Update pre-commit tools and fix issues

Author: Dominik Gresch

.pre-commit-config.yaml

@@ -1,6 +1,6 @@
 repos:
 - repo: git://github.com/pre-commit/mirrors-yapf
-  rev: v0.24.0
+  rev: v0.29.0
   hooks:
   - id: yapf
     language: system

.pylintrc

@@ -50,7 +50,7 @@ confidence=
 # --enable=similarities". If you want to run only the classes checker, but have
 # no Warning level messages displayed, use"--disable=all --enable=classes
 # --disable=W"
-disable=too-few-public-methods,too-many-public-methods,bad-continuation,wrong-import-position,line-too-long,locally-disabled,wildcard-import,locally-enabled,too-many-instance-attributes
+disable=too-few-public-methods,too-many-public-methods,bad-continuation,wrong-import-position,line-too-long,locally-disabled,wildcard-import,locally-enabled,too-many-instance-attributes,cyclic-import
 
 # Enable the message, report, category or checker with the given id(s). You can
 # either give multiple identifier separated by comma (,) or put this option

doc/source/conf.py

@@ -13,14 +13,12 @@
 # serve to show the default.
 
 import os
-import sys
 import time
-import sphinx_rtd_theme
+import contextlib
 
 # If extensions (or modules to document with autodoc) are in another directory,
 # add these directories to sys.path here. If the directory is relative to the
 # documentation root, use os.path.abspath to make it absolute, like shown here.
-#~ sys.path.insert(0, os.path.abspath('../../'))
 import z2pack
 
 # -- General configuration ------------------------------------------------
@@ -119,9 +117,11 @@
 
 # The theme to use for HTML and HTML Help pages.  See the documentation for
 # a list of builtin themes.
-#~ html_theme = 'basicstrap'
-html_theme = 'sphinx_rtd_theme'
-html_theme_path = [sphinx_rtd_theme.get_html_theme_path()]
+if not os.environ.get('READTHEDOCS', None) == 'True':
+    with contextlib.suppress(ImportError):
+        import sphinx_rtd_theme
+        html_theme = 'sphinx_rtd_theme'
+        html_theme_path = [sphinx_rtd_theme.get_html_theme_path()]
 
 # Theme options are theme-specific and customize the look and feel of a theme
 # further.  For a list of options available for each theme, see the

examples/hm/kane_mele_model/run.py

@@ -26,8 +26,8 @@ def inner(k):
         y = (kx + ky) / 2
         return (
             t * (1 + 2 * cos(x) * cos(y)) * kron(pauli_x, identity) +
-            lambda_v * kron(pauli_z, identity) +
-            lambda_R * (1 - cos(x) * cos(y)) * kron(pauli_y, pauli_x) +
+            lambda_v * kron(pauli_z, identity) + lambda_R *
+            (1 - cos(x) * cos(y)) * kron(pauli_y, pauli_x) +
             -sqrt(3) * lambda_R * sin(x) * sin(y) * kron(pauli_y, pauli_y) +
             2 * t * cos(x) * sin(y) * kron(pauli_y, identity) + lambda_SO *
             (2 * sin(2 * x) - 4 * sin(x) * cos(y)) * kron(pauli_z, pauli_z) +

futures/tci.py

@@ -28,9 +28,8 @@ def tci_h(k):
     kz = k[2] * 2 * pi
     t1a, t1b, t2a, t2b, t1, t2, tz = (1.0, -1.0, 0.5, -0.5, 2.5, 0.5, 2.0)
     H = np.matrix([[
-        2 * t1a * cos(kx) + 2 * t2a * cos(kx) * cos(ky),
-        2 * t2a * sin(kx) * sin(ky),
-        t1 + 2 * t2 * (cos(kx) + cos(ky)) + tz * exp(1j * kz), 0
+        2 * t1a * cos(kx) + 2 * t2a * cos(kx) * cos(ky), 2 * t2a * sin(kx) *
+        sin(ky), t1 + 2 * t2 * (cos(kx) + cos(ky)) + tz * exp(1j * kz), 0
     ],
                    [
                        2 * t2a * sin(kx) * sin(ky),
@@ -43,9 +42,8 @@ def tci_h(k):
                        2 * t2b * sin(kx) * sin(ky)
                    ],
                    [
-                       0,
-                       t1 + 2 * t2 * (cos(kx) + cos(ky)) + tz * exp(-1j * kz),
-                       2 * t2b * sin(kx) * sin(ky),
+                       0, t1 + 2 * t2 * (cos(kx) + cos(ky)) +
+                       tz * exp(-1j * kz), 2 * t2b * sin(kx) * sin(ky),
                        2 * t1b * cos(kx) + 2 * t2b * cos(kx) * cos(ky)
                    ]],
                   dtype=complex)

