Merge branch 'main' into lighter_recon

Author: CPernet

.blackignore

@@ -0,0 +1,111 @@
+# Virtual environments
+.venv/
+venv/
+env/
+ENV/
+env.bak/
+venv.bak/
+
+# Python cache
+__pycache__/
+*.py[cod]
+*$py.class
+*.so
+.Python
+.pytest_cache/
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+
+# PyInstaller
+*.manifest
+*.spec
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+.hypothesis/
+.pytest_cache/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# pyenv
+.python-version
+
+# celery beat schedule file
+celerybeat-schedule
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# IDE
+.vscode/
+.idea/
+*.swp
+*.swo
+*~
+
+# OS
+.DS_Store
+.DS_Store?
+._*
+.Spotlight-V100
+.Trashes
+ehthumbs.db
+Thumbs.db
+
+# Project specific
+__MACOSX/
+*.zip
+*.mat
+*.v
+*.v.gz
+*.avi
+*.jpg
+*.bytes 

.codespellrc

@@ -0,0 +1,7 @@
+[codespell]
+# Ref: https://github.com/codespell-project/codespell#using-a-config-file
+skip = .git*,*.pdf,*.lock,.codespellrc
+check-hidden = true
+# Some domain specific variables, names, and some specific variable choices
+ignore-regex =  \b(TE|PROMIS|Claus|nam|bais)\b
+# ignore-words-list =

.github/workflows/codespell.yml

@@ -0,0 +1,25 @@
+# Codespell configuration is within .codespellrc
+---
+name: Codespell
+
+on:
+  push:
+    branches: [main]
+  pull_request:
+    branches: [main]
+
+permissions:
+  contents: read
+
+jobs:
+  codespell:
+    name: Check for spelling errors
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+      - name: Annotate locations with typos
+        uses: codespell-project/codespell-problem-matcher@v1
+      - name: Codespell
+        uses: codespell-project/actions-codespell@v2

.github/workflows/phantoms.yaml

@@ -27,8 +27,8 @@ jobs:
 
     strategy:
       matrix:
-        os: [ubuntu-20.04]
-        python: ["3.10"]
+        os: [ubuntu-latest]
+        python: ["3.12"]
       fail-fast: false
 
     steps:
@@ -37,15 +37,15 @@ jobs:
 
       - name: Cache Node Posix
         if: runner.os != 'Windows' && !env.ACT
-        uses: actions/cache@v3
+        uses: actions/cache@v4
         with:
           path: ~/.npm
           key: npm-${{ runner.os }}-${{ env.cache-name }}
 
       - name: Cache Phantoms
         if: ${{ !env.ACT }}
         id: phantom-cache
-        uses: actions/cache@v3
+        uses: actions/cache@v4
         env:
           cache-name: cache-phantoms
         with:
@@ -67,6 +67,12 @@ jobs:
             brew install dcm2niix
           fi
 
+
+      - name: Check dcm2niix is installed and on path
+        if: runner.os != 'Windows'
+        run:
+          dcm2niix -h 
+
       - name: Install dcm2niix windows
         if: runner.os == 'Windows'
         run: |
@@ -81,23 +87,26 @@ 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
-        uses: actions/setup-node@v3
+        uses: actions/setup-node@v4
 
       - name: Install BIDS Validator
-        run: npm install -g bids-validator
+        run: npm install -g bids-validator@1.14.6
 
       - name: Collect Phantoms
         if: ${{ steps.cache-phantoms.outputs.cache-hit != 'true' }} && ${{ !env.ACT }}
@@ -130,11 +139,15 @@ jobs:
           bash python_conversions.sh
 
       - name: SetupMatlab
-        if: ${{ matrix.os == 'ubuntu-20.04' }}
+        if: ${{ matrix.os == 'ubuntu-latest' }}
         uses: matlab-actions/setup-matlab@v1
+        # note matlab-actions/setup-matlab@v2 breaks this script, don't update unless you're forced to
+        #with:
+          #release: 'R2023a'
+          #cache: true
 
