Merge branch 'gtfs-html-new' of https://github.com/datasciencecampus/…

…transport-network-performance into gtfs-html-new

.github/workflows/all-os-tests.yml

@@ -0,0 +1,34 @@
+# This workflow will install OS dependencies and run a 'base' set of unit tests with Python 3.9
+# For more information see: https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-python
+
+name: Unit tests on macOS/Linux/Windows
+
+on:
+  push:
+  pull_request:
+    branches: [ "dev", "main" ]
+
+jobs:
+  build:
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ["3.9"]
+        os: ["macos-latest", "ubuntu-latest", "windows-latest"]
+    steps:
+    - uses: actions/checkout@v3
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v3
+      with:
+        python-version: ${{ matrix.python-version }}
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install -r requirements.txt
+    - name: Run Integration Tests  # run only those tests marked runinteg & with no osmosis deps
+      run: |
+          pytest -m runinteg --runinteg --deselect tests/osm/
+    - name: Test with pytest  # run only tests with no osmosis deps
+      run: |
+        pytest --deselect tests/osm/

.github/workflows/python-package.yml

@@ -1,4 +1,4 @@
-# This workflow will install Python dependencies, run tests and lint with a variety of Python versions
+# This workflow will install Python dependencies, run tests and lint with Python 3.9
 # For more information see: https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-python
 
 name: Python package
@@ -10,7 +10,6 @@ on:
 
 jobs:
   build:
-
     runs-on: ${{ matrix.os }}
     strategy:
       fail-fast: false
@@ -23,11 +22,6 @@ jobs:
       uses: actions/setup-python@v3
       with:
         python-version: ${{ matrix.python-version }}
-    - name: Install geos  # required for cartopy installation
-      uses: ConorMacBride/install-package@v1
-      with:
-        brew: geos
-        apt: libgeos-dev
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip
@@ -40,11 +34,19 @@ jobs:
     - name: Check Java Install
       run: |
         java --version
-    - name: Install Osmosis
-      uses: ConorMacBride/install-package@v1
-      with:
-        brew: osmosis
-        apt: osmosis
+    - name: Install mac depencies with brew
+      if: runner.os == 'macOS'  # not updating brew version, issue with aom
+      run: |
+        brew install geos
+        brew install osmosis
+      shell: sh
+    - name: Install linux depencies with apt
+      if: runner.os == 'Linux'
+      run: |
+        sudo apt update
+        sudo apt install -y libgeos-dev
+        sudo apt install -y osmosis
+      shell: sh
     - name: Run Integration Tests
       run: |
           pytest -m runinteg --runinteg # run only those tests marked runinteg
@@ -56,10 +58,12 @@ jobs:
       run: |
         pytest
     - name: Generate Report
+      if: runner.os == 'macOS'  # run coverage report only on macOS
       run: |
         coverage run -m pytest
         coverage xml
     - name: Upload coverage reports to Codecov
+      if: runner.os == 'macOS'  # run coverage report only on macOS
       uses: codecov/codecov-action@v3
       with:
         file: ./coverage.xml

notebooks/urban_centres/poc_urban_centres.py

@@ -84,9 +84,13 @@
 AREA_OF_INTEREST = "newport"
 BBOX = BBOX_DICT[AREA_OF_INTEREST]
 
+# bbox
 bbox_npt = gpd.GeoDataFrame(index=[0], crs="epsg:4326", geometry=[box(*BBOX)])
 bbox_npt_r = bbox_npt.to_crs("esri:54009")
-coords = (float(bbox_npt.centroid.y), float(bbox_npt.centroid.x))
+
+# bbox centroid
+bbox_npt_centroid = bbox_npt.to_crs("epsg:27700").centroid.to_crs("epsg:4326")
+coords = (bbox_npt_centroid.y[0], bbox_npt_centroid.x[0])
 
 # pop only criteria
 npt = ucc.UrbanCentre(file=(MERGED_DIR))
@@ -105,9 +109,13 @@
 AREA_OF_INTEREST = "leeds"
 BBOX = BBOX_DICT[AREA_OF_INTEREST]
 
+# bbox
 bbox_lds = gpd.GeoDataFrame(index=[0], crs="epsg:4326", geometry=[box(*BBOX)])
 bbox_lds_r = bbox_lds.to_crs("esri:54009")
-coords = (float(bbox_lds.centroid.y), float(bbox_lds.centroid.x))
+
+# bbox centroid
+bbox_lds_centroid = bbox_lds.to_crs("epsg:27700").centroid.to_crs("epsg:4326")
+coords = (bbox_lds_centroid.y[0], bbox_lds_centroid.x[0])
 
 # pop only criteria
 lds = ucc.UrbanCentre(file=(MERGED_DIR))
@@ -126,9 +134,13 @@
 AREA_OF_INTEREST = "london"
 BBOX = BBOX_DICT[AREA_OF_INTEREST]
 
