Make qml optional dependency.

clusttraj/io.py

@@ -269,9 +269,9 @@ def configure_runtime(args_in: List[str]) -> ClustOptions:
     parser.add_argument(
         "--reorder-alg",
         action="store",
-        default="qml",
+        default="hungarian",
         metavar="METHOD",
-        help="select which reorder algorithm to use; hungarian, brute, distance, qml (default). Warning: brute is VERY slow)",
+        help="select which reorder algorithm to use; hungarian (default), brute, distance, qml. Warning: brute is VERY slow)",
     )
     parser.add_argument(
         "-ns",

pyproject.toml

@@ -42,6 +42,10 @@ clusttraj = "clusttraj.main:main"
 
 [project.optional-dependencies]
 test = ["pytest", "pytest-cov[all]"]
+docs = ["sphinx", "sphinx_rtd_theme"]
+lint = ["ruff", "black"]
+qml = ["qml @ git+https://github.com/hmcezar/qml@develop"]
+all = ["clusttraj[test,docs,lint,qml]"]
 
 [tool.setuptools]
 packages = ["clusttraj"]

requirements.txt

@@ -3,5 +3,4 @@ rmsd
 scipy
 scikit-learn
 matplotlib
-qml @ git+https://github.com/hmcezar/qml@develop
 openbabel-wheel>=3.0