Added qmllib dependency, and removed deprecated. Updated pre-commit (#…

…110)

* Updated pre-commit and ran formatting

* Updated `qml`/`qmllib` dependency to the new package

* Updated actions to https://devguide.python.org/versions/ current live Pythons

* Updated actions to make tests work again

.github/workflows/test.yml

@@ -17,22 +17,20 @@ jobs:
         shell: bash -l {0}
     strategy:
       matrix:
-        python-version: ['3.8', '3.9', '3.10']
+        python-version: ['3.9', '3.10', '3.11', '3.12', '3.13']
     steps:
       - uses: actions/checkout@v2
       - uses: conda-incubator/setup-miniconda@v2
         with:
           activate-environment: rmsd-dev
           environment-file: environment.yml
           python-version: ${{ matrix.python-version }}
-      - run: |
-          pip install git+https://github.com/qmlcode/qml@develop
       - run: |
           ls
           pwd
           which python
           conda info
       - run: |
-          make test
+          make test python=python
       - run: |
-          pre-commit run --all-files
+          make format python=python

.pre-commit-config.yaml

@@ -1,7 +1,7 @@
 repos:
 
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v3.4.0
+    rev: v5.0.0
     hooks:
       - id: trailing-whitespace
         exclude: ^tests/resources/
@@ -21,7 +21,7 @@ repos:
         args: ['--maxkb=3000']
 
   - repo: https://github.com/myint/autoflake
-    rev: v1.4
+    rev: v2.3.1
     hooks:
       - id: autoflake
         name: Removes unused variables
@@ -46,7 +46,7 @@ repos:
         ]
 
   - repo: https://github.com/psf/black
-    rev: 22.3.0
+    rev: 24.10.0
     hooks:
       - id: black
         name: Fixes formatting
@@ -55,7 +55,7 @@ repos:
 
 
   - repo: https://github.com/pycqa/flake8
-    rev: 4.0.1
+    rev: 7.1.1
     hooks:
       - id: flake8
         name: Checks pep8 style

Makefile

@@ -1,13 +1,59 @@
+python=./env/bin/python
+
+## Setup
 
 env:
-	conda env create -f ./environment.yml -p ./env --quiet
-	./env/bin/python -m pip install -e .
+	conda env create -f ./environment.yaml -p ./env --quiet
+	${python} -m pre_commit install
+	${python} -m pip install -e .
+
+## Development
 
-env-qml:
-	./env/bin/pip install git+https://github.com/qmlcode/qml@develop
+update-format:
+	${python} -m pre_commit autoupdate
+
+format:
+	${python} -m pre_commit run --all-files
 
 test:
-	python -m pytest -vrs tests
+	${python} -m pytest -rs ./tests
+
+test-dist:
+	${python} -m twine check dist/*
+
+types:
+	${python} -m monkeytype run $$(which ${pytest}) ./tests
+	${python} -m monkeytype list-modules | grep ${pkg} | parallel -j${j} "${python} -m monkeytype apply {} > /dev/null && echo {}"
+
+cov:
+	${python} -m pytest --cov=${pkg} --cov-config .coveragerc --cov-report html tests
+
+compile:
+	${python} _compile.py
+
+build:
+	${python} -m build --sdist --skip-dependency-check  .
+
+upload:
+	${python} -m twine upload ./dist/*.tar.gz
+
+## Version
+
+## Github
+
+## Clean
+
+clean:
+	find ./rmsd/ -type f \
+		-name "*.so" \
+		-name "*.pyc" \
+		-name ".pyo" \
+		-delete
+	rm -rf ./rmsd/*.egg-info/
+	rm -rf *.whl
+	rm -rf ./build/ ./__pycache__/
+	rm -rf ./dist/
 
-test-cov-html:
-	python -m pytest -vrs --cov=rmsd --cov-report html tests
+clean-env:
+	rm -rf ./env/
+	rm ./.git/hooks/pre-commit

environment.yml

@@ -3,11 +3,6 @@ channels:
   - defaults
   - conda-forge
 dependencies:
-  - matplotlib
-  - mypy
-  - numpy
-  - pre-commit
-  - pylint
-  - pytest
-  - pytest-cov
-  - scipy
+  - pip
+  - pip:
+    - -r requirements.txt

pyproject.toml

@@ -0,0 +1,33 @@
+[build-system]
+requires = ["setuptools"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "rmsd"
+dynamic = ["version"]
+authors = []
+requires-python = ">=3.9"
+readme="README.rst"
+description="Calculate Root-mean-square deviation (RMSD) of two molecules, using rotation, in xyz or pdb format "
+classifiers = [
+    "Intended Audience :: Developers",
+    "Intended Audience :: Science/Research",
+    "License :: OSI Approved :: MIT License",
+    "Programming Language :: Python :: 3",
+    "Programming Language :: Python",
+    "Topic :: Scientific/Engineering :: Chemistry",
+]
+keywords = ["pdb", "atoms", "kabsch", "reordering", "rotation", "xyz", "rmsd"]
+dependencies=["numpy", "scipy"]
+
+[project.urls]
+Homepage = "https://github.com/charnley/rmsd"
+
+[options.packages.find]
+where="."
+
+[tool.setuptools]
+include-package-data = true
+
+[tool.setuptools.dynamic]
+version = {attr = "rmsd.__version__"}

