Changes to requirements and update README.

README.md

@@ -16,23 +16,25 @@ The following libraries are required:
 - [NumPy](http://www.numpy.org/)
 - [OpenBabel](http://openbabel.org/)
 - [RMSD](https://github.com/charnley/rmsd)
-- [QML](https://github.com/qmlcode/qml)
 - [SciPy](https://www.scipy.org/)
 - [scikit-learn](http://scikit-learn.org/stable/index.html)
 - [matplotlib](https://matplotlib.org/)
 
-We use the development branch of `QML` as one of the reordering algorithms.
-Since the development of `QML` has been quite slow, we provide our [own branch](https://github.com/hmcezar/qml/tree/develop) in which installation using modern versions of `numpy` is possible.
+We also have [qmllib](https://github.com/qmlcode/qmllib) as an optional dependency as one of the reordering algorithms.
 
 For `openbabel`, we use the `pip` package `openbabel-wheel` which provides pre-built `openbabel` packages for Linux and MacOS.
 More details can be seen in the [projects' GitHub page](https://github.com/njzjz/openbabel-wheel).
 
-
 You can install the package using `pip`
 ```bash
 pip install clusttraj
 ``` 
 
+If you want to use the `qmllib` reordering algorithm, you can install it with:
+```bash
+pip install clusttraj[qml]
+```
+
 ## Usage
 To see all the options run the script with the `-h` command option:
 ```bash

pyproject.toml

@@ -16,10 +16,10 @@ classifiers = [
   "Intended Audience :: Science/Research",
   "Programming Language :: Python",
   "Programming Language :: Python :: 3 :: Only",
-  "Programming Language :: Python :: 3.8",
   "Programming Language :: Python :: 3.9",
   "Programming Language :: Python :: 3.10",
   "Programming Language :: Python :: 3.11",
+  "Programming Language :: Python :: 3.12",
   "Environment :: Console",
   "License :: OSI Approved :: GNU General Public License v3 (GPLv3)",
   "Operating System :: OS Independent",

requirements.txt

@@ -1,5 +1,5 @@
 numpy
-rmsd
+rmsd>=1.6.0
 scipy
 scikit-learn
 matplotlib