updated docker file (and associated version numbers, incremented to 4…

….4.5, and Docker image) to address #336 and updated test.py to address #337

.ghsci_version

@@ -1 +1 @@
-4.4.3
+4.4.5

.test-compose.yml

@@ -1,7 +1,7 @@
 version: "3"
 services:
   ghsci:
-    image: globalhealthyliveablecities/global-indicators:v4.4.2
+    image: globalhealthyliveablecities/global-indicators:v4.4.5
     container_name: ghsci
     shm_size: 2g
     stdin_open: true # docker run -i

docker-compose.yml

@@ -1,7 +1,7 @@
 version: "3"
 services:
   ghsci:
-    image: globalhealthyliveablecities/global-indicators:v4.4.2
+    image: globalhealthyliveablecities/global-indicators:v4.4.5
     container_name: ghsci
     shm_size: 2g
     stdin_open: true # docker run -i

docker/Dockerfile

@@ -54,7 +54,8 @@ RUN mkdir /env && \
 ENV PATH="/env/bin/:$PATH"
 ENV PROJ_LIB="/env/share/proj"
 
-RUN echo 'alias configure="python configure.py"' >> ~/.bashrc && \
+RUN pip install -e git+https://github.com/wklumpen/gtfs-lite.git#egg=gtfs-lite && \
+    echo 'alias configure="python configure.py"' >> ~/.bashrc && \
     echo 'alias analysis="python analysis.py"' >> ~/.bashrc && \
     echo 'alias generate="python generate.py"' >> ~/.bashrc && \
     echo 'alias compare="python compare.py"' >> ~/.bashrc  && \

docker/environment.yml

@@ -3,10 +3,10 @@ channels:
   - conda-forge
 dependencies:
   - python
-  - osmnx=1.4.* # for constructing network graph from OpenStreetMap using Overpass API
+  - osmnx=1.5.* # for constructing network graph from OpenStreetMap using Overpass API
   - fpdf2=2.7.*
   - sqlalchemy=1.4.*
-  - nicegui=1.2.23
+  - nicegui>=1.2.24
   - cryptography=41.0.*
   - requests=2.31.*
   - tornado>=6.3.2
@@ -27,5 +27,3 @@ dependencies:
   - pyyaml
   - websockets
   - pip
-  - pip:
-    - gtfs-lite

