pylinting + tiny bugfixes

ogs6py/classes/build_tree.py

@@ -51,6 +51,9 @@ def populate_tree(cls, parent, tag, text='', attr=None, overwrite=False):
 
     @classmethod
     def get_child_tag(cls, parent, tag, attr=None, attr_val=None):
+        """
+        search for child tag based on tag and possible attributes
+        """
         q = None
         for child in parent:
             if child.tag == tag:
@@ -63,6 +66,9 @@ def get_child_tag(cls, parent, tag, attr=None, attr_val=None):
 
     @classmethod
     def get_child_tag_for_type(cls, parent, tag, subtagval, subtag="type"):
+        """
+        search for child tag based on subtag type
+        """
         q = None
         for child in parent:
             if child.tag == tag:

ogs6py/classes/geo.py

@@ -26,4 +26,4 @@ def add_geometry(self, filename):
         ----------
         filename : `str`
         """
-        geom = self.populate_tree(self.root, "geometry", text=filename, overwrite=True)
+        self.populate_tree(self.root, "geometry", text=filename, overwrite=True)

ogs6py/classes/linsolvers.py

@@ -39,11 +39,11 @@ def add_lin_solver(self, **args):
         lis : `str` for lis only
         """
         self._convertargs(args)
-        if not "name" in args:
+        if "name" not in args:
             raise KeyError("You need to provide a name for the linear solver.")
         ls = self.populate_tree(self.lss, 'linear_solver', overwrite=True)
         self.populate_tree(ls, 'name', text=args['name'], overwrite=True)
-        if not "kind" in args:
+        if "kind" not in args:
             raise KeyError("No kind given. Please specify the linear \
                         solver library (e.g.: eigen, petsc, lis).")
         if args['kind'] == "eigen":

ogs6py/classes/mesh.py

@@ -7,7 +7,6 @@
 
 """
 # pylint: disable=C0103, R0902, R0914, R0913
-from lxml import etree as ET
 from ogs6py.classes import build_tree
 
 class Mesh(build_tree.BuildTree):
@@ -41,7 +40,7 @@ def add_mesh(self, filename, axially_symmetric=None):
         elif isinstance(axially_symmetric, str):
             attr_dict = {"axially_symmetric": axially_symmetric}
         if self.mesh is not None:
-            if self.mesh.text is "":
+            if self.mesh.text == "":
                 self.populate_tree(self.root, "mesh", text=filename, attr=attr_dict, overwrite=True)
             else:
                 entry = self.mesh.text
@@ -57,12 +56,11 @@ def add_mesh(self, filename, axially_symmetric=None):
                     self.geometry = self.root.find("./geometry")
                 self.populate_tree(self.meshes, "mesh", text=entry, attr=mesh0attr_dict)
                 self.populate_tree(self.meshes, "mesh", text=filename, attr=attr_dict)
-        elif (self.meshes is not None):
+        elif self.meshes is not None:
             self.populate_tree(self.meshes, "mesh", text=filename, attr=attr_dict)
             self.geometry = self.root.find("./geometry")
             if self.geometry is not None:
                 self.geometry.getparent().remove(self.geometry)
                 self.geometry = self.root.find("./geometry")
         else:
             raise RuntimeError("This should not happpen")
-

ogs6py/classes/processes.py

@@ -37,7 +37,7 @@ def add_process_variable(self, process_variable="", process_variable_name=""):
         process_variable_name : `str`
         """
         self.procvars = self.populate_tree(self.process, "process_variables", overwrite=True)
-        if not process_variable == "":
+        if process_variable != "":
             if process_variable_name == "":
                 raise KeyError("process_variable_name missing.")
             self.procvar[process_variable] = self.populate_tree(self.procvars,
@@ -90,7 +90,7 @@ def set_process(self, **args):
             self.populate_tree(self.process, "specific_body_force", text=" ".join(str(x) for x in args['specific_body_force']))
         for key, value in args.items():
             if isinstance(value, str):
-                self.populate_tree(self.process, key, text=args[key])
+                self.populate_tree(self.process, key, text=value)
 
 
     def set_constitutive_relation(self, **args):
@@ -115,15 +115,22 @@ def set_constitutive_relation(self, **args):
 
 
     def add_bhe_type(self, bhe_type):
+        """
+        Adds a BHE type
+        """
         self.borehole_heat_exchangers = self.populate_tree(
                 self.process, "borehole_heat_exchangers", overwrite=True)
         self.borehole_heat_exchanger.append(self.populate_tree(
                         self.borehole_heat_exchangers, "borehole_heat_exchanger"))
         self.populate_tree(self.borehole_heat_exchanger[-1], "type", text = bhe_type)
 
