From f638cf4ee0adce555055474a30ad6cd6aa5cd8e5 Mon Sep 17 00:00:00 2001 From: Anthony Galassi <28850131+bendhouseart@users.noreply.github.com> Date: Thu, 26 Jun 2025 11:11:42 -0400 Subject: [PATCH 1/4] switch to uv and update python supported versions --- .github/workflows/phantoms.yaml | 11 +- .github/workflows/python.yaml | 18 +- Makefile | 28 +- pypet2bids/poetry.lock | 1765 ----------------------- pypet2bids/pypet2bids/__init__.py | 3 + pypet2bids/pyproject.toml | 123 +- pypet2bids/uv.lock | 2218 +++++++++++++++++++++++++++++ scripts/add_python_dependency | 14 +- scripts/installpoetry | 2 - scripts/installuv | 2 + scripts/test_all_python_versions | 203 +++ 11 files changed, 2534 insertions(+), 1853 deletions(-) delete mode 100644 pypet2bids/poetry.lock create mode 100644 pypet2bids/uv.lock delete mode 100755 scripts/installpoetry create mode 100755 scripts/installuv create mode 100755 scripts/test_all_python_versions diff --git a/.github/workflows/phantoms.yaml b/.github/workflows/phantoms.yaml index 69668ed3..d1b8679e 100644 --- a/.github/workflows/phantoms.yaml +++ b/.github/workflows/phantoms.yaml @@ -28,7 +28,7 @@ jobs: strategy: matrix: os: [ubuntu-latest] - python: ["3.10"] + python: ["3.12"] fail-fast: false steps: @@ -87,14 +87,17 @@ jobs: cache-dependency-path: | pypet2bids/pyproject.toml + - name: Install UV + run: curl -LsSf https://astral.sh/uv/install.sh | sh + - name: Install Python Dependencies run: | cd pypet2bids - pip install . + uv sync --dev - - name: Install Poetry Build Package + - name: Install UV Build Package run: | - make installpoetry + make installuv make buildpackage make installpackage dcm2niix4pet -h diff --git a/.github/workflows/python.yaml b/.github/workflows/python.yaml index 52551430..e0fe4d81 100644 --- a/.github/workflows/python.yaml +++ b/.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 @@ -48,13 +48,13 @@ jobs: with: python-version: ${{ matrix.python }} + - name: Install UV + run: curl -LsSf https://astral.sh/uv/install.sh | sh + - 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 + uv sync --dev - name: Collect ECAT and other phantoms if: steps.cache-phantoms.outputs.cache-hit != 'true' @@ -73,12 +73,12 @@ jobs: - name: Test CLI --help run: | cd pypet2bids/ - poetry run python3 -m pypet2bids.ecat_cli --help + uv run 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 + uv run 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 +87,9 @@ jobs: gzip -d ${{ env.SMALLER_ECAT_PATH }} - name: Test ecatread - run: "cd pypet2bids/ && poetry run python3 -m tests.test_ecatread" + run: "cd pypet2bids/ && uv run python3 -m tests.test_ecatread" - name: Run All Other Python Tests w/ Pytest run: | cd pypet2bids - poetry run pytest -k 'not write_pixel_data' -k 'not test_convert_pmod_to_blood' tests/ + uv run pytest -k 'not write_pixel_data' -k 'not test_convert_pmod_to_blood' tests/ diff --git a/Makefile b/Makefile index b3993c7f..15188955 100644 --- a/Makefile +++ b/Makefile @@ -20,21 +20,21 @@ help: %: Makefile @$(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"; \ - 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and blood data to BIDS." -authors = ["anthony galassi <28850131+bendhouseart@users.noreply.github.com>"] -license = "MIT" -include = [ - 'pypet2bids/pyproject.toml', - 'pypet2bids/README.md', - ] -documentation = "https://pypet2bids.readthedocs.io/en/latest/" -repository = "https://github.com/openneuropet/pet2bids/" +authors = [ + {name = "anthony galassi", email = "28850131+bendhouseart@users.noreply.github.com"} +] +license = {text = "MIT"} readme = "README.md" +requires-python = ">=3.8" +classifiers = [ + "Development Status :: 4 - Beta", + "Intended Audience :: Science/Research", + "License :: OSI Approved :: MIT License", + "Programming Language :: Python :: 3", + "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", + "Programming Language :: Python :: 3.13", +] +dependencies = [ + "nibabel>=3.2.1", + "numpy>=1.21.3", + 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pyproject.toml") else: sys.exit(1) diff --git a/scripts/installpoetry b/scripts/installpoetry deleted file mode 100755 index 8aa14baf..00000000 --- a/scripts/installpoetry +++ /dev/null @@ -1,2 +0,0 @@ -#! /usr/bin/env bash -python3 -m pip install poetry==1.6.1 diff --git a/scripts/installuv b/scripts/installuv new file mode 100755 index 00000000..3e9cf57e --- /dev/null +++ b/scripts/installuv @@ -0,0 +1,2 @@ +#! /usr/bin/env bash +curl -LsSf https://astral.sh/uv/install.sh | sh \ No newline at end of file diff --git a/scripts/test_all_python_versions b/scripts/test_all_python_versions new file mode 100755 index 00000000..c3e441b1 --- /dev/null +++ b/scripts/test_all_python_versions @@ -0,0 +1,203 @@ +#!/usr/bin/env bash +# Test pypet2bids installation across multiple Python versions +# This script emulates building and installing pypet2bids for each supported Python version + +set -e # Exit on any error + +# Colors for output +RED='\033[0;31m' +GREEN='\033[0;32m' +YELLOW='\033[1;33m' +BLUE='\033[0;34m' +NC='\033[0m' # No Color + +# Get script directory +SCRIPT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)" +PROJECT_ROOT="$(dirname "$SCRIPT_DIR")" +PYPET2BIDS_DIR="$PROJECT_ROOT/pypet2bids" + +# Python versions to test +PYTHON_VERSIONS=("3.8" "3.9" "3.10" "3.11" "3.12" "3.13") + +# Function to print colored output +print_status() { + echo -e "${BLUE}[INFO]${NC} $1" +} + +print_success() { + echo -e "${GREEN}[SUCCESS]${NC} $1" +} + +print_warning() { + echo -e "${YELLOW}[WARNING]${NC} $1" +} + +print_error() { + echo -e "${RED}[ERROR]${NC} $1" +} + +# Function to check if Python version is available +check_python_version() { + local version=$1 + if command -v "python$version" &> /dev/null; then + local installed_version=$(python$version --version 2>&1 | cut -d' ' -f2) + print_success "Found Python $version ($installed_version)" + return 0 + else + print_warning "Python $version not found, skipping" + return 1 + fi +} + +# Function to test a specific Python version +test_python_version() { + local version=$1 + local python_cmd="python$version" + + print_status "Testing Python $version..." + + # Create a temporary virtual environment + local venv_dir="/tmp/pypet2bids_test_py$version" + rm -rf "$venv_dir" + + print_status "Creating virtual environment with $python_cmd..." + if ! $python_cmd -m venv "$venv_dir"; then + print_error "Failed to create virtual environment for Python $version" + return 1 + fi + + # Activate virtual environment + source "$venv_dir/bin/activate" + + # Upgrade pip and install UV + print_status "Installing UV in Python $version environment..." + if ! pip install --upgrade pip uv; then + print_error "Failed to install UV for Python $version" + deactivate + rm -rf "$venv_dir" + return 1 + fi + + # Change to pypet2bids directory + cd "$PYPET2BIDS_DIR" + + # Try to sync dependencies (without dev dependencies to avoid conflicts) + print_status "Installing dependencies for Python $version..." + if ! uv sync --no-dev --python "$python_cmd"; then + print_error "Failed to sync dependencies for Python $version" + deactivate + rm -rf "$venv_dir" + return 1 + fi + + # Build the package + print_status "Building package for Python $version..." + if ! uv build --python "$python_cmd"; then + print_error "Failed to build package for Python $version" + deactivate + rm -rf "$venv_dir" + return 1 + fi + + # Test importing the package + print_status "Testing package import for Python $version..." + if ! uv run --python "$python_cmd" python -c "import pypet2bids; print('Successfully imported pypet2bids')"; then + print_error "Failed to import pypet2bids for Python $version" + deactivate + rm -rf "$venv_dir" + return 1 + fi + + # Try to get version (optional, don't fail if it doesn't work) + print_status "Attempting to get version for Python $version..." + uv run --python "$python_cmd" python -c "import pypet2bids; print('Version:', getattr(pypet2bids, '__version__', 'unknown'))" || true + + # Test CLI commands + print_status "Testing CLI commands for Python $version..." + if ! uv run --python "$python_cmd" ecatpet2bids --help > /dev/null; then + print_error "Failed to run ecatpet2bids CLI for Python $version" + deactivate + rm -rf "$venv_dir" + return 1 + fi + + if ! uv run --python "$python_cmd" dcm2niix4pet --help > /dev/null; then + print_error "Failed to run dcm2niix4pet CLI for Python $version" + deactivate + rm -rf "$venv_dir" + return 1 + fi + + # Clean up + deactivate + rm -rf "$venv_dir" + + print_success "Python $version: All tests passed!" + return 0 +} + +# Main execution +main() { + print_status "Starting pypet2bids multi-version test suite" + print_status "Project root: $PROJECT_ROOT" + print_status "Testing versions: ${PYTHON_VERSIONS[*]}" + echo + + # Check UV is installed + if ! command -v uv &> /dev/null; then + print_error "UV is not installed. Please run 'make installuv' first." + exit 1 + fi + + local successful_versions=() + local failed_versions=() + local skipped_versions=() + + # Test each Python version + for version in "${PYTHON_VERSIONS[@]}"; do + echo + print_status "=========================================" + print_status "Testing Python $version" + print_status "=========================================" + + if check_python_version "$version"; then + if test_python_version "$version"; then + successful_versions+=("$version") + else + failed_versions+=("$version") + fi + else + skipped_versions+=("$version") + fi + done + + # Print summary + echo + print_status "=========================================" + print_status "TEST SUMMARY" + print_status "=========================================" + + if [ ${#successful_versions[@]} -gt 0 ]; then + print_success "Successful versions: ${successful_versions[*]}" + fi + + if [ ${#failed_versions[@]} -gt 0 ]; then + print_error "Failed versions: ${failed_versions[*]}" + fi + + if [ ${#skipped_versions[@]} -gt 0 ]; then + print_warning "Skipped versions (not installed): ${skipped_versions[*]}" + fi + + echo + if [ ${#failed_versions[@]} -eq 0 ]; then + print_success "All available Python versions passed!" + exit 0 + else + print_error "Some Python versions failed. See details above." + exit 1 + fi +} + +# Run main function +main "$@" \ No newline at end of file From 8d88674b55625acd732cdd19b4bf8ddf9cb43b17 Mon Sep 17 00:00:00 2001 From: Anthony Galassi <28850131+bendhouseart@users.noreply.github.com> Date: Thu, 26 Jun 2025 12:59:15 -0400 Subject: [PATCH 2/4] use pip instead of uv for installs --- .github/workflows/phantoms.yaml | 4 ++-- .github/workflows/python.yaml | 14 ++++++++------ 2 files changed, 10 insertions(+), 8 deletions(-) diff --git a/.github/workflows/phantoms.yaml b/.github/workflows/phantoms.yaml index d1b8679e..2b32590f 100644 --- a/.github/workflows/phantoms.yaml +++ b/.github/workflows/phantoms.yaml @@ -88,12 +88,12 @@ jobs: pypet2bids/pyproject.toml - name: Install UV - run: curl -LsSf https://astral.sh/uv/install.sh | sh + run: curl -LsSf https://astral.sh/uv/install.sh | sh && echo "$HOME/.cargo/bin" >> $GITHUB_PATH - name: Install Python Dependencies run: | cd pypet2bids - uv sync --dev + uv pip install -e .[dev] - name: Install UV Build Package run: | diff --git a/.github/workflows/python.yaml b/.github/workflows/python.yaml index e0fe4d81..5381172b 100644 --- a/.github/workflows/python.yaml +++ b/.github/workflows/python.yaml @@ -47,14 +47,16 @@ jobs: uses: actions/setup-python@v4 with: python-version: ${{ matrix.python }} + cache: 'pip' + cache-dependency-path: 'pypet2bids/pyproject.toml' - name: Install UV - run: curl -LsSf https://astral.sh/uv/install.sh | sh + run: curl -LsSf https://astral.sh/uv/install.sh | sh && echo "$HOME/.cargo/bin" >> $GITHUB_PATH - name: Install dependencies run: | cd pypet2bids - uv sync --dev + uv 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/ - uv run python3 -m pypet2bids.ecat_cli --help + python3 -m pypet2bids.ecat_cli --help - name: Test CLI Ecat Dump run: | cd pypet2bids/ - uv 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/ && uv 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 - uv 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/ From b5b22b4b7e79df28237a955c09a9904cf395a81e Mon Sep 17 00:00:00 2001 From: Anthony Galassi <28850131+bendhouseart@users.noreply.github.com> Date: Thu, 26 Jun 2025 14:42:52 -0400 Subject: [PATCH 3/4] install to system python not venv --- .github/workflows/phantoms.yaml | 4 ++-- .github/workflows/python.yaml | 2 +- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/.github/workflows/phantoms.yaml b/.github/workflows/phantoms.yaml index 2b32590f..735b785d 100644 --- a/.github/workflows/phantoms.yaml +++ b/.github/workflows/phantoms.yaml @@ -93,13 +93,13 @@ jobs: - name: Install Python Dependencies run: | cd pypet2bids - uv pip install -e .[dev] + uv pip install -e .[dev] --system - name: Install UV Build Package run: | make installuv make buildpackage - make installpackage + cd pypet2bids && uv pip install dist/pypet2bids-*.whl --system dcm2niix4pet -h - name: Set Up Node diff --git a/.github/workflows/python.yaml b/.github/workflows/python.yaml index 5381172b..3289c342 100644 --- a/.github/workflows/python.yaml +++ b/.github/workflows/python.yaml @@ -56,7 +56,7 @@ jobs: - name: Install dependencies run: | cd pypet2bids - uv pip install -e .[dev] + uv pip install -e .[dev] --system - name: Collect ECAT and other phantoms if: steps.cache-phantoms.outputs.cache-hit != 'true' From b6e3bda93df2de038d3432df980a9fa64cde5620 Mon Sep 17 00:00:00 2001 From: Anthony Galassi <28850131+bendhouseart@users.noreply.github.com> Date: Thu, 26 Jun 2025 14:46:40 -0400 Subject: [PATCH 4/4] just use pip --- .github/workflows/phantoms.yaml | 2 +- .github/workflows/python.yaml | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/phantoms.yaml b/.github/workflows/phantoms.yaml index 735b785d..c6f7386c 100644 --- a/.github/workflows/phantoms.yaml +++ b/.github/workflows/phantoms.yaml @@ -93,7 +93,7 @@ jobs: - name: Install Python Dependencies run: | cd pypet2bids - uv pip install -e .[dev] --system + pip install -e .[dev] - name: Install UV Build Package run: | diff --git a/.github/workflows/python.yaml b/.github/workflows/python.yaml index 3289c342..f7e035a3 100644 --- a/.github/workflows/python.yaml +++ b/.github/workflows/python.yaml @@ -56,7 +56,7 @@ jobs: - name: Install dependencies run: | cd pypet2bids - uv pip install -e .[dev] --system + pip install -e .[dev] - name: Collect ECAT and other phantoms if: steps.cache-phantoms.outputs.cache-hit != 'true'