refactor: Reformat to respect ruff rules (#77)

* Reformat to respect ruff rules

* ci fix and correction geos-geomechanics package name in ci config

* fix test and linting

Author: mlemayTTE

.github/workflows/typing-check.yml

@@ -16,7 +16,7 @@ jobs:
       max-parallel: 3
       matrix:
         # add packages to check typing
-        package-name: ["hdf5-geomechanics", "geos-posp", "geos-timehistory", "geos-utils", "geos-xml-tools", "hdf5-wrapper"]
+        package-name: ["geos-geomechanics", "geos-posp", "geos-timehistory", "geos-utils", "geos-xml-tools", "hdf5-wrapper"]
 
     steps:
     - uses: actions/checkout@v3

geos-timehistory/src/geos/timehistory/__init__.py

@@ -1 +1 @@
-from .plot_time_history import getHistorySeries
+from .plot_time_history import getHistorySeries  #noqa: F401

geos-timehistory/src/geos/timehistory/plot_time_history.py

@@ -1,40 +1,41 @@
-import numpy as np
+from typing import Any, Optional
 from geos.hdf5_wrapper import wrapper as h5w
-import matplotlib as mpl
 import matplotlib.pyplot as plt
 import os
-import sys
 import argparse
 
 import re
 
 
-def isiterable( obj ):
+def isiterable( obj: Any ) -> bool:
+    """Check if input is iterable."""
     try:
-        it = iter( obj )
+        it = iter( obj )  # noqa: F841
     except TypeError:
         return False
     return True
 
 
-def getHistorySeries( database, variable, setname, indices=None, components=None ):
-    """
-    Retrieve a series of time history structures suitable for plotting in addition to the specific set index and component for the time series
+def getHistorySeries( database: h5w,
+                      variable: str,
+                      setname: str,
+                      indices: Optional[ int | list[ int ] ] = None,
+                      components: Optional[ int | list[ int ] ] = None ) -> Optional[ list[ tuple[ Any, ...] ] ]:
+    """Retrieve a series of time history structures suitable for plotting in addition to the specific set index and component for the time series.
 
     Args:
         database (geos.hdf5_wrapper.hdf5_wrapper): database to retrieve time history data from
         variable (str): the name of the time history variable for which to retrieve time-series data
         setname (str): the name of the index set as specified in the geosx input xml for which to query time-series data
-        indices (int, list): the indices in the named set to query for, if None, defaults to all
-        components (int, list): the components in the flattened data types to retrieve, defaults to all
-    
+        indices (Optional[int | list[ int ]]): the indices in the named set to query for, if None, defaults to all
+        components (Optional[int | list[ int ]]): the components in the flattened data types to retrieve, defaults to all
+
     Returns:
-        list: list of (time, data, idx, comp) timeseries tuples for each time history data component
+        Optional[list[ tuple[ Any, ...] ]]: list of (time, data, idx, comp) timeseries tuples for each time history data component
     """
-
     set_regex = re.compile( variable + '(.*?)', re.IGNORECASE )
     if setname is not None:
-        set_regex = re.compile( variable + '\s*' + str( setname ), re.IGNORECASE )
+        set_regex = re.compile( variable + r'\s*' + str( setname ), re.IGNORECASE )
     time_regex = re.compile( 'Time', re.IGNORECASE )  # need to make this per-set, thought that was in already?
 
     set_match = list( filter( set_regex.match, database.keys() ) )
@@ -62,39 +63,48 @@ def getHistorySeries( database, variable, setname, indices=None, components=None
         print(
             f"Error: The length of the time-series {time_match} and data-series {set_match} do not match: {time_series.shape} and {data_series.shape} !"
         )
-
+    indices1: list[ int ] = []
     if indices is not None:
         if type( indices ) is int:
-            indices = [ indices ]
-        if isiterable( indices ):
-            oob_idxs = list( filter( lambda idx: not 0 <= idx < data_series.shape[ 1 ], indices ) )
+            indices1 = [ indices ]
+        elif isiterable( indices ):
+            oob_idxs: list[ int ] = list(
+                filter(
+                    lambda idx: not 0 <= idx < data_series.shape[ 1 ],  # type: ignore[arg-type]
+                    indices ) )  # type: ignore[arg-type]
             if len( oob_idxs ) > 0:
-                print( f"Error: The specified indices: ({', '.join(oob_idxs)}) " + "\n\t" +
-                       f" are out of the dataset index range: [0,{data_series.shape[1]})" )
-            indices = list( set( indices ) - set( oob_idxs ) )
+                print( f"Error: The specified indices: ({', '.join(map(str, oob_idxs))}) " + "\n\t" +
+                       f" are out of the dataset index range: [0,{data_series.shape[1]})" )  # type: ignore[arg-type]
+            indices1 = list( set( indices ) - set( oob_idxs ) )  # type: ignore[arg-type]
         else:
             print( f"Error: unsupported indices type: {type(indices)}" )
     else:
-        indices = range( data_series.shape[ 1 ] )
+        indices1 = list( range( data_series.shape[ 1 ] ) )
 
