add fix-encoding-pragma hook

.pre-commit-config.yaml

@@ -2,7 +2,7 @@ default_language_version:
   python: python3.7
 default_stages: [commit, push, manual]
 repos:
--   repo: https://github.com/ambv/black
+  - repo: https://github.com/ambv/black
     rev: stable
     hooks:
     - id: black
@@ -13,23 +13,23 @@ repos:
       types: [python]
       files: \.pyi?$
 
--   repo: https://github.com/asottile/blacken-docs
+  - repo: https://github.com/asottile/blacken-docs
     rev: v1.0.0
     hooks:
-    -   id: blacken-docs
-        additional_dependencies: [black==19.3b0]
-        language: python
-        language_version: python3.7
+    - id: blacken-docs
+      additional_dependencies: [black==19.3b0]
+      language: python
+      language_version: python3.7
 
--   repo: https://github.com/pre-commit/pre-commit-hooks
+  - repo: https://github.com/pre-commit/pre-commit-hooks
     rev: v1.2.3
     hooks:
     - id: check-yaml
       language: python
     - id: check-added-large-files
       language: python
-    # - id: fix-encoding-pragma
-    #   language: python
+    - id: fix-encoding-pragma
+      language: python
     - id: check-docstring-first
       language: python
     - id: flake8
@@ -46,7 +46,6 @@ repos:
       language: python
       types: [python]
 
-
 # -   repo: https://github.com/asottile/reorder_python_imports
 #     rev: v1.4.0
 #     hooks:

setup.py

@@ -1,4 +1,4 @@
-# -*- coding: utf-8 -*-
+# -*- coding: utf-8 -*-
 
 from setuptools import Extension
 from setuptools import find_packages

src/c_lib/include/Hamiltonian.h

@@ -6,8 +6,8 @@
 //  Contact email = srivastava.89@osu.edu, deepansh2012@gmail.com
 //
 
-#include "transition_function.h"
 #include "mrsimulator.h"
+#include "transition_function.h"
 
 /*
 ===============================================================================
@@ -18,8 +18,7 @@ spin transition functions.
 */
 static inline void get_nuclear_shielding_hamiltonian_to_first_order(
     double *R0, complex128 *R2, double iso, double zeta, double eta,
-    double *transition)
-{
+    double *transition) {
   // Spin transition contribution
   double transition_fn = p(transition[1], transition[0]);
 
@@ -45,10 +44,10 @@ static inline void get_nuclear_shielding_hamiltonian_to_first_order(
 The Hamiltonian includes the product of second rank tensor and the
 spin transition functions.
 */
-static inline void get_quadrupole_hamiltonian_to_first_order(
-    double *R0, complex128 *R2, double spin, double Cq, double eta,
-    double *transition)
-{
+static inline void
+get_quadrupole_hamiltonian_to_first_order(double *R0, complex128 *R2,
+                                          double spin, double Cq, double eta,
+                                          double *transition) {
   // Spin transition contribution
   double transition_fn = d(transition[1], transition[0]);
 
@@ -79,10 +78,9 @@ The Hamiltonian includes the product of second rank tensor and the
 spin transition functions.
 */
 static inline void get_quadrupole_hamiltonian_to_second_order(
-    double *R0, complex128 *R2, complex128 *R4, double spin,
-    double Cq, double eta, double *transition, double vo,
-    int remove_second_order_quad_iso)
-{
+    double *R0, complex128 *R2, complex128 *R4, double spin, double Cq,
+    double eta, double *transition, double vo,
+    int remove_second_order_quad_iso) {
   // Spin transition contribution
   double c0, c2, c4;
   quad_ci(&c0, &c2, &c4, transition[1], transition[0], spin);
@@ -97,31 +95,30 @@ static inline void get_quadrupole_hamiltonian_to_second_order(
   double eta2 = eta * eta;
 
