Merge pull request #468 from healthysustainablecities/enhancements

Enhancements

.ghsci_version

@@ -1 +1 @@
-4.5.3
+4.6.0

.test-compose.yml

@@ -1,7 +1,6 @@
-version: "3"
 services:
   ghsci:
-    image: globalhealthyliveablecities/global-indicators:v4.5.1
+    image: globalhealthyliveablecities/global-indicators:v4.6.0
     container_name: ghsci
     shm_size: 2g
     stdin_open: true # docker run -i

docker-compose.yml

@@ -1,6 +1,6 @@
 services:
   ghsci:
-    image: globalhealthyliveablecities/global-indicators:v4.5.2
+    image: globalhealthyliveablecities/global-indicators:v4.6.0
     container_name: ghsci
     shm_size: 2g
     stdin_open: true # docker run -i

docker/Dockerfile

@@ -18,7 +18,7 @@
 # >>> docker rmi $(docker images -q) --force
 ##############################################################################
 
-FROM continuumio/miniconda3:latest as build
+FROM continuumio/miniconda3:latest AS build
 LABEL maintainer="Global Healthy Liveable City Indicator Study Collaboration Group"
 LABEL url="https://github.com/global-healthy-liveable-cities/global-indicators"
 
@@ -39,7 +39,7 @@ RUN conda config --set show_channel_urls true && \
 
 # =============================================================================
 # Runtime environment
-FROM debian:stable-slim as runtime
+FROM debian:stable-slim AS runtime
 
 # Install the environment pack
 COPY --from=build /env.tar.gz .

docker/environment.yml

@@ -3,22 +3,19 @@ channels:
   - conda-forge
 dependencies:
   - python
-  - osmnx=1.5.* # OpenStreetMap network retrieval and analysis
+  - osmnx=1.9.3 # OpenStreetMap network retrieval and analysis
+  - geopandas=1.0.*
   - pandas=2.1.*
   - fpdf2=2.7.* # pdf templating
   - sqlalchemy=1.4.* # SQL connectivity with PostgreSQL
-  - nicegui=1.4.26 # web app framework
+  - nicegui=1.4.29 # web app framework
   - cryptography=42.0.*,>=42.0.4
-  - requests=2.31.*
-  - tornado>=6.3.*
+  - tornado=6.4.*,>=6.4.1
   - fonttools=4.43.*
-  - jupyterlab=4.0.* # code notebooks / web interface
-  - jupyter-lsp=2.2.*
-  - urllib3=2.0.*
+  - jupyterlab=4.2.* # code notebooks / web interface
   - pillow=10.*,>=10.3.0
-  - pip>=24.*
+  - pip=24.*
   - pyrosm=0.6.* # possible alternate OSM/network retrieval
-  - orjson=3.9.*,>=3.9.15
   - idna>=3.7
   - tqdm=4.*, >=4.66.3
   - openpyxl
@@ -33,3 +30,4 @@ dependencies:
   - psycopg2 # PostgreSQL connection
   - pyyaml # YAML parsing
   - websockets
+  - zipp=3.19.*, >=3.19.1 # https://github.com/healthysustainablecities/global-indicators/security/dependabot/61

