switched to uv b/c poetry is getting worse by the day

.github/workflows/check_python_compatibility.yaml

@@ -0,0 +1,65 @@
+name: Check Python Compatibility
+
+on:
+  pull_request:
+    branches: [ main ]
+  push:
+    branches: [ main ]
+
+jobs:
+  test-python-compatibility:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ["3.10", "3.11", "3.12", "3.13"]
+        toolchain: [uv, pip]
+
+    steps:
+    - name: Checkout code
+      uses: actions/checkout@v4
+
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v4
+      with:
+        python-version: ${{ matrix.python-version }}
+
+    - name: Install UV
+      if: matrix.toolchain == 'uv'
+      uses: astral-sh/setup-uv@v2
+      with:
+        version: "latest"
+
+    - name: Build package with ${{ matrix.toolchain }}
+      if: matrix.toolchain == 'uv'
+      run: |
+        uv build
+        ls -lh dist/
+
+    - name: Build package with ${{ matrix.toolchain }}
+      if: matrix.toolchain == 'pip'
+      run: |
+        python -m pip install --upgrade pip build
+        python -m build
+        ls -lh dist/
+
+    - name: Install package with ${{ matrix.toolchain }}
+      if: matrix.toolchain == 'uv'
+      run: |
+        uv pip install --system dist/*.whl
+        uv run python -c "import petdeface; print('Package installed successfully')"
+
+    - name: Test CLI
+      if: matrix.toolchain == 'uv'
+      run: |
+        uv run petdeface --help
+
+    - name: Install package with ${{ matrix.toolchain }}
+      if: matrix.toolchain == 'pip'
+      run: |
+        python -m pip install dist/*.whl
+        python -c "import petdeface; print('Package installed successfully')"
+
+    - name: Test CLI
+      if: matrix.toolchain == 'pip'
+      run: |
+        petdeface --help 

.github/workflows/petdeface.yaml

@@ -13,14 +13,28 @@ jobs:
   test_petdeface:
     runs-on: ubuntu-latest
     name: Test petdeface
+    strategy:
+      matrix:
+        toolchain: [uv, pip]
     steps:
       - uses: actions/checkout@v3
-      - name: Install Poetry
-        run: pipx install poetry
       - uses: actions/setup-python@v4
         with:
           python-version: 3.11
-          cache: poetry
-      - run: poetry install
-      - name: Run All Tests
-        run: poetry run make testall
+      - name: Install dependencies (UV)
+        if: matrix.toolchain == 'uv'
+        run: |
+          curl -LsSf https://astral.sh/uv/install.sh | sh
+          echo "$HOME/.cargo/bin" >> $GITHUB_PATH
+          uv sync --dev
+      - name: Install dependencies (pip)
+        if: matrix.toolchain == 'pip'
+        run: |
+          python -m pip install --upgrade pip
+          pip install .[dev]
+      - name: Run All Tests (UV)
+        if: matrix.toolchain == 'uv'
+        run: uv run make testall
+      - name: Run All Tests (pip)
+        if: matrix.toolchain == 'pip'
+        run: make testall

.github/workflows/publish_to_pypi.yaml

@@ -12,25 +12,23 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v3
-
-      - name: Install dependencies
-        run: |
-          pipx install poetry
-          poetry install
-
-      - name: Set up Python
-        uses: actions/setup-python@v4
+      - uses: actions/setup-python@v4
         with:
           python-version: 3.11
-          cache: 'poetry'
+      - name: Build Package
+        run: |
+          curl -LsSf https://astral.sh/uv/install.sh | sh
+          echo "$HOME/.cargo/bin" >> $GITHUB_PATH
+          uv sync --dev
+          uv build
 
-      - name: Build
+      - name: Check PyPI token
         run: |
-          poetry build
+          if [ -z "$PYPI_TOKEN_PETDEFACE" ]; then
+            echo "Error: PYPI_TOKEN_PETDEFACE is not set or is empty check your secrets"
+            exit 1
+          fi
 
