Increase scope of docformatter and black [unitaryhack]

.github/CHANGELOG.md

@@ -12,8 +12,11 @@
 * Added tests for `EGraph` plots. [#60](https://github.com/XanaduAI/flamingpy/pull/60)
 * Added `.gitattributes` to the repository, so git automatically handles consistent `eol`'s for all commits and contributors across different operating systems. [#78](https://github.com/XanaduAI/flamingpy/pull/78)
 * Added `fig, ax` returns for the draw methods in `utils/viz.py` and some additional tests. [#55](https://github.com/XanaduAI/flamingpy/pull/55)
+* Increased the scope of `docformatter` to all `.py` files in the repository. [#79](https://github.com/XanaduAI/flamingpy/pull/79)
+* Increased the scope of `black` formatter to include documentation files. [#79](https://github.com/XanaduAI/flamingpy/pull/79)
 
 ### Documentation changes
+
 * Mention the new graph state functions from `flamingpy.utils.graph_states` in the `run_graph_states.py` tutorial. [#68](https://github.com/XanaduAI/flamingpy/pull/68)
 * Typo fix and minor README change. [#70](https://github.com/XanaduAI/flamingpy/pull/80)
 
@@ -22,7 +25,7 @@
 
 This release contains contributions from (in alphabetical order):
 
-[Joost Bus](https://github.com/soosub), [Sebastián Duque Mesa](https://github.com/sduquemesa), [Luis Mantilla](https://github.com/BestQuark), Nariman Saadatmand
+[Joost Bus](https://github.com/soosub), [Sebastián Duque Mesa](https://github.com/sduquemesa), [Luis Mantilla](https://github.com/BestQuark), Nariman Saadatmand, [WingCode](https://github.com/WingCode) 
 
 See full commit details ...
 

.github/workflows/format.yaml

@@ -28,7 +28,7 @@ jobs:
       - uses: actions/checkout@v2
 
       - name: Run black
-        run: python -m black -l 100 tests flamingpy --check
+        run: python -m black -l 100 tests flamingpy doc --check
 
       - name: Run docformatter
-        run: python -m docformatter --check flamingpy/*/*.py
+        run: python -m docformatter -r --check .

doc/_ext/edit_on_github.py

@@ -24,9 +24,8 @@
 
 
 def get_github_url(app, view, path):
-    """A function to generate github url based on __app__, __view__,
-    and __path__ inputs.
-    """
+    """A function to generate github url based on __app__, __view__, and
+    __path__ inputs."""
     return "https://github.com/{project}/{view}/{branch}/{path}".format(
         project=app.config.edit_on_github_project,
         view=view,
@@ -36,7 +35,7 @@ def get_github_url(app, view, path):
 
 
 def html_page_context(app, pagename, templatename, context, doctree):
-    """A function to set html page context and return warnings as needed"""
+    """A function to set html page context and return warnings as needed."""
     if templatename != "page.html":
         return
 
@@ -56,7 +55,7 @@ def html_page_context(app, pagename, templatename, context, doctree):
 
 
 def setup(app):
-    """A handy function to set up edit_on_github links"""
+    """A handy function to set up edit_on_github links."""
     app.add_config_value("edit_on_github_project", "", True)
     app.add_config_value("edit_on_github_branch", "master", True)
     app.connect("html-page-context", html_page_context)

doc/conf.py

@@ -5,9 +5,7 @@
 # This file does only contain a selection of the most common options. For a
 # full list see the documentation:
 # http://www.sphinx-doc.org/en/master/config
-"""
-flamingpy configuration file for the Sphinx documentation builder.
-"""
+"""flamingpy configuration file for the Sphinx documentation builder."""
 import os
 import sys
 import re
@@ -28,7 +26,7 @@
 
 
 class Mock(MagicMock):
-    """An auxiliary class to create mocked modules"""
+    """An auxiliary class to create mocked modules."""
 
     __name__ = "foo"
 

doc/tutorials/run_error_correction.py

@@ -1,9 +1,7 @@
-"""
-.. _run-error-correction:
+""".. _run-error-correction:
 
 A complete round of error correction
 ====================================
-
 """
 
 

doc/tutorials/run_graph_states.py

@@ -1,9 +1,7 @@
-"""
-.. _graph-states-tutorial:
+""".. _graph-states-tutorial:
 
 Graph States
 ============
-
 """
 
 

flamingpy/_version.py

@@ -15,4 +15,4 @@
 """Version number (major.minor.patch[label])"""
 
 
-__version__ = "0.8.2a5.dev5"
+__version__ = "0.8.2a5.dev6"

flamingpy/examples/surface_code.py

@@ -42,7 +42,7 @@ def illustrate_surface_code(d, boundaries, err, polarity, stabilizer_inds=None,
     # Instantiate a surface code.
     RHG_code = SurfaceCode(d, ec=err, boundaries=boundaries, polarity=polarity)
     RHG_lattice = RHG_code.graph
-    RHG_fig, RHG_ax = RHG_code.draw()
+    _, RHG_ax = RHG_code.draw()
 
     # Check edges between boundaries for periodic boundary conditions.
     if boundaries == "periodic":

flamingpy/simulations.py

@@ -52,7 +52,8 @@ def ec_mc_trial(
     weight_options,
     rng=default_rng(),
 ):
-    """Runs a single trial of Monte Carlo simulations of error-correction for the given code."""
+    """Runs a single trial of Monte Carlo simulations of error-correction for
+    the given code."""
     if passive_objects is not None:
         reduce_macro_and_simulate(*passive_objects, p_swap, delta, rng)
     else:

setup.py

@@ -11,8 +11,7 @@
 # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 # See the License for the specific language governing permissions and
 # limitations under the License.
-"""setup.py instructions for FlamingPy installation from Source
-"""
+"""setup.py instructions for FlamingPy installation from Source."""
 
 # pylint: disable=too-few-public-methods
 
@@ -36,7 +35,7 @@
 
 
 class BinaryDistribution(dist.Distribution):
-    """A class to define Binary Distribution objects"""
+    """A class to define Binary Distribution objects."""
 
     def has_ext_modules(foo):
         """Check for external modules."""
@@ -159,8 +158,10 @@ def build_extension(self, ext):
     "thewalrus>=0.19.0",
 ]
 
-description = ("FlamingPy is a cross-platform Python library with a variety of backends for "
-               "efficient simulations of error correction in fault-tolerant quantum computers.")
+description = (
+    "FlamingPy is a cross-platform Python library with a variety of backends for "
+    "efficient simulations of error correction in fault-tolerant quantum computers."
+)
 
 setup(
     name="flamingpy",

tests/conftest.py

@@ -11,8 +11,8 @@
 # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 # See the License for the specific language governing permissions and
 # limitations under the License.
-"""Default parameters, environment variables, fixtures, and shared objects
-the unit tests and manual checks."""
+"""Default parameters, environment variables, fixtures, and shared objects the
+unit tests and manual checks."""
 import os
 import pytest
 

tests/unit/test_benchmarks_examples.py

@@ -17,7 +17,6 @@
 # pylint: disable=import-outside-toplevel,unused-import
 
 import pytest
-from flamingpy.codes import alternating_polarity
 
 
 @pytest.mark.parametrize("noise", ["cv", "dv"])

tests/unit/test_iid_noise.py

@@ -40,8 +40,7 @@ def test_full_noise():
 
 def test_finite_prob_noise():
     """Check that all bit values are either 0 or 1 when the error probability
-    is between 0 and 1.
-    """
+    is between 0 and 1."""
     code = SurfaceCode(3)
     for prob in [0.1, 0.5, 0.9]:
         noise = IidNoise(code, prob)
@@ -51,8 +50,8 @@ def test_finite_prob_noise():
 
 
 def test_decoding():
-    """Check that we can use the correct function to decode the code
-    after applying iid noise."""
+    """Check that we can use the correct function to decode the code after
+    applying iid noise."""
     code = SurfaceCode(3)
     noise = IidNoise(code, 0.1)
     noise.apply_noise()
@@ -61,7 +60,8 @@ def test_decoding():
 
 @pytest.mark.parametrize("prob", [-0.1, 1.1])
 def test_warning(prob):
-    """Test that a warning is raised when the probability is not between 0 and 1."""
+    """Test that a warning is raised when the probability is not between 0 and
+    1."""
 
     code = SurfaceCode(3)
     with pytest.raises(Exception) as exc:

tests/unit/test_init.py

@@ -11,9 +11,7 @@
 # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 # See the License for the specific language governing permissions and
 # limitations under the License.
-"""
-Unit tests for flamingpy top _init_.py functions.
-"""
+"""Unit tests for flamingpy top _init_.py functions."""
 
 # pylint: disable=protected-access
 

tests/unit/test_matching.py

@@ -74,7 +74,8 @@ def test_matching_has_same_weight(matching_graphs):
 
 @pytest.fixture(scope="module", params=it.product(matching_graph_types, distances))
 def code_matching_graphs(request):
-    """Return a matching graph type built from a surface code with given distance.
+    """Return a matching graph type built from a surface code with given
+    distance.
 
