Switching to poetry + ruff

.github/workflows/main.yml

@@ -0,0 +1,158 @@
+name: bob-the-builder
+
+# only run on pushes to main or pull requests
+on:
+  push:
+    # push to any branch *
+    branches: *
+  pull_request:
+    branches: [ main ]
+
+jobs:
+  lint:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+      - uses: chartboost/ruff-action@v1
+
+  tests:
+    runs-on: ${{ matrix.os }}
+    timeout-minutes: 15 # Consider increasing timeout
+
+    strategy:
+      matrix:
+        os: [ubuntu-latest, macos-latest, macos-14]
+        python-version: ["3.12", "3.11", "3.10"]
+
+    steps:
+      - uses: actions/checkout@v3
+
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v4
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - name: Install poetry
+        uses: snok/install-poetry@v1
+
+      - name: Install dependencies
+        run: poetry install
+
+      - name: Test with pytest
+        run: |
+          # Github action runners now have 4 cores
+          poetry run pytest -s -v -n 4 --cov --cov-report xml:coverage-report/coverage.xml
+
+      - name: Upload coverage report artifact to be used by Codecov
+        # only upload if matrix.os is ubuntu-latest and matrix.python-version is 3.12
+        if: matrix.os == 'ubuntu-latest' && matrix.python-version == '3.12'
+        uses: actions/upload-artifact@v2
+        with:
+          name: coverage-report
+          path: coverage-report
+
+  codecov:
+    needs: tests
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v3
+
+      - name: Download coverage.xml artifact
+        uses: actions/download-artifact@v2
+        with:
+          name: coverage-report
+          path: coverage-report
+
+      - name: Use Codecov to track coverage
+        uses: codecov/codecov-action@v3
+        with:
+          token: ${{ secrets.CODECOV_TOKEN }}
+          files: ./coverage-report/coverage.xml
+          fail_ci_if_error: true
+          verbose: true
+          name: codecov-umbrella
+
+  cd:
+    permissions:
+        contents: write
+        packages: write
+        issues: write
+        pull-requests: write
+
+    needs: [tests]
+
+    # if pulling to main, deploy to PyPI
+    if: github.ref == 'refs/heads/main'
+
+    # Set up operating system
+    runs-on: ubuntu-latest
+
+    outputs:
+      released: ${{ steps.release.outputs.released }}
+      version: ${{ steps.release.outputs.version }}
+      tag: ${{ steps.release.outputs.tag }}
+
+    # Define job steps
+    steps:
+    - name: Set up Python 3.12
+      uses: actions/setup-python@v2
+      with:
+        python-version: 3.12
+
+    - name: Check-out repository
+      uses: actions/checkout@v2
+      with:
+        fetch-depth: 0
+
+  pip-squeak:
+    needs: cd
+    if: needs.cd.outputs.released == 'true'
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout the code with tag ${{ needs.cd.outputs.tag }}
+        uses: actions/checkout@v3
+        with:
+          ref: ${{ needs.cd.outputs.tag }}
+
+      - name: Set up Python 3.12
+        uses: actions/setup-python@v4
+        with:
+          python-version: 3.12
+
+      - name: Install Package Builder
+        run:
+          python3 -m pip install build
+
+      - name: Build package
+        run:
+          python3 -m build --sdist --wheel --outdir dist/
+
+      - name: Publish to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1
+        with:
+          verbose: true
+          user: __token__
+          password: ${{ secrets.PYPI_API_TOKEN }}
+
+
+  does-the-pip-squeak:
+    needs: pip-squeak
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        os: [ubuntu-latest, macos-latest, macos-14]
+        python-version: ["3.12", "3.11", "3.10"]
+
+    steps:
+      - uses: actions/checkout@v3
+
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v4
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - name: Install using PyPi
+        run: |
+          pip install nbiatoolkit==${{ needs.cd.outputs.version }}
+          NBIAToolkit

examples/process_general.py

@@ -1,7 +1,4 @@
-import os, pathlib
-import glob
-from numpy import mod
-import pandas as pd
+import pathlib
 
 from argparse import ArgumentParser
 
@@ -12,7 +9,6 @@
 
 import SimpleITK as sitk
 
-import warnings
 
 
 ###############################################################
@@ -198,7 +194,7 @@ def process_one_subject(self, subject_id):
         n_jobs=args.n_jobs,
         show_progress=args.show_progress)
 
-    print(f'starting Pipeline...')
+    print('starting Pipeline...')
     # == Parallel Processing == 
     pipeline.run()
 
@@ -216,4 +212,4 @@ def process_one_subject(self, subject_id):
     # == Just Uno ==
     # Good for quickly checking on one sample. 
     # pipeline.process_one_subject(5) 
-    print(f'finished Pipeline!')
+    print('finished Pipeline!')

examples/radcure_simple.py

@@ -1,8 +1,7 @@
-import os, pathlib
+import pathlib
 from argparse import ArgumentParser
 
-from imgtools.io import (ImageFileLoader, ImageFileWriter,
-                         read_dicom_rtstruct, read_dicom_series, read_dicom_rtdose, read_dicom_pet)
+from imgtools.io import (read_dicom_rtstruct, read_dicom_series, read_dicom_rtdose, read_dicom_pet)
 from imgtools.ops import StructureSetToSegmentation, ImageFileInput, ImageFileOutput, Resample
 from imgtools.pipeline import Pipeline