mak installation pypi-compatible

Author: sfluegel05

README.md

@@ -6,8 +6,13 @@ A web application for the ensemble is available at https://chebifier.hastingslab
 
 ## Installation
 
-Note: `chebai-graph` and its dependencies cannot be installed automatically. To install it, follow
-the instructions in the [chebai-graph repository](https://github.com/ChEB-AI/python-chebai-graph). Other dependencies are installed automatically.
+Not all models can be installed automatically at the moment:
+- `chebai-graph` and its dependencies. To install them, follow
+the instructions in the [chebai-graph repository](https://github.com/ChEB-AI/python-chebai-graph). 
+- `chemlog-extra` can be installed with `pip install git+https://github.com/ChEB-AI/chemlog-extra.git`
+- The automatically installed version of `c3p` may not work under Windows. If you want to run chebifier on Windows, we 
+recommend using this forked version: `pip install git+https://github.com/sfluegel05/c3p.git`
+
 
 You can get the package from PyPI:
 ```bash

pyproject.toml

@@ -25,9 +25,11 @@ dependencies = [
     "rdkit",
     "chebai>=1.0.1",
     "chemlog>=1.0.4",
-    "chemlog_extra @ git+https://github.com/ChEB-AI/chemlog-extra.git",
+    # pypi does not support git dependencies
+    #"chemlog_extra @ git+https://github.com/ChEB-AI/chemlog-extra.git",
+    "c3p"
     # forked version of c3p is windows-compatible
-    "c3p @ git+https://github.com/sfluegel05/c3p.git"
+    #"c3p @ git+https://github.com/sfluegel05/c3p.git"
 ]