Run test update

.gitignore

@@ -1,6 +1,7 @@
 # dev
 .vim
 env
+*.sqlite3
 
 *.py[cod]
 

Makefile

@@ -1,9 +1,11 @@
 python=./env/bin/python
+pytest=./env/bin/pytest
+package=rmsd
 
 ## Setup
 
 env:
-	conda env create -f ./environment.yaml -p ./env --quiet
+	conda env create -f ./environment.yml -p ./env --quiet
 	${python} -m pre_commit install
 	${python} -m pip install -e .
 
@@ -23,10 +25,10 @@ test-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 {}"
+	${python} -m monkeytype list-modules | grep ${package} | parallel -j1 "${python} -m monkeytype apply {} > /dev/null && echo {}"
 
 cov:
-	${python} -m pytest --cov=${pkg} --cov-config .coveragerc --cov-report html tests
+	${python} -m pytest --cov=${package} --cov-config .coveragerc --cov-report html tests
 
 compile:
 	${python} _compile.py

requirements.txt

@@ -1,5 +1,6 @@
 numpy
 scipy
+scipy-stubs
 matplotlib
 qmllib
 mypy

rmsd/calculate_rmsd.py

@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/env python3
 __doc__ = """
 Calculate Root-mean-square deviation (RMSD) between structure A and B, in XYZ
 or PDB format, using transformation and rotation.
@@ -19,16 +19,16 @@
 
 import numpy as np
 from numpy import ndarray
-from scipy.optimize import linear_sum_assignment  # type: ignore
-from scipy.spatial import distance_matrix  # type: ignore
-from scipy.spatial.distance import cdist  # type: ignore
+from scipy.optimize import linear_sum_assignment
+from scipy.spatial import distance_matrix
+from scipy.spatial.distance import cdist
 
 try:
     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
-    qmllib = None  # pragma: no cover
+except ImportError:
+    qmllib = None
 
 
 METHOD_KABSCH = "kabsch"
@@ -1939,8 +1939,8 @@ def main(args: Optional[List[str]] = None) -> str:
     use_view: bool = True
 
     if settings.ignore_hydrogen:
-        p_view = np.where(p_atoms != 1)  # type: ignore
-        q_view = np.where(q_atoms != 1)  # type: ignore
+        (p_view,) = np.where(p_atoms != 1)
+        (q_view,) = np.where(q_atoms != 1)
 
     elif settings.remove_idx:
         index = np.array(list(set(range(p_size)) - set(settings.remove_idx)))
@@ -2088,5 +2088,5 @@ def main(args: Optional[List[str]] = None) -> str:
 
 
 if __name__ == "__main__":
-    result = main()  # pragma: no cover
+    result = main()
     print(result)