Review reco

.github/workflows/build_and_test_app.yml

@@ -21,10 +21,13 @@ jobs:
       - name: install quality deps
         run: |
           pip install pylint mccabe
-      - name: code quality
+      - name: Run Pylint
+        shell: bash -l {0}
+        run: |
+          pylint --recursive=y --disable=all --fail-under=10 --enable=too-many-statements,too-many-nested-blocks .
+      - name: Run McCabe Complexity Check
+        shell: bash -l {0}
         run: |
-          pylint --disable=all --fail-under=10 --enable=too-many-statements --max-statements=100 .
-          pylint --disable=all --fail-under=10 --enable=too-many-nested-blocks .
           ./continuous_integration/scripts/check_mccabe_complexity.sh 25 .
   test:
     runs-on: ubuntu-22.04
@@ -46,7 +49,6 @@ jobs:
         if [ -f docker/requirements.txt ]; then pip install -r docker/requirements.txt; fi
     - name: pytest
       run: |
-        cd tests
         export CMAKE_PREFIX_PATH=/opt/otb
         export PYTHONPATH=/opt/otb/lib/python3/dist-packages:/opt/otb/lib/otb/python
         export GDAL_DRIVER_PATH=disable
@@ -57,5 +59,13 @@ jobs:
         export OTB_APPLICATION_PATH=/opt/otb/lib/otb/applications
         export OTB_INSTALL_DIR=/opt/otb
         export LC_NUMERIC=C
-
-        pytest -s --cov-fail-under=65
+
+        pytest --cov=tests --cov-report=xml:.ci-reports-alcd/coverage_alcd.xml --cov-report html:cov_html_alcd --cov-report=term --junitxml=pytest-results-alcd.xml
+    - name: Upload Coverage Report
+      uses: actions/upload-artifact@v4
+      with:
+        name: coverage-report-alcd
+        path: |
+          .ci-reports-alcd/
+          cov_html_alcd/
+          pytest-results-alcd.xml

L1C_band_composition.py

@@ -419,49 +419,21 @@ def create_image_compositions(global_parameters, location, paths_parameters, cur
 
     # Create new indices if needed
     new_indices = global_parameters["features"]["special_indices"]
-    for indice in new_indices:
-        out_tif = op.join(out_dir_bands, (indice + '.tif'))
-        create_specific_indices(bands_dir, out_tif, indice_name=indice, resolution=resolution)
-        additional_bands.append(str(out_tif))
+    create_new_indices(additional_bands, bands_dir, new_indices, out_dir_bands, resolution)
 
     # Create the ratios
     ratios = create_ratio_bands(global_parameters, bands_dir, out_dir_bands, resolution=60)
     additional_bands.extend(ratios)
 
-    use_DTM = str2bool(global_parameters["features"]["DTM"])
-    if use_DTM:
-        # Append the DTM model
-        out_dtm = op.join(out_dir_bands, ('DTM.tif'))
-        # try to append it. If an error occurs, the DTM probably does not exist
-        # and we will therefore skip this band
-        try:
-            dtm_addition(location, out_dtm, resolution=resolution)
-            additional_bands.append(str(out_dtm))
-        except:
-            print('ERROR : THE DTM DOES NOT EXIST !!!')
+    use_dtm(additional_bands, global_parameters, location, out_dir_bands, resolution)
 
     create_textures = str2bool(global_parameters["features"]["textures"])
     # Create the texture features
     if create_textures:
-        band_used_for_contours = 2
-        in_tif = glob.glob(
-            op.join(bands_dir, '*{}*{:02}.jp2'.format(band_prefix, band_used_for_contours)))[0]
-        in_channel = 1
-
-        out_tif = op.join(out_dir_bands, 'density_contours.tif')
-        create_contours_density(in_tif, in_channel, out_tif, radius=3)
-        additional_bands.append(str(out_tif))
-        out_tif = op.join(out_dir_bands, 'variation_coeff.tif')
-        create_variation_coeff(in_tif, in_channel, out_tif, radius=3)
-        additional_bands.append(str(out_tif))
+        create_texture_feat(additional_bands, band_prefix, bands_dir, out_dir_bands)
 