       - name: Run Matlab Conversion Script on Phantoms
-        if: ${{ matrix.os == 'ubuntu-20.04' }}
+        if: ${{ matrix.os == 'ubuntu-latest' }}
         uses: matlab-actions/run-command@v1
         with:
           command: |
@@ -154,6 +167,13 @@ jobs:
         run: |
           bids-validator OpenNeuroPET-Phantoms/python
 
+      - name: Debug
+        uses: mxschmitt/action-tmate@v3
+        if: ${{ github.event_name == 'workflow_dispatch' && inputs.debug_enabled }}
+        timeout-minutes: 15
+        with:
+          limit-access-to-actor: true
+
       - name: Validate Matlab Conversion
         run: |
           bids-validator OpenNeuroPET-Phantoms/matlab

.github/workflows/python.yaml

@@ -30,15 +30,15 @@ jobs:
     strategy:
       matrix:
         os: [macOS-latest, ubuntu-latest]
-        python: ['3.8', '3.9', '3.10']
+        python: ['3.8', '3.9', '3.10', '3.11', '3.12', '3.13']
 
     steps:
       - name: Checkout Repo
         uses: actions/checkout@v2
 
       - name: Cache Phantoms
         id: cache-phantoms
-        uses: actions/cache@v2
+        uses: actions/cache@v4
         with:
           path: US-sourced-OpenNeuroPET-Phantoms.zip
           key: ${{ runner.os }}-phantoms
@@ -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
-          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/

.github/workflows/windows.yaml

@@ -13,7 +13,7 @@ jobs:
     strategy:
       matrix:
         os: [windows-latest]
-        python: ['3.8', '3.9', '3.10']
+        python: ['3.9', '3.10']
 
     steps:
       - name: Checkout Repo

.gitignore

@@ -58,3 +58,12 @@ D:\\BIDS*
 *OpenNeuroPET-Phantoms*
 **PHANTOMS.zip
 ecat_validation/ECAT7_multiframe.v
+variables.env
+ecat_testing/matlab/
+ecat_testing/steps/
+ecat_testing/**/*.nii*
+*osem*
+*fbp*
+
+matlab/SiemensHRRTparameters.txt
+

.readthedocs.yaml

@@ -11,26 +11,20 @@ submodules:
     - golden_ecat.py
     - tests
 
-
 # Set the version of Python and other tools you might need
 build:
   os: ubuntu-22.04
   tools:
     python: "3.11"
-  jobs:
-    post_create_environment:
-      - cp -r metadata pypet2bids/pypet2bids/
-      # install poetry
-      - pip install poetry
-      - poetry config virtualenvs.create false
-      # just use poetry to export a requirements.txt as that worked much better than the previous attempts
-      - cd pypet2bids && poetry lock && poetry export --without-hashes --with dev --format=requirements.txt > requirements.txt
+
+# Install Python dependencies
+python:
+  install:
+    - method: pip
+      path: pypet2bids
+      extra_requirements:
+        - dev
 
 # Build documentation in the docs/ directory with Sphinx
 sphinx:
    configuration: docs/conf.py
-
-# Optionally declare the Python requirements required to build your docs
-python:
-   install:
-   - requirements: pypet2bids/requirements.txt

CITATION.cff

@@ -31,11 +31,17 @@ authors:
 - family-names: "Ganz-Benjaminsen"
   given-names: "Melanie"
   orcid: "https://orcid.org/0000-0002-9120-8098"
+- family-names: "Bilgel"
+  given-names: "Murat"
+  orcid: "https://orcid.org/0000-0001-5042-7422"
+- family-names: "Eierud"
+  given-names: "Cyrus"
+  orcid: "https://orcid.org/0000-0002-9942-676X"
 - family-names: "Pernet"
   given-names: "Cyril"
   orcid: "https://orcid.org/0000-0003-4010-4632"
 title: "PET2BIDS"
-version: 1.0.0
+version: 1.3.20240502
 url: "https://github.com/openneuropet/PET2BIDS"
 date-released: 2022-10-01
 license: MIT