+    components1: list[ int ] = []
     if components is not None:
         if type( components ) is int:
-            components = [ components ]
-        if isiterable( components ):
-            oob_comps = list( filter( lambda comp: not 0 <= comp < data_series.shape[ 2 ], components ) )
+            components1 = [ components ]
+        elif isiterable( components ):
+            oob_comps: list[ int ] = list(
+                filter(
+                    lambda comp: not 0 <= comp < data_series.shape[ 2 ],  # type: ignore[arg-type]
+                    components ) )  # type: ignore[arg-type]
             if len( oob_comps ) > 0:
-                print( f"Error: The specified components: ({', '.join(oob_comps)}) " + "\n\t" +
+                print( f"Error: The specified components: ({', '.join(map(str, oob_comps))}) " + "\n\t" +
                        " is out of the dataset component range: [0,{data_series.shape[1]})" )
-            components = list( set( components ) - set( oob_comps ) )
+            components1 = list( set( components ) - set( oob_comps ) )  # type: ignore[arg-type]
         else:
             print( f"Error: unsupported components type: {type(components)}" )
     else:
-        components = range( data_series.shape[ 2 ] )
+        components1 = list( range( data_series.shape[ 2 ] ) )
 
-    return [ ( time_series[ :, 0 ], data_series[ :, idx, comp ], idx, comp ) for idx in indices for comp in components ]
+    return [ ( time_series[ :, 0 ], data_series[ :, idx, comp ], idx, comp ) for idx in indices1
+             for comp in components1 ]
 
 
-def commandLinePlotGen():
+def commandLinePlotGen() -> int:
+    """Parse commande line."""
     parser = argparse.ArgumentParser(
         description="A script that parses geosx HDF5 time-history files and produces time-history plots using matplotlib"
     )

geos-trame/pyproject.toml

@@ -46,6 +46,7 @@ dependencies = [
     "colorcet==3.1.0",
     "funcy==2.0",
     "typing_inspect==0.9.0",
+    "typing_extensions>=4.12",
 ]
 
 [project.optional-dependencies]

geos-xml-tools/pyproject.toml

@@ -16,7 +16,8 @@ requires-python = ">=3.8"
 dependencies = [
     "lxml>=4.5.0",
     "parameterized",
-    "numpy"
+    "numpy>=1.16.2",
+    "typing_extensions>=4.12"
 ]
 
 [project.scripts]
@@ -25,3 +26,14 @@ dependencies = [
     test_geosx_xml_tools = "geos.xml_tools.tests.test_manager:main"
     check_xml_attribute_coverage = "geos.xml_tools.attribute_coverage:main"
     check_xml_redundancy = "geos.xml_tools.xml_redundancy_check:main"
+
+[tool.pytest.ini_options]
+addopts = "--import-mode=importlib"
+console_output_style = "count"
+pythonpath = [".", "src"]
+python_classes = "Test"
+python_files = "test*.py"
+python_functions = "test*"
+testpaths = ["tests"]
+norecursedirs = "bin"
+filterwarnings = []

geos-xml-tools/src/geos/xml_tools/__init__.py

@@ -1,3 +1 @@
-"""
-A python module that enables advanced xml features for GEOSX.
-"""
+"""A python module that enables advanced xml features for GEOSX."""

geos-xml-tools/src/geos/xml_tools/attribute_coverage.py

@@ -12,7 +12,7 @@ def parse_schema_element( root: ElementTree.Element,
                           xsd: str = '{http://www.w3.org/2001/XMLSchema}',
                           recursive_types: Iterable[ str ] = [ 'PeriodicEvent', 'SoloEvent', 'HaltEvent' ],
                           folders: Iterable[ str ] = [ 'src', 'examples' ] ) -> record_type:
-    """Parse the xml schema at the current level
+    """Parse the xml schema at the current level.
 
     Args:
         root (lxml.etree.Element): the root schema node
@@ -24,7 +24,6 @@ def parse_schema_element( root: ElementTree.Element,
     Returns:
         dict: Dictionary of attributes and children for the current node
     """
-
     element_type = node.get( 'type' )
     element_name = node.get( 'name' )
     element_def = root.find( "%scomplexType[@name='%s']" % ( xsd, element_type ) )
@@ -49,7 +48,7 @@ def parse_schema_element( root: ElementTree.Element,
 
 
 def parse_schema( fname: str ) -> record_type:
-    """Parse the schema file into the xml attribute usage dict
+    """Parse the schema file into the xml attribute usage dict.
 
     Args:
         fname (str): schema name
@@ -64,14 +63,14 @@ def parse_schema( fname: str ) -> record_type:
 
 
 def collect_xml_attributes_level( local_types: record_type, node: ElementTree.Element, folder: str ) -> None:
-    """Collect xml attribute usage at the current level
+    """Collect xml attribute usage at the current level.
 
