Merge pull request #67 from neuro-ml/develop

Develop

.github/workflows/tests.yml

@@ -0,0 +1,63 @@
+name: Test
+
+on: [ pull_request ]
+
+env:
+  MODULE_NAME: dpipe
+
+jobs:
+  test:
+    runs-on: ubuntu-20.04
+    strategy:
+      matrix:
+        python-version: [ 3.6, 3.7, 3.8, 3.9, '3.10' ]
+
+    steps:
+      - uses: actions/checkout@v2
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v2
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - name: Check the version and build the package
+        run: |
+          VERSION=$(python -c "from pathlib import Path; import runpy; folder, = {d.parent for d in Path().resolve().glob('*/__init__.py') if d.parent.is_dir() and (d.parent / '__version__.py').exists()}; print(runpy.run_path(folder / '__version__.py')['__version__'])")
+          MATCH=$(pip index versions deep-pipe | grep "Available versions:" | grep $VERSION) || echo
+          echo $MATCH
+          if [ "$GITHUB_BASE_REF" = "master" ] && [ "$MATCH" != "" ]; then exit 1; fi
+          python setup.py sdist
+
+      - name: Install
+        run: |
+          pip install dist/*
+          pip install -r tests/requirements.txt
+
+          cd tests
+          export MODULE_PARENT=$(python -c "import $MODULE_NAME, os; print(os.path.dirname($MODULE_NAME.__path__[0]))")
+          export MODULE_PARENT=${MODULE_PARENT%"/"}
+          cd ..
+          echo $MODULE_PARENT
+          echo "MODULE_PARENT=$(echo $MODULE_PARENT)" >> $GITHUB_ENV
+
+      - name: Test with pytest
+        run: |
+          pytest tests -m "not integration and not cuda" --junitxml=reports/junit-${{ matrix.python-version }}.xml --cov="$MODULE_PARENT/$MODULE_NAME" --cov-report=xml --cov-branch
+      - name: Generate coverage report
+        run: |
+          coverage xml -o reports/coverage-${{ matrix.python-version }}.xml
+          sed -i -e "s|$MODULE_PARENT/||g" reports/coverage-${{ matrix.python-version }}.xml
+          sed -i -e "s|$(echo $MODULE_PARENT/ | tr "/" .)||g" reports/coverage-${{ matrix.python-version }}.xml
+
+      - name: Upload artifacts
+        uses: actions/upload-artifact@v2
+        with:
+          name: reports-${{ matrix.python-version }}
+          path: reports/*-${{ matrix.python-version }}.xml
+        if: ${{ always() }}
+
+      - name: Upload coverage results
+        uses: codecov/codecov-action@v3
+        with:
+          fail_ci_if_error: true
+          files: reports/coverage-${{ matrix.python-version }}.xml
+          verbose: true

MANIFEST.in

@@ -1,4 +1,4 @@
-include *.md
+include README.md
 include requirements.txt
 include LICENSE
 recursive-include dpipe *.py

dpipe/__init__.py

@@ -1 +1 @@
-__version__ = '0.1.2'
+from .__version__ import __version__

dpipe/__version__.py

@@ -0,0 +1 @@
+__version__ = '0.2.0'

dpipe/im/preprocessing.py

@@ -1,5 +1,5 @@
 import numpy as np
-from skimage.measure import label
+from imops.measure import label
 
 from dpipe.itertools import negate_indices
 from .axes import AxesLike, check_axes, AxesParams
@@ -99,14 +99,16 @@ def describe_connected_components(mask: np.ndarray, background: int = 0, drop_ba
     volumes
         a list of corresponding labels' volumes.
     """
-    label_map = label(mask, background=background)
-    labels, volumes = np.unique(label_map, return_counts=True)
+    label_map, labels, volumes = label(mask, background=background, return_labels=True, return_sizes=True)
+
+    if not drop_background:
+        # background's label is always 0
+        labels = np.append(labels, 0)
+        volumes = np.append(volumes, label_map.size - volumes.sum(dtype=int))
+
     idx = volumes.argsort()[::-1]
     labels, volumes = labels[idx], volumes[idx]
-    if drop_background:
-        # background's label is always 0
-        foreground = labels != 0
-        labels, volumes = labels[foreground], volumes[foreground]
+
     return label_map, labels, volumes