   // Scaled R00
-  if (remove_second_order_quad_iso == 0)
-  {
+  if (remove_second_order_quad_iso == 0) {
     R0[0] += (eta2 * 0.33333333333 + 1.0) * 0.07453559925 * scale * c0;
   }
 
   /* Scaled R2m containing the components of the quad second rank tensor in
   its principal axis frame. */
   double temp = -eta * 0.07273929675 * scale * c2;
   double temp2 = 0.08908708064 * (eta2 * 0.33333333333 - 1.0) * scale * c2;
-  complex128_add_inplace(R2[0], temp);                                                      // R2-2
-  complex128_add_inplace(R2[1], 0.0);                                                       // R2-1
+  complex128_add_inplace(R2[0], temp);  // R2-2
+  complex128_add_inplace(R2[1], 0.0);   // R2-1
   complex128_add_inplace(R2[2], temp2); // R2 0
-  complex128_add_inplace(R2[3], 0.0);                                                       // R2 1
-  complex128_add_inplace(R2[4], temp);                                                      // R2 2
+  complex128_add_inplace(R2[3], 0.0);   // R2 1
+  complex128_add_inplace(R2[4], temp);  // R2 2
 
   /* Scaled R4m containing the components of the quad second rank tensor in
   its principal axis frame. */
   temp = eta2 * 0.02777777778 * scale * c4;
   temp2 = -0.06299407883 * eta * scale * c4;
   double temp4 = 0.1195228609 * (eta2 * 0.05555555556 + 1.0) * scale * c4;
-  complex128_add_inplace(R4[0], temp);                                                     // R4-4
-  complex128_add_inplace(R4[2], temp2);                                                    // R4-2
+  complex128_add_inplace(R4[0], temp);  // R4-4
+  complex128_add_inplace(R4[2], temp2); // R4-2
   complex128_add_inplace(R4[4], temp4); // R4 0
-  complex128_add_inplace(R4[6], temp2);                                                    // R4 2
-  complex128_add_inplace(R4[8], temp);                                                     // R4 4
+  complex128_add_inplace(R4[6], temp2); // R4 2
+  complex128_add_inplace(R4[8], temp);  // R4 4
 }
 
 /*
@@ -132,8 +129,7 @@ The Hamiltonian includes the product of second rank tensor and the
 spin transition functions in the weak coupling limit.
 */
 static inline void get_weakly_coupled_direct_dipole_hamiltonian_to_first_order(
-    double *R0, complex128 *R2, double D, double *transition)
-{
+    double *R0, complex128 *R2, double D, double *transition) {
   // Spin transition contribution
   double transition_fn = dIS(transition[0], transition[1], 0.5, 0.5);
 

src/c_lib/include/config.h

@@ -82,6 +82,4 @@ inline complex128 complex128_add_inplace(complex128 a, double b) {
 // // printf("Using upto %d threads for simulation.\n", max_threads);
 // #endif
 
-
-
 #endif

src/c_lib/include/isotopomer_ravel.h

@@ -32,7 +32,6 @@ struct __isotopomers_list {
   isotopomer_ravel *isotopomers;
 };
 
-
 typedef struct __isotopomers_list isotopomers_list;
 
 #endif /* isotopomer_h */

src/c_lib/include/spinning_sidebands.h

@@ -24,7 +24,7 @@ extern void spinning_sideband_core(
                                       // the second order quad Hamiltonian.
 
