Release 0.5.0

.github/workflows/README.md

@@ -0,0 +1,16 @@
+# MedPy's CI/CD workflows
+
+## Build & release
+Upon creating a release or a pre-release on GitHub, the package is *build* and *published* to [test.pypi.org](https://test.pypi.org).
+
+Install from test PyPi with `python -m pip install --index-url https://test.pypi.org/simple/ --extra-index-url https://pypi.org/simple medpy==x.y.z.`. This ensures that the dependencies are installed from the proper PyPI.
+
+After making sure that the package published there is installable and passes all tests, the final *publish* to [pypi.org](https://pypi.org) can be triggered manually from the GitHub UI.
+
+Note that publishing only works for releases created directly from the `master` branch. Releasees published from other branches should always be pre-releases and never published to [pypi.org](https://pypi.org), but only [test.pypi.org](https://test.pypi.org).
+
+## pre-commit.yml
+Makes sure that all PRs and all releases adhere to the pre-commit rules.
+
+## run-test*.yml
+Makes sure that all PRs and all releases pass the tests.

.github/workflows/build-publish-test.yml

@@ -0,0 +1,54 @@
+# Build package & publish a release to PyPI (test)
+# Given a tag, downloads the associated code, builds the package, and uploads the source tarball as artifact
+# This version releases to https://test.pypi.org/ for testing purposes
+# Triggers on: all published releases (incl pre-releases)
+
+name: Build package & release to PyPI (test)
+
+on:
+  release:
+    types: [published]
+
+permissions:
+  contents: read
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: 3.x
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install build
+      - name: Build a source tarball
+        run: python -m build --sdist
+      - name: Store the distribution packages
+        uses: actions/[email protected]
+        with:
+          name: python-package-distributions-${{ github.ref_name }}
+          path: dist/
+
+  publish-test:
+    needs:
+      - build
+    runs-on: ubuntu-latest
+    environment:
+      name: pypi-publish-test
+      url: https://test.pypi.org/p/medpy
+    permissions:
+      id-token: write # IMPORTANT: mandatory for trusted publishing
+    steps:
+      - name: Download dists
+        uses: actions/[email protected] # make sure that same major version as actions/upload-artifact
+        with:
+          name: python-package-distributions-${{ github.ref_name }}
+          path: dist/
+      - name: Publish package
+        uses: pypa/[email protected]
+        with:
+          repository-url: https://test.pypi.org/legacy/ # test publish platform

.github/workflows/pre-commit.yml

@@ -0,0 +1,30 @@
+# Runs the pre-commit hooks to make sure that all changes are properly formatted and such
+# Triggers on: All PRs that are mergable, but not for draft PRs
+# Triggers on: all published releases (incl draft releases)
+
+name: Pre-commit hooks
+
+on:
+  pull_request:
+    types: [opened, synchronize, reopened, ready_for_review]
+  release:
+    types: [published]
+
+permissions:
+  contents: read
+
+jobs:
+  pre-commit:
+    if: github.event.pull_request.draft == false
+
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@v4
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: 3.x
+      - uses: pre-commit/[email protected]
+      - uses: pre-commit-ci/[email protected]
+        if: always()

.github/workflows/publish.yml

@@ -0,0 +1,56 @@
+# Publish a release to PyPI
+# Requires build package workflow to run first
+# This version releases to https://pypi.org/, only trigger if the release has been thorough tested
+
+name: Build package & release to PyPI
+
+on:
+  workflow_dispatch:
+    inputs:
+      tag:
+        description: "Select release to publish"
+        required: true
+
+permissions:
+  contents: read
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          ref: ${{ inputs.tag }}
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: 3.x
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install build
+      - name: Build a source tarball
+        run: python -m build --sdist
+      - name: Store the distribution packages
+        uses: actions/[email protected]
+        with:
+          name: python-package-distributions-${{ inputs.tag }}
+          path: dist/
+
+  publish:
+    needs:
+      - build
+    runs-on: ubuntu-latest
+    environment:
+      name: pypi-publish
+      url: https://pypi.org/p/medpy
+    permissions:
+      id-token: write # IMPORTANT: mandatory for trusted publishing
+    steps:
+      - name: Download dists
+        uses: actions/[email protected] # make sure that same major version as actions/upload-artifact
+        with:
+          name: python-package-distributions-${{ inputs.tag }}
+          path: dist/
+      - name: Publish package
+        uses: pypa/[email protected]