-      - name: Publish
-        if: ${{ !contains(github.ref_name, 'test') }}
+      - name: Publish Package
         run: |
-          echo "Publishing to PyPI..."
-          poetry config pypi-token.pypi $PYPI_TOKEN
-          poetry publish
+          uv publish --token $PYPI_TOKEN_PETDEFACE

.gitignore

@@ -4,13 +4,17 @@
 
 # ignore virtualenv
 venv/
+.venv/
 
 # ignore pycache
 __pycache__/
 
 # ignore dist
 dist/
 
+# ignore egg-info
+petdeface.egg-info/
+
 # nipype generates pickle files, we need to redirect where it stores them,
 # but until then hack fix
 *.pkl

.readthedocs.yaml

@@ -2,33 +2,27 @@
 # Read the Docs configuration file
 # See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
 
-# Required
 version: 2
 
-# Set the OS, Python version and other tools you might need
+# Build environment
 build:
   os: ubuntu-22.04
   tools:
     python: "3.12"
-  jobs:
-    post_create_environment:
-      - pip install poetry
-      - poetry config virtualenvs.create false
-    post_install:
-      - VIRTUAL_ENV=$READTHEDOCS_VIRTUALENV_PATH poetry install --with=dev
+
+# Python environment setup
+python:
+  install:
+    - method: pip
+      path: .
+      extra_requirements:
+        - dev
 
 # Build documentation in the "docs/" directory with Sphinx
 sphinx:
-   configuration: docs/conf.py
+  configuration: docs/conf.py
 
 # Optionally build your docs in additional formats such as PDF and ePub
 # formats:
 #    - pdf
 #    - epub
-
-# Optional but recommended, declare the Python requirements required
-# to build your documentation
-# See https://docs.readthedocs.io/en/stable/guides/reproducible-builds.html
-# python:
-#    install:
-#    - requirements: docs/requirements.txt

README.md

@@ -14,6 +14,9 @@ This software can be installed via source or via pip from PyPi with `pip install
 |---------| ------ |
 | `docker build . -t petdeface` | ![docker_build](https://codebuild.us-east-1.amazonaws.com/badges?uuid=eyJlbmNyeXB0ZWREYXRhIjoiYzdXV0tYSkQzTVNkcG04cHA2S055UXlKRlZTU1VONThUMVRoZVcwU3l1aHFhdVBlNDNaRGVCYzdWM1Q0WjYzQ1lRU2ZTSHpmSERPWFRkVXVyb3k3RTZBPSIsIml2UGFyYW1ldGVyU3BlYyI6IjRCZFFIQnNGT2lKcDA1VG4iLCJtYXRlcmlhbFNldFNlcmlhbCI6MX0%3D&branch=main) |
 | `docker push` | ![docker push icon](https://codebuild.us-east-1.amazonaws.com/badges?uuid=eyJlbmNyeXB0ZWREYXRhIjoia0c1bEJYUGI2SXlWYi9JMm1tcGtiYWVTdVd3bmlnOUFaTjN4QjJITU5PTVpvQnN3TlowajhxNmhHY2RwQ2Z5SU93OExqc2xvMzFnTHFvajlqVk1MV2FzPSIsIml2UGFyYW1ldGVyU3BlYyI6Ikl6SzRyc1RabzBnSkplTjciLCJtYXRlcmlhbFNldFNlcmlhbCI6MX0%3D&branch=main) |
+| `Python 3.14 >= 3.10` | [![Check Python Compatibility](https://github.com/openneuropet/petdeface/actions/workflows/check_python_compatibility.yaml/badge.svg)](https://github.com/openneuropet/petdeface/actions/workflows/check_python_compatibility.yaml) |
+| `packaging` | [![Publish to PyPI](https://github.com/openneuropet/petdeface/actions/workflows/publish_to_pypi.yaml/badge.svg)](https://github.com/openneuropet/petdeface/actions/workflows/publish_to_pypi.yaml) |
+| `Docs` | ![RTD BADGE](https://app.readthedocs.org/projects/petdeface/badge/?version=latest&style=default) |
 
 ## Requirements
 
@@ -161,12 +164,27 @@ trouble running this container in singularity/apptainer.
 
 ## Development
 
-This project uses poetry to package and build, to create a pip installable version of the package run:
+This project supports both [UV](https://github.com/astral-sh/uv) and standard Python (pip + build) workflows for development and packaging.
+
+### Using UV (recommended for speed)
+
+```bash
+git clone https://github.com/openneuropet/petdeface.git
+cd petdeface
+uv build
+pip install dist/petdeface-<X.X.X>-py3-none-any.whl # where X.X.X is the version number of the generated file
+```
+
+### Using pip and python (no UV required)
 
 ```bash
 git clone https://github.com/openneuropet/petdeface.git
 cd petdeface
-poetry build
+pip install --upgrade pip
+pip install .[dev]
+# To build a wheel or sdist:
+pip install build
+python -m build
 pip install dist/petdeface-<X.X.X>-py3-none-any.whl # where X.X.X is the version number of the generated file
 ```
 

docs/installation.rst

@@ -9,11 +9,22 @@ PETdeface can be installed via PyPi_::
 
     pip install petdeface
 
-Or cloned and installed from source::
+Or cloned and installed from source (using UV)::
 
     git clone https://github.com/openneuropet/petdeface.git
     cd petdeface
-    poetry build
+    uv build
+    pip install dist/petdeface-<X.X.X>-py3-none-any.whl 
+    # where X.X.X is the version number of the generated file
+
+Or cloned and installed from source (using pip and python)::
+
+    git clone https://github.com/openneuropet/petdeface.git
+    cd petdeface
+    pip install --upgrade pip
+    pip install .[dev]
+    pip install build
+    python -m build
     pip install dist/petdeface-<X.X.X>-py3-none-any.whl 
     # where X.X.X is the version number of the generated file
 

data/participants.tsv → petdeface/data/participants.tsv

@@ -1,4 +1,4 @@
-participant_id	height	weight	age	gender
-sub-01	178	58	28	male
-sub-mni305	200	65	10	n/a
-sub-02	178	58	28	male
+participant_id	height	weight	age	gender
+sub-01	178	58	28	male
+sub-mni305	200	65	10	n/a
+sub-02	178	58	28	male

petdeface/noanat.py

@@ -29,19 +29,25 @@ def get_data_path(filename: str) -> Path:
     FileNotFoundError
         If the requested file is not found in the package data
     """
-    # Get the path to the data directory
-    data_dir = Path(__file__).parent.parent / "data"
+    # First try the top-level data directory (for development)
+    project_root = Path(__file__).parent.parent.parent
+    top_level_data_dir = project_root / "data"
+    file_path = top_level_data_dir / filename
 
-    # Construct the full path
-    full_path = data_dir / filename
+    if file_path.exists():
+        return file_path
+    # Fallback: try to find the file in the installed package data
+    module_dir = Path(__file__).parent
+    package_data_dir = module_dir / "data"
+    file_path = package_data_dir / filename
 
-    # Check if the file exists
-    if not full_path.exists():
-        raise FileNotFoundError(
-            f"Could not find data file {filename} in data directory"
-        )
+    if file_path.exists():
+        return file_path
 
-    return full_path
+    # If neither location works, raise an error
+    raise FileNotFoundError(
+        f"Could not find data file {filename} in package data at {package_data_dir / filename} or {top_level_data_dir / filename}"
+    )
 
 
 def get_default_anat(anat) -> Path:
@@ -302,7 +308,7 @@ def remove_default_anat(
         anat_dir = subject_dir / "anat"
 
         # Define the file paths
-        target_nii = anat_dir / f"sub-{extracted_id}_T1w.nii"
+        target_nii = anat_dir / f"sub-{extracted_id}_T1w.nii.gz"
         target_json = anat_dir / f"sub-{extracted_id}_T1w.json"
 
         # Check if the files exist