     // spin rate, spin angle and number spinning sidebands
-    int number_of_sidebands,          // The number of sidebands
+    int number_of_sidebands,                // The number of sidebands
     double sample_rotation_frequency_in_Hz, // The rotor spin frequency
     double rotor_angle_in_rad, // The rotor angle relative to lab-frame z-axis
 

src/c_lib/include/transition_function.h

@@ -36,7 +36,6 @@
  */
 static inline double p(double mf, double mi) { return (mf - mi); }
 
-
 /**
  * @brief The @f$\mathbb{d}@f$ spin transition symmetry function.
  *
@@ -53,12 +52,10 @@ static inline double p(double mf, double mi) { return (mf - mi); }
  * @param mi The quantum number associated with the initial energy state.
  * @return The spin transition symmetry function @f$\mathbb{d}@f$.
  */
-static inline double d(double mf, double mi)
-{
-    return 1.2247448714 * (mf * mf - mi * mi);
+static inline double d(double mf, double mi) {
+  return 1.2247448714 * (mf * mf - mi * mi);
 }
 
-
 /**
  * @brief The @f$\mathbb{f}@f$ spin transition symmetry function.
  *
@@ -75,13 +72,12 @@ static inline double d(double mf, double mi)
  * @param mi The quantum number associated with the initial energy state.
  * @return The spin transition symmetry function @f$\mathbb{f}@f$.
  */
-static inline double f(double mf, double mi, double spin)
-{
-    double f_ = 1.0 - 3.0 * spin * (spin + 1.0);
-    f_ *= (mf - mi);
-    f_ += 5.0 * (mf * mf * mf - mi * mi * mi);
-    f_ *= 0.316227766;
-    return f_;
+static inline double f(double mf, double mi, double spin) {
+  double f_ = 1.0 - 3.0 * spin * (spin + 1.0);
+  f_ *= (mf - mi);
+  f_ += 5.0 * (mf * mf * mf - mi * mi * mi);
+  f_ *= 0.316227766;
+  return f_;
 }
 
 /**
@@ -104,18 +100,17 @@ static inline double f(double mf, double mi, double spin)
  * @param mSf The quantum number associated with the final state of spin S.
  * @return The spin transition symmetry function @f$\mathbb{d_{IS}}@f$.
  */
-static inline double dIS(double mIf, double mIi, double mSf, double mSi)
-{
-    return mIf * mSf - mIi * mSi;
+static inline double dIS(double mIf, double mIi, double mSf, double mSi) {
+  return mIf * mSf - mIi * mSi;
 }
 
-static inline void quad_ci(double *c0, double *c2, double *c4, double mf, double mi, double spin)
-{
-    double f_ = f(mf, mi, spin);
-    double p_ = p(mf, mi);
+static inline void quad_ci(double *c0, double *c2, double *c4, double mf,
+                           double mi, double spin) {
+  double f_ = f(mf, mi, spin);
+  double p_ = p(mf, mi);
 
-    double temp = spin * (spin + 1.0) - 0.75;
-    c0[0] = 0.3577708764 * temp * p_ + 0.8485281374 * f_;
-    c2[0] = 0.1069044968 * temp * p_ + -1.0141851057 * f_;
-    c4[0] = -0.1434274331 * temp * p_ + -1.2850792082 * f_;
+  double temp = spin * (spin + 1.0) - 0.75;
+  c0[0] = 0.3577708764 * temp * p_ + 0.8485281374 * f_;
+  c2[0] = 0.1069044968 * temp * p_ + -1.0141851057 * f_;
+  c4[0] = -0.1434274331 * temp * p_ + -1.2850792082 * f_;
 }

src/c_lib/lib/angular_momentum.c

@@ -99,7 +99,7 @@ void __wigner_d_matrix_cosine(const int l, const int n, const double *cos_angle,
 
       wigner[12] = 1.5 * cx2 - .5; // 0,  0 // 12
 
-      wigner+=25;
+      wigner += 25;
     }
   }
   if (l == 4) {
@@ -250,7 +250,7 @@ void __wigner_d_matrix_cosine(const int l, const int n, const double *cos_angle,
       temp = 0.125 * (3. - 30. * cx2 + 35 * cx2 * cx2);
       wigner[40] = temp; //  0,  0 // 40
 
