Update requirements and installation

README.md

@@ -23,40 +23,16 @@ There is a series of detailed tutorials for *PolyConf* in the folder [polyconf_e
 
 ## Quick and dirty installation
 
-From your home directory, clone *PolyConstruct* from this repository:
-
-```bash
-cd ~
-git clone https://github.com/OMaraLab/polyconstruct.git
-```
-
-Then navigate to `~/polyconstruct`
-
-```bash
-cd polyconstruct
-```
-
-Create a python environment and setup *PolyConstruct*:
+Create and activate a new python environment:
 
 ```bash
 conda create --name polyconstruct python=3.10
 conda activate polyconstruct
-
-pip install -r requirements.txt
 ```
 
-Then, build the *PolyTop*, *PolyConf* and *PolyBuild* packages:
+Install dependencies and *PolyConstruct*:
 
 ```bash
-cd polytop
-
-pip install -e .
-
-cd ../polyconf
-
-pip install -e .
-
-cd ../polybuild
-
-pip install -e .
+pip install "polyconstruct@git+https://github.com/OMaraLab/polyconstruct.git"
 ```
+

pyproject.toml

@@ -13,13 +13,20 @@ license = { text = "MIT License" }
 
 # Dependencies required for your project
 dependencies = [
-    "numpy",
-    "mdanalysis",
-    "click",
-    "py3Dmol",
-    "rdkit",
+    "numpy==2.2.6",
+    "MDAnalysis==2.9.0",
+    "click==8.3.0",
+    "py3Dmol==2.5.2",
+    "rdkit==2025.3.6",
+    "networkx==3.4.2",
+    "pandas==2.3.2",
+    "tqdm==4.67.1"
 ]
 
-[tool.setuptools.packages.find]
-where = ["."]
-include = ["*"]
+[tool.setuptools]
+packages = ["polybuild", "polybuild.polybuild", "polyconf", "polyconf.polyconf", "polytop", "polytop.polytop"]
+
+[tool.setuptools.package-dir]
+polybuild.polybuild = "polybuild"
+polyconf.polyconf = "polyconf"
+polytop.polytop = "polytop"