Updated python types and environment (#113)

.gitignore

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

.pre-commit-config.yaml

@@ -20,22 +20,24 @@ repos:
       - id: check-added-large-files
         args: ['--maxkb=3000']
 
+
   - repo: https://github.com/myint/autoflake
     rev: v2.3.1
     hooks:
       - id: autoflake
-        name: Removes unused variables
+        name: removes unused variables
         args:
           - --in-place
           - --remove-all-unused-imports
           - --expand-star-imports
           - --ignore-init-module-imports
 
+
   - repo: https://github.com/pre-commit/mirrors-isort
     rev: v5.10.1
     hooks:
       - id: isort
-        name: Sorts imports
+        name: sorts imports
         args: [
           # Align isort with black formatting
           "--multi-line=3",
@@ -45,11 +47,12 @@ repos:
           "--line-width=99",
         ]
 
+
   - repo: https://github.com/psf/black
     rev: 24.10.0
     hooks:
       - id: black
-        name: Fixes formatting
+        name: fixes formatting
         language_version: python3
         args: ["--line-length=99"]
 
@@ -58,7 +61,7 @@ repos:
     rev: 7.1.1
     hooks:
       - id: flake8
-        name: Checks pep8 style
+        name: checks pep8 style
         args: [
           "--max-line-length=99",
           # Ignore imports in init files
@@ -69,16 +72,11 @@ repos:
           "--ignore=E501,E203,W503",
         ]
 
-  # - repo: https://github.com/pre-commit/mirrors-mypy
-  #   rev: v0.782
-  #   hooks:
-  #   - id: mypy
-  #     args: [--ignore-missing-imports]
 
   - repo: local
     hooks:
       - id: mypy
-        name: Checking types
+        name: checking types
         entry: mypy
         language: system
         types: [ python ]
@@ -87,12 +85,6 @@ repos:
   - repo: local
     hooks:
 
-      # - id: mypy
-      #   name: Static type checking
-      #   entry: mypy
-      #   files: \.py$
-      #   language: python
-
       - id: jupyisort
         name: Sorts ipynb imports
         entry: jupytext --pipe-fmt ".py" --pipe "isort - --multi-line=3 --trailing-comma --force-grid-wrap=0 --use-parentheses --line-width=99" --sync

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

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

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.
@@ -27,8 +27,8 @@
     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)