phasorpy 0.1__tar.gz → 0.2__tar.gz

phasorpy-0.2/.codecov.yml

@@ -0,0 +1,11 @@
+codecov:
+  notify:
+    require_ci_to_pass: false
+    after_n_builds: 1
+coverage:
+  status:
+    project:
+      default:
+        threshold: 0.1%
+        informational: true
+comment: off

phasorpy-0.2/.github/ISSUE_TEMPLATE/bug_report.md

@@ -0,0 +1,36 @@
+---
+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, preferably on [Zenodo.org](https://zenodo.org/communities/phasorpy/).
+
+Information how PhasorPy was installed (pip, conda, or other) and the console output of:
+
+```
+$ python -m phasorpy versions
+```

phasorpy-0.2/.github/dependabot.yml

@@ -0,0 +1,11 @@
+version: 2
+
+updates:
+  - package-ecosystem: "github-actions"
+    directory: "/"
+    schedule:
+      interval: "monthly"
+    groups:
+      github-actions:
+        patterns:
+          - "*"

phasorpy-0.2/.github/pull_request_template.md

@@ -0,0 +1,15 @@
+## Description
+
+...
+
+## Checklist
+
+- [ ] The pull request title and description are concise.
+- [ ] Related issues are linked in the description.
+- [ ] New dependencies are explained.
+- [ ] The source code and documentation can be distributed under the [MIT license](https://www.phasorpy.org/docs/stable/license/).
+- [ ] The source code adheres to [code standards](https://www.phasorpy.org/docs/stable/contributing/#code-standards).
+- [ ] New classes, functions, and features are thoroughly [tested](https://www.phasorpy.org/docs/stable/contributing/#tests).
+- [ ] New, user-facing classes, functions, and features are [documented](https://www.phasorpy.org/docs/stable/contributing/#documentation).
+- [ ] New features are covered in tutorials.
+- [ ] No files other than source code, documentation, and project settings are added to the repository.

phasorpy-0.2/.github/workflows/build_sdist.yml

@@ -0,0 +1,77 @@
+name: Build sdist
+
+on:
+  push:
+    tags:
+      - "*"
+    branches:
+      - main
+  pull_request:
+    branches:
+      - main
+  workflow_dispatch:
+
+jobs:
+  build_artifacts:
+    name: Build sdist
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          submodules: true
+          fetch-depth: 0
+      - uses: actions/setup-python@v5
+        with:
+          python-version: "3.12"
+      - name: Install PyBuild
+        run: |
+          python -m pip install -U build
+      - name: Build sdist
+        run: |
+          python -m build --sdist .
+      - uses: actions/upload-artifact@v4
+        with:
+          name: sdist
+          path: dist
+
+  test_artifacts:
+    name: Test sdist
+    needs: [build_artifacts]
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/download-artifact@v4
+        with:
+          name: sdist
+          path: dist
+      - uses: actions/setup-python@v5
+        with:
+          python-version: "3.12"
+      - run: |
+          ls
+          ls dist
+          python -m pip install -U twine setuptools build wheel numpy Cython
+          python -m twine check dist/*
+          python -m pip install --upgrade --no-build-isolation --no-cache-dir --no-deps --pre --no-index --find-links=dist phasorpy
+          python -c"from phasorpy import __version__;print(__version__)"
+
+# Upload sdist and wheels manually for now
+#
+#  upload_artifacts:
+#    name: Upload release to PyPI
+#    needs: [test_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@v4
+#        with:
+#          name: releases
+#          path: dist
+#      - uses: pypa/gh-action-pypi-publish@release/v1

phasorpy-0.2/.github/workflows/build_wheels.yml

@@ -0,0 +1,43 @@
+name: Build wheels
+
+on:
+  push:
+    tags:
+      - "*"
+    branches:
+      - main
+  # pull_request:
+  #   branches:
+  #     - main
+  workflow_dispatch:
+
+env:
+  MPLBACKEND: agg
+
+jobs:
+  build:
+    name: Build wheels on ${{ matrix.os }}
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        os: [ubuntu-22.04, macos-13, windows-2019]
+    steps:
+      - uses: actions/checkout@v4
+      # - name: Set up QEMU
+      #   if: runner.os == 'Linux'
+      #   uses: docker/setup-qemu-action@v3
+      #   with:
+      #     platforms: all
+      - uses: pypa/cibuildwheel@v2.21.3
+        env:
+          # Building and testing manylinux2014_aarch64 too is slow.
+          # See https://github.com/phasorpy/phasorpy/pull/135
+          # CIBW_ARCHS_LINUX: x86_64 aarch64
+          CIBW_ARCHS_LINUX: auto
+          CIBW_ARCHS_MACOS: x86_64 arm64
+          CIBW_ARCHS_WINDOWS: AMD64 ARM64
+          CIBW_BUILD_VERBOSITY: 2
+      - uses: actions/upload-artifact@v4
+        with:
+          path: ./wheelhouse/*.whl
+          name: wheels-${{ matrix.os }}

phasorpy-0.2/.github/workflows/coverage.yml

@@ -0,0 +1,40 @@
+name: Code coverage
+
+on:
+  push:
+    branches:
+      - main
+  pull_request:
+    branches:
+      - main
+  workflow_dispatch:
+
+jobs:
+  code_coverage:
+    name: Code coverage
+    runs-on: "ubuntu-latest"
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ["3.12"]
+    steps:
+      - uses: actions/checkout@v4
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v5
+        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: Generate coverage report
+        run: |
+          pytest --cov=phasorpy --cov-report=xml tests
+      - name: Upload coverage to Codecov
+        uses: codecov/codecov-action@v4
+        with:
+          env_vars: OS,PYTHON
+          fail_ci_if_error: false
+          token: ${{ secrets.PHASORPY_CODECOV_TOKEN }}
+          verbose: true

