Merge #3203

3203: Code cleanup with pylint r=KaiSzuttor a=jngrad

Follow-up to #3194

Description of changes:
- remove unused imports
- rewrite wildcard imports as explicit imports
- replace mutable optional parameters by immutable equivalents
- fix LB thermostat checkpointing mechanism
- cleanup and simplify conditional statements
- refactor code with numpy and new espresso methods
- remove unused variables/arguments
- rename unused loop variables from `i` to `_`
- fix broken numpy commands in parts of the testsuite that aren't executed
- remove trailling whitespaces


Co-authored-by: Jean-Noël Grad <[email protected]>
Co-authored-by: Kai Szuttor <[email protected]>

maintainer/CI/dox_warnings.py

@@ -55,14 +55,14 @@
 # filter out non-critical warnings
 warnings = {}
 for (filepath, lineno, warning), warning_list in raw_warnings.items():
-    if re.search('^member \S+ belongs to two different groups\. '
-                 'The second one found here will be ignored\.$', warning):
+    if re.search(r'^member \S+ belongs to two different groups\. '
+                 r'The second one found here will be ignored\.$', warning):
         # happens when a function is declared in a group in the .hpp file but
         # defined in another group in the .cpp file; this is usually caused by
         # the "Private functions" and "Exported functions" groups in .hpp files
         continue
-    if re.search(
-            '^documented symbol `\S+\' was not declared or defined\.$', warning):
+    if re.search(r'^documented symbol `\S+\' was not declared or defined\.$',
+                 warning):
         # known bug, fixed in 1.8.16
         continue
     if re.search('^no uniquely matching class member found for $', warning):
@@ -75,7 +75,7 @@
         # warning, when in reality the warning is silenced because the text on
         # the following line is captured and becomes the argument description
         continue
-    filepath = re.sub('^.*(?=src/)', '', filepath)
+    filepath = re.sub(r'^.*(?=src/)', '', filepath)
     if filepath not in warnings:
         warnings[filepath] = {}
     warnings[filepath][(lineno, warning)] = warning_list
@@ -94,7 +94,7 @@
         f.write(filepath + ':\n')
         for (lineno, warning) in sorted(warnings[filepath].keys()):
             warning_list = warnings[filepath][(lineno, warning)]
-            s = re.sub('\(.*\)', '()', warning)
+            s = re.sub(r'\(.*\)', '()', warning)
             if warning_list:
                 s += ': ' + ', '.join(x.strip() for x in warning_list)
             f.write('  line {}: {}\n'.format(lineno, s))

maintainer/benchmarks/lj.py

@@ -58,7 +58,6 @@
 
 
 import espressomd
-from espressomd import thermostat
 if args.visualizer:
     from espressomd import visualization
     from threading import Thread

maintainer/benchmarks/p3m.py

@@ -58,11 +58,9 @@
 
 
 import espressomd
-from espressomd import thermostat
 from espressomd import electrostatics
 if args.visualizer:
     from espressomd import visualization
-    from threading import Thread
 
 required_features = ["P3M", "LENNARD_JONES", "MASS"]
 espressomd.assert_features(required_features)
@@ -101,7 +99,7 @@
 # Integration parameters
 #############################################################
 system.time_step = 0.01
-system.cell_system.skin = .4 
+system.cell_system.skin = .4
 system.thermostat.turn_off()
 
 

maintainer/gh_post_docs_warnings.py

@@ -22,7 +22,6 @@
 import os
 import sys
 import requests
-import subprocess
 
 if not os.environ['CI_COMMIT_REF_NAME'].startswith('PR-'):
     exit(0)

maintainer/gh_post_style_patch.py

@@ -60,5 +60,5 @@
     comment += 'You can run `gitlab-runner exec docker style` afterwards to check if your changes worked out properly.\n\n'
     comment += 'Please note that there are often multiple ways to correctly format code. As I am just a robot, I sometimes fail to identify the most aesthetically pleasing way. So please look over my suggested changes and adapt them where the style does not make sense.'
 
-    if len(patch) > 0:
+    if patch:
         requests.post(URL, json={'body': comment})

maintainer/git2changelog.py

@@ -16,7 +16,6 @@
 # You should have received a copy of the GNU General Public License
 # along with this program.  If not, see <http://www.gnu.org/licenses/>.
 #
-import string
 import re
 import os
 
@@ -52,14 +51,14 @@
         continue
 
     # Match the author line and extract the part we want
-    m = re.match('^Author:\s*(.*)\s*$', line)
+    m = re.match(r'^Author:\s*(.*)\s*$', line)
     if m is not None:
         author = m.group(1)
         authorFound = True
         continue
 
     # Match the date line
-    m = re.match('^Date:\s*(.*)\s*$', line)
+    m = re.match(r'^Date:\s*(.*)\s*$', line)
     if m is not None:
         date = m.group(1)
         dateFound = True
@@ -92,7 +91,7 @@
         continue
     # Collect the files for this commit. FIXME: Still need to add +/- to files
     elif authorFound & dateFound & messageFound:
-        fileList = re.split(' \| ', line, 2)
+        fileList = re.split(r' \| ', line, 2)
         if len(fileList) > 1:
             if files:
                 files = files + ", " + fileList[0].strip()

src/config/defines.py

@@ -21,9 +21,10 @@
 
 class Defines:
 
-    def __init__(self, compiler, flags=[]):
+    def __init__(self, compiler, flags=()):
         self._compiler = compiler
-        self._flags = flags + ["-E", "-dM"]
+        assert isinstance(flags, (list, tuple))
+        self._flags = list(flags) + ["-E", "-dM"]
 
         build_in = self._build_in_defs()
         self._buildin = set(build_in)

src/config/featuredefs.py

@@ -20,11 +20,10 @@
 # This module parses the feature definition file features.def
 #
 import fileinput
-import string
 import re
 
 
-class SyntaxError:
+class SyntaxError(Exception):
 
     def __init__(self, message, instead):
         self.message = message
@@ -171,7 +170,7 @@ def check_validity(self, activated):
         for feature in allfeatures:
             featurevars[feature] = feature in newset
 
-        for feature, expr, undef in self.requirements:
+        for feature, expr, _ in self.requirements:
             # print 'Requirement: ', feature, ' -> ', expr
             if feature in newset:
                 if not eval(expr, featurevars):

src/config/gen_sampleconfig.py

@@ -20,8 +20,6 @@
 # This script appends the sample list of features to the file
 #   myconfig-sample.h.
 #
-import time
-import string
 import fileinput
 import inspect
 import sys

src/python/espressomd/MDA_ESP/__init__.py

@@ -210,9 +210,9 @@ def _read_first_frame(self):
         with util.openany(self.filename, 'rt') as espfile:
             n_atoms = 1
             for pos, line in enumerate(espfile, start=-3):
-                if (pos == -3):
+                if pos == -3:
                     time = float(line[1:-1])
-                elif(pos == -2):
+                elif pos == -2:
                     n_atoms = int(line)
                     self.n_atoms = n_atoms
                     positions = np.zeros(
@@ -224,13 +224,13 @@ def _read_first_frame(self):
                     self.ts = ts = self._Timestep(
                         self.n_atoms, **self._ts_kwargs)
                     self.ts.time = time
-                elif(pos == -1):
+                elif pos == -1:
                     self.ts._unitcell[:3] = np.array(
                         list(map(float, line[1:-2].split())))
-                elif(pos < n_atoms):
+                elif pos < n_atoms:
                     positions[pos] = np.array(
                         list(map(float, line[1:-2].split())))
-                elif(pos < 2 * n_atoms):
+                elif pos < 2 * n_atoms:
                     velocities[pos - n_atoms] = np.array(
                         list(map(float, line[1:-2].split())))
                 else:

src/python/espressomd/accumulators.py

@@ -241,10 +241,10 @@ def result(self):
         -------
 
         numpy.ndarray
-            The result of the correlation function as a 2d-array. 
+            The result of the correlation function as a 2d-array.
             The first column contains the values of the lag time tau.
             The second column contains the number of values used to
-            perform the averaging of the correlation. Further columns contain 
+            perform the averaging of the correlation. Further columns contain
             the values of the correlation function. The number of these columns
             is the dimension of the output of the correlation operation.
         """

src/python/espressomd/checkpointing.py

@@ -17,7 +17,6 @@
 # along with this program.  If not, see <http://www.gnu.org/licenses/>.
 #
 from collections import OrderedDict
-import sys
 import inspect
 import os
 import re
@@ -97,7 +96,6 @@ def __setattr_submodule(self, obj, name, value):
 
         """
         names = name.split('.')
-        tmp_obj = obj
         for i in range(len(names) - 1):
             obj = getattr(obj, names[i], None)
 

src/python/espressomd/constraints.py

@@ -15,7 +15,6 @@
 # You should have received a copy of the GNU General Public License
 # along with this program.  If not, see <http://www.gnu.org/licenses/>.
 from .script_interface import ScriptObjectRegistry, ScriptInterfaceHelper, script_interface_register
-from espressomd.utils import is_valid_type
 import numpy as np
 from itertools import product
 

src/python/espressomd/ekboundaries.py

@@ -14,7 +14,7 @@
 #
 # You should have received a copy of the GNU General Public License
 # along with this program.  If not, see <http://www.gnu.org/licenses/>.
-from .script_interface import ScriptInterfaceHelper, script_interface_register
+from .script_interface import script_interface_register
 from .__init__ import has_features
 import espressomd.lbboundaries
 

src/python/espressomd/io/writer/vtf.py

@@ -40,7 +40,7 @@ def vtf_pid_map(system, types='all'):
     id_to_write = []
     for p in system.part:
         for t in types:
-            if p.type == t or t == "all":
+            if t in (p.type, "all"):
                 id_to_write.append(p.id)
     return dict(zip(id_to_write, range(len(id_to_write))))
 
@@ -70,7 +70,7 @@ def writevsf(system, fp, types='all'):
                                                               system.part[pid].type))
     for pid, vtf_id, in vtf_index.items():
         for b in system.part[pid].bonds:
-            if (system.part[b[1]].id in vtf_index):
+            if system.part[b[1]].id in vtf_index:
                 fp.write("bond {}:{}\n".format(
                     vtf_id, vtf_index[system.part[b[1]].id]))
 

src/python/object_in_fluid/__init__.py

@@ -14,32 +14,15 @@
 #
 # You should have received a copy of the GNU General Public License
 # along with this program.  If not, see <http://www.gnu.org/licenses/>.
-from .oif_classes import \
-    FixedPoint, \
-    PartPoint, \
-    Edge, \
-    Triangle, \
-    Angle, \
-    ThreeNeighbors, \
-    Mesh, \
-    OifCellType,\
-    OifCell
-
-from .oif_utils import \
-    custom_str, \
-    get_triangle_normal, \
-    norm, \
-    vec_distance, \
-    area_triangle, \
-    angle_btw_triangles, \
-    discard_epsilon, \
-    oif_neo_hookean_nonlin, \
-    oif_calc_stretching_force, \
-    oif_calc_linear_stretching_force, \
-    oif_calc_bending_force, \
-    oif_calc_local_area_force, \
-    oif_calc_global_area_force, \
-    oif_calc_volume_force, \
-    output_vtk_rhomboid, \
-    output_vtk_cylinder, \
-    output_vtk_lines
+from .oif_classes import (
+    FixedPoint, PartPoint, Edge, Triangle, Angle, ThreeNeighbors, Mesh,
+    OifCellType, OifCell
+)
+from .oif_utils import (
+    custom_str, get_triangle_normal, norm, vec_distance, area_triangle,
+    angle_btw_triangles, discard_epsilon, oif_neo_hookean_nonlin,
+    oif_calc_stretching_force, oif_calc_linear_stretching_force,
+    oif_calc_bending_force, oif_calc_local_area_force,
+    oif_calc_global_area_force, oif_calc_volume_force, output_vtk_rhomboid,
+    output_vtk_cylinder, output_vtk_lines
+)