Merge branch 'kassoulet-feature/display_csv_content_in_test_log' into develop

# Conflicts:
#	.github/workflows/ubuntu.yml
#	environment.yml
#	tests/end_to_end/ref_data/test_full/KLT_matcher_L2F_T12SYH_20220824T175017_LS9_R035_B04_10m_T12SYH_20220514T175909_B04.csv
#	tests/end_to_end/ref_data/test_full/kp_delta.json
#	tests/end_to_end/test_main.py

Author: telespazio-tim

.github/workflows/code-quality.yml

@@ -0,0 +1,56 @@
+name: Code Quality
+
+on:
+  push:
+    branches: [ main ]
+  pull_request:
+    branches: [ main ]
+
+jobs:
+  code-quality:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: [3.12]
+
+    steps:
+    - uses: actions/checkout@v4
+
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v5
+      with:
+        python-version: ${{ matrix.python-version }}
+        cache: 'pip'
+
+    - name: Install Conda
+      uses: conda-incubator/setup-miniconda@v3
+      with:
+        activate-environment: karios
+        python-version: ${{ matrix.python-version }}
+        auto-activate-base: false
+
+    - name: Install dependencies
+      run: |
+        pip install -e .
+        pip install -r requirements_dev.txt
+        # Install tools needed for pre-commit checks
+        pip install black isort bandit pydocstyle pre-commit
+
+    - name: Run license headers check
+      run: |
+        python -c "import licenseheaders; print('licenseheaders available')"
+        # Check if license headers are properly applied
+        python -m licenseheaders -cy -o "Telespazio France" -n "KARIOS" -t apache-2.tmpl -u "https://github.com/telespazio-tim/karios" -d karios --checkonly .
+      continue-on-error: true
+
+    - name: Run import sorting check (isort)
+      run: |
+        isort --check-only .
+
+    - name: Run code formatting check (black)
+      run: |
+        black -l 100 --check .
+
+    - name: Run security check (bandit)
+      run: |
+        bandit .

.github/workflows/ubuntu.yml

@@ -37,42 +37,32 @@ jobs:
         environment-file: environment.yml
         activate-environment: karios
 
-    - name: Test conda installation
-      shell: bash -l {0}
-      run: conda info
-
-    # - name: Install dependencies manually using conda install
-    #   shell: bash -l {0}
-    #   run: |
-    #     conda install --yes \
-    #       numpy=1.26.* \
-    #       matplotlib-base=3.9.* \
-    #       gdal=3.8.1 \
-    #       opencv=4.8.1 \
-    #       pandas=2.1.4 \
-    #       python=3.12 \
-    #       scikit-image=0.22.0 \
-    #       rich-click=1.8.9
+    - name: Install system dependencies
+      run: |
+        sudo apt-get update
+        sudo apt-get install -y libglx0
 
     - name: Install package in development mode
       shell: bash -l {0}
       run: |
         python -m pip install --upgrade pip
         pip install setuptools>=77.0
         pip install -e .
+      shell: bash -l {0}
 
     - name: Install dev dependencies for testing
       shell: bash -l {0}
       run: |
         pip install pytest
         if [ -f requirements_dev.txt ]; then
           pip install -r requirements_dev.txt
-
           # conda install -n karios -c conda-forge --file requirements_dev.txt
         fi
+      shell: bash -l {0}
 
     - name: Run tests
       shell: bash -l {0}
       continue-on-error: true
       run: |
-        python -m pytest tests/ -v
+        python -m pytest tests/ -v
+      shell: bash -l {0}

.github/workflows/windows64.yml

@@ -52,4 +52,4 @@ jobs:
         
     - name: Run tests
       run: |
-        python -m pytest tests/ -v
+        python -m pytest tests/ -v

.pre-commit-config.yaml

@@ -46,7 +46,7 @@ repos:
      require_serial: true
      pass_filenames: false # avoid files to be passed to pytest as args
      always_run: true
-     stages: [push]
+     stages: [pre-push]
   #  - id: docstyle
   #    name: docstyle
   #    entry: pydocstyle --convention=google

environment.yml

@@ -2,13 +2,11 @@ name: karios
 channels:
   - conda-forge
 dependencies:
-  # - python=3.11
   - pip
-  - numpy
-  - matplotlib-base=3.9.*
-  - gdal=3.8.1
-  - opencv=4.8.1
-  - pandas=2.1.4
+  - gdal=3.8.*
+  - matplotlib-base=3.8.*
+  - opencv=4.8.*
+  - pandas=2.1.*
   - python=3.12
-  - scikit-image=0.22.0
-  - rich-click=1.8.9
+  - scikit-image=0.24.*
+  - rich-click=1.8.*

karios/cli/commands.py

@@ -119,10 +119,12 @@ def cli() -> None:
     short_help="Performs image matching to detect pixel-level shifts between a monitored image and a reference image"
 )
 @click.argument(
-    "monitored_image", type=click.Path(exists=True, file_okay=True, dir_okay=False, path_type=Path)
+    "monitored_image",
+    type=click.Path(exists=True, file_okay=True, dir_okay=False, path_type=Path),
 )
 @click.argument(
-    "reference_image", type=click.Path(exists=True, file_okay=True, dir_okay=False, path_type=Path)
+    "reference_image",
+    type=click.Path(exists=True, file_okay=True, dir_okay=False, path_type=Path),
 )
 @click.argument(
     "mask_file",

karios/report/chip_service.py

@@ -492,7 +492,9 @@ def _create_vrt(self, directory_path: Path, output_vrt_name="chips.vrt"):
 
             # Build VRT options
             vrt_options = gdal.BuildVRTOptions(
-                separate=False, srcNodata=None, VRTNodata=0  # False for mosaic (single band)
+                separate=False,
+                srcNodata=None,
+                VRTNodata=0,  # False for mosaic (single band)
             )
 
             # Create the VRT

karios/report/overview_plot.py

@@ -197,7 +197,12 @@ def _create_error_scatter(
         axes.axis("scaled")
 
         scatter = axes.scatter(
-            self._points["x0"], self._points["y0"], c=values, cmap=colormap, s=1, **kwargs
+            self._points["x0"],
+            self._points["y0"],
+            c=values,
+            cmap=colormap,
+            s=1,
+            **kwargs,
         )
 
         axes.grid()