docker/requirements.txt

@@ -1,5 +1,5 @@
 affine==2.4.0
-aiofiles==23.2.1
+aiofiles==24.1.0
 aiohttp==3.9.5
 aiosignal==1.3.1
 annotated-types==0.7.0
@@ -18,7 +18,7 @@ branca==0.7.2
 Brotli==1.1.0
 cached-property==1.5.2
 Cartopy==0.23.0
-certifi==2024.2.2
+certifi==2024.7.4
 cffi==1.16.0
 charset-normalizer==3.3.2
 click==8.1.7
@@ -28,34 +28,33 @@ colorama==0.4.6
 comm==0.2.2
 contextily==1.6.0
 contourpy==1.2.1
-cryptography==42.0.7
+cryptography==42.0.8
 cycler==0.12.1
 cykhash==2.0.1
 Cython==3.0.10
 dataclasses==0.8
-debugpy==1.8.1
+debugpy==1.8.2
 decorator==5.1.1
 defusedxml==0.7.1
 docutils==0.21.2
 entrypoints==0.4
 et-xmlfile==1.1.0
-exceptiongroup==1.2.0
+exceptiongroup==1.2.2
 executing==2.0.1
 fastapi==0.109.2
-fastjsonschema==2.19.1
-fiona==1.9.6
-folium==0.16.0
+fastjsonschema==2.20.0
+folium==0.17.0
 fonttools==4.43.1
 fpdf2==2.7.9
 fqdn==1.5.1
 frozenlist==1.4.1
-GDAL==3.8.5
-GeoAlchemy2==0.14.7
+GDAL==3.9.1
+GeoAlchemy2==0.15.2
 geographiclib==2.0
-geopandas==0.14.4
+geopandas==1.0.1
 geopy==2.4.1
 greenlet==3.0.3
-gtfs-lite==0.2.1
+gtfs-lite==0.2.2
 h11==0.14.0
 h2==4.1.0
 hpack==4.0.0
@@ -64,36 +63,36 @@ httpx==0.27.0
 hyperframe==6.0.1
 idna==3.7
 ifaddr==0.2.0
-importlib_metadata==7.1.0
+importlib_metadata==8.0.0
 importlib_resources==6.4.0
-ipykernel==6.29.3
-ipython==8.25.0
+ipykernel==6.29.5
+ipython==8.26.0
 ipywidgets==8.1.3
 isoduration==20.11.0
 itsdangerous==2.2.0
 jedi==0.19.1
 Jinja2==3.1.4
 joblib==1.4.2
 json5==0.9.25
-jsonpointer==2.4
-jsonschema==4.22.0
+jsonpointer==3.0.0
+jsonschema==4.23.0
 jsonschema-specifications==2023.12.1
 jupyter_client==8.6.2
 jupyter_core==5.7.2
 jupyter-events==0.10.0
 jupyter-lsp==2.2.5
-jupyter_server==2.14.1
+jupyter_server==2.14.2
 jupyter_server_terminals==0.5.3
-jupyterlab==4.0.13
+jupyterlab==4.2.3
 jupyterlab_pygments==0.3.0
-jupyterlab_server==2.27.2
+jupyterlab_server==2.27.3
 jupyterlab_widgets==3.0.11
 kiwisolver==1.4.5
 lxml==5.2.2
 mapclassify==2.6.1
-markdown2==2.4.13
+markdown2==2.5.0
 MarkupSafe==2.1.5
-matplotlib==3.8.4
+matplotlib==3.9.1
 matplotlib-inline==0.1.7
 mercantile==1.2.1
 mistune==3.0.2
@@ -104,39 +103,40 @@ nbconvert==7.16.4
 nbformat==5.10.4
 nest_asyncio==1.6.0
 networkx==3.3
-nicegui==1.4.25.dev0
+nicegui==1.4.28.dev0
 notebook_shim==0.2.4
 numexpr==2.10.0
 numpy==1.26.4
-openpyxl==3.1.2
-orjson==3.9.15
-osmnx==1.5.1
+openpyxl==3.1.4
+orjson==3.10.6
+osmnx==1.9.3
 overrides==7.7.0
 OWSLib==0.31.0
-packaging==24.0
+packaging==24.1
 pandana==0.7
 pandas==2.1.4
 pandocfilters==1.5.0
 parso==0.8.4
 pexpect==4.9.0
 pickleshare==0.7.5
-pillow==10.3.0
+pillow==10.4.0
 pip==24.0
 pkgutil_resolve_name==1.3.10
 platformdirs==4.2.2
 prometheus_client==0.20.0
-prompt-toolkit==3.0.42
+prompt_toolkit==3.0.47
 pscript==0.7.7
-psutil==5.9.8
+psutil==6.0.0
 psycopg2==2.9.9
 ptyprocess==0.7.0
 pure-eval==0.2.2
 py-cpuinfo==9.0.0
 pycparser==2.22
-pydantic==2.7.2
-pydantic_core==2.18.3
+pydantic==2.8.2
+pydantic_core==2.20.1
 pygeometa==0.15.3
 Pygments==2.18.0
+pyogrio==0.9.0
 pyparsing==3.1.2
 pyproj==3.6.1
 pyrobuf==0.9.3
@@ -147,23 +147,22 @@ python-dateutil==2.9.0
 python-engineio==4.9.1
 python-json-logger==2.0.7
 python-multipart==0.0.9
-python-rapidjson==1.17
-python-socketio==5.11.2
+python-rapidjson==1.18
+python-socketio==5.11.3
 pytz==2024.1
 PyYAML==6.0.1
 pyzmq==26.0.3
 rasterio==1.3.10
 referencing==0.35.1
-requests==2.31.0
+requests==2.32.3
 rfc3339-validator==0.1.4
 rfc3986-validator==0.1.1
-rpds-py==0.18.1
-Rtree==1.2.0
-scikit-learn==1.5.0
-scipy==1.13.1
+rpds-py==0.19.0
+scikit-learn==1.5.1
+scipy==1.14.0
 Send2Trash==1.8.3
-setuptools==70.0.0
-shapely==2.0.4
+setuptools==71.0.1
+shapely==2.0.5
 simple-websocket==1.0.0
 six==1.16.0
 sniffio==1.3.1
@@ -178,27 +177,28 @@ terminado==0.18.1
 threadpoolctl==3.5.0
 tinycss2==1.3.0
 tomli==2.0.1
-tornado==6.4
+tornado==6.4.1
 tqdm==4.66.4
 traitlets==5.14.3
 types-python-dateutil==2.9.0.20240316
-typing_extensions==4.12.1
+typing_extensions==4.12.2
 typing-utils==0.1.0
 tzdata==2024.1
-uharfbuzz==0.39.1
+uharfbuzz==0.39.3
 uri-template==1.3.0
-urllib3==2.0.7
-uvicorn==0.30.0
+urllib3==2.2.2
+uvicorn==0.30.1
 vbuild==0.8.2
 watchfiles==0.22.0
 wcwidth==0.2.13
-webcolors==1.13
+webcolors==24.6.0
 webencodings==0.5.1
 websocket-client==1.8.0
 websockets==12.0
 wheel==0.43.0
 widgetsnbextension==4.0.11
 wsproto==1.2.0
-xyzservices==2024.4.0
+xyzservices==2024.6.0
 yarl==1.9.4
-zipp==3.17.0
+zipp==3.19.2
+zstandard==0.23.0

