Develop

.github/workflows/test-coverage.yml

@@ -21,8 +21,10 @@ jobs:
         sudo apt-get update
         sudo apt-get install -y libgdal-dev
         pip install GDAL==$(gdal-config --version)
-        pip install pytest codecov coverage pytest-cov
-        pip install -r requirements.txt
+        pip install .[dev]
+    - name: Lint with ruff
+      run: |
+        ruff check .
     - name: Run tests with coverage
       run: |
         pytest --cov --cov-report xml:results.xml --cov-report json --disable-warnings

aemworkflow/aemworkflow.py

@@ -1,10 +1,12 @@
 import sys
+
 import click
+
 from .conversion import main as conversion
-from .validation import main as validation
-from .pre_interpretation import main as pre_interpretation
-from .interpretation import main as interpretation
 from .exports import main as exports
+from .interpretation import main as interpretation
+from .pre_interpretation import main as pre_interpretation
+from .validation import main as validation
 
 
 @click.group()

aemworkflow/commands.py

@@ -1,16 +1,17 @@
 """
 GA AEM interpretation workflow, awk2python script translation
 """
-from pathlib import Path
-import os
-import glob
 import argparse
+import glob
+import os
 import re
-import pandas as pd
+from pathlib import Path
+from typing import List, TextIO, Tuple
 
+import pandas as pd
 from loguru import logger
-from typing import List, Tuple, TextIO
-from aemworkflow.utilities import get_ogr_path, run_command, validate_file, get_make_srt_dir
+
+from aemworkflow.utilities import get_make_srt_dir, get_ogr_path, run_command, validate_file
 
 
 def first(shp_dir: str, wrk_dir: str) -> None:

aemworkflow/conversion.py

@@ -1,14 +1,15 @@
-import os
 import glob
+import os
 import re
 import warnings
-
 from pathlib import Path
-import pandas as pd
 from typing import List, Tuple
-from osgeo import osr
+
+import pandas as pd
 from loguru import logger
-from aemworkflow.utilities import get_ogr_path, get_make_srt_dir, validate_file, run_command
+from osgeo import osr
+
+from aemworkflow.utilities import get_make_srt_dir, get_ogr_path, run_command, validate_file
 
 
 def conversion_zedfix_gmt_to_srt(wrk_dir: str, path_dir: str, ext_file: str, logger_session=logger) -> List[int]:

aemworkflow/exports.py

@@ -1,11 +1,12 @@
-import sys
 import csv
 import os
+import re
+import sys
 from pathlib import Path
+from typing import List
+
 import pandas as pd
-import re
 from loguru import logger
-from typing import List
 
 
 def gmtsddd_to_egs(wrk_dir: str, alt_colors: str, nm_list: List[int]) -> None:

aemworkflow/interpretation.py

@@ -1,14 +1,15 @@
 import decimal
-import os
 import glob
+import os
 import sys
-import geopandas
-import folium
 import warnings
+from pathlib import Path
 
+import folium
+import geopandas
 from osgeo import osr
-from pathlib import Path
-from aemworkflow.utilities import get_ogr_path, validate_file, run_command, validate_shapefile
+
+from aemworkflow.utilities import find_geometry_file, get_ogr_path, run_command, validate_file, validate_shapefile
 
 header = 0
 xpo = 0.5
@@ -110,10 +111,8 @@ def main(input_directory, output_directory, crs=28349, gis="esri_arcmap_0.5", li
         for shp in shp_list:
             fname = Path(shp).stem
             prefix = fname.split("_")[0]
-            extent_file_path = os.path.join(shp_dir, f'{prefix}.extent.txt')
-            print(f'extent file {extent_file_path} exists: {os.path.isfile(extent_file_path)}')
-            path_file_path = os.path.join(shp_dir, f'{prefix}.path.txt')
-            print(f'path file {path_file_path} exists: {os.path.isfile(path_file_path)}')
+            extent_file_path, extent_suffix = find_geometry_file(shp_dir, prefix, "extent")
+            path_file_path, path_suffix = find_geometry_file(shp_dir, prefix, "path")
             active_extent_control_file(extent_file_path,
                                        path_file_path,
                                        active_gmt_out_file_path,
@@ -122,7 +121,7 @@ def main(input_directory, output_directory, crs=28349, gis="esri_arcmap_0.5", li
                                        gis,
                                        mode)
 
