switched requirements.txt to pyproject.toml

.devcontainer/devcontainer.json

@@ -14,7 +14,7 @@
 		"ghcr.io/devcontainers/features/git:1": {}
 	},
 	//"onCreateCommand": "apt-get update && apt-get install -y python3-pip pipenv",
-	"postCreateCommand": "pipenv --python 3 && pipenv run pip install -r requirements.txt",
+	"postCreateCommand": "pipenv --python 3 && pipenv run pip install -e .",
 
 	//"postCreateCommand": "id",
 	"customizations": {

Dockerfile

@@ -9,11 +9,7 @@ RUN apt-get update && \
 
 WORKDIR /app
 
-COPY requirements.txt .
-RUN pipenv --python 3 && pipenv install -r requirements.txt
-
 COPY . .
+RUN pipenv --python 3 && pipenv run pip install -e .
 
-RUN chmod +x cbsurge.sh
-
-CMD [ "./cbsurge.sh", "--help"]
+CMD [ "pipenv", "run", "rapida", "--help"]

Makefile

@@ -21,7 +21,7 @@ test:
 	@echo "------------------------------------------------------------------"
 	@echo "Execute test cases"
 	@echo "------------------------------------------------------------------"
-	pipenv run python -m pytest cbsurge/stats
+	pipenv run python -m pytest tests
 
 build:
 	@echo

README.md

@@ -3,16 +3,22 @@ A repo to hold python tools that facilitate the assessment of natural hazards ov
 
 ## Usage
 
-Install dependencies to virtual environment as below.
+Install the project with dependencies to virtual environment as below.
 
 ```shell
-pipenv install -r requirements.txt
+pipenv run pip install -e .
 ```
 
 Then, run the below command to show help menu.
 
 ```shell
-pipenv run python -m cbsurge.cli --help
+pipenv run rapida --help
+```
+
+To uninstall the project from Python environment, execute the following command.
+
+```shell
+pipenv run pip uninstall geo-cb-surge
 ```
 
 ## Admin
@@ -22,13 +28,13 @@ pipenv run python -m cbsurge.cli --help
 - OSM
 
 ```shell
-pipenv run python -m cbsurge.cli admin osm --help
+pipenv run rapida admin osm --help
 ```
 
 - ocha
 
 ```shell
-pipenv run python -m cbsurge.cli admin ocha --help
+pipenv run rapida admin ocha --help
 ```
 
 ## Run test
@@ -59,5 +65,5 @@ make down
 
 ```shell
 make shell
-./cbsurge.sh --help # run CLI in shell on docker container
+pipenv run rapida --help # run CLI in shell on docker container
 ```

cbsurge/admin/__init__.py

@@ -100,7 +100,7 @@ def osm(bbox=None,admin_level=None, osm_level=None, clip=False, h3id_precision=7
 
     To save the result as a file, for instance, the following command can be executed to extract admin 0 data for Rwanda and Burundi as GeoJSON file:
 
-    python -m  cbsurge.cli admin osm -b "27.767944,-5.063586,31.734009,-0.417477" -l 0 > osm.geojson
+    rapida admin osm -b "27.767944,-5.063586,31.734009,-0.417477" -l 0 > osm.geojson
     """
     silence_httpx_az()
     logging.basicConfig(level=logging.DEBUG if debug else logging.INFO)
@@ -156,7 +156,7 @@ def ocha(bbox=None,admin_level=None,  clip=False, h3id_precision=7, debug=False)
 
     To save the result as a file, for instance, the following command can be executed to extract admin 0 data for Rwanda and Burundi as GeoJSON file:
 
-    python -m  cbsurge.cli admin ocha -b "27.767944,-5.063586,31.734009,-0.417477" -l 0 > ocha.geojson
+    rapida admin ocha -b "27.767944,-5.063586,31.734009,-0.417477" -l 0 > ocha.geojson
     """
     silence_httpx_az()
     logging.basicConfig(level=logging.DEBUG if debug else logging.INFO)

cbsurge/stats/__init__.py

@@ -73,10 +73,10 @@ def compute(
 
     Usage: \n
         The below command provides how to use the command to compute zonal statistics.\n
-        python -m cbsurge.cli stats compute --help
+        rapida stats compute --help
 
