Python version and CI update

.github/workflows/publish-on-pypi.yml

@@ -22,11 +22,11 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
     - name: Set up Python
       uses: actions/setup-python@v4
       with:
-        python-version: '3.8'
+        python-version: '3.12'
     # This second step is unnecessary but highly recommended because
     # It will cache database and saves time re-downloading it if database isn't stale.
     - name: Cache pip
@@ -39,13 +39,13 @@ jobs:
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip
-        pip install scikit-build
-        pip install -e .
-        pip install build
+        pip install uv
+        uv pip install scikit-build build --system
+        uv pip install -e . --system
     - name: Build package
       run: python -m build
     - name: Publish package
-      uses: pypa/gh-action-pypi-publish@27b31702a0e7fc50959f5ad993c78deac1bdfc29
+      uses: pypa/gh-action-pypi-publish@master
       with:
         user: __token__
         password: ${{ secrets.PYPI_API_TOKEN }}

.github/workflows/test.yml

@@ -0,0 +1,58 @@
+# This workflow will install Python dependencies, run tests and lint with a variety of Python versions
+# For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions
+
+name: Build & Tests
+
+on:
+  push:
+    branches: [ main ]
+  pull_request:
+    branches: [ main ]
+
+jobs:
+  build:
+
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        os: [ubuntu-latest, macos-latest, windows-latest]
+        python-version: ["3.9", "3.10", "3.11", "3.12"]
+
+    steps:
+    - uses: actions/checkout@v4
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v4
+      with:
+        python-version: ${{ matrix.python-version }}
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install uv
+        uv pip install scikit-build build --system
+        uv pip install -e . --system
+    - name: Run through staple
+      run: |
+        python fusion_run -inputs ./data/unet.nii.gz,./data/resunet.nii.gz -output ./data/test_staple.nii.gz -classes 0,1,2,4 -method staple 
+        python -c "from LabelFusion.itkUtils import *; sys.exit('fail') if(not (imageComparision('./data/baseline_staple.nii.gz', './data/test_staple.nii.gz'))) else print('pass')"
+    - name: Run through itkvoting
+      run: |
+        python fusion_run -inputs ./data/unet.nii.gz,./data/resunet.nii.gz -output ./data/test_itkvoting.nii.gz -classes 0,1,2,4 -method itkvoting 
+        python -c "from LabelFusion.itkUtils import *; sys.exit('fail') if(not (imageComparision('./data/baseline_itkvoting.nii.gz', './data/test_itkvoting.nii.gz'))) else print('pass')"
+    - name: Run through majorityvoting
+      run: |
+        python fusion_run -inputs ./data/unet.nii.gz,./data/resunet.nii.gz -output ./data/test_majorityvoting.nii.gz -classes 0,1,2,4 -method majorityvoting 
+        python -c "from LabelFusion.itkUtils import *; sys.exit('fail') if(not (imageComparision('./data/baseline_majorityvoting.nii.gz', './data/test_majorityvoting.nii.gz'))) else print('pass')"
+    - name: Run through simple
+      run: |
+        python fusion_run -inputs ./data/unet.nii.gz,./data/resunet.nii.gz -output ./data/test_simple.nii.gz -classes 0,1,2,4 -method simple 
+        python -c "from LabelFusion.itkUtils import *; sys.exit('fail') if(not (imageComparision('./data/baseline_simple.nii.gz', './data/test_simple.nii.gz'))) else print('pass')"
+
+    - name: Build distributions
+      run: python setup.py sdist
+
+    - name: Publish package to PyPI
+      if: github.repository == 'CBICA/FigureGenerator' && github.event_name == 'push' && startsWith(github.ref, 'refs/tags')
+      uses: pypa/gh-action-pypi-publish@master
+      with:
+        user: __token__
+        password: ${{ secrets.pypi_password }}

fusion_run

@@ -13,7 +13,7 @@ from LabelFusion.utils import *
 from LabelFusion.wrapper import *
 
 def main():
-  copyrightMessage = 'Contact: software@cbica.upenn.edu\n\n' + 'This program is NOT FDA/CE approved and NOT intended for clinical use.\nCopyright (c) ' + str(date.today().year) + ' University of Pennsylvania. All rights reserved.' 
+  copyrightMessage = 'Contact: admin@fets.ai\n\n' + 'This program is NOT FDA/CE approved and NOT intended for clinical use.\nCopyright (c) ' + str(date.today().year) + ' University of Pennsylvania. All rights reserved.' 
   parser = argparse.ArgumentParser(prog='LabelFusion', formatter_class=argparse.RawTextHelpFormatter, description = "Fusion of different labels together.\n\n" + copyrightMessage)
   parser.add_argument('-inputs', type=str, help = 'The absolute, comma-separated paths of labels that need to be fused', required=True)
   parser.add_argument('-classes', type=str, help = 'The expected labels; for example, for BraTS, this should be \'0,1,2,4\'; this is not needed for STAPLE|ITKVoting', default='0,1')

setup.py

@@ -8,22 +8,24 @@
     readme = readme_file.read()
 
 requirements = [
-    "numpy",
+    "numpy>=1.19.2",
     "SimpleITK!=2.0.*",
     "SimpleITK!=2.2.1",  # https://github.com/mlcommons/GaNDLF/issues/536
     "setuptools",
     "wheel",
     "twine",
     "keyring",
     "black",
+    "psutil",
+    "requests",
 ]
 
 setup(
     name="LabelFusion",
-    version="1.0.14",  # dev: development release; this should be changed when tagging
+    version="1.0.15",  # dev: development release; this should be changed when tagging
     author="Megh Bhalerao, Sarthak Pati",
     author_email="admin@fets.ai",
-    python_requires=">=3.8",
+    python_requires=">=3.9",
     packages=find_packages(),
     scripts=["fusion_run"],
     classifiers=[
@@ -32,9 +34,10 @@
         "License :: OSI Approved :: Apache Software License",
         "Natural Language :: English",
         "Operating System :: OS Independent",
-        "Programming Language :: Python :: 3.8",
         "Programming Language :: Python :: 3.9",
         "Programming Language :: Python :: 3.10",
+        "Programming Language :: Python :: 3.11",
+        "Programming Language :: Python :: 3.12",
     ],
     description=("Label fusion strategies for multi-class labels."),
     url="https://github.com/FETS-AI/LabelFusion",