fix: update pre-commit config so that isort works (#267)

.pre-commit-config.yaml

@@ -32,6 +32,15 @@ repos:
         - --extra-keys
         - "metadata.colab metadata.kernelspec cell.metadata.colab cell.metadata.executionInfo cell.metadata.id cell.metadata.outputId"
 
+# ----- isort - imports sorting
+- repo: https://github.com/pycqa/isort
+  rev: 5.12.0
+  hooks:
+      - id: isort
+        name: isort (python)
+        types: [python]
+        args: [ "--profile", "black", "--filter-files" ]
+
 # ----- black - code formatting
 - repo: https://github.com/psf/black
   rev: 22.3.0 # Replace by any tag/version: https://github.com/psf/black/tags
@@ -49,15 +58,6 @@ repos:
     - id: flake8
       name: flake8 - Python linting
 
-# ----- isort - imports sorting
-- repo: https://github.com/pycqa/isort
-  rev: 5.12.0
-  hooks:
-    - id: isort
-      name: isort - Sort Python imports (auto-fixes)
-      types: [ cython, pyi, python ]
-      args: [ "--profile", "black", "--filter-files" ]
-
 # ----- nbQA - notebook quality assuring
 - repo: https://github.com/nbQA-dev/nbQA
   rev: 0.12.0

notebooks/e2e/e2e_leeds.py

@@ -10,29 +10,27 @@
 Call in script wide imports and the configuration information.
 """
 
-# %%
-import toml
-import os
 import datetime
+import os
+
+import folium
 import geopandas as gpd
-import pandas as pd
 import gtfs_kit as gk
-import folium
+import pandas as pd
 import seaborn as sns
 
+# %%
+import toml
+from folium.map import Icon
 from pyprojroot import here
+from r5py import TransportMode, TransportNetwork, TravelTimeMatrixComputer
 from shapely.geometry import box
-from folium.map import Icon
-from r5py import (
-    TransportNetwork,
-    TravelTimeMatrixComputer,
-    TransportMode,
-)
-from transport_performance.urban_centres.raster_uc import UrbanCentre
-from transport_performance.population.rasterpop import RasterPop
+
 from transport_performance.gtfs.gtfs_utils import bbox_filter_gtfs
 from transport_performance.gtfs.validation import GtfsInstance
 from transport_performance.osm.osm_utils import filter_osm
+from transport_performance.population.rasterpop import RasterPop
+from transport_performance.urban_centres.raster_uc import UrbanCentre
 from transport_performance.utils.raster import (
     merge_raster_files,
     sum_resample_file,

notebooks/e2e/e2e_london.py

@@ -10,8 +10,6 @@
 Call in script wide imports and the configuration information.
 """
 
-# %%
-import toml
 import os
 
 # import datetime
@@ -20,27 +18,29 @@
 # import pandas as pd
 import gtfs_kit as gk
 
-# import folium
-
+# %%
+import toml
 from pyprojroot import here
 from shapely.geometry import box
 
+from transport_performance.gtfs.gtfs_utils import bbox_filter_gtfs
+from transport_performance.gtfs.validation import GtfsInstance
+from transport_performance.osm.osm_utils import filter_osm
+from transport_performance.population.rasterpop import RasterPop
+
 # from folium.map import Icon
 # from r5py import (
 #     TransportNetwork,
 #     TravelTimeMatrixComputer,
 #    TransportMode,
 # )
 from transport_performance.urban_centres.raster_uc import UrbanCentre
-from transport_performance.population.rasterpop import RasterPop
-from transport_performance.gtfs.gtfs_utils import bbox_filter_gtfs
-from transport_performance.gtfs.validation import GtfsInstance
-from transport_performance.osm.osm_utils import filter_osm
-
 from transport_performance.utils.raster import (
     merge_raster_files,
-    # sum_resample_file,
-)
+)  # sum_resample_file,
+
+# import folium
+
 
