switch to uv and update python supported versions (#355)

switch to uv from poetry; allows more python supported versions

Author: bendhouseart

.github/workflows/phantoms.yaml

@@ -28,7 +28,7 @@ jobs:
     strategy:
       matrix:
         os: [ubuntu-latest]
-        python: ["3.10"]
+        python: ["3.12"]
       fail-fast: false
 
     steps:
@@ -87,16 +87,19 @@ jobs:
           cache-dependency-path: |
             pypet2bids/pyproject.toml
 
+      - name: Install UV
+        run: curl -LsSf https://astral.sh/uv/install.sh | sh && echo "$HOME/.cargo/bin" >> $GITHUB_PATH
+
       - name: Install Python Dependencies
         run: |
           cd pypet2bids
-          pip install .
+          pip install -e .[dev]
 
-      - name: Install Poetry Build Package
+      - name: Install UV Build Package
         run: |
-          make installpoetry
+          make installuv
           make buildpackage
-          make installpackage
+          cd pypet2bids && uv pip install dist/pypet2bids-*.whl --system
           dcm2niix4pet -h
 
       - name: Set Up Node

.github/workflows/python.yaml

@@ -30,7 +30,7 @@ jobs:
     strategy:
       matrix:
         os: [macOS-latest, ubuntu-latest]
-        python: ['3.9', '3.10']
+        python: ['3.8', '3.9', '3.10', '3.11', '3.12', '3.13']
 
     steps:
       - name: Checkout Repo
@@ -47,14 +47,16 @@ jobs:
         uses: actions/setup-python@v4
         with:
           python-version: ${{ matrix.python }}
+          cache: 'pip'
+          cache-dependency-path: 'pypet2bids/pyproject.toml'
+
+      - name: Install UV
+        run: curl -LsSf https://astral.sh/uv/install.sh | sh && echo "$HOME/.cargo/bin" >> $GITHUB_PATH
 
       - name: Install dependencies
-        if: steps.cached-poetry-dependencies.outputs.cache-hit != 'true'
         run: |
           cd pypet2bids
-          python -m pip install --upgrade pip
-          pip install poetry==1.6.1
-          poetry install --with dev
+          pip install -e .[dev] 
 
       - name: Collect ECAT and other phantoms
         if: steps.cache-phantoms.outputs.cache-hit != 'true'
@@ -73,12 +75,12 @@ jobs:
       - name: Test CLI --help
         run: |
           cd pypet2bids/
-          poetry run python3 -m pypet2bids.ecat_cli --help
+          python3 -m pypet2bids.ecat_cli --help
 
       - name: Test CLI Ecat Dump
         run: |
           cd pypet2bids/
-          poetry run python3 -m pypet2bids.ecat_cli ${{ env.REAL_ECAT_TEST_PATH }} --dump
+          python3 -m pypet2bids.ecat_cli ${{ env.REAL_ECAT_TEST_PATH }} --dump
 
       # the larger real data file uses too much ram for the github runner, we use the small file for
       # heavy io operations instead
@@ -87,9 +89,9 @@ jobs:
           gzip -d ${{ env.SMALLER_ECAT_PATH }}
       
       - name: Test ecatread
-        run: "cd pypet2bids/ && poetry run python3 -m tests.test_ecatread"
+        run: "cd pypet2bids/ && python3 -m tests.test_ecatread"
 
       - name: Run All Other Python Tests w/ Pytest
         run: |
           cd pypet2bids
-          poetry run pytest -k 'not write_pixel_data' -k 'not test_convert_pmod_to_blood' tests/
+          python -m pytest -k 'not write_pixel_data' -k 'not test_convert_pmod_to_blood' tests/

Makefile

@@ -20,21 +20,21 @@ help:
 %: Makefile
 	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
 
-# add a dependency, this is an alias for poetry add that also updates the requirements.txt file
+# add a dependency, this is an alias for uv add that also updates the pyproject.toml file
 add:
 	@scripts/add_python_dependency $(ARGUMENTS)
 
-# copies metadata to path included in pypet2bids project to enable packaging of those files w/ poetry
+# builds package using standard Python packaging tools
 buildpackage:
 	@cp pypet2bids/pyproject.toml pypet2bids/pypet2bids/pyproject.toml
 	@rm -rf pypet2bids/dist
-	@cd pypet2bids && poetry lock && poetry build
+	@cd pypet2bids && uv build
 
 publish:
-	@cd pypet2bids && poetry publish
+	@cd pypet2bids && uv publish
 
-installpoetry:
-	@cd scripts && ./installpoetry
+installuv:
+	@cd scripts && ./installuv
 
 # installs latest package
 installpackage:
@@ -43,14 +43,18 @@ installpackage:
 testphantoms:
 	@scripts/testphantoms
 
+# test package across all supported Python versions
+test-all-python-versions:
+	@scripts/test_all_python_versions
+
 html:
 	@cd docs && make html
 
 installdependencies:
 	@cd pypet2bids; \
 	python -m pip install --upgrade pip; \
-	pip install poetry; \
-	poetry install --with dev
+	pip install uv; \
+	uv sync --dev
 
 collectphantoms:
 ifeq (, $(wildcard ./PHANTOMS.zip))
@@ -64,20 +68,20 @@ decompressphantoms:
 
 testecatcli:
 	@cd pypet2bids; \
-	poetry run python -m pypet2bids.ecat_cli --help; \
-	poetry run python -m pypet2bids.ecat_cli ../OpenNeuroPET-Phantoms/sourcedata/SiemensHRRT-JHU/Hoffman.v --dump
+	uv run python -m pypet2bids.ecat_cli --help; \
+	uv run python -m pypet2bids.ecat_cli ../OpenNeuroPET-Phantoms/sourcedata/SiemensHRRT-JHU/Hoffman.v --dump
 
 testecatread:
 	@cd pypet2bids; \
 	export TEST_ECAT_PATH="../OpenNeuroPET-Phantoms/sourcedata/SiemensHRRT-JHU/Hoffman.v"; \
 	export READ_ECAT_SAVE_AS_MATLAB="$$PWD/tests/ECAT7_multiframe.mat"; \
 	export NIBABEL_READ_ECAT_SAVE_AS_MATLAB="$$PWD/tests/ECAT7_multiframe.nibabel.mat"; \
-	poetry run python3 -m tests.test_ecatread
+	uv run python3 -m tests.test_ecatread
 
 testotherpython:
 	cd pypet2bids; \
 	export TEST_DICOM_IMAGE_FOLDER="../OpenNeuroPET-Phantoms/sourcedata/SiemensBiographPETMR-NIMH/AC_TOF"; \
-	poetry run pytest --ignore=tests/test_write_ecat.py tests/ -vvv
+	uv run pytest --ignore=tests/test_write_ecat.py tests/ -vvv
 
 pythongithubworkflow: installdependencies collectphantoms decompressphantoms testecatread testecatcli testotherpython
 	@echo finished running python tests