     Also return the corresponding NxMatchingGraph for comparison.
     """

tests/unit/test_stabilizer_graph.py

@@ -11,8 +11,7 @@
 # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 # See the License for the specific language governing permissions and
 # limitations under the License.
-"""
-Unit tests for StablizerGraph classes in stab_graph.py.
+"""Unit tests for StablizerGraph classes in stab_graph.py.
 
 The networkx implementation is used as a reference.
 """

tests/unit/test_uf_decoder.py

@@ -68,10 +68,8 @@ def enc_state(request):
 
 @pytest.fixture(scope="module", params=code_params)
 def enc_state_swap_list(request):
-    """
-    In this function, lattice is generated based on a list of psqueezed states,
-    which are generated randomly.
-    """
+    """In this function, lattice is generated based on a list of psqueezed
+    states, which are generated randomly."""
     distance, ec, boundaries, delta = request.param
 
     if boundaries == "periodic":
@@ -172,7 +170,7 @@ def test_support(self, enc_state_swap_list):
                     assert support.status[frozenset((edge[0], edge[1]))] == "grown"
 
     def test_support_value(self, enc_state_swap_list):
-        """Test Support function assignments"""
+        """Test Support function assignments."""
         CV_decoder(enc_state_swap_list[0])
         assign_weights(enc_state_swap_list[0], "UF")
 
@@ -230,7 +228,7 @@ def test_boundary(self, enc_state):
 
 
 class TestUnionFindFunctions:
-    """Test function members of UnionFind decoder"""
+    """Test function members of UnionFind decoder."""
 
     def test_union(self):
         """Test the union of trees."""
@@ -338,10 +336,11 @@ def test_initialize_cluster_trees(self, enc_state):
 
 
 class PeelingDecoder:
-    """A class to host methods for testing peeling decoder assignments"""
+    """A class to host methods for testing peeling decoder assignments."""
 
     def test_peeling(self):
-        """Test the peeling decoder for the surface code with periodic boundary conditions."""
+        """Test the peeling decoder for the surface code with periodic boundary
+        conditions."""
         # Test 1: Check if the peeling decoder works fine for one even cluster
         spanning_forest = rx.PyGraph()
 
@@ -443,9 +442,8 @@ def test_uf_erasure(self, enc_state_swap_list):
         assert set(enc_state_swap_list[2]) == set(erased_qubits)
 
     def test_assign_weight_UF(self):
-        """
-        Testing the different types of weights and number of weight levels in
-        different weighted UF decoders in UFdecoder.py
+        """Testing the different types of weights and number of weight levels
+        in different weighted UF decoders in UFdecoder.py.
 
         The graph considered is
         (0,0,0) A'p' -
@@ -457,10 +455,8 @@ def test_assign_weight_UF(self):
         """
 
         class MinimalCode:
-            """
-            A class similar to SurfaceCode class but only with
-            attributes that are required for the testing.
-            """
+            """A class similar to SurfaceCode class but only with attributes
+            that are required for the testing."""
 
             def __init__(self, G, synd_coords):
                 self.graph = G
@@ -505,9 +501,7 @@ def __init__(self, G, synd_coords):
         assert G.nodes[(6, 3, 2)]["weight"] == 2
 
     def test_UF(self):
-        """
-        Testing the UFdecoder
-        """
+        """Testing the UFdecoder."""
         syndrome_dict = {1: 1, 2: 0, 3: 1, 4: 0, 5: 0, 6: 1, 7: 1, 8: 0, 9: 0}
         syndrome_nodes = []
         for i in range(len(syndrome_dict)):

tests/unit/test_utils_graphstates.py

@@ -11,7 +11,7 @@
 # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 # See the License for the specific language governing permissions and
 # limitations under the License.
-""""Unit tests for the utils.graph_states module"""
+""""Unit tests for the utils.graph_states module."""
 import pytest
 from flamingpy.utils import graph_states
 
@@ -28,7 +28,7 @@ def test_star_graph():
 
 
 def test_star_graph_inputs():
-    """Check that invalid inputs in star_graph raise a warning"""
+    """Check that invalid inputs in star_graph raise a warning."""
     n = 0
     with pytest.raises(Exception) as e:
         graph_states.star_graph(n)
@@ -56,7 +56,7 @@ def test_complete_graph():
 
 
 def test_complete_graph_inputs():
-    """Check that invalid inputs in complete_graph raise a warning"""
+    """Check that invalid inputs in complete_graph raise a warning."""
     n = 0
     with pytest.raises(Exception) as e:
         graph_states.complete_graph(n)

tests/unit/test_viz.py

@@ -12,9 +12,7 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 """"Unit tests for functions in the viz module."""
-
 import math
-from datetime import datetime
 
 import numpy as np
 from numpy.random import default_rng as rng