From ce095db7d80140530cb1d84afabed991598e7660 Mon Sep 17 00:00:00 2001
From: Timo Koch <timo.koch@iws.uni-stuttgart.de>
Date: Fri, 30 Jul 2021 23:04:46 +0200
Subject: [PATCH] [bin][python] Make flake8 happy and add to CI
---
.flake8 | 3 +
.gitlab-ci/default.yml | 1 +
bin/doc/getparameterlist.py | 28 +++----
bin/installdumux.py | 27 ++++---
bin/installexternal.py | 35 ++++----
bin/postprocessing/exportscreenshot2d.py | 65 +++++++++------
bin/postprocessing/extractlinedata.py | 16 ++--
.../extractpointdataovertime.py | 18 +++--
bin/postprocessing/l2error.py | 7 +-
bin/remove_clutter_after_last_endif.py | 1 +
bin/testing/fuzzycomparedata.py | 12 +--
bin/testing/fuzzycomparevtu.py | 79 ++++++++++---------
bin/testing/runtest.py | 27 +++++--
bin/util/common.py | 1 -
bin/util/installscript.py | 2 +-
bin/util/installscript_writer.py | 6 +-
16 files changed, 197 insertions(+), 131 deletions(-)
diff --git a/.flake8 b/.flake8
index a41b8c9c4d..4cf0f63e70 100644
--- a/.flake8
+++ b/.flake8
@@ -1,4 +1,7 @@
[flake8]
+ignore =
+ # Ignore whitespace before colon which gives false positive for list slice (black does it correct)
+ E203
max-line-length = 100
per-file-ignores =
# imported but unused and unable to detect undefined names
diff --git a/.gitlab-ci/default.yml b/.gitlab-ci/default.yml
index 93b3c5c5f0..ff98f7be11 100644
--- a/.gitlab-ci/default.yml
+++ b/.gitlab-ci/default.yml
@@ -51,6 +51,7 @@ pylint-flake8 (python):
if [ -d build-cmake/python/dumux ] ; then
pylint --rcfile=.pylintrc build-cmake/python/dumux
flake8 build-cmake/python/dumux
+ flake8 bin
fi
needs:
- job: configure
diff --git a/bin/doc/getparameterlist.py b/bin/doc/getparameterlist.py
index 8f6b474ec7..7a9afefe51 100644
--- a/bin/doc/getparameterlist.py
+++ b/bin/doc/getparameterlist.py
@@ -7,6 +7,7 @@ for usage of getParam or getParamFromGroup.
import os
+
# find the content of the given string between the first matching pair of opening/closing keys
def getEnclosedContent(string, openKey, closeKey):
@@ -91,9 +92,9 @@ def getParamsFromFile(file):
# print encountered errors
if errors:
print(
- "\n\n{} parameter{} in file {} could not be retrieved automatically. Please check them yourself:".format(
- len(errors), "s" if len(errors) > 1 else "", file
- )
+ f"\n\n{len(errors)} parameter{'s' if len(errors) > 1 else ''}"
+ f"in file {file} could not be retrieved automatically. "
+ "Please check them yourself:"
)
for lineIdx in errors:
print("\n\t-> line {}: {}".format(lineIdx, errors[lineIdx]["line"]))
@@ -140,7 +141,9 @@ for key in parameterDict:
groupEntry = "-" if not hasGroup else entry["paramName"].split(".")[0]
paramName = entry["paramName"] if not hasGroup else entry["paramName"].partition(".")[2]
- # In case of multiple occurrences, we use the first entry that is not None and print the others for possible manual editing
+ # In case of multiple occurrences,
+ # we use the first entry that is not None
+ # and print the others for possible manual editing
paramType = entry["paramType"][0]
defaultValue = next((e for e in entry["defaultValue"] if e), "-")
@@ -154,27 +157,24 @@ for key in parameterDict:
)
if hasMultiplePT or hasMultipleDV:
print(
- "\nFound multiple occurrences of parameter "
- + paramName
- + " with differing specifications: "
+ f"\nFound multiple occurrences of parameter {paramName}",
+ " with differing specifications: "
)
if hasMultiplePT:
print(" -> Specified type names:")
for typeName in entry["paramType"]:
print(" " * 8 + typeName)
print(
- " ---> For the parameters list, "
- + paramType
- + " has been chosen. Please adapt manually if desired."
+ " ---> For the parameters list, {paramType}"
+ " has been chosen. Please adapt manually if desired."