requirements.txt

@@ -1,2 +1,14 @@
 numpy
 scipy
+matplotlib
+qmllib
+mypy
+numpy
+pre-commit
+pylint
+pytest
+pytest-cov
+scipy
+build
+twine
+monkeytype

rmsd/calculate_rmsd.py

@@ -24,9 +24,11 @@
 from scipy.spatial.distance import cdist  # type: ignore
 
 try:
-    import qml  # type: ignore
+    import qmllib  # type: ignore
+    from qmllib.kernels import laplacian_kernel  # type: ignore
+    from qmllib.representations import generate_fchl19  # type: ignore
 except ImportError:  # pragma: no cover
-    qml = None  # pragma: no cover
+    qmllib = None  # pragma: no cover
 
 
 METHOD_KABSCH = "kabsch"
@@ -812,7 +814,7 @@ def hungarian_vectors(
 
     if use_kernel:
         # Calculate cost matrix from similarity kernel
-        K = qml.kernels.laplacian_kernel(p_vecs, q_vecs, sigma)
+        K = laplacian_kernel(p_vecs, q_vecs, sigma)
         K *= -1.0
         K += 1.0
 
@@ -858,13 +860,6 @@ def reorder_similarity(
              coordinates of the atoms
     """
 
-    if qml is None:
-        raise ImportError(  # pragma: no cover
-            "QML is not installed. Package is avaliable from"
-            "\n github.com/qmlcode/qml"
-            "\n pip install qml"
-        )
-
     elements = np.unique(p_atoms)
     n_atoms = p_atoms.shape[0]
     distance_cut = 20.0
@@ -876,9 +871,9 @@ def reorder_similarity(
         "acut": distance_cut,
     }
 
-    p_vecs = qml.representations.generate_fchl_acsf(p_atoms, p_coord, **parameters)
+    p_vecs = generate_fchl19(p_atoms, p_coord, **parameters)
 
-    q_vecs = qml.representations.generate_fchl_acsf(q_atoms, q_coord, **parameters)
+    q_vecs = generate_fchl19(q_atoms, q_coord, **parameters)
 
     # generate full view from q shape to fill in atom view on the fly
     view_reorder = np.zeros(q_atoms.shape, dtype=int)
@@ -1837,7 +1832,7 @@ def parse_arguments(arguments: Optional[Union[str, List[str]]] = None) -> argpar
             "error: Cannot reorder atoms and print structure, "
             "when excluding atoms (such as --ignore-hydrogen)"
         )
-        sys.exit()
+        sys.exit(5)
 
     if (
         args.use_reflections
@@ -1848,7 +1843,7 @@ def parse_arguments(arguments: Optional[Union[str, List[str]]] = None) -> argpar
             "error: Cannot use reflections on atoms and print, "
             "when excluding atoms (such as --ignore-hydrogen)"
         )
-        sys.exit()
+        sys.exit(5)
 
     # Check methods
     args.rotation = args.rotation.lower()
@@ -1857,7 +1852,7 @@ def parse_arguments(arguments: Optional[Union[str, List[str]]] = None) -> argpar
             f"error: Unknown rotation method: '{args.rotation}'. "
             f"Please use {valid_rotation_methods}"
         )
-        sys.exit()
+        sys.exit(5)
 
     # Check reorder methods
     args.reorder_method = args.reorder_method.lower()
@@ -1866,7 +1861,7 @@ def parse_arguments(arguments: Optional[Union[str, List[str]]] = None) -> argpar
             f'error: Unknown reorder method: "{args.reorder_method}". '
             f"Please use {valid_reorder_methods}"
         )
-        sys.exit()
+        sys.exit(5)
 
     # Check fileformat
     if args.format is None:
@@ -1885,6 +1880,13 @@ def parse_arguments(arguments: Optional[Union[str, List[str]]] = None) -> argpar
 
         args.format = ext
 
+    # Check QML is installed
+    if args.reorder_method == REORDER_QML and qmllib is None:
+        print(
+            "'qmllib' is not installed. Package is avaliable from: github.com/qmlcode/qmllib or pip install qmllib."
+        )
+        sys.exit(1)
+
     return args
 
 

tests/test_main.py

@@ -5,7 +5,7 @@
 from context import RESOURCE_PATH, call_main
 
 import rmsd as rmsdlib
-from rmsd.calculate_rmsd import get_coordinates_pdb, get_coordinates_xyz, get_coordinates_xyz_lines
+from rmsd.calculate_rmsd import get_coordinates_xyz_lines
 
 
 def test_print_reflection_reorder() -> None:

tests/test_reorder_print.py

@@ -1,5 +1,5 @@
 import numpy as np
-from context import RESOURCE_PATH, call_main
+from context import RESOURCE_PATH
 
 import rmsd as rmsdlib
 from rmsd import get_coordinates_xyz, get_coordinates_xyz_lines

tests/test_reorder_qml.py

@@ -6,7 +6,7 @@
 
 import rmsd as rmsdlib
 
-qml = pytest.importorskip("qml")
+qmllib = pytest.importorskip("qmllib")
 
 
 def test_reorder_qml() -> None: