Merge pull request #29 from greschd/dev

Release/0.1.1

.gitignore

@@ -24,3 +24,6 @@ tests/.cache
 htmlcov
 .pytest-score
 htmlscore
+
+# editor related
+.vscode

.pre-commit-config.yaml

@@ -1,13 +1,15 @@
 repos:
 - repo: git://github.com/pre-commit/mirrors-yapf
-  sha: v0.24.0
+  rev: v0.29.0
   hooks:
   - id: yapf
     language: system
 
-- repo: git://github.com/guykisel/prospector-mirror
-  sha: 7ff847e779347033ebbd9e3b88279e7f3a998b45
+- repo: local
   hooks:
   - id: prospector
+    name: prospector
+    entry: prospector
+    types: [file, python]
     language: system
     exclude: '^(doc/)|(examples/)'

.pylintrc

@@ -15,7 +15,7 @@ ignore-patterns=
 
 # Python code to execute, usually for sys.path manipulation such as
 # pygtk.require().
-#init-hook=
+init-hook="import os, sys; from pylint.config import find_pylintrc; sys.path.append(os.path.join(os.path.dirname(find_pylintrc()), 'tests'))"
 
 # Use multiple processes to speed up Pylint.
 jobs=1

.readthedocs.yml

@@ -0,0 +1,22 @@
+# .readthedocs.yml
+# Read the Docs configuration file
+# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
+
+# Required
+version: 2
+
+# Build documentation in the doc/ directory with Sphinx
+sphinx:
+  configuration: doc/source/conf.py
+
+# Optionally build your docs in additional formats such as PDF and ePub
+formats: []
+
+# Optionally set the version of Python and requirements required to build your docs
+python:
+  version: 3.7
+  install:
+    - method: pip
+      path: .
+      extra_requirements:
+        - doc

.travis-data/install_script.sh

@@ -0,0 +1,23 @@
+#!/bin/bash
+
+# Author: Dominik Gresch <greschd@gmx.ch>
+
+# Be verbose, and stop with error as soon there's one
+set -ev
+
+cd ${TRAVIS_BUILD_DIR}
+
+pip install git+https://github.com/greschd/pytest-score.git
+
+case "$INSTALL_TYPE" in
+    dev)
+        pip install .[dev]
+        ;;
+    test)
+        pip install .[test]
+        ;;
+    test_sdist)
+        python setup.py sdist
+        ls -1 dist/ | xargs -I % pip install dist/%[test]
+        ;;
+esac

.travis-data/test_script.sh

@@ -0,0 +1,16 @@
+#!/bin/bash
+
+# © 2017-2019, ETH Zurich, Institut für Theoretische Physik
+# Author: Dominik Gresch <greschd@gmx.ch>
+
+# Be verbose, and stop with error as soon there's one
+set -ev
+
+case "$TEST_TYPE" in
+    test)
+        cd ${TRAVIS_BUILD_DIR}/tests; pytest --no-plot-compare
+        ;;
+    precommit)
+        pre-commit run --all-files
+        ;;
+esac

.travis.yml

@@ -1,20 +1,21 @@
 language: python
 cache: pip
 python:
-  - "3.5"
   - "3.6"
-
+  - "3.7"
+  - "3.8"
 env:
   - TEST_TYPE="test"
-matrix:
+    INSTALL_TYPE="test"
+  - TEST_TYPE="test"
+    INSTALL_TYPE="test_sdist"
+jobs:
   include:
-    - python: 3.6
-      env: TEST_TYPE="compliance"
-
+    - python: "3.7"
+      env:
+        - TEST_TYPE="precommit"
+          INSTALL_TYPE="dev"
 install:
-  - pip install -U pytest
-  - pip install --process-dependency-links .[test]
-
+  - ./.travis-data/install_script.sh
 script:
-  - if [ "$TEST_TYPE" == "compliance" ] ; then pip install .[dev]; pre-commit run --all-files ; fi
-  - if [ "$TEST_TYPE" == "test" ] ; then cd tests; pytest --no-plot-compare ; fi
+  - ./.travis-data/test_script.sh

README.md

@@ -7,4 +7,7 @@ The goal of this code is to identify nodal features in potential landscapes, usi
 
 The initial use-case for this code is to find gapless features in three-dimensional materials.
 
+Documentation: https://nodefinder.greschd.ch
+
+[![Documentation Status](https://readthedocs.org/projects/nodefinder/badge/?version=latest)](https://nodefinder.greschd.ch/en/latest/?badge=latest)
 [![Build Status](https://travis-ci.org/greschd/NodeFinder.svg?branch=master)](https://travis-ci.org/greschd/NodeFinder)

doc/source/conf.py

@@ -3,8 +3,8 @@
 # © 2017-2019, ETH Zurich, Institut für Theoretische Physik
 # Author: Dominik Gresch <greschd@gmx.ch>
 
+import os
 import time
-import sphinx_rtd_theme
 
 # 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
@@ -54,11 +54,8 @@
 # General information about the project.
 project = u'NodeFinder'
 year = time.localtime().tm_year
-team = 'ETH Zurich'
-if year == 2017:
-    copyright = u'2017, {}'.format(team)
-else:
-    copyright = u'2017-{}, {}'.format(year, team)
+team = 'ETH Zurich; Dominik Gresch'
+copyright = u'2017-{}, {}'.format(year, team)
 