)
if hasMultipleDV:
print(" -> Specified default values:")
for default in entry["defaultValue"]:
print(" " * 8 + (default if default else "- (none given)"))
print(
- " ---> For the parameters list, "
- + defaultValue
- + " has been chosen. Please adapt manually if desired."
+ f" ---> For the parameters list, {defaultValue}"
+ " has been chosen. Please adapt manually if desired."
)
maxGroupWidth = max(maxGroupWidth, len(groupEntry) + 3) # +3 because \b will be added later
@@ -219,7 +219,7 @@ tableEntries = tableEntriesWithoutGroup + tableEntriesWithGroup
header = """/*!
*\\file
- *\ingroup Parameter
+ *\\ingroup Parameter
*
*\\brief List of currently useable run-time parameters
*
diff --git a/bin/installdumux.py b/bin/installdumux.py
index 5ff12c02eb..4ccafe1bc1 100755
--- a/bin/installdumux.py
+++ b/bin/installdumux.py
@@ -7,6 +7,7 @@ import os
import sys
import argparse
import subprocess
+import textwrap
from distutils.spawn import find_executable
from distutils.version import LooseVersion
@@ -65,14 +66,17 @@ def run_command(command, workdir="."):
print(line, end="")
popen.stdout.close()
popen.stderr.close()
- return_code = popen.wait()
- if return_code:
- print("\n")
- message = "\n (Error) The command {} returned with non-zero exit code\n".format(
- command
+ returnCode = popen.wait()
+ if returnCode:
+ message = textwrap.dedent(
+ f"""\
+
+ (Error) The command {command} returned with non-zero exit code
+ If you can't fix the problem yourself consider reporting your issue
+ on the mailing list (dumux@listserv.uni-stuttgart.de) and
+ attach the file 'installdumux.log'
+ """
)
- message += "\n If you can't fix the problem yourself consider reporting your issue\n"
- message += " on the mailing list (dumux@listserv.uni-stuttgart.de) and attach the file 'installdumux.log'\n"
show_message(message)
sys.exit(1)
@@ -125,7 +129,8 @@ os.makedirs("./dumux", exist_ok=True)
os.chdir("dumux")
show_message(
- "(2/3) Cloning repositories. This may take a while. Make sure to be connected to the internet..."
+ "(2/3) Cloning repositories. This may take a while. "
+ "Make sure to be connected to the internet..."
)
# the core modules
@@ -152,7 +157,8 @@ show_message("(2/3) Step completed. All repositories have been cloned into a con
#################################################################
#################################################################
show_message(
- "(3/3) Configure and build dune modules and dumux using dunecontrol. This may take several minutes..."
+ "(3/3) Configure and build dune modules and dumux using dunecontrol. "
+ "This may take several minutes..."
)
# run dunecontrol
@@ -172,7 +178,8 @@ else:
test_path += "/implicit/isothermal"
show_message(
- "(Installation complete) To test if everything works, please run the following commands (can be copied to command line):\n\n"
+ "(Installation complete) To test if everything works, "
+ "please run the following commands (can be copied to command line):\n\n"
" cd {}\n"
" make test_1p_tpfa\n"
" ./test_1p_tpfa\n"
diff --git a/bin/installexternal.py b/bin/installexternal.py
index d99a9e261c..416fcfacd9 100755
--- a/bin/installexternal.py
+++ b/bin/installexternal.py
@@ -4,13 +4,14 @@
install external stuff for dumux
"""
import os
-import urllib.request
+import shutil
+import re
+import urllib
import tarfile
import sys
import subprocess
-import shutil
-import re
import argparse
+import textwrap
class ChoicesAction(argparse._StoreAction):
@@ -38,7 +39,8 @@ def show_message(message):
if len(sys.argv) == 1:
show_message(
- "No options given. For more information run the following command: \n ./installexternal.py --help"
+ "No options given. For more information "
+ "run the following command: \n ./installexternal.py --help"
)
sys.exit()
@@ -111,11 +113,14 @@ def run_command(command, currentdir="."):
return_code = popen.wait()
if return_code:
print("\n")
- message = "\n (Error) The command {} returned with non-zero exit code\n".format(
- command
+ message = textwrap.dedent(
+ f"""\
+ (Error) The command {command} returned with non-zero exit code
+ If you can't fix the problem yourself consider reporting your issue
+ on the mailing list (dumux@listserv.uni-stuttgart.de) and
+ attach the file 'installexternal.log'
+ """
)
- message += "\n If you can't fix the problem yourself consider reporting your issue\n"
- message += " on the mailing list (dumux@listserv.uni-stuttgart.de) and attach the file 'installexternal.log'\n"
show_message(message)
sys.exit(1)
@@ -124,7 +129,7 @@ def git_clone(url, branch=None):
clone = ["git", "clone"]
if branch:
clone += ["-b", branch]
- result = run_command(command=[*clone, url])
+ run_command(command=[*clone, url])
def install_external(args):
@@ -244,7 +249,7 @@ def install_external(args):
run_command(configcmd, currentdir=ext_dir)
try:
run_command("make", currentdir=ext_dir)
- except:
+ except subprocess.CalledProcessError:
raise Exception("{} installation has failed.".format(package))
# Save message to be shown at the end
if os.path.exists(ext_dir + "/" + package):
@@ -281,7 +286,9 @@ def install_external(args):
# Save post installation message about dunecontrol if need be.
if not cleanup and any(x in pkg for pkg in packages for x in ["dumux", "dune", "opm"]):
final_message.append(
- "\n\nPlease run the following command (can be copied to command line):\n\n ./dune-common/bin/dunecontrol --opts=./dumux/cmake.opts all"
+ "\n\nPlease run the following command "
+ "(can be copied to command line):\n\n "
+ "./dune-common/bin/dunecontrol --opts=./dumux/cmake.opts all"
)
# If cleanup and only logfile in the external directory, remove the directory
@@ -295,7 +302,7 @@ def install_external(args):
#################################################################
#################################################################
-## (1/3) Define th necessary packages and their urls
+# (1/3) Define th necessary packages and their urls
#################################################################
#################################################################
dune_git_baseurl = "https://gitlab.dune-project.org/"
@@ -362,7 +369,7 @@ messages = {
#################################################################
#################################################################
-## (2/3) Download/Config/Clean the requested packages
+# (2/3) Download/Config/Clean the requested packages
#################################################################
#################################################################
# Start download/configuration/cleaning tasks
@@ -370,7 +377,7 @@ final_message = install_external(args)
#################################################################
#################################################################
-## (3/3) Show the final message
+# (3/3) Show the final message
#################################################################
#################################################################
# Show final message
diff --git a/bin/postprocessing/exportscreenshot2d.py b/bin/postprocessing/exportscreenshot2d.py
index 2032ff41a1..8ff909a342 100644
--- a/bin/postprocessing/exportscreenshot2d.py
+++ b/bin/postprocessing/exportscreenshot2d.py
@@ -1,20 +1,42 @@
-#### TODO:
-# - different colors for legend
-# - read-in pvds with time outputs
-# - read-in multiple vtus, e.g. for multidomain
-# - rendering method 2d and 3d
+"""
+Script for exporting 2d screenshots from ParaView
+
+TODO:
+- different colors for legend
+- read-in pvds with time outputs
+- read-in multiple vtus, e.g. for multidomain
+- rendering method 2d and 3d
+"""
# parse arguments
import argparse
import os
import sys
+try:
+ from paraview.simple import (
+ XMLUnstructuredGridReader,
+ GetActiveView,
+ CreateRenderView,
+ Show,
+ ColorBy,
+ GetColorTransferFunction,
+ GetScalarBar,
+ RenderAllViews,
+ SaveScreenshot,
+ )
+except ImportError:
+ print("`paraview.simple` not found. Make sure using pvbatch.")
+
bool = ["True", "False"]
parameterType = ["CELLS", "POINTS"]
legendOrientation = ["Horizontal", "Vertical"]
parser = argparse.ArgumentParser(
prog="\033[1m\033[94m" + "pvbatch" + "\033[0m" + " " + sys.argv[0],
- description="Export a screenshot of a standard 2D plot. To change the color palette, change the default in the paraview GUI.",
+ description=(
+ "Export a screenshot of a standard 2D plot. "
+ "To change the color palette, change the default in the paraview GUI."
+ ),
)
# on/off-type features
offscreen = parser.add_mutually_exclusive_group(required=False)
@@ -158,11 +180,6 @@ parser.add_argument(
parser.add_argument("-v", "--verbosity", type=int, default=2, help="Verbosity of the output")
args = vars(parser.parse_args())
-try:
- from paraview.simple import *
-except ImportError:
- print("`paraview.simple` not found. Make sure using pvbatch.")
-
# import locations
commonOutDirectory = False
outDirectory = args["outputDirectory"]
@@ -189,7 +206,8 @@ for curFile in args["files"]:
vtuFile = XMLUnstructuredGridReader(FileName=curFile)
if args["parameter"] == "":
print(
- "\nNo parameter was specified, use '-p PARAMETER' to specify it. Available parameters are:"
+ "\nNo parameter was specified, use '-p PARAMETER' to specify it. "
+ "Available parameters are:"
)
if args["parameterType"] == "CELLS":
print(vtuFile.CellArrayStatus)
@@ -204,18 +222,19 @@ for curFile in args["files"]:
renderView1 = CreateRenderView()
# print additional help message for large picture sizes
- if (args["size"][0] > 1024 or args["size"][1] > 1024) and args["offscreen"] == False:
- print(
- "\nIt seems like you want to export a picture greater then your actual screen size. Use:"
+ if (args["size"][0] > 1024 or args["size"][1] > 1024) and not args["offscreen"]:
+ raise IOError(
+ "\nIt seems like you want to export a picture greater "
+ "than your actual screen size. Use:\n"
+ "pvbatch --use-offscreen-rendering SCRIPT OPTIONS --offscreen"
)
- print("pvbatch --use-offscreen-rendering SCRIPT OPTIONS --offscreen")
- exit(2)
+
renderView1.ViewSize = args["size"]
- if args["showOrientationAxes"] == False:
+ if not args["showOrientationAxes"]:
renderView1.OrientationAxesVisibility = 0
- if args["showAxesGrid"] == True:
+ if args["showAxesGrid"]:
renderView1.AxesGrid.Visibility = 1
# show data in view
@@ -229,7 +248,7 @@ for curFile in args["files"]:
ColorBy(vtuFileDisplay, (args["parameterType"], args["parameter"]))
# show color bar/color legend
- if args["showLegend"] == True:
+ if args["showLegend"]:
vtuFileDisplay.SetScalarBarVisibility(renderView1, True)
# get color transfer function/color map for the parameter
@@ -241,7 +260,7 @@ for curFile in args["files"]:
parameterLUT.VectorComponent = args["parameterComponent"]
# if args['parameterRange'][0] == 0 and args['parameterRange'][1] == 0:
# vtuFileDisplay.RescaleTransferFunctionToDataRange(False)
- if args["showLegend"] == True:
+ if args["showLegend"]:
velocityLUTColorBar = GetScalarBar(parameterLUT, renderView1)
velocityLUTColorBar.Title = args["parameter"]
velocityLUTColorBar.ComponentTitle = str(args["parameterComponent"])
@@ -272,11 +291,11 @@ for curFile in args["files"]:
legend.ComponentTitle = args["legendComponentTitle"]
# set a white background color and black color for fonts and the grid
- if args["whiteBackground"] == True:
+ if args["whiteBackground"]:
renderView1.Background = [255, 255, 255]
legend.TitleColor = [0.0, 0.0, 0.0]
legend.LabelColor = [0.0, 0.0, 0.0]
- if args["showAxesGrid"] == True:
+ if args["showAxesGrid"]:
renderView1.AxesGrid.GridColor = [0.0, 0.0, 0.0]
renderView1.AxesGrid.XTitleColor = [0.0, 0.0, 0.0]
renderView1.AxesGrid.YTitleColor = [0.0, 0.0, 0.0]
diff --git a/bin/postprocessing/extractlinedata.py b/bin/postprocessing/extractlinedata.py
index 7f5a7817d1..041fb6e1c7 100644
--- a/bin/postprocessing/extractlinedata.py
+++ b/bin/postprocessing/extractlinedata.py
@@ -3,6 +3,17 @@ import csv
import sys
import os
+try:
+ from paraview.simple import (
+ XMLPolyDataReader,
+ XMLUnstructuredGridReader,
+ SetActiveSource,
+ PlotOverLine,
+ CreateWriter,
+ )
+except ImportError:
+ raise ImportError("`paraview.simple` not found. Make sure using pvpython instead of python.")
+
# parse arguments
parser = argparse.ArgumentParser(
prog="\033[1m\033[94m" + "pvpython" + "\033[0m" + " " + sys.argv[0],
@@ -48,11 +59,6 @@ parser.add_argument(
)
args = vars(parser.parse_args())
-try:
- from paraview.simple import *
-except:
- raise ImportError("`paraview.simple` not found. Make sure using pvpython instead of python.")
