Merge pull request #5 from Z2PackDev/add_rtd_build

Add rtd build

.gitignore

@@ -27,3 +27,6 @@ tests/.coverage
 
 # Atom
 .ropeproject
+
+# VSCode
+.vscode

.pre-commit-config.yaml

@@ -1,6 +1,6 @@
 repos:
 - repo: git://github.com/pre-commit/mirrors-yapf
-  rev: v0.25.0
+  rev: v0.29.0
   hooks:
   - id: yapf
     language: system

README.md

@@ -1,5 +1,6 @@
 A simple tool to describe symmetry operations and their representations.
 
-Documentation: http://z2pack.ethz.ch/symmetry-representation
+Documentation: https://symmetry-representation.greschd.ch
 
+[![Documentation Status](https://readthedocs.org/projects/symmetry-representation/badge/?version=latest)](https://symmetry-representation.greschd.ch/en/latest/?badge=latest)
 [![Build Status](https://travis-ci.org/Z2PackDev/symmetry_representation.svg?branch=master)](https://travis-ci.org/Z2PackDev/symmetry_representation)

setup.py

@@ -5,14 +5,11 @@
 # Author: Dominik Gresch <greschd@gmx.ch>
 
 import re
-try:
-    from setuptools import setup
-except ImportError:
-    from distutils.core import setup
+from setuptools import setup, find_packages
 
 import sys
-if sys.version_info < (3, 5):
-    raise 'must use Python version 3.5 or higher'
+if sys.version_info < (3, 6):
+    raise 'must use Python version 3.6 or higher'
 
 README = """A tool to describe symmetry operations and their representation."""
 
@@ -23,8 +20,8 @@
 EXTRAS_REQUIRE = {
     'doc': ['sphinx', 'sphinx-rtd-theme', 'sphinx-click', 'ipython>=6.2'],
     'dev': [
-        'pytest', 'pytest-cov', 'yapf==0.25', 'pre-commit==1.11.1',
-        'prospector==1.1.6.*', 'pylint==2.1.*'
+        'pytest', 'pytest-cov', 'yapf==0.29', 'pre-commit',
+        'prospector==1.2.0', 'pylint==2.4.4'
     ]
 }
 
@@ -33,7 +30,7 @@
 setup(
     name='symmetry-representation',
     version=VERSION,
-    url='http://z2pack.ethz.ch/symmetry-representation',
+    url='https://symmetry-representation.greschd.ch',
     author='Dominik Gresch',
     author_email='greschd@gmx.ch',
     license='Apache 2.0',
@@ -56,9 +53,7 @@
         'Topic :: Scientific/Engineering :: Physics',
         'Development Status :: 4 - Beta'
     ],
-    packages=[
-        'symmetry_representation', 'symmetry_representation._get_repr_matrix'
-    ],
+    packages=find_packages(),
     entry_points='''
         [console_scripts]
         symmetry-repr=symmetry_representation._cli:cli

symmetry_representation/__init__.py

@@ -3,6 +3,7 @@
 
 # (c) 2017-2018, ETH Zurich, Institut fuer Theoretische Physik
 # Author: Dominik Gresch <greschd@gmx.ch>
+# pylint: disable=cyclic-import
 """
 A tool for describing symmetry operations and their representations.
 """

symmetry_representation/_cli.py

@@ -53,7 +53,7 @@ def filter_symmetries(symmetries, lattice, output):
     click.echo("Loading structure from file '{}'...".format(lattice))
     structure = mg.Structure.from_file(lattice)
     click.echo("Filtering symmetries...")
-    filtered_symmetries = filter_compatible(symmetries, structure=structure)  # pylint: disable=assignment-from-no-return
+    filtered_symmetries = filter_compatible(symmetries, structure=structure)
     click.echo("Saving filtered symmetries to file '{}'...".format(output))
     io.save(filtered_symmetries, output)
     click.echo("Done!")

symmetry_representation/_compatibility.py

@@ -43,7 +43,7 @@ def is_compatible(*, structure, symmetry):
 
 @export
 @singledispatch
-def filter_compatible(symmetries, *, structure):  # pylint: disable=unused-argument
+def filter_compatible(symmetries, *, structure):
     """
     Returns the symmetries which are compatible with the given structure.
 