-      wigner+=81;
+      wigner += 81;
     }
   }
 }

src/mrsimulator/parseable.py

@@ -1,3 +1,4 @@
+# -*- coding: utf-8 -*-
 from pydantic import BaseModel
 from mrsimulator.unit import string_to_quantity
 from typing import ClassVar, Dict

src/mrsimulator/python/Hamiltonian.py

@@ -1,3 +1,4 @@
+# -*- coding: utf-8 -*-
 import numpy as np
 
 # from . import transition_function as tf

src/mrsimulator/python/angular_momentum.py

@@ -1,3 +1,4 @@
+# -*- coding: utf-8 -*-
 import numpy as np
 
 __author__ = "Deepansh J. Srivastava"

src/mrsimulator/python/orientation.py

@@ -1,3 +1,4 @@
+# -*- coding: utf-8 -*-
 import numpy as np
 
 __author__ = "Deepansh J. Srivastava"

src/mrsimulator/python/simulator.py

@@ -1,3 +1,4 @@
+# -*- coding: utf-8 -*-
 from numpy.fft import fft, fftfreq
 import numpy as np
 from numpy import dot, exp

src/mrsimulator/python/transition_function.py

@@ -1,3 +1,4 @@
+# -*- coding: utf-8 -*-
 """Transition symmetry functions from irreducible tensors.
 
 .. seealso::

src/mrsimulator/python/utils.py

@@ -1,3 +1,4 @@
+# -*- coding: utf-8 -*-
 import numpy as np
 
 __author__ = "Deepansh J. Srivastava"

src/mrsimulator/site.py

@@ -1,3 +1,4 @@
+# -*- coding: utf-8 -*-
 from typing import ClassVar, Optional
 from mrsimulator import Parseable, SymmetricTensor, AntisymmetricTensor
 

src/mrsimulator/spectrum.py

@@ -1,3 +1,4 @@
+# -*- coding: utf-8 -*-
 import os.path
 import re
 from monty.serialization import loadfn

src/mrsimulator/tensors.py

@@ -1,3 +1,4 @@
+# -*- coding: utf-8 -*-
 from typing import ClassVar, Optional
 from mrsimulator import Parseable
 

src/mrsimulator/tests/__init__.py

@@ -1,3 +1,4 @@
+# -*- coding: utf-8 -*-
 import os.path
 import pytest
 from monty.serialization import loadfn

src/mrsimulator/tests/test_core.py

@@ -1,4 +1,4 @@
-# coding: utf-8
+# -*- coding: utf-8 -*-
 """
 Tests for the base Parseable pattern
 """

src/mrsimulator/tests/test_parseable.py

@@ -1,4 +1,4 @@
-# coding: utf-8
+# -*- coding: utf-8 -*-
 """
 Tests for the base Parseable pattern
 """

src/mrsimulator/tests/test_simulator.py

@@ -1,4 +1,4 @@
-# coding: utf-8
+# -*- coding: utf-8 -*-
 """
 Tests for the base Parseable pattern
 """

tests/orientations_test.py

@@ -1,3 +1,4 @@
+# -*- coding: utf-8 -*-
 import numpy as np
 from mrsimulator.python.orientation import cosine_of_polar_angles_and_amplitudes
 from mrsimulator.python.orientation import triangle_interpolation

tests/phase_test.py

@@ -1,3 +1,4 @@
+# -*- coding: utf-8 -*-
 import mrsimulator.sandbox as clib
 from mrsimulator.python.utils import pre_phase_components
 import numpy as np

tests/wigner/wigner_matrix_test.py

@@ -1,3 +1,4 @@
+# -*- coding: utf-8 -*-
 import mrsimulator.sandbox as clib
 from mrsimulator.python.angular_momentum import (
     wigner_d_matrix_cosines,

tests/wigner/wigner_rotation_test.py

@@ -1,3 +1,4 @@
+# -*- coding: utf-8 -*-
 import mrsimulator.sandbox as clib
 from mrsimulator.python.angular_momentum import wigner_rotation
 import numpy as np