 # %%
 # config filepath, and loading

notebooks/e2e/e2e_marseille.py

@@ -10,30 +10,28 @@
 Call in script wide imports and the configuration information.
 """
 
-# %%
-import toml
+import datetime
 import glob
 import os
-import datetime
+
+import folium
 import geopandas as gpd
-import pandas as pd
 import gtfs_kit as gk
-import folium
+import pandas as pd
 import seaborn as sns
 
+# %%
+import toml
+from folium.map import Icon
 from pyprojroot import here
+from r5py import TransportMode, TransportNetwork, TravelTimeMatrixComputer
 from shapely.geometry import box
-from folium.map import Icon
-from r5py import (
-    TransportNetwork,
-    TravelTimeMatrixComputer,
-    TransportMode,
-)
-from transport_performance.urban_centres.raster_uc import UrbanCentre
-from transport_performance.population.rasterpop import RasterPop
+
 from transport_performance.gtfs.gtfs_utils import bbox_filter_gtfs
 from transport_performance.gtfs.validation import GtfsInstance
 from transport_performance.osm.osm_utils import filter_osm
+from transport_performance.population.rasterpop import RasterPop
+from transport_performance.urban_centres.raster_uc import UrbanCentre
 from transport_performance.utils.raster import (
     merge_raster_files,
     sum_resample_file,

notebooks/e2e/e2e_newport.py

@@ -10,29 +10,27 @@
 Call in script wide imports and the configuration information.
 """
 
-# %%
-import toml
-import os
 import datetime
+import os
+
+import folium
 import geopandas as gpd
-import pandas as pd
 import gtfs_kit as gk
-import folium
+import pandas as pd
 import seaborn as sns
 
+# %%
+import toml
+from folium.map import Icon
 from pyprojroot import here
+from r5py import TransportMode, TransportNetwork, TravelTimeMatrixComputer
 from shapely.geometry import box
-from folium.map import Icon
-from r5py import (
-    TransportNetwork,
-    TravelTimeMatrixComputer,
-    TransportMode,
-)
-from transport_performance.urban_centres.raster_uc import UrbanCentre
-from transport_performance.population.rasterpop import RasterPop
+
 from transport_performance.gtfs.gtfs_utils import bbox_filter_gtfs
 from transport_performance.gtfs.validation import GtfsInstance
 from transport_performance.osm.osm_utils import filter_osm
+from transport_performance.population.rasterpop import RasterPop
+from transport_performance.urban_centres.raster_uc import UrbanCentre
 from transport_performance.utils.raster import (
     merge_raster_files,
     sum_resample_file,

notebooks/gtfs/check_unmatched_id_warnings.py

@@ -3,9 +3,9 @@
 # %%
 # imports
 import gtfs_kit as gk
-from pyprojroot import here
-import pandas as pd
 import numpy as np
+import pandas as pd
+from pyprojroot import here
 
 # %%
 # initialise my feed from GTFS test data

notebooks/gtfs/stop_id_check.py

@@ -1,8 +1,8 @@
 """A notebook containing viable code for additional stop_id validation."""
 # %%
 # IMPORTS
-from transport_performance.gtfs.validation import GtfsInstance
 from transport_performance.gtfs.gtfs_utils import _add_validation_row
+from transport_performance.gtfs.validation import GtfsInstance
 
 
 # %%

notebooks/metrics/metrics_experiments.py

@@ -9,23 +9,21 @@
 Call in script wide imports and the configuration information.
 """
 
-# %%
-import folium
-import geopandas as gpd
 import os
-import pandas as pd
 import pathlib
 import pickle
+from typing import Union
 
+# %%
+import folium
+import geopandas as gpd
+import pandas as pd
 from folium.map import Icon
 from haversine import haversine_vector
 from pyprojroot import here
 from tqdm import tqdm
-from typing import Union
 
-from transport_performance.utils.defence import (
-    _check_parent_dir_exists,
-)
+from transport_performance.utils.defence import _check_parent_dir_exists
 