     Example: \n
-        python -m cbsurge.cli stats compute ./cbsurge/stats/tests/assets/admin2.geojson ./cbsurge/stats/tests/assets/admin2_stats.fgb -r ./cbsurge/stats/tests/assets/rwa_m_5_2020_constrained_UNadj.tif -r ./cbsurge/stats/tests/assets/rwa_f_5_2020_constrained_UNadj.tif -o sum -c male_5_sum -c female_5_sum
+        rapida stats compute ./cbsurge/stats/tests/assets/admin2.geojson ./cbsurge/stats/tests/assets/admin2_stats.fgb -r ./cbsurge/stats/tests/assets/rwa_m_5_2020_constrained_UNadj.tif -r ./cbsurge/stats/tests/assets/rwa_f_5_2020_constrained_UNadj.tif -o sum -c male_5_sum -c female_5_sum
     """
     logging.basicConfig(level=logging.DEBUG if debug else logging.INFO)
     with ZonalStats(input_file, target_srid=54009) as st:

docker-compose.yaml

@@ -8,4 +8,5 @@ services:
     command: "pipenv run python -m cbsurge.cli --help"
     volumes:
       - ./Makefile:/app/Makefile
-      - ./cbsurge:/app/cbsurge # mount app folder to container
+      - ./cbsurge:/app/cbsurge # mount app folder to container
+      - ./tests:/app/tests

pyproject.toml

@@ -0,0 +1,69 @@
+[project]
+name = "geo-cb-surge"
+version = "0.0.1"
+description = "python tools that facilitate the assessment of natural hazards over various domains like population, landuse, infrastructure, etc"
+requires-python = ">=3.12"
+authors = [
+    { name = 'Ioan Ferencik'},
+    { name = 'Joseph Thuha'},
+    { name = 'Jin Igarashi'},
+    { name = "United Nations Development Programme", email = "[email protected]" }
+]
+readme = "README.md"
+dependencies = [
+    "httpx",
+    "osm2geojson",
+    "shapely",
+    "h3",
+    "tqdm",
+    "GDAL==3.10.0",
+    "azure-storage-blob",
+    "overturemaps",
+    "async",
+    "aiofiles",
+    "aiohttp",
+    "azure-storage-blob",
+    "asyncclick",
+    "rio-cogeo",
+    "exactextract",
+    "pycountry",
+    "click",
+    "pyarrow",
+    "azure-core",
+    "rasterio",
+    "geopandas",
+    "pytest"
+]
+
+[project.scripts]
+rapida = "cbsurge.cli:cli"
+
+[tool.setuptools]
+py-modules = ["cbsurge"]
+
+[project.urls]
+Homepage = "https://github.com/UNDP-Data/geo-cb-surge"
+Documentation = "https://github.com/UNDP-Data/geo-cb-surge"
+Repository = "https://github.com:UNDP-Data/geo-cb-surge.git"
+Issues = "https://github.com/UNDP-Data/geo-cb-surge/issues"
+#Changelog = "https://github.com/UNDP-Data/geo-cb-surge/blob/master/CHANGELOG.md"
+
+[tool.hatch.build.targets.wheel]
+    packages = ["cbsurge"]
+
+[tool.hatch.build.targets.sdist]
+exclude = [
+    ".devcontainer",
+    ".github",
+    ".dockerignore",
+    "docker-compose.yml",
+    "Dockerfile",
+    ".gitignore",
+    ".pre-commit-config.yaml",
+    "tests",
+    "Makefile"
+]
+
+[build-system]
+requires = ["hatchling"]
+build-backend = "hatchling.build"

cbsurge/stats/tests/test_ZonalStats.py → tests/cbsurge/stats/test_ZonalStats.py

@@ -2,7 +2,7 @@
 import pytest
 from cbsurge.stats.ZonalStats import ZonalStats
 
-TEST_DIR = "./cbsurge/stats/tests"
+TEST_DIR = "./tests/cbsurge/stats"
 
 def get_test_path(relative_path):
     """Helper function to generate absolute paths for test assets."""