v3
+        with:
+          submodules: true
+          fetch-depth: 0
+      - uses: actions/setup-python@v4
+        with:
+          python-version: "3.11"
+      - name: Install PyBuild
+        run: |
+          python -m pip install build
+      - name: Build wheel and sdist
+        run: |
+          python -m build .
+      - uses: actions/upload-artifact@v3
+        with:
+          name: releases
+          path: dist
+
+  test_artifacts:
+    name: Test sdist and wheel
+    needs: [build_artifacts]
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/download-artifact@v3
+        with:
+          name: releases
+          path: dist
+      - uses: actions/setup-python@v4.6.0
+        with:
+          python-version: "3.11"
+      - run: |
+          ls
+          ls dist
+          python -m pip install -U twine
+          python -m twine check dist/*
+          python -m pip install --upgrade --no-cache-dir --no-deps --pre --no-index --find-links=dist phasorpy
+          python -c"from phasorpy import __version__;print(__version__)"
+
+  upload_artifacts:
+    name: Upload release to PyPI
+    needs: [build_artifacts]
+    runs-on: ubuntu-latest
+    environment:
+      name: pypi
+      url: https://pypi.org/p/phasorpy
+    permissions:
+      id-token: write
+    if: github.event_name == 'push' && startsWith(github.event.ref, 'refs/tags/v')
+    steps:
+      - uses: actions/download-artifact@v3
+        with:
+          name: releases
+          path: dist
+      - uses: pypa/gh-action-pypi-publish@release/v1
diff --git a/.github/workflows/run-tests.yml b/.github/workflows/run-tests.yml
@@ -0,0 +1,96 @@
+name: Run tests
+
+on:
+  push:
+    branches:
+      - main
+  pull_request:
+    branches:
+      - main
+
+jobs:
+  test:
+    name: Test library and docs
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        os: ["ubuntu-20.04"]
+        python-version: ["3.10", "3.11"]
+    steps:
+    - uses: actions/checkout@v3
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v3
+      with:
+        python-version: ${{ matrix.python-version }}
+    - name: Editable install
+      run: |
+        python -m pip install --upgrade pip
+        python -m pip install --editable .
+        python -m pip install -r requirements_dev.txt
+    - name: Print dependency versions
+      run: |
+        phasorpy --versions
+    - name: Test with pytest
+      run: |
+        python -X dev -m pytest
+    - name: Build docs
+      run: |
+        cd docs
+        make html
+
+  test_win_mac:
+    name: Test Windows and macOS
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        os: ["windows-2019", "macos-12"]
+        python-version: ["3.10"]
+    steps:
+    - uses: actions/checkout@v3
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v3
+      with:
+        python-version: ${{ matrix.python-version }}
+    - name: Editable install
+      run: |
+        python -m pip install --upgrade pip
+        python -m pip install --editable .
+        python -m pip install -r requirements_dev.txt
+    - name: Test with pytest
+      run: |
+        python -X dev -m pytest
+    - name: Build docs
+      run: |
+        cd docs
+        make html
+
+  static_analysis:
+    name: Static code analysis
+    runs-on: "ubuntu-latest"
+    strategy:
+      fail-fast: false
+    steps:
+    - uses: actions/checkout@v3
+    - name: Set up Python 3.10
+      uses: actions/setup-python@v3
+      with:
+        python-version: "3.10"
+    - name: Editable install
+      run: |
+        python -m pip install --upgrade pip
+        python -m pip install --editable .
+        python -m pip install -r requirements_dev.txt
+    - name: Test with black
+      run: |
+        python -m black --check src/phasorpy tutorials docs
+    - name: Test with mypy
+      run: |
+        python -m mypy
+    - name: Test with isort
+      run: |
+        python -m isort --check src/phasorpy tutorials
+    - name: Check spelling
+      run: |
+        python -m codespell_lib
diff --git a/.gitignore b/.gitignore
@@ -1,3 +1,18 @@
+_/*
+data/*
+tutorials/data/*
+*.tif
+*.tiff
+*.lsm
+*.ome.tif
+*.sdt
+*.b64
+*.r64
+*.npy
+*.flif
+*.lif
+*.czi
+
 # Byte-compiled / optimized / DLL files
 __pycache__/
 *.py[cod]
@@ -7,6 +22,7 @@ __pycache__/
 *.so
 
 # Distribution / packaging
+setup.cfg
 .Python
 build/
 develop-eggs/
@@ -37,6 +53,7 @@ pip-log.txt
 pip-delete-this-directory.txt
 
 # Unit test / coverage reports
+_htmlcov/
 htmlcov/
 .tox/
 .nox/
@@ -49,6 +66,7 @@ coverage.xml
 *.py,cover
 .hypothesis/
 .pytest_cache/
+.ruff_cache/
 cover/
 
 # Translations
@@ -69,7 +87,11 @@ instance/
 .scrapy
 
 # Sphinx documentation
+_build/
+docs/build/
 docs/_build/
+docs/examples/
+docs/tutorials/
 
 # PyBuilder
 .pybuilder/
@@ -85,25 +107,25 @@ 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
+.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
+Pipfile.lock
 
 # 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
+poetry.lock
 
 # pdm
 #   Similar to Pipfile.lock, it is generally recommended to include pdm.lock in version control.
-#pdm.lock
+pdm.lock
 #   pdm stores project-wide configurations in .pdm.toml, but it is recommended to not include it
 #   in version control.
 #   https://pdm.fming.dev/#use-with-ide
@@ -152,9 +174,15 @@ dmypy.json
 # Cython debug symbols
 cython_debug/
 
+.vs
+.vscode
+*.code-workspace
+
 # PyCharm
 #  JetBrains specific template is maintained 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/
+.idea/
+
+.benchmarks
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -0,0 +1 @@
+See the [PhasorPy release notes](docs/release.rst).
diff --git a/CODE_OF_CONDUCT.md b/CODE_OF_CONDUCT.md
@@ -0,0 +1 @@
+See the [PhasorPy code of conduct](docs/code_of_conduct.rst).
diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md
@@ -0,0 +1 @@
+See the [PhasorPy contributing guide](docs/contributing.rst).
diff --git a/LICENSE → LICENSE.txt b/LICENSE → LICENSE.txt
@@ -1,6 +1,6 @@
 MIT License
 
-Copyright (c) 2023 PhasorPy Developers
+Copyright (c) 2022-2023 PhasorPy Contributors
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal
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		See the [PhasorPy release notes](docs/release.rst).
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		See the [PhasorPy code of conduct](docs/code_of_conduct.rst).
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		@@ -0,0 +1 @@
		See the [PhasorPy contributing guide](docs/contributing.rst).