-
# import locations
outDirectory = args["outputDirectory"]
if outDirectory.strip():
diff --git a/bin/postprocessing/extractpointdataovertime.py b/bin/postprocessing/extractpointdataovertime.py
index 6c4132dad6..1063c86463 100644
--- a/bin/postprocessing/extractpointdataovertime.py
+++ b/bin/postprocessing/extractpointdataovertime.py
@@ -3,6 +3,19 @@ import csv
import os
import sys
+try:
+ from paraview.simple import (
+ PVDReader,
+ IDSelectionSource,
+ ExtractSelection,
+ servermanager,
+ ProbeLocation,
+ PlotSelectionOverTime,
+ CreateWriter,
+ )
+except ImportError:
+ print("`paraview.simple` not found. Make sure using pvpython instead of python.")
+
# parse arguments
parser = argparse.ArgumentParser(
prog="\033[1m\033[94m" + "pvpython" + "\033[0m" + " " + sys.argv[0],
@@ -33,11 +46,6 @@ parser.add_argument(
)
args = vars(parser.parse_args())
-try:
- from paraview.simple import *
-except ImportError:
- print("`paraview.simple` not found. Make sure using pvpython instead of python.")
-
# import locations
commonOutDirectory = False
outDirectory = args["outputDirectory"]
diff --git a/bin/postprocessing/l2error.py b/bin/postprocessing/l2error.py
index cc75447368..bd1c1a0675 100644
--- a/bin/postprocessing/l2error.py
+++ b/bin/postprocessing/l2error.py
@@ -122,10 +122,9 @@ for i in range(1, len(reference)):
float(reference[2][indexReferenceX]) - float(reference[1][indexReferenceX])
)
elif i == len(reference) - 1:
- distance = 0.5 * (
- float(reference[len(reference) - 1][indexReferenceX])
- - float(reference[len(reference) - 2][indexReferenceX])
- )
+ distA = float(reference[len(reference) - 1][indexReferenceX])
+ distB = float(reference[len(reference) - 2][indexReferenceX])
+ distance = 0.5 * (distA - distB)
else:
distance = 0.5 * (
float(reference[i + 1][indexReferenceX]) - float(reference[i - 1][indexReferenceX])
diff --git a/bin/remove_clutter_after_last_endif.py b/bin/remove_clutter_after_last_endif.py
index 84b8e6900f..c21bbff427 100644
--- a/bin/remove_clutter_after_last_endif.py
+++ b/bin/remove_clutter_after_last_endif.py
@@ -1,6 +1,7 @@
#!/usr/bin/env python3
import os
+
# replace everything after last #endif with new line
def clearAfterLastEndIf(filename):
with open(filename, "r") as header:
diff --git a/bin/testing/fuzzycomparedata.py b/bin/testing/fuzzycomparedata.py
index a8625668d8..5d2207eb66 100644
--- a/bin/testing/fuzzycomparedata.py
+++ b/bin/testing/fuzzycomparedata.py
@@ -46,11 +46,10 @@ def compare_data(
"""
if verbose:
- print("Comparing {} and {}".format(dataFile1, dataFile2))
print(
- "... with a maximum relative error of {} and a maximum absolute error of {}*max_abs_parameter_value.".format(
- relative, absolute
- )
+ f"Comparing {dataFile1} and {dataFile2}\n"
+ f"... with a maximum relative error of {relative} and "
+ f"a maximum absolute error of {absolute}*max_abs_parameter_value."
)
# construct element tree from data files
@@ -116,7 +115,10 @@ if __name__ == "__main__":
"--zeroThreshold",
type=json.loads,
default="{}",
- help='Thresholds for treating numbers as zero for a parameter as a python dict e.g. {"vel":1e-7,"delP":1.0}',
+ help=(
+ "Thresholds for treating numbers as zero for a parameter as a python dict "
+ 'e.g. {"vel":1e-7,"delP":1.0}'
+ ),
)
args = vars(parser.parse_args())
diff --git a/bin/testing/fuzzycomparevtu.py b/bin/testing/fuzzycomparevtu.py
index c42923a97a..f8c04e311e 100644
--- a/bin/testing/fuzzycomparevtu.py
+++ b/bin/testing/fuzzycomparevtu.py
@@ -12,11 +12,9 @@ import json
import sys
import math
import os
-import re
-import glob
import functools
-# fuzzy compare VTK tree from VTK strings
+
def compare_vtk(vtk1, vtk2, absolute=1.5e-7, relative=1e-2, zeroValueThreshold={}, verbose=True):
"""take two vtk files and compare them. Returns an exit key as returnvalue.
