Bugfix release 0.403 / first ogstools release

ogs6py/_version.py

@@ -1,3 +1,3 @@
 # -*- coding: utf-8 -*-
 """Provide a central version."""
-__version__ = "0.402"
+__version__ = "0.403"

ogs6py/classes/__init__.py

@@ -1,3 +1,11 @@
+# Copyright (c) 2012-2024, OpenGeoSys Community (http://www.opengeosys.org)
+#            Distributed under a Modified BSD License.
+#            See accompanying file LICENSE.txt or
+#            http://www.opengeosys.org/project/license
+#
+
+# Author: Joerg Buchwald (Helmholtz Centre for Environmental Research GmbH - UFZ)
+
 from . import display
 from . import mesh
 from . import geo

ogs6py/classes/build_tree.py

@@ -1,56 +1,77 @@
-# -*- coding: utf-8 -*-
 """
 Copyright (c) 2012-2021, OpenGeoSys Community (http://www.opengeosys.org)
             Distributed under a Modified BSD License.
               See accompanying file LICENSE or
               http://www.opengeosys.org/project/license
 
 """
+
+
+from typing import TypeAlias
+
 from lxml import etree as ET
 
+OptionalETElement: TypeAlias = (
+    ET.Element
+)  # ToDo this should be Optional[ET.Element]
+
+
 # pylint: disable=C0103, R0902, R0914, R0913
 class BuildTree:
-    """ helper class to create a nested dictionary
+    """helper class to create a nested dictionary
     representing the xml structure
     """
-    def __init__(self, tree):
+
+    def __init__(self, tree: ET.ElementTree) -> None:
         self.tree = tree
 
-    def _get_root(self):
-        root = self.tree.getroot()
-        return root
+    def _get_root(self) -> ET.Element:
+        return self.tree.getroot()
 
     @classmethod
-    def _convertargs(cls, args):
+    def _convertargs(cls, args: dict[str, str]) -> None:
         """
         convert arguments that are not lists or dictionaries to strings
         """
         for item, value in args.items():
-            if not isinstance(value, (list, dict)):
+            if not isinstance(value, list | dict):
                 args[item] = str(value)
 
     @classmethod
-    def populate_tree(cls, parent, tag, text=None, attr=None, overwrite=False):
+    def populate_tree(
+        cls,
+        parent: ET.Element,
+        tag: str,
+        text: str | None = None,
+        attr: dict[str, str] | None = None,
+        overwrite: bool = False,
+    ) -> ET.Element:
         """
         method to create dictionary from an xml entity
         """
         q = None
-        if not tag is None:
+        if tag is not None:
             if overwrite is True:
                 for child in parent:
                     if child.tag == tag:
                         q = child
             if q is None:
                 q = ET.SubElement(parent, tag)
-            if not text is None:
+            if text is not None:
                 q.text = str(text)
-            if not attr is None:
+            if attr is not None:
                 for key, val in attr.items():
                     q.set(key, str(val))
         return q
 
     @classmethod
-    def get_child_tag(cls, parent, tag, attr=None, attr_val=None):
+    def get_child_tag(
+        cls,
+        parent: ET.Element,
+        tag: str,
+        attr: dict[str, str] | None = None,
+        attr_val: str | None = None,
+    ) -> OptionalETElement:
         """
         search for child tag based on tag and possible attributes
         """
@@ -65,15 +86,18 @@ def get_child_tag(cls, parent, tag, attr=None, attr_val=None):
         return q
 
     @classmethod
-    def get_child_tag_for_type(cls, parent, tag, subtagval, subtag="type"):
+    def get_child_tag_for_type(
+        cls, parent: ET.Element, tag: str, subtagval: str, subtag: str = "type"
+    ) -> OptionalETElement:
         """
         search for child tag based on subtag type
         """
         q = None
         for child in parent:
             if child.tag == tag:
                 for subchild in child:
-                    if subchild.tag == subtag:
-                        if subchild.text == subtagval:
-                            q = child
+                    if (subchild.tag == subtag) and (
+                        subchild.text == subtagval
+                    ):
+                        q = child
         return q

ogs6py/classes/curves.py

@@ -1,24 +1,29 @@
-# -*- coding: utf-8 -*-
 """
-Copyright (c) 2012-2021, OpenGeoSys Community (http://www.opengeosys.org)
+Copyright (c) 2012-2024, OpenGeoSys Community (http://www.opengeosys.org)
             Distributed under a Modified BSD License.
               See accompanying file LICENSE or
               http://www.opengeosys.org/project/license
 
