use setuptools instead of pdm for package build (#26)

* remove pdm and tox and adapt pyproject.toml

* clean up build process

* work on package build

* renew build workflow

* add package install

* run tests only on python 3.9 and 3.11

* test with two tf versions

* add new publish to pypi workflow

---------

Co-authored-by: Georg Schramm <georg@Georgs-MacBook-Pro-9.local>

.github/workflows/build_python.yaml

@@ -1,43 +1,62 @@
-# Workflow to build the parallelproj C/CUDA libs (incl. installation of CUDA)
-name: python build
+name: Build and Test
 
 on:
   push:
-    branches: [ "master" ]
+    branches:
+      - master
   pull_request:
-    branches: [ "master" ]
 
 jobs:
-  Testing:
-    runs-on: ${{ matrix.os }}
+  build-and-test:
+    runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ['3.9','3.10']
-        os: [ubuntu-latest]
-  
+        python-version: [3.9, 3.11]
+        tensorflow-version: [2.13, 2.15]
+
     steps:
-      - uses: actions/checkout@v4
+      # Checkout the repository
+      - name: Checkout code
+        uses: actions/checkout@v3
         with:
-          fetch-depth: 0 # default 1 is, which doesnt allow to get all tags which we need for version from scm
-          fetch-tags: true
-      - name: Set up PDM
-        uses: pdm-project/setup-pdm@v4
+          fetch-depth: 0 # Fetch all history to ensure tags are available
+
+      # Set up Python
+      - name: Set up Python
+        uses: actions/setup-python@v4
         with:
           python-version: ${{ matrix.python-version }}
 
-      - name: Show package version
+      # Install dependencies
+      - name: Install dependencies
         run: |
-          git describe --tags
-          pdm show --version
-      - name: Install dependencies and package
+          python -m pip install --upgrade pip
+          pip install build
+
+      # Build the package
+      - name: Build the package
         run: |
-          pdm update -d -G test
-          pdm list
-      - name: Test CLI
+          python -m build
+
+      # Install tensorflow
+      - name: Install tensorflow
         run: |
-          pdm run pyapetnet_list_models
-          pdm run pyapetnet_predict_from_nifti -h
-          pdm run pyapetnet_predict_from_dicom -h
-      - name: Run Tests
+          pip install tensorflow==${{ matrix.tensorflow-version }}
+
+      # Install the package
+      - name: Install the package
+        run: |
+          pip install dist/*.whl
+
+      # Run tests
+      - name: Run tests
+        run: |
+          pip install pytest
+          pytest -vv tests
+
+      # Test entry points
+      - name: Test entry points
         run: |
-          pdm run tox
+          pyapetnet_list_models
+          pyapetnet_predict_from_nifti -h
+          pyapetnet_predict_from_dicom -h

.github/workflows/publish-to-pypi.yaml

@@ -0,0 +1,41 @@
+name: Publish Python distributions to PyPI
+
+on:
+  push:
+    tags:
+      - "v[0-9]+"
+      - "v[0-9]+.[0-9]+"
+      - "v[0-9]+.[0-9]+.[0-9]+"
+      - "v[0-9]+[a-z][0-9]+"
+      - "v[0-9]+.[0-9]+[a-z][0-9]+"
+      - "v[0-9]+.[0-9]+.[0-9]+[a-z][0-9]+"
+
+jobs:
+  build-n-publish:
+    name: Build and publish Python distributions package to PyPI
+    runs-on: ubuntu-latest
+
+    permissions:
+      id-token: write
+      contents: read
+
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0 # Fetch all history to ensure tags are available
+      - name: Set up Python 3.11
+        uses: actions/setup-python@v4
+        with:
+          python-version: "3.11"
+
+      - name: Install pypa/build
+        run: |
+          python -m pip install build --user
+      - name: Build a binary wheel and a source tarball
+        run: |
+          python -m build --sdist --wheel --outdir dist/ .
+
+      - name: Publish distribution package to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1
+        with:
+          password: ${{ secrets.PYPI_API_TOKEN }}

MANIFEST.in

@@ -0,0 +1,24 @@
+# Include necessary metadata files
+include LICENSE
+include README.md
+include pyproject.toml
+
+# Include only the package files
+graft src/pyapetnet
+
+# Include trained models
+recursive-include src/pyapetnet/trained_models
+
+# Exclude unwanted directories
+prune .git
+prune .github
+prune binder
+prune demo_data
+prune demos
+prune figures
+prune notebooks
+prune scripts
+prune tests
+
+# Exclude unwanted files
+global-exclude *.pyc *.pyo __pycache__