Type hinting (#127)

- implemented the basic infrastructure for type-hints

- added a couple of type hints. 

- defined a custom `numba.njit` wrapper, that preserves the type information and sets `cache=True` by default. (related to and relevant for numba/numba#7424)

.circleci/config.yml

@@ -36,10 +36,6 @@ run_tests: &run_tests
       - run:
           name: Running tests
           command: python3 -m pytest -Werror --cov=./src/chemcoord tests/
-      - run:
-          name: Upload coverage reports to Codecov
-          command: |
-            bash <(curl -s https://codecov.io/bash)
       - run:
           name: Prepare documentation
           command: pip3 install -r docs/requirements.txt

.gitignore

@@ -66,3 +66,6 @@ cealign-0.8-RBS
 #pytest
 *.chache/*
 .cache/
+
+
+.mypy_cache/

setup.py

@@ -17,6 +17,7 @@
     "sympy",
     "six",
     "pymatgen",
+    "typing_extensions",
 ]
 KEYWORDS = [
     "chemcoord",

src/chemcoord/_cartesian_coordinates/_cart_transformation.py

@@ -1,13 +1,13 @@
 import numba as nb
 import numpy as np
-from numba import njit
 from numba.extending import overload
 from numpy import arccos, arctan2, sqrt
 
 import chemcoord.constants as constants
 from chemcoord._cartesian_coordinates.xyz_functions import (
     _jit_normalize,
 )
+from chemcoord._utilities._decorators import njit
 from chemcoord.exceptions import ERR_CODE_OK, ERR_CODE_InvalidReference
 
 
@@ -44,12 +44,12 @@ def f(X, indices):
         raise AssertionError("Should not be here")
 
 
-@njit(cache=True)
+@njit
 def get_ref_pos(X, indices):
     return _stub_get_ref_pos(X, indices)
 
 
-@njit(cache=True)
+@njit
 def get_B(X, c_table, j):
     B = np.empty((3, 3))
     ref_pos = get_ref_pos(X, c_table[:, j])
@@ -66,7 +66,7 @@ def get_B(X, c_table, j):
     return (ERR_CODE_OK, B)
 
 
-@njit(cache=True)
+@njit
 def get_grad_B(X, c_table, j):
     grad_B = np.empty((3, 3, 3, 3))
     ref_pos = get_ref_pos(X, c_table[:, j])
@@ -1130,7 +1130,7 @@ def get_grad_S_inv(v):
     return grad_S_inv
 
 
-@njit(cache=True)
+@njit
 def get_T(X, c_table, j):
     err, B = get_B(X, c_table, j)
     if err == ERR_CODE_OK:
@@ -1141,7 +1141,7 @@ def get_T(X, c_table, j):
     return err, result
 
 
-@njit(cache=True)
+@njit
 def get_C(X, c_table):
     C = np.empty((3, c_table.shape[1]))
 
@@ -1154,7 +1154,7 @@ def get_C(X, c_table):
     return (ERR_CODE_OK, C)
 
 
-@njit(cache=True)
+@njit
 def get_grad_C(X, c_table):
     n_atoms = X.shape[1]
     grad_C = np.zeros((3, n_atoms, n_atoms, 3))