@@ -63,11 +61,10 @@ def compare_vtk(vtk1, vtk2, absolute=1.5e-7, relative=1e-2, zeroValueThreshold={
sortedroot2 = sort_vtk(root2)
if verbose:
- print("Comparing {} and {}".format(vtk1, vtk2))
print(
- "... with a maximum relative error of {} and a maximum absolute error of {}*max_abs_parameter_value.".format(
- relative, absolute
- )
+ f"Comparing {vtk1} and {vtk2}\n"
+ f"... with a maximum relative error of {relative} and "
+ f"a maximum absolute error of {absolute}*max_abs_parameter_value."
)
# sort the vtk file so that the comparison is independent of the
@@ -150,7 +147,8 @@ def convert_pvtu_to_vtu(pvturoot, filename):
newvalue = " " + str(int(value) + offsets_offset) + " "
rootOffsets.text += newvalue
- # compute offset for the connectivity vector (it's the number of points of the current root piece)
+ # compute offset for the connectivity vector
+ # (it's the number of points of the current root piece)
rootNumPoints = int(root.findall(".//Piece")[0].attrib["NumberOfPoints"])
rootNumCells = int(root.findall(".//Piece")[0].attrib["NumberOfCells"])
@@ -177,7 +175,10 @@ def convert_pvtu_to_vtu(pvturoot, filename):
root.findall(".//Piece")[0].attrib["NumberOfCells"] = str(newNumCells)
# for debugging the merged vtu file can be written out and viewed in paraview
- # testname = os.path.join(dirname, "comparisontemp-" + os.path.basename(pvturoot.findall(".//Piece")[0].attrib["Source"]))
+ # sourcename = pvturoot.findall(".//Piece")[0].attrib["Source"]
+ # testname = os.path.join(
+ # dirname, "comparisontemp-" + os.path.basename(vtuname)
+ # )
# vtu = ET.ElementTree(root)
# vtu.write(testname)
@@ -214,7 +215,7 @@ def is_fuzzy_equal_node(
else:
return False
if node1child.text or node2child.text:
- if node1child.get("NumberOfComponents") == None:
+ if node1child.get("NumberOfComponents") is None:
numberOfComponents = 1
else:
numberOfComponents = int(node1child.attrib["NumberOfComponents"])
@@ -267,7 +268,8 @@ def is_fuzzy_equal_text(
lists2.append(list2[i::numComp])
if numComp > 1:
parameters.append("{}_{}".format(parameter, i))
- # if zero threshold was set for all components one component inherits it from the parameter
+ # if zero threshold was set for all components,
+ # one component inherits it from the parameter
if parameter in zeroValueThreshold:
zeroValueThreshold["{}_{}".format(parameter, i)] = zeroValueThreshold[parameter]
else:
@@ -293,23 +295,19 @@ def is_fuzzy_equal_text(
print("Parameter {} contains inf!".format(parameter))
return False
- # manipulate the data set for the sake of sensible comparison
- # if the parameter is listed in the zeroThreshold dictionary replace all float under threshold with zero.
- # only replace them with zero if the parameters in both lists are under the threshold. Otherwise we
- # compare a non-zero value with 0 later.
+ # Manipulate the data set for the sake of sensible comparison.
+ # If the parameter is listed in the zeroThreshold dictionary,
+ # replace all float under threshold with zero.
+ # Only replace them with zero if the parameters in both lists are under the threshold.
+ # Otherwise we compare a non-zero value with 0 later.
if parameter in zeroValueThreshold:
+ zeroThr = float(zeroValueThreshold[parameter])
floatList1 = [
- 0.0
- if abs(i) < float(zeroValueThreshold[parameter])
- and abs(j) < float(zeroValueThreshold[parameter])
- else i
+ 0.0 if (abs(i) < zeroThr) and (abs(j) < zeroThr) else i
for i, j in zip(floatList1, floatList2)
]
floatList2 = [
- 0.0
- if abs(i) < float(zeroValueThreshold[parameter])
- and abs(j) < float(zeroValueThreshold[parameter])
- else j
+ 0.0 if (abs(i) < zeroThr) and (abs(j) < zeroThr) else j
for i, j in zip(floatList1, floatList2)
]
@@ -347,18 +345,16 @@ def is_fuzzy_equal_text(
return False
if verbose and max_relative_difference != 0.0:
- print("\nData differs in parameter: {}".format(parameter))
- print(message)
print(
- "Info for {}: max_abs_parameter_value={} and min_abs_parameter_value={}.".format(
- parameter, magnitude, minimal
- )
+ f"\nData differs in parameter: {parameter}\n",
+ message,
+ f"Info for {parameter}: "
+ f"max_abs_parameter_value={magnitude} and min_abs_parameter_value={minimal}.",
)
if parameter in zeroValueThreshold:
print(
- "For parameter {} a zero value threshold of {} was given.".format(
- parameter, zeroValueThreshold[parameter]
- )
+ f"For parameter {parameter} a zero value threshold"
+ f" of {zeroValueThreshold[parameter]} was given."
)
return is_equal
@@ -390,7 +386,7 @@ def sort_elements(items, newroot):
# Create a new item to represent the sorted version
# of the next item, and copy the tag name and contents
newitem = ET.Element(item.tag)
- if item.text and item.text.isspace() == False:
+ if item.text and not item.text.isspace():
newitem.text = item.text
# Copy the attributes (sorted by key) to the new item
@@ -442,7 +438,7 @@ def sort_vtk_by_coordinates(root1, root2, verbose, convertedFromParallelVtu=Fals
cellDataArrays.append(dataArray.attrib["Name"])
for dataArray in root.findall(".//DataArray"):
dataArrays[dataArray.attrib["Name"]] = dataArray.text
- if dataArray.get("NumberOfComponents") == None:
+ if dataArray.get("NumberOfComponents") is None:
numberOfComponents[dataArray.attrib["Name"]] = 1
else:
numberOfComponents[dataArray.attrib["Name"]] = dataArray.attrib[
@@ -459,7 +455,7 @@ def sort_vtk_by_coordinates(root1, root2, verbose, convertedFromParallelVtu=Fals
if convertedFromParallelVtu:
uniqueIdx = []
for i in range(len(coords) // dim):
- pos = [float(c) for c in coords[i * dim : i * dim + dim]]
+ pos = [float(c) for c in coords[(i * dim) : (i * dim + dim)]]
if pos in vertexArray:
uIdx = vertexArray.index(pos)
else:
@@ -468,7 +464,7 @@ def sort_vtk_by_coordinates(root1, root2, verbose, convertedFromParallelVtu=Fals
uniqueIdx.append(uIdx)
else:
for i in range(len(coords) // dim):
- vertexArray.append([float(c) for c in coords[i * dim : i * dim + dim]])
+ vertexArray.append([float(c) for c in coords[(i * dim) : (i * dim + dim)]])
# group the cells into vertex index tuples
cellArray = []
@@ -518,6 +514,7 @@ def sort_vtk_by_coordinates(root1, root2, verbose, convertedFromParallelVtu=Fals
bBoxMax = max(vertexArray)
bBoxMin = min(vertexArray)
epsilon = math.sqrt(sum([(a - b) ** 2 for a, b in zip(bBoxMax, bBoxMin)])) * 1e-7
+
# first compare by coordinates, if the same compare largestCellMidPointForVertex
# TODO: is there a more pythonic way?
def vertex_cmp(a, b):
@@ -550,9 +547,10 @@ def sort_vtk_by_coordinates(root1, root2, verbose, convertedFromParallelVtu=Fals
for j, vertexIndex in enumerate(cell):
cellArray[i][j] = vertexIndexMap[vertexIndex]
- # sort the indices of all cells in case the two grids have different orientation of the elements
- # this doesn't necessarily have to be a valid vtk order, it's just temporary for a sorted literal comparison
- # of the files
+ # Sort the indices of all cells in case the two grids
+ # have different orientation of the elements.
+ # This doesn't necessarily have to be a valid vtk order,
+ # it's just temporary for a sorted literal comparison of the files
for i, cell in enumerate(cellArray):
cellArray[i] = sorted(cell)
@@ -633,7 +631,10 @@ if __name__ == "__main__":
"--zeroThreshold",
type=json.loads,
default="{}",
- help='Thresholds for treating numbers as zero for a parameter as a python dict e.g. {"vel":1e-7,"delP":1.0}',
+ help=(
+ "Thresholds for treating numbers as zero for a parameter as a python dict"
+ 'e.g. {"vel":1e-7,"delP":1.0}'
+ ),
)
parser.add_argument("-v", "--verbose", dest="verbose", action="store_true")
parser.add_argument("--no-verbose", dest="verbose", action="store_false")
diff --git a/bin/testing/runtest.py b/bin/testing/runtest.py
index 480a22de32..1b9c7de159 100755
--- a/bin/testing/runtest.py
+++ b/bin/testing/runtest.py
@@ -1,7 +1,8 @@
#!/usr/bin/env python3
import argparse
import shlex
-import os, sys
+import os
+import sys
import subprocess
import json
from fuzzycomparevtu import compare_vtk
@@ -20,13 +21,19 @@ parser.add_argument(
"-s",
"--script",
nargs=1,
- help="The comparison script. [fuzzy, fuzzyData, exact, <path_to_script>] where the script takes two files as arguments.",
+ help=(
+ "The comparison script. [fuzzy, fuzzyData, exact, <path_to_script>]"
+ " where the script takes two files as arguments."
