Adding mypy types

.github/workflows/test.yml

@@ -4,35 +4,35 @@ name: Test Python package
 on:
   push:
     branches:
-      - 'master'
-      - 'dev'
+      - '**'
   pull_request:
     branches: [ master ]
 
 jobs:
-  build:
-
-    runs-on: ubuntu-latest
+  test:
+    name: Testing
+    runs-on: "ubuntu-latest"
+    defaults:
+      run:
+        shell: bash -l {0}
     strategy:
       matrix:
-        python-version: [3.6, 3.7, 3.8]
-
+        python-version: ['3.7', '3.8', '3.9', '3.10']
     steps:
-    - uses: actions/checkout@v2
-    - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v2
-      with:
-        python-version: ${{ matrix.python-version }}
-    - name: Install dependencies
-      run: |
-        python -m pip install --upgrade pip
-        if test -f requirements.txt; then pip install -r requirements.txt; fi
-        if test -f requirements.dev.txt; then pip install -r requirements.dev.txt; fi
-        python -m pip install git+https://github.com/qmlcode/qml@develop
-        python -m pip install pre-commit
-    - name: Test format
-      run: |
-        pre-commit run --all-files
-    - name: Test with pytest
-      run: |
-        make test
+      - 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
+      - run: |
+          pre-commit run --all-files

.gitignore

@@ -1,8 +1,13 @@
 # dev
 .vim
+env
 
 *.py[cod]
 
+# Test coverage
+htmlcov
+*,cover
+
 # setup.py output
 files.txt
 

.pre-commit-config.yaml

@@ -75,6 +75,15 @@ repos:
   #   - id: mypy
   #     args: [--ignore-missing-imports]
 
+  - repo: local
+    hooks:
+      - id: mypy
+        name: Checking types
+        entry: mypy
+        language: system
+        types: [ python ]
+
+
   - repo: local
     hooks:
 

Makefile

@@ -1,4 +1,9 @@
-python = python
+
+env:
+	conda env create -f ./environment.yml -p ./env --quiet
 
 test:
-	${python} -m pytest -vrs tests
+	python -m pytest -vrs tests
+
+test-cov-html:
+	python -m pytest -vrs --cov=rmsd --cov-report html tests

environment.yml

@@ -0,0 +1,13 @@
+name: rmsd-dev
+channels:
+  - defaults
+  - conda-forge
+dependencies:
+  - matplotlib
+  - mypy
+  - numpy
+  - pre-commit
+  - pylint
+  - pytest
+  - pytest-cov
+  - scipy

example.py

@@ -1,14 +1,15 @@
 #!/usr/bin/env python
 
-from __future__ import print_function
+from pathlib import Path
 
-import matplotlib.pyplot as plt
+import matplotlib.pyplot as plt  # type: ignore
 import numpy as np
+from numpy import ndarray
 
 import rmsd
 
 
-def rotation_matrix(sigma):
+def rotation_matrix(sigma: float) -> ndarray:
     """
 
     https://en.wikipedia.org/wiki/Rotation_matrix
@@ -27,7 +28,7 @@ def rotation_matrix(sigma):
     return R
 
 
-def save_plot(A, B, filename):
+def save_plot(A: ndarray, B: ndarray, filename: Path) -> None:
 
     Ax = A[:, 0]
     Ay = A[:, 1]
@@ -42,12 +43,9 @@ def save_plot(A, B, filename):
     plt.xlim([-2.5, 2.5])
     plt.grid(True)
     plt.tick_params(labelsize=15)
-    plt.savefig(filename + ".png")
-
+    plt.savefig(filename.with_suffix(".png"))
     plt.clf()
 
-    return
-
 
 A = np.array([[1.0, 1.0], [1.0, 2.0], [2.0, 1.5]])
 
@@ -63,17 +61,17 @@ def save_plot(A, B, filename):
 B = np.dot(B, rotation_matrix(90))
 
 print("Normal RMSD", rmsd.rmsd(A, B))
-save_plot(A, B, "plot_beginning")
+save_plot(A, B, Path("plot_beginning"))
 
 # Manipulate
 A -= rmsd.centroid(A)
 B -= rmsd.centroid(B)
 
 print("Translated RMSD", rmsd.rmsd(A, B))
-save_plot(A, B, "plot_translated")
+save_plot(A, B, Path("plot_translated"))
 
 U = rmsd.kabsch(A, B)
 A = np.dot(A, U)
 
 print("Rotated RMSD", rmsd.rmsd(A, B))
-save_plot(A, B, "plot_rotated")
+save_plot(A, B, Path("plot_rotated"))

requirements.txt

@@ -1,2 +1,2 @@
-scipy
 numpy
+scipy

rmsd/__init__.py

@@ -12,18 +12,23 @@
     "get_coordinates_pdb",
     "get_coordinates_xyz",
     "hungarian",
+    "int_atom",
     "kabsch",
     "kabsch_rmsd",
     "kabsch_rotate",
+    "kabsch_fit",
     "quaternion_rmsd",
     "quaternion_rotate",
     "quaternion_transform",
     "reorder_brute",
     "reorder_distance",
     "reorder_hungarian",
+    "reorder_inertia_hungarian",
+    "reorder_similarity",
     "rmsd",
     "set_coordinates",
+    "str_atom",
 ]
 
 if __name__ == "__main__":
-    calculate_rmsd.main()
+    calculate_rmsd.main()  # pragma: no cover