Merge pull request #21 from DEMENT-Model/iss12-env-dependency

Iss12 env dependency

Author: omarjamil

.pre-commit-config.yml

@@ -0,0 +1,12 @@
+repos:
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+  # Ruff version.
+    rev: v0.11.4
+    hooks:
+      # Run the linter.
+      - id: ruff
+        types_or: [ python, pyi ]
+        args: [ --fix ]
+      # Run the formatter.
+      - id: ruff-format
+

README.md

@@ -57,12 +57,20 @@ git clone https://github.com/bioatmosphere/DEMENTpy
 
 **Run DEMENTpy**:
 
-- Configure Environment
-- - Python >= 3.7
-- - Numpy >= 1.16.4
-- - Pandas >= 0.24.2
+[UV](https://github.com/astral-sh/uv) can be used to manage dependencies in `pyproject.toml`. In order to create a virtual ennviroment with DEMENTpy dependencies, do the following: 
 
-A simple example of bash script, dementpy.sh, for running jobs on HPC is provided.
+```
+uv venv
+uv sync --dev 
+source .venv/bin/activate
+```
+if you are not running as developer then leave off the `--dev` switch.
+
+A simple example of bash script, dementpy.sh, for running jobs on HPC is provided. For testing, a simple run can be carried out as follows:
+
+```
+python dementpy.py grassland output 20250402 scrubland
+```
 
 ### Contribution
 

pyproject.toml

@@ -0,0 +1,16 @@
+[project]
+name = "dementpy"
+version = "0.1.0"
+description = "DEMENT (Decomposition Model of Enzymatic Traits): A trait- and individual-based spatially explicit soil microbial systems modelling framework"
+readme = "README.md"
+requires-python = ">=3.12"
+dependencies = [
+    "pandas>=2.2.3",
+    "scipy>=1.15.2",
+]
+
+[dependency-groups]
+dev = [
+    "pre-commit>=4.2.0",
+    "ruff>=0.11.4",
+]