 # %%
 # name of area and source of metrics inputs

notebooks/osm/01-visualise-osm.py

@@ -1,6 +1,7 @@
 """Visualise OMS spatial features."""
 # %%
 from pyprojroot import here
+
 from transport_performance.osm import validate_osm as osmval
 
 # %%

notebooks/population/grid_pop_experiment.py

@@ -49,34 +49,35 @@
 
 """
 
-# %%
-import rasterio as rio
+import logging
 import os
 import sys
-import logging
-import numpy as np
-import pandas as pd
-import geopandas as gpd
-import matplotlib.pyplot as plt
-import seaborn as sns
+import textwrap
+from datetime import datetime
+
 import cartopy.crs as ccrs
 import cartopy.io.img_tiles as cimgt
+import geopandas as gpd
+import matplotlib.pyplot as plt
+import numpy as np
+import pandas as pd
+
+# %%
+import rasterio as rio
+import requests
 import rioxarray
+import seaborn as sns
 import xarray as xr
-import requests
-import textwrap
-
-from datetime import datetime
-from pyproj import Transformer
-from pyprojroot import here
+from geocube.vector import vectorize
 from matplotlib import colormaps
 from matplotlib.colors import LogNorm
 from matplotlib.ticker import AutoMinorLocator
+from pyproj import Transformer
+from pyprojroot import here
 from rasterio.warp import Resampling
-from geocube.vector import vectorize
-from rioxarray.merge import merge_arrays
-from rioxarray.exceptions import NoDataInBounds
 from requests.exceptions import HTTPError
+from rioxarray.exceptions import NoDataInBounds
+from rioxarray.merge import merge_arrays
 from shapely.geometry.polygon import Polygon
 from xarray import DataArray
 

notebooks/urban_centres/poc_urban_centres.py

@@ -27,13 +27,13 @@
 # %%
 import os
 
+import folium
 import geopandas as gpd
-from shapely.geometry import box
-from pyprojroot import here
+import matplotlib.pyplot as plt
 import rioxarray as rxr
+from pyprojroot import here
 from rioxarray.merge import merge_arrays
-import matplotlib.pyplot as plt
-import folium
+from shapely.geometry import box
 
 import transport_performance.urban_centres.raster_uc as ucc
 

pipeline/gtfs/01-validate-gtfs.py

@@ -10,10 +10,11 @@
 8. new - modalities available (including extended spec)
 9. new - feed stats by is-weekend
 """
+import subprocess
+import time
+
 import toml
 from pyprojroot import here
-import time
-import subprocess
 
 from transport_performance.gtfs.validation import GtfsInstance
 from transport_performance.utils.defence import _is_expected_filetype

pipeline/osm/01-validate-osm.py

@@ -6,14 +6,16 @@
 4. Inspect tags by feature type.
 """
 
+import time
+
 import toml
 from pyprojroot import here
+
 from transport_performance.osm.validate_osm import (
     FindIds,
-    FindTags,
     FindLocations,
+    FindTags,
 )
-import time
 
 CONFIG = toml.load(here("pipeline/osm/config/01-validate-osm.toml"))
 OSM_PTH = CONFIG["OSM"]["PATH"]

pyproject.toml

@@ -47,6 +47,8 @@ exclude_lines = [
 # `isort` configurations
 [tool.isort]
 profile = "black"
+skip_glob = ["notebooks/*"]
+line_length = 79
 
 # `pytest` configurations
 [tool.pytest.ini_options]

scripts/prep-fixtures.py

@@ -12,14 +12,14 @@
 station, filtered to a date of 20230613.
 """
 import os
-import gtfs_kit as gk
+
 import geopandas as gpd
-from shapely.geometry import box
+import gtfs_kit as gk
 from pyprojroot import here
+from shapely.geometry import box
 
 from transport_performance.osm.osm_utils import filter_osm
 
-
 fix_dat = os.path.join("tests", "data", "gtfs")
 gtfs_zip = [
     os.path.join(fix_dat, x) for x in os.listdir(fix_dat) if x.endswith(".zip")