+# bbox
 bbox_lnd = gpd.GeoDataFrame(index=[0], crs="epsg:4326", geometry=[box(*BBOX)])
 bbox_lnd_r = bbox_lnd.to_crs("esri:54009")
-coords = (float(bbox_lnd.centroid.y), float(bbox_lnd.centroid.x))
+
+# bbox centroid
+bbox_lnd_centroid = bbox_lnd.to_crs("epsg:27700").centroid.to_crs("epsg:4326")
+coords = (bbox_lnd_centroid.y[0], bbox_lnd_centroid.x[0])
 
 # pop only criteria
 lnd = ucc.UrbanCentre(file=(MERGED_DIR))
@@ -146,9 +158,13 @@
 AREA_OF_INTEREST = "marseille"
 BBOX = BBOX_DICT[AREA_OF_INTEREST]
 
+# bbox
 bbox_mrs = gpd.GeoDataFrame(index=[0], crs="epsg:4326", geometry=[box(*BBOX)])
 bbox_mrs_r = bbox_mrs.to_crs("esri:54009")
-coords = (float(bbox_mrs.centroid.y), float(bbox_mrs.centroid.x))
+
+# bbox centroid
+bbox_mrs_centroid = bbox_mrs_r.centroid.to_crs("epsg:4326")
+coords = (bbox_mrs_centroid.y[0], bbox_mrs_centroid.x[0])
 
 # pop only criteria
 mrs = ucc.UrbanCentre(file=(MERGED_DIR))

requirements.txt

@@ -2,7 +2,7 @@ pre-commit
 r5py>=0.0.4
 gtfs_kit==5.2.7
 rasterio
-matplotlib
+matplotlib>=3.7.0
 scipy
 rioxarray
 geopandas
@@ -13,7 +13,7 @@ coverage
 pyprojroot
 pytest-lazy-fixture
 ipykernel==6.23.1
-pandas
+pandas<2.1.0
 beautifulsoup4
 requests
 pytest-mock

src/transport_performance/gtfs/gtfs_utils.py

@@ -9,8 +9,7 @@
 from transport_performance.utils.defence import (
     _is_expected_filetype,
     _check_list,
-    _dataframe_defence,
-    _bool_defence,
+    _type_defence,
 )
 
 
@@ -109,8 +108,8 @@ def convert_pandas_to_plotly(
         }
     }
     # defences
-    _dataframe_defence(df, "df")
-    _bool_defence(return_html, "return_html")
+    _type_defence(df, "df", pd.DataFrame)
+    _type_defence(return_html, "return_html", bool)
     if scheme not in list(schemes.keys()):
         raise LookupError(
             f"{scheme} is not a valid colour scheme."

src/transport_performance/gtfs/report/report_utils.py

@@ -5,9 +5,8 @@
 import os
 
 from transport_performance.utils.defence import (
-    _bool_defence,
-    _string_defence,
-    _is_path_like,
+    _type_defence,
+    _handle_path_like,
     _check_parent_dir_exists,
 )
 
@@ -76,7 +75,7 @@ def __init__(self, path: Union[str, pathlib.Path]) -> None:
         None
 
         """
-        _is_path_like(path, "path")
+        _handle_path_like(path, "path")
         with open(path, "r", encoding="utf8") as f:
             self.template = f.read()
         return None
@@ -109,9 +108,9 @@ def insert(
             place-holder but 'replace_multiple' is not True
 
         """
-        _string_defence(placeholder, "placeholder")
-        _string_defence(value, "value")
-        _bool_defence(replace_multiple, "replace_multiple")
+        _type_defence(placeholder, "placeholder", str)
+        _type_defence(value, "value", str)
+        _type_defence(replace_multiple, "replace_multiple", bool)
         occurences = len(self.template.split(f"[{placeholder}]")) - 1
         if occurences > 1 and not replace_multiple:
             raise ValueError(

src/transport_performance/gtfs/routes.py

@@ -4,7 +4,7 @@
 import requests
 import warnings
 
-from transport_performance.utils.defence import _url_defence, _bool_defence
+from transport_performance.utils.defence import _url_defence, _type_defence
 
 warnings.filterwarnings(
     action="ignore", category=DeprecationWarning, module=".*pkg_resources"
@@ -98,7 +98,7 @@ def scrape_route_type_lookup(
     for url in [gtfs_url, ext_spec_url]:
         _url_defence(url)
 
-    _bool_defence(extended_schema, "extended_schema")
+    _type_defence(extended_schema, "extended_schema", bool)
     # Get the basic scheme lookup
     resp_txt = _get_response_text(gtfs_url)
     soup = BeautifulSoup(resp_txt, "html.parser")

src/transport_performance/gtfs/validation.py

@@ -23,12 +23,7 @@
     _check_namespace_export,
     _check_parent_dir_exists,
     _check_column_in_df,
-    _bool_defence,
-    _integer_defence,
-    _string_defence,
-    _dataframe_defence,
-    _dict_defence,
-    _string_and_nonetype_defence,
+    _type_defence,
 )
 
 from transport_performance.gtfs.report.report_utils import (
@@ -738,17 +733,17 @@ def _plot_summary(
 