-            gmt_file_path = os.path.join(output_directory, 'interp', f'{prefix}_interp.gmt')
+            gmt_file_path = os.path.join(output_directory, 'interp', f'{prefix}{extent_suffix}_interp.gmt')
             active_shp_to_gmt(shp, gmt_file_path)
 
             bdf_file_path = os.path.join(output_directory, 'interp', 'met.bdf')

aemworkflow/pre_interpretation.py

@@ -1,14 +1,15 @@
 import decimal
-import sys
-import os
 import glob
-import geopandas
-import folium
+import os
+import sys
 import warnings
+from pathlib import Path
 
+import folium
+import geopandas
 from osgeo import osr
-from pathlib import Path
-from aemworkflow.utilities import get_ogr_path, validate_file, run_command
+
+from aemworkflow.utilities import get_ogr_path, run_command, validate_file
 
 decimal.getcontext().rounding = decimal.ROUND_HALF_UP
 

aemworkflow/utilities.py

@@ -1,13 +1,15 @@
 import os
-import sys
 import shutil
 import subprocess  # nosec B404: subprocess usage is controlled and arguments are not user-supplied
-import fiona
+import sys
+from pathlib import Path
+from typing import List, Tuple
 
+import fiona
 from fiona.errors import DriverError
 from loguru import logger
-from typing import List
-from pathlib import Path
+
+BASE_SUFFIX = ("", "_high", "_mid", "_low")
 
 
 def get_ogr_path():
@@ -108,3 +110,15 @@ def get_make_srt_dir(wrk_dir: str, logger_session=logger) -> None:
     except OSError as osx:
         logger_session.error(osx.args)
         sys.exit()
+
+
+def find_geometry_file(shp_dir, prefix, geometryfile, logger_session=logger) -> Tuple[Path, str]:
+    required_suffix = '.path.txt' if geometryfile == 'path' else '.extent.txt'
+    for base_suffix in BASE_SUFFIX:
+        geometry_file_path = Path(shp_dir) / f'{prefix}{base_suffix}{required_suffix}'
+        if geometry_file_path.is_file():
+            logger_session.info(f'{geometryfile} file ../{geometry_file_path.name} exists: True')
+            return geometry_file_path, base_suffix
+
+    logger_session.error(f'No {geometryfile} file found for "{prefix}".')
+    raise FileNotFoundError(f'No {geometryfile} file found for "{prefix}"')

aemworkflow/validation.py

@@ -1,6 +1,7 @@
 import os
 from datetime import date
 from pathlib import Path
+
 from loguru import logger
 
 

docs/source/conf.py

@@ -9,10 +9,10 @@
 
 # If extensions (or modules to document with autodoc) are in another directory,
 # add these directories to sys.path here.
-#import os
-#import sys
-#sys.path.insert(0, pathlib.Path(__file__).parents[2].resolve().as_posix())
-#sys.path.insert(0, os.path.abspath('../..'))
+# import os
+# import sys
+# sys.path.insert(0, pathlib.Path(__file__).parents[2].resolve().as_posix())
+# sys.path.insert(0, os.path.abspath('../..'))
 
 # -- Project information -----------------------------------------------------
 

pyproject.toml

@@ -22,12 +22,20 @@ dependencies = [
     "geopandas==1.1.2",
     "importlib-metadata==8.6.1",
     "loguru==0.7.3",
-    "markdown==3.7",
     "pandas==2.2.3",
     "pytz==2025.1",
     "pyyaml==6.0.2",
 ]
 
+[project.optional-dependencies]
+dev = [
+    "pytest",
+    "pytest-cov",
+    "codecov",
+    "coverage",
+    "ruff",
+]
+
 [project.scripts]
 aemworkflow = "aemworkflow.aemworkflow:cli"
 
@@ -44,6 +52,7 @@ Issues = "https://github.com/GeoscienceAustralia/aem-interpretation-conversion/i
 filterwarnings = [
     "ignore::RuntimeWarning",
     "ignore::DeprecationWarning",
+    "ignore::FutureWarning",
 ]
 addopts = [
     "--cov=aemworkflow",
@@ -54,6 +63,9 @@ addopts = [
     "-o junit_family=legacy",
 ]
 
-[tool.flake8]
-max-line-length = 120
-ignore = ["E402", "F401", "F841"]
+[tool.ruff]
+line-length = 120
+preview = true
+
+[tool.ruff.lint]
+select = ["E", "F", "I"]