     def add_bhe_component(self, index=0, **args):
+        """
+        adds a BHE component
+        """
         self._convertargs(args)
-        if not 'comp_type' in args:
+        bhe_type = ""
+        if 'comp_type' not in args:
             raise KeyError("No BHE component name specified.")
         bhecomponent = self.populate_tree(self.borehole_heat_exchanger[index], args['comp_type'])
         if bhecomponent.tag == "borehole":
@@ -133,10 +140,9 @@ def add_bhe_component(self, index=0, **args):
             for element in self.borehole_heat_exchanger[index]:
                 if element.tag == "type":
                     bhe_type = element.text
-            if bhe_type == "1U" or bhe_type == "2U":
-                inlet_text = "inlet"
-                outlet_text = "outlet"
-            elif bhe_type == "CXA" or bhe_type == "CXC":
+            inlet_text = "inlet"
+            outlet_text = "outlet"
+            if bhe_type in ("CXA", "CXC"):
                 inlet_text = "inner"
                 outlet_text = "outer"
             inlet = self.populate_tree(bhecomponent, inlet_text)

ogs6py/classes/python_script.py

@@ -26,4 +26,4 @@ def set_pyscript(self, filename):
         ----------
         filename : `str`
         """
-        self.populate_tree(self.root, "python_script", text=args['filename'], overwrite=True)
+        self.populate_tree(self.root, "python_script", text=filename, overwrite=True)

ogs6py/ogs.py

@@ -19,11 +19,11 @@
 import shutil
 import pandas as pd
 from lxml import etree as ET
-from ogs6py.classes import (display, geo, mesh, python_script, processes, media, timeloop, 
+from ogs6py.classes import (display, geo, mesh, python_script, processes, media, timeloop,
         local_coordinate_system, parameters, curves, processvars, linsolvers, nonlinsolvers)
 import ogs6py.log_parser.log_parser as parser
 import ogs6py.log_parser.common_ogs_analyses as parse_fcts
-from ogs6py.classes.properties import * 
+from ogs6py.classes.properties import *
 
 class OGS:
     """Class for an OGS6 model.
@@ -77,24 +77,6 @@ def __init__(self, **args):
         else:
             self.inputfile = None
             self.root = ET.Element("OpenGeoSysProject")
-            """if len(self.geo.tree['geometry']['text']) > 0:
-                self.__dict2xml(self.root, self.geo.tree)
-            self.__dict2xml(self.root, self.mesh.tree)
-            if len(self.pyscript.tree['pythonscript']['text']) > 0:
-                self.__dict2xml(self.root, self.pyscript.tree)
-            self.__dict2xml(self.root, self.processes.tree)
-            if len(self.media.tree['media']['children']) > 0:
-                self.__dict2xml(self.root, self.media.tree)
-            self.__dict2xml(self.root, self.timeloop.tree)
-            if len(self.local_coordinate_system.tree['local_coordinate_system']['children']) > 0:
-                self.__dict2xml(self.root, self.local_coordinate_system.tree)
-            self.__dict2xml(self.root, self.parameters.tree)
-            if len(self.curves.tree['curves']['children']) > 0:
-                self.__dict2xml(self.root, self.curves.tree)
-            self.__dict2xml(self.root, self.processvars.tree)
-            self.__dict2xml(self.root, self.nonlinsolvers.tree)
-            self.__dict2xml(self.root, self.linsolvers.tree))
-            self._add_includes(self.root)"""
             # Reparsing for pretty_print to work properly
             parse = ET.XMLParser(remove_blank_text=True, huge_tree=True)
             tree_string = ET.tostring(self.root, pretty_print=True)
@@ -117,15 +99,6 @@ def __init__(self, **args):
         self.nonlinear_solvers = nonlinsolvers.NonLinSolvers(self.tree)
         self.linear_solvers = linsolvers.LinSolvers(self.tree)
 