 """
 # pylint: disable=C0103, R0902, R0914, R0913
-from ogs6py.classes import build_tree
+from typing import Any
+
+from lxml import etree as ET
+
+from ogstools.ogs6py import build_tree
+
 
 class Curves(build_tree.BuildTree):
     """
     Class to create the curve section of the project file.
     """
-    def __init__(self, tree):
+
+    def __init__(self, tree: ET.ElementTree) -> None:
         self.tree = tree
         self.root = self._get_root()
         self.curves = self.populate_tree(self.root, "curves", overwrite=True)
 
-    def add_curve(self, **args):
+    def add_curve(self, **args: Any) -> None:
         """
         Adds a new curve.
 
@@ -29,23 +34,28 @@ def add_curve(self, **args):
         values : `list`
         """
         if "name" not in args:
-            raise KeyError("No curve name given.")
+            msg = "No curve name given."
+            raise KeyError(msg)
         if "coords" not in args:
-            raise KeyError("No coordinates given.")
+            msg = "No coordinates given."
+            raise KeyError(msg)
         if "values" not in args:
-            raise KeyError("No values given.")
+            msg = "No values given."
+            raise KeyError(msg)
         if len(args["coords"]) != len(args["values"]):
-            raise ValueError("Number of time coordinate points differs from number of values")
+            msg = """Number of time coordinate points differs \
+                     from number of values"""
+            raise ValueError(msg)
         curve = self.populate_tree(self.curves, "curve")
-        self.populate_tree(curve, "name", args['name'])
+        self.populate_tree(curve, "name", args["name"])
         coord_str = ""
         value_str = ""
         for i, coord in enumerate(args["coords"]):
-            if i < (len(args["coords"])-1):
+            if i < (len(args["coords"]) - 1):
                 coord_str = coord_str + str(coord) + " "
                 value_str = value_str + str(args["values"][i]) + " "
-            if i == (len(args["coords"])-1):
+            if i == (len(args["coords"]) - 1):
                 coord_str = coord_str + str(coord)
                 value_str = value_str + str(args["values"][i])
-        self.populate_tree(curve, 'coords', text=coord_str)
-        self.populate_tree(curve, 'values', text=value_str)
+        self.populate_tree(curve, "coords", text=coord_str)
+        self.populate_tree(curve, "values", text=value_str)

ogs6py/classes/display.py

@@ -1,53 +1,106 @@
-# -*- coding: utf-8 -*-
 """
 Copyright (c) 2012-2021, OpenGeoSys Community (http://www.opengeosys.org)
             Distributed under a Modified BSD License.
               See accompanying file LICENSE or
               http://www.opengeosys.org/project/license
 
 """
+from contextlib import suppress
+
+from lxml import etree as ET
+
 try:
-    from IPython.display import display, Markdown, Latex
+    from IPython.display import Markdown, display
+
     verbose = True
 except ImportError:
     verbose = False
 