setup.py

@@ -26,10 +26,10 @@
 EXTRAS = {
     'plot': ['matplotlib'],
     'tb': ['tbmodels>=1.1.1'],
-    'doc': ['sphinx', 'sphinx_rtd_theme', 'sphinx-pyreverse', 'pylint==2.1.1'],
+    'doc': ['sphinx', 'sphinx-rtd-theme', 'sphinx-pyreverse', 'pylint==2.4.4'],
     'dev': [
-        'prospector==1.1.2', 'pytest>=3.4', 'pytest-cov', 'yapf==0.24',
-        'pre-commit==1.11.1', 'pylint==2.1.1'
+        'prospector==1.2.0', 'pytest>=3.4', 'pytest-cov', 'yapf==0.29',
+        'pre-commit', 'pylint==2.4.4'
     ],
 }
 EXTRAS['dev'] += EXTRAS['plot'] + EXTRAS['tb'] + EXTRAS['doc']

tests/conftest.py

@@ -15,7 +15,7 @@
 from z2pack._utils import _get_max_move
 
 
-def pytest_addoption(parser):  # pylint: disable=missing-docstring
+def pytest_addoption(parser):  # pylint: disable=missing-function-docstring
     parser.addoption('-A', action='store_true', help='run ABINIT tests')
     parser.addoption('-V', action='store_true', help='run VASP tests')
     parser.addoption(
@@ -28,7 +28,7 @@ def pytest_addoption(parser):  # pylint: disable=missing-docstring
     )
 
 
-def pytest_configure(config):  # pylint: disable=missing-docstring
+def pytest_configure(config):  # pylint: disable=missing-function-docstring
     # register additional marker
     config.addinivalue_line(
         "markers", "abinit: mark tests which run with ABINIT"
@@ -39,7 +39,7 @@ def pytest_configure(config):  # pylint: disable=missing-docstring
     )
 
 
-def pytest_runtest_setup(item):  # pylint: disable=missing-docstring
+def pytest_runtest_setup(item):  # pylint: disable=missing-function-docstring
     try:
         abinit_marker = item.get_marker("abinit")
         vasp_marker = item.get_marker("vasp")
@@ -68,7 +68,6 @@ def test_name(request):
 @pytest.fixture
 def compare_data(request, test_name, scope="session"):
     """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 '')
         val = request.config.cache.get(full_name, None)
@@ -80,13 +79,10 @@ def inner(compare_fct, data, tag=None):
                 )
             )
             raise ValueError('Reference data does not exist.')
-        else:
-            assert compare_fct(
-                val,
-                json.loads(
-                    json.dumps(data, default=z2pack.io._encoding.encode)
-                )
-            )  # get rid of json-specific quirks
+        assert compare_fct(
+            val,
+            json.loads(json.dumps(data, default=z2pack.io._encoding.encode))
+        )  # get rid of json-specific quirks
 
     return inner
 
@@ -99,7 +95,6 @@ def compare_equal(compare_data):
 @pytest.fixture
 def compare_wcc(compare_data):
     """Checks whether two lists of WCC (or nested lists of WCC) are almost equal, up to a periodic shift."""
-
     def check_wcc(wcc0, wcc1):
         """
         Check that two sets of WCC are equal.
@@ -119,7 +114,6 @@ def sample():
     """
     Returns the path to the sample of the given name.
     """
-
     def inner(name):
         return os.path.join(
             os.path.join(

tests/ctrl_base_tester.py

@@ -14,7 +14,6 @@ def test_ctrl_base():
     """
     Test that a control class is a subclass of the right abstract classes.
     """
-
     def inner(ctrl):
         assert issubclass(ctrl, AbstractControl)
         if hasattr(ctrl, 'converged'):

tests/fp/test_abinit.py

@@ -17,7 +17,6 @@ def abinit_system(sample):
     """
     Create ABINIT system.
     """
-
     def inner(build_dir):
         sample_dir = sample('abinit')
         input_files = [

tests/fp/test_espresso.py

@@ -19,7 +19,6 @@ def qe_system(request, sample):
     """
     Creates a QE system.
     """
-
     def inner(build_dir, num_wcc=None):
         sample_dir = sample('espresso')
         shutil.copytree(
@@ -37,8 +36,8 @@ def inner(build_dir, num_wcc=None):
         pw2wancmd = mpirun + qedir + '/pw2wannier90.x '
         wancmd = wandir + '/wannier90.x'
         z2cmd = (
-            wancmd + ' bi -pp;' + pwcmd + '< bi.nscf.in >& pw.log;' + pw2wancmd
-            + '< bi.pw2wan.in >& pw2wan.log;'
+            wancmd + ' bi -pp;' + pwcmd + '< bi.nscf.in >& pw.log;' +
+            pw2wancmd + '< bi.pw2wan.in >& pw2wan.log;'
         )
 
         return z2pack.fp.System(