 # The version info for the project you're documenting, acts as replacement for
 # |version| and |release|, also used in various other places throughout the
@@ -115,8 +112,10 @@
 # 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':
+    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/kdotp_weyl/kdotp.py

@@ -21,18 +21,20 @@ class Pauli:
 def Hamilton_general(k, *, a, b, c, d, e, f, g, h, j, l, m, n, o, p, q, r):
     kx, ky, kz = k
     H = (
-        a * np.kron(Pauli.zero, Pauli.zero) + b * np.kron(Pauli.z, Pauli.zero)
-        + c * (kx + ky) * np.kron(Pauli.x, Pauli.z) +
-        d * (kx + ky) * np.kron(Pauli.y, Pauli.zero) + e * (kx - ky) *
-        np.kron(Pauli.x, Pauli.x) + f * (kx - ky) * np.kron(Pauli.x, Pauli.y) +
+        a * np.kron(Pauli.zero, Pauli.zero) +
+        b * np.kron(Pauli.z, Pauli.zero) + c *
+        (kx + ky) * np.kron(Pauli.x, Pauli.z) + d *
+        (kx + ky) * np.kron(Pauli.y, Pauli.zero) + e *
+        (kx - ky) * np.kron(Pauli.x, Pauli.x) + f *
+        (kx - ky) * np.kron(Pauli.x, Pauli.y) +
         g * kz * np.kron(Pauli.x, Pauli.x) +
-        h * kz * np.kron(Pauli.x, Pauli.y) +
-        j * (kx**2 + ky**2) * np.kron(Pauli.zero, Pauli.zero) +
-        l * (kx**2 + ky**2) * np.kron(Pauli.z, Pauli.zero) +
+        h * kz * np.kron(Pauli.x, Pauli.y) + j *
+        (kx**2 + ky**2) * np.kron(Pauli.zero, Pauli.zero) + l *
+        (kx**2 + ky**2) * np.kron(Pauli.z, Pauli.zero) +
         m * kx * ky * np.kron(Pauli.zero, Pauli.zero) +
-        n * kx * ky * np.kron(Pauli.z, Pauli.zero) +
-        o * (kx * kz - ky * kz) * np.kron(Pauli.zero, Pauli.zero) +
-        p * (kx * kz - ky * kz) * np.kron(Pauli.z, Pauli.zero) +
+        n * kx * ky * np.kron(Pauli.z, Pauli.zero) + o *
+        (kx * kz - ky * kz) * np.kron(Pauli.zero, Pauli.zero) + p *
+        (kx * kz - ky * kz) * np.kron(Pauli.z, Pauli.zero) +
         q * kz**2 * np.kron(Pauli.zero, Pauli.zero) +
         r * kz**2 * np.kron(Pauli.z, Pauli.zero)
     )

examples/kdotp_weyl/run.py

@@ -67,7 +67,8 @@ def get_chern(splitting, k):
     loop = asyncio.get_event_loop()
     executor = ProcessPoolExecutor(max_workers=4)
     res = pm.run(
-        lambda pos: phase_func([pos[0], 0, pos[1]], loop=loop, executor=executor),
+        lambda pos:
+        phase_func([pos[0], 0, pos[1]], loop=loop, executor=executor),
         limits=[(-0.3, 0.3)] * 2,
         mesh=3,
         num_steps=5,

examples/kdotp_weyl/splitting_fct.py

@@ -16,8 +16,8 @@
 
 def c00(k, a, j, m, o, q, **kwargs):
     kx, ky, kz = k
-    return a + j * (kx**2 + ky**
-                    2) + m * kx * ky + o * (kx * kz - ky * kz) + q * kz**2
+    return a + j * (kx**2 +
+                    ky**2) + m * kx * ky + o * (kx * kz - ky * kz) + q * kz**2
 
 
 def cxz(k, c, **kwargs):
@@ -32,8 +32,8 @@ def cy0(k, d, **kwargs):
 
 def cz0(k, b, l, n, p, r, **kwargs):
     kx, ky, kz = k
-    return b + l * (kx**2 + ky**
-                    2) + n * kx * ky + p * (kx * kz - ky * kz) + r * kz**2
+    return b + l * (kx**2 +
+                    ky**2) + n * kx * ky + p * (kx * kz - ky * kz) + r * kz**2
 
 
 def cxx(k, e, g, **kwargs):

nodefinder/__init__.py

@@ -5,7 +5,7 @@
 """A tool to find and identify nodal features in band structures.
 """
 