.github/workflows/run-tests-gc.yml

@@ -0,0 +1,55 @@
+# Install the package and run the graph-cut tests
+# This test is kept separate, as the graphcut functionality is optional and unstable
+# Triggers on: All PRs that are mergable, but not for draft PRs
+# Triggers on: all published releases (incl pre-releases)
+
+# Note: the dependency libboost_python will always be installed against the OS's main python version,
+# independent of the python version set-up. They are 22.04 = 3.10 and 20.04 = 3.8.
+
+name: Run tests (graphcut only)
+
+on:
+  pull_request:
+    types: [opened, synchronize, reopened, ready_for_review]
+  release:
+    types: [published]
+
+permissions:
+  contents: read
+
+jobs:
+  run-tests-gc-ubuntu-22_04:
+    if: github.event.pull_request.draft == false
+    runs-on: ubuntu-22.04
+    steps:
+      - uses: actions/checkout@v4
+      - name: Set up Python 3.10
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.10"
+      - name: Install system dependencies for graphcut functionality
+        run: sudo apt-get install -y libboost-python-dev build-essential
+      - name: Install with test dependencies
+        run: |
+          python -m pip install --upgrade pip
+          python -m pip install -v .[test]
+      - name: Test with pytest (graphcut test only)
+        run: cd tests && pytest graphcut_/*
+
+  run-tests-gc-test-ubuntu-20_04:
+    if: github.event.pull_request.draft == false
+    runs-on: ubuntu-20.04
+    steps:
+      - uses: actions/checkout@v4
+      - name: Set up Python 3.8
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.8"
+      - name: Install system dependencies for graphcut functionality
+        run: sudo apt-get install -y libboost-python-dev build-essential
+      - name: Install with test dependencies
+        run: |
+          python -m pip install --upgrade pip
+          python -m pip install -v .[test]
+      - name: Test with pytest (graphcut test only)
+        run: cd tests && pytest graphcut_/*

.github/workflows/run-tests.yml

@@ -0,0 +1,43 @@
+# Install the package and run all tests except the graph-cut ones
+# Triggers on: All PRs that are mergable, but not for draft PRs
+# Triggers on: all published releases (incl pre-releases)
+
+name: Run tests (wo graphcut)
+
+on:
+  pull_request:
+    types: [opened, synchronize, reopened, ready_for_review]
+  release:
+    types: [published]
+
+permissions:
+  contents: read
+
+jobs:
+  run-tests:
+    if: github.event.pull_request.draft == false
+
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ["3.8", "3.9", "3.10", "3.11"]
+        os: [ubuntu-latest, macos-latest]
+
+    runs-on: ${{ matrix.os }}
+
+    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 with test dependencies
+        run: |
+          python -m pip install --upgrade pip
+          python -m pip install .[test]
+      - name: Test with pytest
+        run: |
+          pytest tests/features_/*
+          pytest tests/filter_/*
+          pytest tests/io_/*
+          pytest tests/metric_/*

.gitignore

@@ -1,38 +1,35 @@
 TODO.txt
 
-# Images #
-##########
+
+# Images
 *.nii
 *.mhd
 *.raw
 
-# DOC dirs #
-############
+# Local virtual envs
+.venv/
+
+# DOC dirs
 doc/build/
 doc/generated/
 doc/source/generated/
 
-# Notebooks dirs #
-##################
+# Notebooks dirs
 .ipynb_checkpoints
 
-# BUILD dirs #
-##############
+# BUILD dirs
 build/
 dist/
 MedPy.egg-info/
 
-# Only locally used, temporary .py scripts. #
-#############################################
+# Only locally used, temporary .py scripts.
 _*.py
 !__init__.py
 
-# Backup files #
-################
+# Backup files
 *.bak
 
-# Compiled source #
-###################
+# Compiled source
 *.com
 *.class
 *.dll
@@ -42,8 +39,7 @@ _*.py
 *.pyc
 *.pyo
 
-# Packages #
-############
+# Packages
 # it's better to unpack these files and commit the raw source
 # git has its own built in compression methods
 *.7z
@@ -55,29 +51,25 @@ _*.py
 *.tar
 *.zip
 
-# Logs and databases #
-######################
+# Logs and databases
 *.log
 *.sql
 *.sqlite
 
-# OS generated files #
-######################
+# OS generated files
 .DS_Store*
 ehthumbs.db
 Icon?
 Thumbs.db
 *~
 
-# Eclipse and PyDev project files #
-###################################
+# Eclipse and PyDev project files
 .project
 .pydevproject
 .settings/
 .metadata/
 
-# Suggestions by GitHub for Python projects #
-#############################################
+# Suggestions by GitHub for Python projects
 # Packages
 *.egg
 *.egg-info
@@ -96,6 +88,7 @@ pip-log.txt
 # Unit test / coverage reports
 .coverage
 .tox
+.hypothesis
 
 #Translations
 *.mo