+ ),
)
parser.add_argument(
"-f",
"--files",
nargs="+",
- help="Pairs of file names (first reference, then current). Usage: '[-f ref1 cur1 [[ref2] [cur2] ...]]'",
+ help=(
+ "Pairs of file names (first reference, then current). "
+ "Usage: '[-f ref1 cur1 [[ref2] [cur2] ...]]'"
+ ),
)
parser.add_argument(
"-d", "--delimiter", type=str, default=",", help="Column delimiter for data files"
@@ -50,7 +57,10 @@ parser.add_argument(
"--zeroThreshold",
type=json.loads,
default="{}",
- help='Thresholds for treating numbers as zero for a parameter as a python dict e.g. {"vel":1e-7,"delP":1.0}',
+ help=(
+ "Thresholds for treating numbers as zero for"
+ ' a parameter as a python dict e.g. {"vel":1e-7,"delP":1.0}'
+ ),
)
args = vars(parser.parse_args())
@@ -58,7 +68,8 @@ args = vars(parser.parse_args())
if args["script"]:
if len(args["files"]) % 2 != 0 or not args["files"]:
sys.stderr.write(
- "The files have to be pairs of reference and current solution files. Usage '-f [ref1] [cur1] [[ref2] [cur2] ...]'"
+ "The files have to be pairs of reference and current solution files."
+ " Usage '-f [ref1] [cur1] [[ref2] [cur2] ...]'"
)
parser.print_help()
sys.exit(1)
@@ -67,7 +78,9 @@ if args["script"]:
ref_dir = os.path.dirname(os.path.abspath(__file__)).rstrip("bin") + "test/references"
if os.path.dirname(args["files"][(i * 2) + 1]) == ref_dir:
sys.stderr.write(
- "Tried to delete a reference solution. Specify reference file first, then the current solution. Usage: '[-f ref1 cur1 [[ref2] [cur2] ...]]'"
+ "Tried to delete a reference solution. "
+ "Specify reference file first, then the current solution. "
+ "Usage: '[-f ref1 cur1 [[ref2] [cur2] ...]]'"
)
sys.exit(1)
subprocess.call(["rm", "-fv", args["files"][(i * 2) + 1]])
@@ -76,7 +89,7 @@ if args["script"]:
res = 1
try:
res = subprocess.call(shlex.split(args["command"][0]))
-except OSError as e:
+except OSError:
print(args["command"][0].split())
print("OSError: Command not found. Most likely the executable specified doesn't exist.")
sys.exit(1)
diff --git a/bin/util/common.py b/bin/util/common.py
index e8a7dc201d..cf80279391 100644
--- a/bin/util/common.py
+++ b/bin/util/common.py
@@ -5,7 +5,6 @@ import fnmatch
import functools
import subprocess
import traceback
-import datetime
import shlex
diff --git a/bin/util/installscript.py b/bin/util/installscript.py
index c65125bd34..10636bcf37 100644
--- a/bin/util/installscript.py
+++ b/bin/util/installscript.py
@@ -185,7 +185,7 @@ def printFinalMessage(scriptName, topFolderName=None):
)
else:
description = textwrap.dedent(
- f"""\
+ """\
Running this script will clone all modules into the folder from which it is
called, configure the entire project and build the contained applications
"""
diff --git a/bin/util/installscript_writer.py b/bin/util/installscript_writer.py
index 72884693de..40e99c0776 100644
--- a/bin/util/installscript_writer.py
+++ b/bin/util/installscript_writer.py
@@ -1,7 +1,5 @@
"""Language-specific backends for install script generation"""
-import os
-import sys
import textwrap
from abc import ABC, abstractmethod
from util.common import addPrefixToLines, escapeCharacters
@@ -197,7 +195,9 @@ class InstallScriptWriterPython(InstallScriptWriterInterface):
runFromSubFolder(['git', 'checkout', branch], subFolder)
runFromSubFolder(['git', 'reset', '--hard', revision], subFolder)
else:
- print(f'Skip cloning {{url}} since target folder "{{targetFolder}}" already exists.')
+ print(
+ f"Skip cloning {{url}} since target "{{targetFolder}}" already exists."
+ )
def applyPatch(subFolder, patch):
--
GitLab