switched

Author: bendhouseart

.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 +12,21 @@ 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: |
+          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

@@ -4,6 +4,7 @@
 
 # ignore virtualenv
 venv/
+.venv/
 
 # ignore pycache
 __pycache__/

.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

@@ -161,12 +161,27 @@ 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
 

pyproject.toml

@@ -1,69 +1,69 @@
-[tool.poetry]
+[project]
 name = "petdeface"
 version = "0.3.0"
 description = "A nipype PET and MR defacing pipeline for BIDS datasets utilizing FreeSurfer's MiDeFace."
-authors = ["Martin Nørgaard <[email protected]>", "Anthony Galassi <[email protected]>", "Murat Bilgel <[email protected]>"]
-license = "MIT"
+authors = [
+    {name = "Martin Nørgaard", email = "[email protected]"},
+    {name = "Anthony Galassi", email = "[email protected]"},
+    {name = "Murat Bilgel", email = "[email protected]"}
+]
+license = {text = "MIT"}
 readme = "README.md"
-include = [
-    "petdeface/*",
-    "pyproject.toml",
-    "data/sub-01/ses-baseline/anat/sub-01_ses-baseline_T1w.nii.gz",
-    "data/sub-01/ses-baseline/anat/sub-01_ses-baseline_T1w.json",
-    "data/sub-mni305/anat/sub-mni305_T1w.nii.gz",
-    "data/sub-mni305/anat/sub-mni305_T1w.json",
+requires-python = ">=3.10"
+dependencies = [
+    "setuptools>=68.1.2",
+    "petutils>=0.0.1",
+    "niworkflows>=1.11.0",
+    "matplotlib>=3.10.1",
+    "niftifixer @ git+https://github.com/openneuropet/nifti_fixer.git",
+    "bids-validator-deno>=2.0.5",
+    "nipreps>=1.0",
+    "nireports>=25.2.0",
+    "nibabel>=5.3.2",
+    "nilearn>=0.10.4",
+    "numpy>=2.1.3",
+    "scipy>=1.14.1",
+    "seaborn>=0.13.2",
+    "pillow>=11.0.0",
+    "imageio>=2.36.0",
+]
+
+[project.optional-dependencies]
+dev = [
+    "black>=23.7.0",
+    "flake8>=6.1.0",
+    "isort>=5.12.0",
+    "pre-commit>=3.3.3",
+    "pytest>=7.4.2",
+    "sphinx>=7.2.6",
+    "sphinx-rtd-theme>=3.0.1",
+    "jupyterlab>=4.4.1",
+    "notebook>=7.4.1",
+    "nbconvert>=7.16.6",
+    "ipywidgets>=8.1.6",
+    "matplotlib>=3.10.1",
+    "pandas>=2.2.3",
+    "pyqt6>=6.9.0",
 ]
 
+[project.scripts]
+petdeface = "petdeface.petdeface:main"
+
 # please update the bids version to the latest compliant version when making modifications to this code here
 [tool.bids]
 bids_version = "1.8.0"
 
-[tool.poetry.dependencies]
-python = ">=3.10, <4.0"
-setuptools = "^68.1.2"
-petutils = "^0.0.1"
-niworkflows = "^1.11.0"
-matplotlib = "^3.10.1"
-niftifixer = {git = "https://github.com/openneuropet/nifti_fixer.git"}
-bids-validator-deno = "^2.0.5"
-nipreps = "^1.0"
-nireports = "^25.2.0"
-nibabel = "^5.3.2"
-nilearn = "^0.10.4"
-numpy = "^2.1.3"
-scipy = "^1.14.1"
-seaborn = "^0.13.2"
-pillow = "^11.0.0"
-imageio = "^2.36.0"
-
-
-[tool.poetry.group.dev.dependencies]
-black = "^23.7.0"
-flake8 = "^6.1.0"
-isort = "^5.12.0"
-pre-commit = "^3.3.3"
-pytest = "^7.4.2"
-sphinx = "^7.2.6"
-sphinx-rtd-theme = "^3.0.1"
-jupyterlab = "^4.4.1"
-notebook = "^7.4.1"
-nbconvert = "^7.16.6"
-ipywidgets = "^8.1.6"
-matplotlib = "^3.10.1"
-pandas = "^2.2.3"
-pyqt6 = "^6.9.0"
-
 [tool.isort]
 profile = "black"
 force_single_line = true
 lines_after_imports = 2
 
 [build-system]
-requires = ["poetry-core", "setuptools>=61.0"]
-build-backend = "poetry.core.masonry.api"
+requires = ["hatchling"]
+build-backend = "hatchling.build"
+
+[tool.hatch.metadata]
+allow-direct-references = true
 
 [tool.setuptools]
 package-data = { "petdeface" = [ "data/sub-01/ses-baseline/anat/*.nii", "data/sub-01/ses-baseline/anat/*.json", "data/sub-mni305/anat/sub-mni305_T1w.nii.gz", "data/sub-mni305/anat/sub-mni305_T1w.json"]}
-
-[tool.poetry.scripts]
-petdeface = 'petdeface.petdeface:main'