chore: rename averaged -> average (#123)

* chore: rename averaged -> average * chore: add setuptools to requirements.txt * chore: update requirements.txt and revert addition of setuptools
Exabyte-io · Nov 15, 2022 · 3f124d3 · 3f124d3
1 parent 04ed9ea
commit 3f124d3
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Showing 7 changed files with 18 additions and 18 deletions.
diff --git a/express/parsers/apps/espresso/formats/txt.py b/express/parsers/apps/espresso/formats/txt.py
@@ -810,7 +810,7 @@ def final_lattice_vectors(self, text):
         if cell_parameters_last_index < 0: return self.initial_lattice_vectors(text)
         return self._extract_lattice(text[cell_parameters_last_index:])
 
-    def averaged_quantity(self, stdout_file: str) -> np.ndarray:
+    def average_quantity(self, stdout_file: str) -> np.ndarray:
         """
         Extract planar and macroscopic averages of a quantity from the output of average.x (output file or avg.dat)
         The format is as follows:
@@ -835,5 +835,5 @@ def averaged_quantity(self, stdout_file: str) -> np.ndarray:
             average_file = find_file(stdout_file, self.work_dir)
         if type(average_file) == str and os.path.isfile(average_file):
             dtype = np.dtype([("x", float), ("planar_average", float), ("macroscopic_average", float)])
-            data = np.fromregex(average_file, settings.REGEX["averaged_quantity"]["regex"], dtype)
+            data = np.fromregex(average_file, settings.REGEX["average_quantity"]["regex"], dtype)
             return data
diff --git a/express/parsers/apps/espresso/parser.py b/express/parsers/apps/espresso/parser.py
@@ -333,8 +333,8 @@ def final_structure_strings(self):
                 pass
         return structures
 
-    def averaged_potential(self):
-        data = self.txt_parser.averaged_quantity(self.stdout_file)
+    def average_potential(self):
+        data = self.txt_parser.average_quantity(self.stdout_file)
         data["x"] *= Constant.BOHR  # convert to angstrom
         data["planar_average"] *= Constant.RYDBERG  # convert to eV
         data["macroscopic_average"] *= Constant.RYDBERG  # convert to eV

diff --git a/express/parsers/apps/espresso/settings.py b/express/parsers/apps/espresso/settings.py
@@ -140,7 +140,7 @@
         "occurrences": 0,
         "output_type": "str",
     },
-    "averaged_quantity": {
+    "average_quantity": {
         "regex": r"\s*({0})\s+({0})\s+({0})".format(DOUBLE_REGEX),
     },
 }

diff --git a/...sional_plot/averaged_potential_profile.py → ...nsional_plot/average_potential_profile.py b/...sional_plot/averaged_potential_profile.py → ...nsional_plot/average_potential_profile.py
@@ -1,14 +1,14 @@
 from express.properties.non_scalar.two_dimensional_plot import TwoDimensionalPlotProperty
 
 
-class AveragedPotentialProfile(TwoDimensionalPlotProperty):
+class AveragePotentialProfile(TwoDimensionalPlotProperty):
     """
-    Averaged potential profile plot.
+    Average potential profile plot.
     """
 
     def __init__(self, name: str, parser, *args, **kwargs):
         super().__init__(name, parser, *args, **kwargs)
 
-        self.data = self.safely_invoke_parser_method("averaged_potential")
+        self.data = self.safely_invoke_parser_method("average_potential")
         self.xDataArray = self.data["x"].tolist()
         self.yDataSeries = [self.data["planar_average"].tolist(), self.data["macroscopic_average"].tolist()]
diff --git a/express/settings.py b/express/settings.py
@@ -94,8 +94,8 @@
     'file_content': {
         'reference': 'express.properties.non_scalar.file_content.FileContent'
     },
-    'averaged_potential_profile': {
-        'reference': 'express.properties.non_scalar.two_dimensional_plot.averaged_potential_profile.AveragedPotentialProfile'
+    'average_potential_profile': {
+        'reference': 'express.properties.non_scalar.two_dimensional_plot.average_potential_profile.AveragePotentialProfile'
     },
 }
 

diff --git a/requirements-dev.txt b/requirements-dev.txt
@@ -5,7 +5,7 @@ click==7.0
 coverage==5.3
 cycler==0.10.0
 decorator==4.4.2
-esse==2022.11.10.post0
+esse==2022.11.15.post0
 exabyte-json-include==2021.05.06
 flask==1.0.2
 idna==2.7

diff --git a/...l_plot/test_averaged_potential_profile.py → ...al_plot/test_average_potential_profile.py b/...l_plot/test_averaged_potential_profile.py → ...al_plot/test_average_potential_profile.py
@@ -1,11 +1,11 @@
 from mock import MagicMock
 import numpy as np
 from tests.unit import UnitTestBase
-from express.properties.non_scalar.two_dimensional_plot.averaged_potential_profile import AveragedPotentialProfile
+from express.properties.non_scalar.two_dimensional_plot.average_potential_profile import AveragePotentialProfile
 
 
 AVG_POTENTIAL = {
-    "name": "averaged_potential_profile",
+    "name": "average_potential_profile",
     "xDataArray": [0, 2.0943951, 4.1887902, 6.28318531],
     "yDataSeries": [[0, 0, 0, 0], [1.0, -0.5, -0.5, 1.0]],
     "yAxis": {
@@ -19,7 +19,7 @@
 }
 
 
-class AveragedPotentialProfileTest(UnitTestBase):
+class AveragePotentialProfileTest(UnitTestBase):
     def setUp(self):
         super().setUp()
 
@@ -39,9 +39,9 @@ def create_mock_data(self, n_points: int = 300):
         dtype = np.dtype([("x", float), ("planar_average", float), ("macroscopic_average", float)])
         return np.array(list(zip(x, p_x, m_x)), dtype=dtype)
 
-    def test_averaged_potential(self):
-        averaged_potential_data = self.create_mock_data(n_points=4)
+    def test_average_potential(self):
+        average_potential_data = self.create_mock_data(n_points=4)
         parser = MagicMock()
-        parser.attach_mock(MagicMock(return_value=averaged_potential_data), "averaged_potential")
-        property_ = AveragedPotentialProfile("averaged_potential_profile", parser)
+        parser.attach_mock(MagicMock(return_value=average_potential_data), "average_potential")
+        property_ = AveragePotentialProfile("average_potential_profile", parser)
         self.assertDeepAlmostEqual(property_.serialize_and_validate(), AVG_POTENTIAL, places=6)