-    def __dict2xml(self, parent, dictionary):
-        for entry in dictionary:
-            self.tag.append(ET.SubElement(parent, dictionary[entry]['tag']))
-            self.tag[-1].text = str(dictionary[entry]['text'])
-            for attr in dictionary[entry]['attr']:
-                self.tag[-1].set(attr, dictionary[entry]['attr'][attr])
-            if len(dictionary[entry]['children']) > 0:
-                self.__dict2xml(self.tag[-1], dictionary[entry]['children'])
-
     def __replace_blocks_by_includes(self):
         for i, file in enumerate(self.include_files):
             parent_element = self.include_elements[i].getparent()
@@ -371,7 +344,7 @@ def remove_element(self, xpath, tag = None, text = None):
         """
         root = self._get_root()
         elements = root.findall(xpath)
-        if tag == None:
+        if tag is None:
             for element in elements:
                 element.getparent().remove(element)
         else:
@@ -576,8 +549,8 @@ def set(self, **args):
                 "compensate_displacement": "./process_variables/process_variable[name='displacement']/compensate_non_equilibrium_initial_residuum",
                 "compensate_all": "./process_variables/process_variable/compensate_non_equilibrium_initial_residuum"
                 }
-        for arg in args:
-            self.replace_text(args[arg], xpath=property_db[arg])
+        for key, val in args.items():
+            self.replace_text(val, xpath=property_db[key])
 
 
     def restart(self, restart_suffix="_restart", t_initial=None, t_end=None, zero_displacement=False):
@@ -768,32 +741,6 @@ def run_model(self, logfile="out.log", path=None, args=None, container_path=None
                         print(line)
             raise RuntimeError('OGS execution was not successful.')
 
-    """def build_tree(self):
-        self.root = ET.Element("OpenGeoSysProject")
-        if len(self.geo.tree['geometry']['text']) > 0:
-            self.__dict2xml(self.root, self.geo.tree)
-        self.__dict2xml(self.root, self.mesh.tree)
-        if len(self.pyscript.tree['pythonscript']['text']) > 0:
-            self.__dict2xml(self.root, self.pyscript.tree)
-        self.__dict2xml(self.root, self.processes.tree)
-        if len(self.media.tree['media']['children']) > 0:
-            self.__dict2xml(self.root, self.media.tree)
-        self.__dict2xml(self.root, self.timeloop.tree)
-        if len(self.local_coordinate_system.tree['local_coordinate_system']['children']) > 0:
-            self.__dict2xml(self.root, self.local_coordinate_system.tree)
-        self.__dict2xml(self.root, self.parameters.tree)
-        if len(self.curves.tree['curves']['children']) > 0:
-            self.__dict2xml(self.root, self.curves.tree)
-        self.__dict2xml(self.root, self.processvars.tree)
-        self.__dict2xml(self.root, self.nonlinsolvers.tree)
-        self.__dict2xml(self.root, self.linsolvers.tree)
-        self._add_includes(self.root)
-        # Reparsing for pretty_print to work properly
-        parse = ET.XMLParser(remove_blank_text=True)
-        tree_string = ET.tostring(self.root, pretty_print=True)
-        tree_ = ET.fromstring(tree_string, parser=parse)
-        self.tree = ET.ElementTree(tree_)
-    """
 
     def write_input(self, keep_includes=False):
         """Writes the projectfile to disk
@@ -819,16 +766,7 @@ def write_input(self, keep_includes=False):
                             xml_declaration=True,
                             pretty_print=True)
             return True
-        raise RuntimeError("Something went wrong")
-        self.build_tree()
-        ET.indent(self.tree, space="    ")
-        if self.verbose is True:
-            display.Display(self.tree)
-        self.tree.write(self.prjfile,
-                         encoding="ISO-8859-1",
-                         xml_declaration=True,
-                         pretty_print=True)
-        return True
+        raise RuntimeError("No tree has been build.")
 
     def parse_out(self, logfile=None, filter=None, maximum_lines=None, reset_index=True):
         """Parses the logfile
@@ -880,7 +818,7 @@ def property_dataframe(self, mediamapping=None):
         for i in range(numofmedia):
             multidim_prop[i] = {}
         ## preprocessing
-        # write elastic properties to MPL       
+        # write elastic properties to MPL
         for entry in newtree.findall("./processes/process/constitutive_relation"):
             medium = self._get_medium_pointer(root, entry.attrib["id"])
             parent = medium.find("./phases/phase[type='Solid']/properties")
@@ -909,7 +847,7 @@ def property_dataframe(self, mediamapping=None):
                     property_value = newtree.findall(f"./media/medium/{location_pointer[location]}properties/property[parameter_name='{parameter_name}']/parameter_name")
                     for entry in property_value:
                         entry.tag = "value"
-                        entry.text = param_value[0].text            
+                        entry.text = param_value[0].text
             # expand tensors
             expand_tensors(self, numofmedia, multidim_prop, root, location)
             expand_van_genuchten(self, numofmedia, root, location)