phasorpy-0.2/.github/workflows/deploy-docs.yml

@@ -0,0 +1,54 @@
+name: Deploy documentation
+
+on:
+  push:
+    tags:
+      - "*"
+    branches:
+      - main
+  pull_request:
+    branches:
+      - main
+  workflow_dispatch:
+
+env:
+  MPLBACKEND: agg
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ["3.12"]
+
+    steps:
+      - uses: actions/checkout@v4
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v5
+        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 dirhtml
+      - name: Upload artifacts
+        uses: actions/upload-artifact@v4
+        with:
+          name: docs
+          path: docs/_build/dirhtml
+      - name: Deploy docs
+        if: github.event_name == 'push'
+        uses: peaceiris/actions-gh-pages@v4
+        with:
+          personal_token: ${{ secrets.PHASORPY_DOC_DEPLOY_KEY }}
+          external_repository: phasorpy/phasorpy.github.io
+          publish_dir: docs/_build/dirhtml
+          publish_branch: main
+          destination_dir: docs/${{github.ref_name}}
+          # cname: phasorpy.org

phasorpy-0.2/.github/workflows/run-tests.yml

@@ -0,0 +1,162 @@
+name: Run tests
+
+on:
+  push:
+    branches:
+      - main
+  pull_request:
+    branches:
+      - main
+  workflow_dispatch:
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+env:
+  MPLBACKEND: agg
+
+jobs:
+  test:
+    name: Test library and docs
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        os: ["ubuntu-20.04"]
+        python-version: ["3.10", "3.12"]
+        # 3.11 tested with cibuildwheel
+    steps:
+      - uses: actions/checkout@v4
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v5
+        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
+          python -m pip install -r requirements_min.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 dirhtml
+
+  test_win_mac:
+    name: Test Windows and macOS
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        os: ["windows-2019", "macos-13"]
+        python-version: ["3.10"]
+        # 3.12 tested with cibuildwheel
+    steps:
+      - uses: actions/checkout@v4
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v5
+        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
+          python -m pip install -r requirements_min.txt
+      - name: Test with pytest
+        run: |
+          python -X dev -m pytest
+      - name: Build docs
+        run: |
+          cd docs
+          make dirhtml
+
+  build_wheels:
+    name: Test cibuildwheel
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        os: ["ubuntu-22.04", "windows-2019", "macos-13"]
+    steps:
+      - uses: actions/checkout@v4
+      - uses: pypa/cibuildwheel@v2.21.3
+        env:
+          # CIBW_ENVIRONMENT: "PIP_PRE=1"
+          CIBW_BUILD_VERBOSITY: 3
+          CIBW_BUILD: "cp311-manylinux_x86_64 cp312-win_amd64 cp312-macosx_x86_64"
+          CIBW_SKIP:
+      - uses: actions/upload-artifact@v4
+        with:
+          path: ./wheelhouse/*.whl
+          name: wheels-${{ matrix.os }}
+
+  # Building and testing manylinux2014_aarch64 too is slow.
+  # See https://github.com/phasorpy/phasorpy/pull/135
+  #
+  #  build_wheels_arm64:
+  #    name: Test Linux on AArch64
+  #    runs-on: ${{ matrix.os }}
+  #    strategy:
+  #      fail-fast: false
+  #      matrix:
+  #        os: ["ubuntu-latest"]
+  #    steps:
+  #      - uses: actions/checkout@v4
+  #      - name: Set up QEMU
+  #        if: runner.os == 'Linux'
+  #        uses: docker/setup-qemu-action@v3
+  #        with:
+  #          platforms: all
+  #      - uses: pypa/cibuildwheel@v2.21.3
+  #        env:
+  #          CIBW_ARCHS_LINUX: aarch64
+  #          CIBW_BUILD_VERBOSITY: 2
+  #          CIBW_BUILD: "cp311*"
+  #          CIBW_SKIP: "*musllinux*"
+  #      - uses: actions/upload-artifact@v4
+  #        with:
+  #          path: ./wheelhouse/*.whl
+  #          name: wheels-aarch64
+
+  static_analysis:
+    name: Static code analysis
+    runs-on: "ubuntu-latest"
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ["3.12"]
+    steps:
+      - uses: actions/checkout@v4
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v5
+        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
+          python -m pip install -r requirements_min.txt
+      - name: Test with black
+        run: |
+          python -m black --check src/phasorpy tutorials docs
+      - name: Test with blackdoc
+        run: |
+          python -m blackdoc --check src/phasorpy
+      - 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

phasorpy-0.2/.gitignore

@@ -0,0 +1,203 @@
+_/*
+data/*
+testdata/*
+test_data/*
+tests/data/*
+tutorials/data/*
+*.tif
+*.tiff
+*.lsm
+*.ome.tif
+*.sdt
+*.b64
+*.r64
+*.ref
+*.npy
+*.flif
+*.lif
+*.czi
+*.ptu
+*.lnk
+.DS_Store
+
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+*.pdb
+
+# generated by Cython
+_*.c
+
+# Distribution / packaging
+setup.cfg
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+*.whl
+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/
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py,cover
+.hypothesis/
+.pytest_cache/
+.ruff_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
+_build/
+docs/build/
+docs/_build/
+docs/examples/
+docs/tutorials/
+docs/sg_execution_times.rst
+
+# 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
+
+# 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
+
+# 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
+
+# pdm
+#   Similar to Pipfile.lock, it is generally recommended to include pdm.lock in version control.
+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
+.pdm.toml
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow and github.com/pdm-project/pdm
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+phasorpy_dev
+phasorpy-dev
+
+# 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/
+
+.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/
+
+.benchmarks