     # Create time difference features
-    bands_num = [int(band) for band in global_parameters["features"]["time_difference_bands"]]
-    out_dir_bands = op.join(global_parameters["user_choices"]["main_dir"], 'Intermediate')
-    for band_num in bands_num:
-        out_tif = op.join(out_dir_bands, ('time_' + str(band_num) + '.tif'))
-        create_time_difference_band(global_parameters, paths_parameters, band_num, out_tif, resolution=resolution)
-        additional_bands.append(str(out_tif))
+    time_diff_feat(additional_bands, global_parameters, paths_parameters, resolution)
 
     # --- Create the main TIF with low resolution
     # create intermediate resolution files
@@ -501,10 +473,7 @@ def create_image_compositions(global_parameters, location, paths_parameters, cur
         new_indices = ['NDVI', 'NDWI']
         out_dir_bands = op.join(global_parameters["user_choices"]["main_dir"], 'Intermediate')
         additional_bands = []
-        for indice in new_indices:
-            out_tif = op.join(out_dir_bands, (indice + '.tif'))
-            create_specific_indices(bands_dir, out_tif, indice_name=indice, resolution=resolution)
-            additional_bands.append(str(out_tif))
+        create_new_indices(additional_bands, bands_dir, new_indices, out_dir_bands, resolution)
 
         # create intermediate resolution files
         intermediate_bands_dir = op.join(
@@ -513,15 +482,8 @@ def create_image_compositions(global_parameters, location, paths_parameters, cur
         pixelresY = resolution
 
         # The bands to put into the heavy file
-        bands_num = [2, 3, 4, 10]
-
-        intermediate_sizes_paths = []
-        for band in bands_num:
-            in_band = str(op.join(bands_dir, band_prefix) + '{:02d}'.format(band)+'.jp2')
-            out_band = op.join(intermediate_bands_dir, op.basename(in_band)[0:-4]+'.tif')
-
-            resize_band(in_band, out_band, pixelresX, pixelresY)
-            intermediate_sizes_paths.append(out_band)
+        intermediate_sizes_paths = put_band_heavy_tif(band_prefix, bands_dir, intermediate_bands_dir,
+                                                      intermediate_sizes_paths, pixelresX, pixelresY)
 
         out_heavy_tif = op.join(global_parameters["user_choices"]["main_dir"], 'In_data',
                                 'Image', global_parameters["user_choices"]["raw_img"])[0:-4]+'_H.tif'
@@ -531,7 +493,6 @@ def create_image_compositions(global_parameters, location, paths_parameters, cur
         compose_bands_heavy(intermediate_sizes_paths, str(out_heavy_tif))
 
     if "user_function" in list(global_parameters["user_choices"].keys()) and global_parameters["user_choices"]["user_function"] != None:
-        print('ENTERED')
         user_process(raw_img = out_all_bands_tif,
                  main_dir = global_parameters["user_choices"]["main_dir"],
                  module_path = global_parameters["user_choices"]["user_module"],
@@ -541,6 +502,61 @@ def create_image_compositions(global_parameters, location, paths_parameters, cur
     return
 