@@ -61,24 +61,24 @@ def filter_compatible(symmetries, *, structure):  # pylint: disable=unused-argum
 
 
 @filter_compatible.register(Iterable)
-def _(symmetries, *, structure):  # pylint: disable=missing-docstring
+def _(symmetries, *, structure):  # pylint: disable=missing-function-docstring
     filtered_syms = [
         filter_compatible(s, structure=structure) for s in symmetries
     ]
     return [s for s in filtered_syms if s is not None]
 
 
 @filter_compatible.register(SymmetryOperation)
-def _(symmetry, *, structure):  # pylint: disable=missing-docstring
+def _(symmetry, *, structure):  # pylint: disable=missing-function-docstring
     if is_compatible(symmetry=symmetry, structure=structure):
         return symmetry
     else:
         return None
 
 
 @filter_compatible.register(SymmetryGroup)
-def _(symmetry_group, *, structure):  # pylint: disable=missing-docstring
-    filtered_syms = filter_compatible(  # pylint: disable=assignment-from-no-return
+def _(symmetry_group, *, structure):  # pylint: disable=missing-function-docstring
+    filtered_syms = filter_compatible(
         symmetry_group.symmetries, structure=structure
     )
     if filtered_syms:

symmetry_representation/_get_repr_matrix/_get_repr_matrix.py

@@ -172,12 +172,12 @@ def _get_repr_matrix_impl(  # pylint: disable=too-many-locals
     repr_matrix_numeric = np.array(repr_matrix).astype(complex)
     if not np.allclose(
         repr_matrix_numeric @ repr_matrix_numeric.conj().T,
-        np.eye(*repr_matrix_numeric.shape)
+        np.eye(*repr_matrix_numeric.shape)  # pylint: disable=not-an-iterable
     ):
         max_mismatch = np.max(
             np.abs(
                 repr_matrix_numeric @ repr_matrix_numeric.conj().T -
-                np.eye(*repr_matrix_numeric.shape)
+                np.eye(*repr_matrix_numeric.shape)  # pylint: disable=not-an-iterable
             )
         )
         raise ValueError(

symmetry_representation/_sym_op.py

@@ -3,6 +3,7 @@
 
 # (c) 2017-2018, ETH Zurich, Institut fuer Theoretische Physik
 # Author: Dominik Gresch <greschd@gmx.ch>
+# pylint: disable=cyclic-import
 """
 Defines symmetry operations and groups.
 """
@@ -128,7 +129,7 @@ def from_orbitals(
             Determines whether a numeric (numpy) or analytic (sympy)
             representation matrix is constructed.
         """
-        from . import _get_repr_matrix
+        from . import _get_repr_matrix  # pylint: disable=import-outside-toplevel
         if kwargs.get('repr_has_cc', False):
             raise NotImplementedError
         repr_matrix = _get_repr_matrix.get_repr_matrix(
@@ -367,14 +368,15 @@ def __init__(self, matrix, has_cc=False, numeric=None):
         if numeric:
             matrix = np.array(matrix).astype(complex)
             if not np.allclose(
-                matrix @ matrix.T.conjugate(), np.eye(matrix.shape[0])
+                matrix @ matrix.T.conjugate(),
+                np.eye(matrix.shape[0])  # pylint: disable=unsubscriptable-object
             ):
                 raise ValueError(
                     'Input matrix is not unitary: {}'.format(matrix)
                 )
         else:
             matrix = sp.Matrix(matrix)
-            if not sp.eye(*matrix.shape).equals(matrix @ matrix.H):  # pylint: disable=not-an-iterable
+            if not sp.eye(*matrix.shape).equals(matrix @ matrix.H):
                 raise ValueError(
                     'Input matrix is not unitary: {}'.format(matrix)
                 )

tests/conftest.py

@@ -20,7 +20,6 @@ def sample():
     """
     Returns the path to the sample of the given name.
     """
-
     def inner(name):
         return os.path.join(
             os.path.join(
@@ -40,7 +39,6 @@ def test_name(request):
 @pytest.fixture
 def compare_data(request, test_name, scope="session"):  # pylint: disable=unused-argument,redefined-outer-name
     """Returns a function which either saves some data to a file or (if that file exists already) compares it to pre-existing data using a given comparison function."""
-
     def inner(compare_fct, data, tag=None):
         full_name = test_name + (tag or '')
 
@@ -53,8 +51,7 @@ def inner(compare_fct, data, tag=None):
         if val is None:
             request.config.cache.set(full_name, data_str)
             raise ValueError('Reference data does not exist.')
-        else:
-            assert compare_fct(val, data)
+        assert compare_fct(val, data)
 