+
 # pylint: disable=C0103, R0902, R0914, R0913
 class Display:
-    """ helper class to create a nested dictionary
+    """helper class to create a nested dictionary
     representing the xml structure
     """
-    def __init__(self,tree):
+
+    def __init__(self, tree: ET.ElementTree):
         if verbose is True:
-            display(Markdown('## OpenGeoSys project file'))
-            display(Markdown('### Main Info'))
-            display(Markdown(f"**Process name:** {tree.find('./processes/process/name').text}"))
-            display(Markdown(f"**Process type:** {tree.find('./processes/process/type').text}"))
-            t_end = float(tree.find('./time_loop/processes/process/time_stepping/t_end').text)
-            t_init = float(tree.find('./time_loop/processes/process/time_stepping/t_initial').text)
-            display(Markdown(f"**Simulation time:** {t_end-t_init}"))
-            proc_vars = tree.findall("./process_variables/process_variable")
-            display(Markdown(f"**Output prefix:** {tree.find('./time_loop/output/prefix').text}"))
-            display(Markdown('### Boundary conditions'))
-            for var in proc_vars:
-                proc_var_entries = var.getchildren()
-                for entry in proc_var_entries:
-                    if entry.tag == "name":
-                        display(Markdown(f"**Process Variable:** {entry.text}"))
-                    if entry.tag == "initial_condition":
-                        display(Markdown(f" - **Initial Condition:** {entry.text}"))
-                    if entry.tag == "order":
-                        display(Markdown(f" - **Order:** {entry.text}"))
-                    if entry.tag == "boundary_conditions":
-                        bcs = entry.getchildren()
-                        for bc in bcs:
-                            bc_entries = bc.getchildren()
-                            for subentry in bc_entries:
-                                if subentry.tag == "type":
-                                    display(Markdown(f" - **Type:** {subentry.text}"))
-                                if subentry.tag == "mesh":
-                                    display(Markdown(f" - **Mesh:** {subentry.text}"))
-                                if subentry.tag == "geometrical_set":
-                                    display(Markdown(f" - **Geometrical Set:** {subentry.text}"))
-                                if subentry.tag == "geometry":
-                                    display(Markdown(f" - **Geometry:** {subentry.text}"))
+            display(Markdown("## OpenGeoSys project file"))
+            display(Markdown("### Main Info"))
+            with suppress(AttributeError):
+                display(
+                    Markdown(
+                        f"**Process name:** {tree.find('./processes/process/name').text}"
+                    )
+                )
+            with suppress(AttributeError):
+                display(
+                    Markdown(
+                        f"**Process type:** {tree.find('./processes/process/type').text}"
+                    )
+                )
+            with suppress(AttributeError):
+                t_end = float(
+                    tree.find(
+                        "./time_loop/processes/process/time_stepping/t_end"
+                    ).text
+                )
+                t_init = float(
+                    tree.find(
+                        "./time_loop/processes/process/time_stepping/t_initial"
+                    ).text
+                )
+                display(Markdown(f"**Simulation time:** {t_end-t_init}"))
+            with suppress(AttributeError):
+                proc_vars = tree.findall("./process_variables/process_variable")
+                with suppress(AttributeError):
+                    display(
+                        Markdown(
+                            f"**Output prefix:** {tree.find('./time_loop/output/prefix').text}"
+                        )
+                    )
+                display(Markdown("### Boundary conditions"))
+                for var in proc_vars:
+                    proc_var_entries = var.getchildren()
+                    for entry in proc_var_entries:
+                        if entry.tag == "name":
+                            display(
+                                Markdown(f"**Process Variable:** {entry.text}")
+                            )
+                        if entry.tag == "initial_condition":
+                            display(
+                                Markdown(
+                                    f" - **Initial Condition:** {entry.text}"
+                                )
+                            )
+                        if entry.tag == "order":
+                            display(Markdown(f" - **Order:** {entry.text}"))
+                        if entry.tag == "boundary_conditions":
+                            bcs = entry.getchildren()
+                            for bc in bcs:
+                                bc_entries = bc.getchildren()
+                                for subentry in bc_entries:
+                                    if subentry.tag == "type":
+                                        display(
+                                            Markdown(
+                                                f" - **Type:** {subentry.text}"
+                                            )
+                                        )
+                                    if subentry.tag == "mesh":
+                                        display(
+                                            Markdown(
+                                                f" - **Mesh:** {subentry.text}"
+                                            )
+                                        )
+                                    if subentry.tag == "geometrical_set":
+                                        display(
+                                            Markdown(
+                                                f" - **Geometrical Set:** {subentry.text}"
+                                            )
+                                        )
+                                    if subentry.tag == "geometry":
+                                        display(
+                                            Markdown(
+                                                f" - **Geometry:** {subentry.text}"
+                                            )
+                                        )

ogs6py/classes/geo.py

@@ -1,24 +1,27 @@
-# -*- coding: utf-8 -*-
 """
-Copyright (c) 2012-2021, OpenGeoSys Community (http://www.opengeosys.org)
+Copyright (c) 2012-2024, OpenGeoSys Community (http://www.opengeosys.org)
             Distributed under a Modified BSD License.
               See accompanying file LICENSE or
               http://www.opengeosys.org/project/license
 
 """
 # pylint: disable=C0103, R0902, R0914, R0913
-from ogs6py.classes import build_tree
+from lxml import etree as ET
+
+from ogstools.ogs6py import build_tree
+
 
 class Geo(build_tree.BuildTree):
     """
     Class containing the geometry file.
     """
-    def __init__(self, tree):
+
+    def __init__(self, tree: ET.ElementTree) -> None:
         self.tree = tree
         self.root = self._get_root()
         self.populate_tree(self.root, "geometry", overwrite=True)
 
-    def add_geometry(self, filename):
+    def add_geometry(self, filename: str) -> None:
         """
         Adds a geometry file.