process/analysis.py

@@ -161,6 +161,7 @@ def analysis(r):
                 "When using psql, you can type '\\dt' to list database tables, '\\d <table_name>' to list table columns, and 'SELECT * FROM <table_name> LIMIT 10;' to view the first 10 rows of a table.  To exit psql, enter '\\q'."
                 '\n\n',
             )
+        append_to_log_file.close()
 
 
 def main():

process/example.ipynb

@@ -424,7 +424,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.12.3"
+   "version": "3.12.4"
   }
  },
  "nbformat": 4,

process/subprocesses/bulk_gdal_merge.py

@@ -24,10 +24,16 @@ def valid_path(arg):
     description='Generate origin destination matrix',
 )
 parser.add_argument(
-    '-dir', help='parent directory', default=cwd, type=valid_path,
+    '-dir',
+    help='parent directory',
+    default=cwd,
+    type=valid_path,
 )
 parser.add_argument(
-    '-outfile', help='outfile name', default='gdal_merged.tif', type=str,
+    '-outfile',
+    help='outfile name',
+    default='gdal_merged.tif',
+    type=str,
 )
 parser.add_argument(
     '-gdal_loc',
@@ -39,7 +45,7 @@ def valid_path(arg):
 
 # initialise tif list file
 tif_list_name = 'tif_list_{date:%Y-%m-%d}.txt'.format(
-    date=datetime.datetime.now(),
+    date=datetime.datetime.now(datetime.UTC),
 )
 tif_list_path = os.path.join(args.dir, tif_list_name)
 tif_list = open(tif_list_path, 'w')