     return inner
 

tests/sym_op/test_real_space_operator.py

@@ -13,12 +13,12 @@
 
 @pytest.mark.parametrize(['real_space_op', 'vec', 'res'], [
     (
-        sr.RealSpaceOperator(np.eye(3), [0.1, 0.2, 0.3]), [0.2, 0.7, 0.1],
-        [0.3, 0.9, 0.4]
+        sr.RealSpaceOperator(np.eye(3), [0.1, 0.2, 0.3]), [0.2, 0.7, 0.1
+                                                           ], [0.3, 0.9, 0.4]
     ),
     (
-        sr.RealSpaceOperator([[0, 1], [1, 1]], [0.1, 0.2]), [0.3, 0.6],
-        [0.7, 1.1]
+        sr.RealSpaceOperator([[0, 1], [1, 1]], [0.1, 0.2]), [0.3, 0.6
+                                                             ], [0.7, 1.1]
     ),
 ])
 def test_apply(real_space_op, vec, res):

tests/sym_op/test_representation.py

@@ -15,10 +15,10 @@
 @pytest.mark.parametrize(
     ['mat_1', 'has_cc_1', 'mat_2', 'has_cc_2', 'mat_res', 'has_cc_res'],
     [
-        ([[0, 1], [1, 0]], False, [[0, 1], [1, 0]], True, [[1, 0], [0, 1]],
-         True),
-        ([[1, 0], [0, 1]], True, [[0, sp.I], [-sp.I, 0]], False,
-         [[0, -sp.I], [sp.I, 0]], True),
+        ([[0, 1], [1, 0]], False, [[0, 1], [1, 0]], True, [[1, 0], [0, 1]
+                                                           ], True),
+        ([[1, 0], [0, 1]], True, [[0, sp.I], [-sp.I, 0]
+                                  ], False, [[0, -sp.I], [sp.I, 0]], True),
     ]  # pylint: disable=too-many-arguments
 )
 def test_representation_mul(

tests/test_auto_repr.py

@@ -71,8 +71,9 @@ def test_auto_repr(sample):
     ('orbitals', 'result_repr_matrix'),
     [
         ([
-            sr.
-            Orbital(position=(0.1, 0.2, 0.3), function_string='1', spin=None)
+            sr.Orbital(
+                position=(0.1, 0.2, 0.3), function_string='1', spin=None
+            )
         ], sp.Matrix([[1]])),
         ([
             sr.Orbital(
@@ -85,8 +86,9 @@ def test_auto_repr(sample):
             )
         ], sp.Matrix([[0, -sp.I], [sp.I, 0]])),
         ([
-            sr.
-            Orbital(position=(0.1, 0.2, 0.3), function_string='x', spin=None)
+            sr.Orbital(
+                position=(0.1, 0.2, 0.3), function_string='x', spin=None
+            )
         ], sp.Matrix([[1]])),
     ],
 )
@@ -132,8 +134,8 @@ def test_time_reversal(orbitals, result_repr_matrix, numeric):
 
 
 @pytest.mark.parametrize(['orbitals', 'rotation_matrix', 'reference'], [
-    ([sr.Orbital(position=(0, 0, 0), function_string='1', spin=None)],
-     np.array([[0, 1, 0], [1, 0, 0], [0, 0, 1]]), sp.eye(1, 1)),
+    ([sr.Orbital(position=(0, 0, 0), function_string='1', spin=None)
+      ], np.array([[0, 1, 0], [1, 0, 0], [0, 0, 1]]), sp.eye(1, 1)),
     ([
         sr.Orbital(position=(0, 0, 0), function_string='x', spin=None),
         sr.Orbital(position=(0, 0, 0), function_string='y', spin=None)
@@ -164,8 +166,8 @@ def test_time_reversal(orbitals, result_repr_matrix, numeric):
     ([
         sr.Orbital(position=(0, 0, 0), function_string='1', spin=sr.SPIN_UP),
         sr.Orbital(position=(0, 0, 0), function_string='1', spin=sr.SPIN_DOWN)
-    ], np.array([[-1, 0, 0], [0, -1, 0], [0, 0, 1]]),
-     sp.Matrix([[-sp.I, 0], [0, sp.I]])),
+    ], np.array([[-1, 0, 0], [0, -1, 0], [0, 0, 1]]
+                ), sp.Matrix([[-sp.I, 0], [0, sp.I]])),
     ([
         sr.Orbital(position=(0, 0, 0), function_string='1', spin=sr.SPIN_UP),
         sr.Orbital(position=(0, 0, 0), function_string='1', spin=sr.SPIN_DOWN)

tests/test_compatible.py

@@ -61,9 +61,8 @@ def check(sym):
         return False
 
     for sym in all_symmetries:
-        assert sr.is_compatible(
-            structure=strained_structure, symmetry=sym
-        ) == check(sym)
+        assert sr.is_compatible(structure=strained_structure,
+                                symmetry=sym) == check(sym)
 
 
 def test_filter_compatible(unstrained_structure, all_symmetries):  # pylint: disable=redefined-outer-name