 
+def put_band_heavy_tif(band_prefix, bands_dir, intermediate_bands_dir, intermediate_sizes_paths, pixelresX, pixelresY):
+    bands_num = [2, 3, 4, 10]
+    intermediate_sizes_paths = []
+    for band in bands_num:
+        in_band = str(op.join(bands_dir, band_prefix) + '{:02d}'.format(band) + '.jp2')
+        out_band = op.join(intermediate_bands_dir, op.basename(in_band)[0:-4] + '.tif')
+
+        resize_band(in_band, out_band, pixelresX, pixelresY)
+        intermediate_sizes_paths.append(out_band)
+    return intermediate_sizes_paths
+
+
+def create_new_indices(additional_bands, bands_dir, new_indices, out_dir_bands, resolution):
+    for indice in new_indices:
+        out_tif = op.join(out_dir_bands, (indice + '.tif'))
+        create_specific_indices(bands_dir, out_tif, indice_name=indice, resolution=resolution)
+        additional_bands.append(str(out_tif))
+
+
+def time_diff_feat(additional_bands, global_parameters, paths_parameters, resolution):
+    bands_num = [int(band) for band in global_parameters["features"]["time_difference_bands"]]
+    out_dir_bands = op.join(global_parameters["user_choices"]["main_dir"], 'Intermediate')
+    for band_num in bands_num:
+        out_tif = op.join(out_dir_bands, ('time_' + str(band_num) + '.tif'))
+        create_time_difference_band(global_parameters, paths_parameters, band_num, out_tif, resolution=resolution)
+        additional_bands.append(str(out_tif))
+
+
+def use_dtm(additional_bands, global_parameters, location, out_dir_bands, resolution):
+    use_DTM = str2bool(global_parameters["features"]["DTM"])
+    if use_DTM:
+        # Append the DTM model
+        out_dtm = op.join(out_dir_bands, ('DTM.tif'))
+        # try to append it. If an error occurs, the DTM probably does not exist
+        # and we will therefore skip this band
+        try:
+            dtm_addition(location, out_dtm, resolution=resolution)
+            additional_bands.append(str(out_dtm))
+        except:
+            print('ERROR : THE DTM DOES NOT EXIST !!!')
+
+
+def create_texture_feat(additional_bands, band_prefix, bands_dir, out_dir_bands):
+    band_used_for_contours = 2
+    in_tif = glob.glob(
+        op.join(bands_dir, '*{}*{:02}.jp2'.format(band_prefix, band_used_for_contours)))[0]
+    in_channel = 1
+    out_tif = op.join(out_dir_bands, 'density_contours.tif')
+    create_contours_density(in_tif, in_channel, out_tif, radius=3)
+    additional_bands.append(str(out_tif))
+    out_tif = op.join(out_dir_bands, 'variation_coeff.tif')
+    create_variation_coeff(in_tif, in_channel, out_tif, radius=3)
+    additional_bands.append(str(out_tif))
+
+
 def create_no_data_tif(global_parameters, paths_parameters, out_tif, dilation_radius=10):
     '''
     Create the no_data TIF using both the clear and cloudy date.

alcd_params/global_parameters.py

@@ -191,12 +191,12 @@ class UserChoices(BaseModel):
     """
     user_function: Optional[str] = None
     user_module: Optional[str] = None
-    clear_date: str
-    current_date: str
-    location: str
+    clear_date: Optional[str] = None
+    current_date: Optional[str] = None
+    location: Optional[str] = None
     main_dir: str
     raw_img: str
-    tile: str
+    tile: Optional[str] = None
 
     @field_validator("clear_date", "current_date")
     def parse_yyyymmdd(cls, value: str, info: ValidationInfo) -> str:

alcd_params/paths_parameters.py

@@ -1,5 +1,5 @@
 from pydantic import BaseModel, DirectoryPath
-from typing import Dict
+from typing import Dict, Optional
 
 
 class GlobalChainsPaths(BaseModel):
@@ -24,12 +24,12 @@ class GlobalChainsPaths(BaseModel):
         Path to the resized DTM directory.
     """
     L1C: DirectoryPath
-    maja: str
-    sen2cor: str
-    fmask: str
-    fmask3: str
-    DTM_input: str
-    DTM_resized: str
+    maja: Optional[str] = None
+    sen2cor: Optional[str] = None
+    fmask: Optional[str] = None
+    fmask3: Optional[str] = None
+    DTM_input: Optional[str] = None
+    DTM_resized: Optional[str] = None
 
 
 class DataPaths(BaseModel):
@@ -44,7 +44,7 @@ class DataPaths(BaseModel):
         Path to the PCC data directory.
     """
     data_alcd: DirectoryPath
-    data_pcc: str
+    data_pcc: Optional[str] = None
 
 
 class TileLocation(BaseModel):