docker/requirements.txt

@@ -13,6 +13,7 @@ beautifulsoup4==4.12.2
 bidict==0.22.1
 bleach==6.0.0
 branca==0.6.0
+Brotli==1.0.9
 Cartopy==0.21.1
 certifi==2023.5.7
 cffi==1.15.1
@@ -34,7 +35,7 @@ decorator==5.1.1
 defusedxml==0.7.1
 entrypoints==0.4
 et-xmlfile==1.1.0
-exceptiongroup==1.1.1
+exceptiongroup==1.1.2
 executing==1.2.0
 fastapi==0.92.0
 fastapi-socketio==0.0.10
@@ -55,14 +56,14 @@ h11==0.14.0
 idna==3.4
 importlib-metadata==6.7.0
 importlib-resources==5.12.0
-ipykernel==6.23.3
+ipykernel==6.24.0
 ipython==8.14.0
 ipywidgets==8.0.6
 itsdangerous==2.1.2
 jedi==0.18.2
 Jinja2==3.1.2
-joblib==1.2.0
-json5==0.9.5
+joblib==1.3.0
+json5==0.9.14
 jsonschema==4.17.3
 jupyter_client==8.3.0
 jupyter_core==5.3.1
@@ -78,14 +79,14 @@ kiwisolver==1.4.4
 libpysal==4.7.0
 lxml==4.9.2
 mapclassify==2.5.0
-markdown2==2.4.8
+markdown2==2.4.9
 MarkupSafe==2.1.3
 matplotlib==3.7.1
 matplotlib-inline==0.1.6
 mercantile==1.2.1
 mistune==3.0.0
 momepy==0.0.0
-munch==3.0.0
+munch==4.0.0
 munkres==1.1.4
 nbclient==0.8.0
 nbconvert==7.6.0
@@ -98,17 +99,17 @@ numexpr==2.8.4
 numpy==1.25.0
 openpyxl==3.1.2
 orjson==3.8.14
-osmnx==1.4.0
+osmnx==1.5.0
 overrides==7.3.1
 OWSLib==0.29.2
 packaging==23.1
 pandana==0.6.1
-pandas==2.0.2
+pandas==2.0.3
 pandocfilters==1.5.0
 parso==0.8.3
 pexpect==4.8.0
 pickleshare==0.7.5
-Pillow==9.5.0
+Pillow==10.0.0
 pip==23.1.2
 pkgutil_resolve_name==1.3.10
 platformdirs==3.8.0
@@ -123,7 +124,7 @@ ptyprocess==0.7.0
 pure-eval==0.2.2
 py-cpuinfo==9.0.0
 pycparser==2.21
-pydantic==1.10.9
+pydantic==1.10.10
 pygeometa==0.15.0
 pygeos==0.14
 Pygments==2.15.1
@@ -143,21 +144,21 @@ python-socketio==5.8.0
 pytz==2023.3
 PyYAML==6.0
 pyzmq==25.1.0
-rasterio==1.3.7
+rasterio==1.3.8
 requests==2.31.0
 rfc3339-validator==0.1.4
 rfc3986-validator==0.1.1
 Rtree==1.0.1
-scikit-learn==1.2.2
-scipy==1.11.0
+scikit-learn==1.3.0
+scipy==1.11.1
 Send2Trash==1.8.2
 setuptools==68.0.0
 shapely==2.0.1
 six==1.16.0
 sniffio==1.3.0
 snuggs==1.4.7
 soupsieve==2.3.2.post1
-SQLAlchemy==1.4.46
+SQLAlchemy==1.4.48
 stack-data==0.6.2
 starlette==0.25.0
 tables==3.8.0
@@ -169,7 +170,7 @@ tomli==2.0.1
 tornado==6.3.2
 tqdm==4.65.0
 traitlets==5.9.0
-typing_extensions==4.6.3
+typing_extensions==4.7.1
 typing-utils==0.1.0
 tzdata==2023.3
 unicodedata2==15.0.0

process/tests/tests.py

@@ -25,7 +25,7 @@
 import unittest
 
 try:
-    import subprocesses.ghsci
+    from subprocesses import ghsci
 
     project_setup = True
 except ImportError as e:
@@ -45,6 +45,41 @@ def test_project_setup(self):
         """Check if _project_setup.py imported successfully."""
         self.assertTrue(project_setup)
 
+    def test_load_example_region(self):
+        """Load example region."""
+        codename = 'example_ES_Las_Palmas_2023'
+        r = ghsci.Region(codename)
+
+    def test_example_analysis(self):
+        """Analyse example region."""
+        codename = 'example_ES_Las_Palmas_2023'
+        r = ghsci.Region(codename)
+        r.analysis()
+
+    def test_example_generate(self):
+        """Generate resources for example region."""
+        codename = 'example_ES_Las_Palmas_2023'
+        r = ghsci.Region(codename)
+        r.generate()
+
+    def test_sensitivity(self):
+        """Test sensitivity analysis of urban intersection parameter."""
+        reference = 'example_ES_Las_Palmas_2023'
+        comparison = 'ES_Las_Palmas_2023_test_not_urbanx'
+        # create modified version of reference configuration
+        with open(f'./configuration/regions/{reference}.yml') as file:
+            configuration = file.read()
+            configuration = configuration.replace(
+                'ghsl_urban_intersection: true',
+                'ghsl_urban_intersection: false',
+            )
+        with open(f'./configuration/regions/{comparison}.yml', 'w') as file:
+            file.write(configuration)
+        r = ghsci.Region(comparison)
+        r.analysis()
+        r.generate()
+        r.compare(reference, comparison)
+
 
 def calculate_line_endings(path):
     """