     Args:
         local_types (dict): dictionary containing attribute usage
         node (lxml.etree.Element): current xml node
         folder (str): the source folder for the current file
     """
-    for ka in node.attrib.keys():
+    for ka in node.attrib:
         local_types[ 'attributes' ][ ka ][ folder ].append( node.get( ka ) )
 
     for child in node:
@@ -80,7 +79,7 @@ def collect_xml_attributes_level( local_types: record_type, node: ElementTree.El
 
 
 def collect_xml_attributes( xml_types: record_type, fname: str, folder: str ) -> None:
-    """Collect xml attribute usage in a file
+    """Collect xml attribute usage in a file.
 
     Args:
         xml_types (dict): dictionary containing attribute usage
@@ -97,15 +96,15 @@ def collect_xml_attributes( xml_types: record_type, fname: str, folder: str ) ->
 def write_attribute_usage_xml_level( local_types: record_type,
                                      node: ElementTree.Element,
                                      folders: Iterable[ str ] = [ 'src', 'examples' ] ) -> None:
-    """Write xml attribute usage file at a given level
+    """Write xml attribute usage file at a given level.
 
     Args:
         local_types (dict): dict containing attribute usage at the current level
         node (lxml.etree.Element): current xml node
+        folders (Iterable[ str ]): folders. Defaults to [ 'src', 'examples' ].
     """
-
     # Write attributes
-    for ka in local_types[ 'attributes' ].keys():
+    for ka in local_types[ 'attributes' ]:
         attribute_node = ElementTree.Element( ka )
         node.append( attribute_node )
 
@@ -129,7 +128,7 @@ def write_attribute_usage_xml_level( local_types: record_type,
 
 
 def write_attribute_usage_xml( xml_types: record_type, fname: str ) -> None:
-    """Write xml attribute usage file
+    """Write xml attribute usage file.
 
     Args:
         xml_types (dict): dictionary containing attribute usage by xml type
@@ -143,13 +142,12 @@ def write_attribute_usage_xml( xml_types: record_type, fname: str ) -> None:
 
 
 def process_xml_files( geosx_root: str, output_name: str ) -> None:
-    """Test for xml attribute usage
+    """Test for xml attribute usage.
 
     Args:
         geosx_root (str): GEOSX root directory
         output_name (str): output file name
     """
-
     # Parse the schema
     geosx_root = os.path.expanduser( geosx_root )
     schema = '%ssrc/coreComponents/schema/schema.xsd' % ( geosx_root )
@@ -168,13 +166,12 @@ def process_xml_files( geosx_root: str, output_name: str ) -> None:
 
 
 def main() -> None:
-    """Entry point for the xml attribute usage test script
+    """Entry point for the xml attribute usage test script.
 
     Args:
         -r/--root (str): GEOSX root directory
         -o/--output (str): output file name
     """
-
     # Parse the user arguments
     parser = command_line_parsers.build_attribute_coverage_input_parser()
     args = parser.parse_args()

geos-xml-tools/src/geos/xml_tools/command_line_parsers.py

@@ -3,7 +3,7 @@
 
 
 def build_preprocessor_input_parser() -> argparse.ArgumentParser:
-    """Build the argument parser
+    """Build the argument parser.
 
     Returns:
         argparse.ArgumentParser: The parser
@@ -29,7 +29,7 @@ def build_preprocessor_input_parser() -> argparse.ArgumentParser:
 
 
 def parse_xml_preprocessor_arguments() -> Tuple[ argparse.Namespace, Iterable[ str ] ]:
-    """Parse user arguments
+    """Parse user arguments.
 
     Args:
         -i/--input (str): Input file name (multiple allowed)
@@ -46,12 +46,11 @@ def parse_xml_preprocessor_arguments() -> Tuple[ argparse.Namespace, Iterable[ s
 
 
 def build_xml_formatter_input_parser() -> argparse.ArgumentParser:
-    """Build the argument parser
+    """Build the argument parser.
 
     Returns:
         argparse.ArgumentParser: the parser instance
     """
-
     parser = argparse.ArgumentParser()
     parser.add_argument( 'input', type=str, help='Input file name' )
     parser.add_argument( '-i', '--indent', type=int, help='Indent size', default=2 )
@@ -64,25 +63,23 @@ def build_xml_formatter_input_parser() -> argparse.ArgumentParser:
 
 
 def build_attribute_coverage_input_parser() -> argparse.ArgumentParser:
-    """Build attribute coverage redundancy input parser
+    """Build attribute coverage redundancy input parser.
 
     Returns:
         argparse.ArgumentParser: parser instance
     """
-
     parser = argparse.ArgumentParser()
     parser.add_argument( '-r', '--root', type=str, help='GEOSX root', default='' )
     parser.add_argument( '-o', '--output', type=str, help='Output file name', default='attribute_test.xml' )
     return parser
 
 
 def build_xml_redundancy_input_parser() -> argparse.ArgumentParser:
-    """Build xml redundancy input parser
+    """Build xml redundancy input parser.
 
     Returns:
         argparse.ArgumentParser: parser instance
     """
-
     parser = argparse.ArgumentParser()
     parser.add_argument( '-r', '--root', type=str, help='GEOSX root', default='' )
     return parser