         """
         # parameter type defences
-        _dataframe_defence(summary_df, "summary_df")
-        _string_defence(day_column, "day_column")
-        _string_defence(target_column, "target_column")
-        _dict_defence(plotly_kwargs, "plotly_kwargs")
-        _bool_defence(return_html, "return_html")
-        _integer_defence(width, "width")
-        _integer_defence(height, "height")
-        _string_and_nonetype_defence(xlabel, "xlabel")
-        _string_and_nonetype_defence(ylabel, "ylabel")
-        _bool_defence(save_html, "save_html")
-        _bool_defence(save_image, "save_iamge")
+        _type_defence(summary_df, "summary_df", pd.DataFrame)
+        _type_defence(day_column, "day_column", str)
+        _type_defence(target_column, "target_column", str)
+        _type_defence(plotly_kwargs, "plotly_kwargs", dict)
+        _type_defence(return_html, "return_html", bool)
+        _type_defence(width, "width", int)
+        _type_defence(height, "height", int)
+        _type_defence(xlabel, "xlabel", (str, type(None)))
+        _type_defence(ylabel, "ylabel", (str, type(None)))
+        _type_defence(save_html, "save_html", bool)
+        _type_defence(save_image, "save_iamge", bool)
         _check_parent_dir_exists(save_pth, "save_pth", create=True)
 
         # orientation input defences
@@ -1269,8 +1264,8 @@ def html_report(
             An error raised if the type of summary passed is invalid
 
         """
-        _bool_defence(overwrite, "overwrite")
-        _string_defence(summary_type, "summary_type")
+        _type_defence(overwrite, "overwrite", bool)
+        _type_defence(summary_type, "summary_type", str)
         set_up_report_dir(path=report_dir, overwrite=overwrite)
         summary_type = summary_type.lower()
         if summary_type not in ["mean", "min", "max", "median"]:

src/transport_performance/osm/osm_utils.py

@@ -3,7 +3,7 @@
 from pyprojroot import here
 
 from transport_performance.utils.defence import (
-    _bool_defence,
+    _type_defence,
     _check_list,
     _check_parent_dir_exists,
     _is_expected_filetype,
@@ -54,7 +54,7 @@ def filter_osm(
         "tag_filter": tag_filter,
         "install_osmosis": install_osmosis,
     }.items():
-        _bool_defence(val, param_nm=nm)
+        _type_defence(val, nm, bool)
     # check bbox values makes sense, else osmosis will error
     if not bbox[0] < bbox[2]:
         raise ValueError(

src/transport_performance/population/rasterpop.py

@@ -34,7 +34,7 @@ class RasterPop:
     pop_gdf : gpd.GeoDataFrame
         A geopandas dataframe of the input data, with gridded geometry. This is
         in the same CRS as the input raster data.
-    centroid_gdf
+    centroid_gdf : gpd.GeoDataFrame
         A geopandas dataframe of grid centroids, converted to EPSG:4326 for
         transport analysis.
 
@@ -153,7 +153,7 @@ def plot(
         save : str, optional
             Filepath to save file, with the file extension, by default None
             meaning a file will not be saved.
-        **kwargs
+        kwargs : dict, optional
             Extra arguments passed to plotting functions to configure the plot
             styling. See Notes for more support.
 
@@ -177,9 +177,10 @@ def plot(
         -----
         Calling `help` as follows will provide more insights on possible kwarg
         arguments for the valid plotting backends:
-            - Folium backend: `help(RasterPop._plot_folium)
-            - Matplotlib backend: `help(RasterPop._plot_matplotlib)
-            - Cartopy backend: `help(RasterPop._plot_cartopy)
+
+        - Folium backend: `help(RasterPop._plot_folium)`
+        - Matplotlib backend: `help(RasterPop._plot_matplotlib)`
+        - Cartopy backend: `help(RasterPop._plot_cartopy)`
 
         """
         # record of valid which values
@@ -463,18 +464,30 @@ def _plot_folium(
         )
 
         # add the centroids to a separate layer
-        self.centroid_gdf.explore(
-            self.__UC_COL_NAME,
-            name="Centroids",
-            m=m,
-            show=False,
-            style_kwds={
+        # conditionally style plot based on whether UC is provided
+        if self._uc_gdf is not None:
+            centroid_plot_col = self.__UC_COL_NAME
+            # this dict will change the centriod color in/out the UC.
+            centroid_style_dict = {
                 "style_function": lambda x: {
                     "color": "#BC544B"
                     if x["properties"][self.__UC_COL_NAME] is False
                     else "#8B0000"
                 }
-            },
+            }
+        else:
+            centroid_plot_col = None
+            centroid_style_dict = {
+                "style_function": lambda x: {"color": "#BC544B"}
+            }
+
+        # add in the centroid layer with the conditional styling
+        self.centroid_gdf.explore(
+            centroid_plot_col,
+            name="Centroids",
+            m=m,
+            show=False,
+            style_kwds=centroid_style_dict,
             legend=False,
         )