-__version__ = '0.1.0'
+__version__ = '0.1.1'
 
 from . import coordinate_system
 from . import search

nodefinder/_common_plot.py

@@ -11,12 +11,12 @@ def _setup_plot(limits, axis=None):
     """Sets up the figure axes and handles options common to all plots."""
     # import is here s.t. the import of the package does not fail
     # if matplotlib is not present
-    import matplotlib.pyplot as plt
+    import matplotlib.pyplot as plt  # pylint: disable=import-outside-toplevel
 
     dim = len(limits)
     if dim == 3:
         is_3d = True
-        from mpl_toolkits.mplot3d import Axes3D  # pylint: disable=unused-variable
+        from mpl_toolkits.mplot3d import Axes3D  # pylint: disable=import-outside-toplevel,unused-import
     else:
         is_3d = False
         assert dim == 2

nodefinder/identify/_cluster.py

@@ -39,8 +39,8 @@ def create_clusters(positions, *, feature_size, coordinate_system):
         coordinate_system=coordinate_system
     )
     return [
-        nx.freeze(subgraph)
-        for subgraph in nx.algorithms.connected_component_subgraphs(graph)
+        nx.freeze(graph.subgraph(nodes).copy())
+        for nodes in nx.algorithms.connected_components(graph)
     ]
 
 

nodefinder/identify/_evaluate/_line/_ballistic.py

@@ -42,7 +42,6 @@ class _BallisticLineImpl:
     """
     Implementation class for the 'ballistic' line evaluation.
     """
-
     def __init__(self, *, graph, coordinate_system, feature_size):
         self.graph = graph
         self.coordinate_system = coordinate_system
@@ -113,7 +112,7 @@ def find_loop(self, *, starting_node, initial_direction):
                 )
                 assert previous_direction is not None
                 break
-            elif new_node in self.result_graph:
+            if new_node in self.result_graph:
                 if on_graph:
                     IDENTIFY_LOGGER.debug(
                         "Loop search finished -- reached existing result nodes."
@@ -131,7 +130,7 @@ def get_next_pos(self, *, node, previous_direction):  # pylint: disable=too-many
         Determine the next node based on the current node and previous step
         direction.
         """
-        neighbors_all = [nbr for nbr in self.graph.neighbors(node)]
+        neighbors_all = list(self.graph.neighbors(node))
 
         deltas_all = self.coordinate_system.connecting_vector(
             np.array(node), np.array(neighbors_all)

nodefinder/identify/_evaluate/_line/_shortest_path.py

@@ -111,12 +111,10 @@ def _evaluate_line_shortest_path(  # pylint: disable=too-many-locals,too-many-st
 
                 tmp_graph.remove_nodes_from(nodes_to_remove)
 
-            if num_paths > 0:  # pylint: disable=undefined-loop-variable
+            if num_paths > 0:
                 IDENTIFY_LOGGER.debug(
                     'Found {} path(s) from point {} to point {}.'.format(
-                        num_paths,  # pylint: disable=undefined-loop-variable
-                        start_pos,
-                        end_pos
+                        num_paths, start_pos, end_pos
                     )
                 )
             else:

nodefinder/identify/plot.py

@@ -50,7 +50,7 @@ def _plot_positions(positions, *, axis, color):
 
 
 @singledispatch
-def _plot_result(shape, axis, color, feature_size):  # pylint: disable=unused-argument
+def _plot_result(shape, axis, color, feature_size):
     raise NotImplementedError
 
 
@@ -103,9 +103,9 @@ def nodal_line(shape, *, axis, color, feature_size=None):
 
     if paths:
         for path in paths:
-            axis.plot(*np.array(path).T, color=color)
+            axis.plot(*np.array(path).T, color=color)  # pylint: disable=not-an-iterable
     else:
-        axis.scatter(*np.array(list(graph.nodes)).T, color=color)
+        axis.scatter(*np.array(list(graph.nodes)).T, color=color)  # pylint: disable=not-an-iterable
 
 
 def _get_graph_paths(graph, feature_size):
@@ -125,8 +125,9 @@ def _get_graph_paths(graph, feature_size):
             except StopIteration:
                 paths.append(curr_path)
                 break
-            if la.norm(np.array(next_node) -
-                       np.array(curr_node)) > 2 * feature_size:
+            if la.norm(
+                np.array(next_node) - np.array(curr_node)
+            ) > 2 * feature_size:
                 paths.append(curr_path)
                 curr_path = [next_node]
             else:

nodefinder/identify/result/_containers.py

@@ -82,11 +82,11 @@ def to_hdf5(self, hdf5_handle):
     def from_hdf5(cls, hdf5_handle):
         shape = from_hdf5(hdf5_handle['shape'])
         try:
-            dimension = hdf5_handle['dimension'].value
+            dimension = hdf5_handle['dimension'][()]
         except AttributeError:
             dimension = from_hdf5(hdf5_handle['dimension'])
         try:
-            positions = [tuple(x) for x in hdf5_handle['positions'].value]
+            positions = [tuple(x) for x in hdf5_handle['positions'][()]]
         except AttributeError:
             positions = from_hdf5(hdf5_handle['positions'])
         return cls(positions=positions, dimension=dimension, shape=shape)

nodefinder/identify/result/_shapes.py

@@ -43,7 +43,6 @@ class NodalLine(SimpleNamespace):
     graph : networkx.Graph
         A graph describing the line.
     """
-
     def __init__(self, graph, degree_count):
         self.graph = graph
         self.degree_count = degree_count