Enable Code Formatting Checks

.github/workflows/python-package.yml

@@ -30,10 +30,10 @@ jobs:
         python -m pip install --upgrade pip
         python -m pip install pytest yapf toml
         python -m pip install .
-    # - name: Lint with yapf
-    #   working-directory: ./${{ matrix.package-name }}
-    #   run: |
-    #     yapf -r --diff .
+    - name: Lint with yapf
+      working-directory: ./${{ matrix.package-name }}
+      run: |
+        yapf -r --diff . --style ../.style.yapf
     # - name: Test with pytest
     #   working-directory: ./${{ matrix.package-name }}
     #   run: |

.style.yapf

@@ -0,0 +1,6 @@
+[style]
+based_on_style = pep8
+spaces_before_comment = 2
+split_before_logical_operator = true
+column_limit = 120
+space_inside_brackets = true

docs/conf.py

@@ -18,16 +18,10 @@
 
 # Add python modules to be documented
 python_root = '..'
-python_modules = ('geosx_mesh_tools_package',
-                  'geosx_xml_tools_package',
-                  'geosx_mesh_doctor',
-                  'geos_ats_package',
-                  'hdf5_wrapper_package',
-                  'pygeosx_tools_package',
-                  'timehistory_package')
+python_modules = ( 'geosx_mesh_tools_package', 'geosx_xml_tools_package', 'geosx_mesh_doctor', 'geos_ats_package',
+                   'hdf5_wrapper_package', 'pygeosx_tools_package', 'timehistory_package' )
 for m in python_modules:
-    sys.path.insert(0, os.path.abspath(os.path.join(python_root, m)))
-
+    sys.path.insert( 0, os.path.abspath( os.path.join( python_root, m ) ) )
 
 # -- Project information -----------------------------------------------------
 
@@ -40,7 +34,6 @@
 # The full version, including alpha/beta/rc tags
 release = u''
 
-
 # -- General configuration ---------------------------------------------------
 
 # If your documentation needs a minimal Sphinx version, state it here.
@@ -51,18 +44,11 @@
 # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
 # ones.
 extensions = [
-    'sphinx_design',
-    'sphinx.ext.todo',
-    'sphinx.ext.autodoc',
-    'sphinx.ext.doctest',
-    'sphinx.ext.imgmath',
-    'sphinxarg.ext',
-    'sphinx.ext.napoleon',
-    'sphinxcontrib.programoutput'
+    'sphinx_design', 'sphinx.ext.todo', 'sphinx.ext.autodoc', 'sphinx.ext.doctest', 'sphinx.ext.imgmath',
+    'sphinxarg.ext', 'sphinx.ext.napoleon', 'sphinxcontrib.programoutput'
 ]
 
-
-autodoc_mock_imports = ["pygeosx", "pylvarray", "meshio", "lxml", "mpi4py", "h5py", "ats", "scipy"]
+autodoc_mock_imports = [ "pygeosx", "pylvarray", "meshio", "lxml", "mpi4py", "h5py", "ats", "scipy" ]
 
 # The suffix(es) of source filenames.
 # You can specify multiple suffix as a list of string:
@@ -83,34 +69,28 @@
 # List of patterns, relative to source directory, that match files and
 # directories to ignore when looking for source files.
 # This pattern also affects html_static_path and html_extra_path .
-exclude_patterns = [u'_build', 'Thumbs.db', '.DS_Store', 'cmake/*']
+exclude_patterns = [ u'_build', 'Thumbs.db', '.DS_Store', 'cmake/*' ]
 
 todo_include_todos = True
 
 # The name of the Pygments (syntax highlighting) style to use.
 pygments_style = 'sphinx'
 
-
 # -- Theme options ----------------------------------------------
 extensions += [
     'sphinx_rtd_theme',
 ]
 
 html_theme = "sphinx_rtd_theme"
 
-html_theme_options = {
-    'navigation_depth': -1,
-    'collapse_navigation': False
-}
+html_theme_options = { 'navigation_depth': -1, 'collapse_navigation': False }
 
-html_static_path = ['./_static']
+html_static_path = [ './_static' ]
 
 html_css_files = [
     'theme_overrides.css',
 ]
 
-
 # -- Options for HTMLHelp output ---------------------------------------------
 # Output file base name for HTML help builder.
 htmlhelp_basename = 'geosPythonPackagesDoc'
-

geos_ats_package/geos_ats/__init__.py

@@ -3,4 +3,4 @@
 
 # Add the machines module to the ats.atsMachines submodule,
 # So that ats can find our custom definitions at runtime
-sys.modules['ats.atsMachines.machines'] = machines
+sys.modules[ 'ats.atsMachines.machines' ] = machines

geos_ats_package/geos_ats/command_line_parsers.py

@@ -36,49 +36,58 @@
 
 
 def build_command_line_parser():
-    parser = argparse.ArgumentParser(description="Runs GEOS integrated tests")
+    parser = argparse.ArgumentParser( description="Runs GEOS integrated tests" )
 
-    parser.add_argument("geos_bin_dir", type=str, help="GEOS binary directory.")
+    parser.add_argument( "geos_bin_dir", type=str, help="GEOS binary directory." )
 
-    parser.add_argument("-w", "--workingDir", type=str, help="Initial working directory")
+    parser.add_argument( "-w", "--workingDir", type=str, help="Initial working directory" )
 
-    action_names = ','.join(action_options.keys())
-    parser.add_argument("-a", "--action", type=str, default="run", help=f"Test actions options ({action_names})")
+    action_names = ','.join( action_options.keys() )
+    parser.add_argument( "-a", "--action", type=str, default="run", help=f"Test actions options ({action_names})" )
 
-    check_names = ','.join(check_options.keys())
-    parser.add_argument("-c", "--check", type=str, default="all", help=f"Test check options ({check_names})")
+    check_names = ','.join( check_options.keys() )
+    parser.add_argument( "-c", "--check", type=str, default="all", help=f"Test check options ({check_names})" )
 
-    verbosity_names = ','.join(verbose_options.keys())
-    parser.add_argument("-v", "--verbose", type=str, default="info", help=f"Log verbosity options ({verbosity_names})")
+    verbosity_names = ','.join( verbose_options.keys() )
+    parser.add_argument( "-v",
+                         "--verbose",
+                         type=str,
+                         default="info",
+                         help=f"Log verbosity options ({verbosity_names})" )
 
-    parser.add_argument("-d", "--detail", action="store_true", default=False, help="Show detailed action/check options")
+    parser.add_argument( "-d",
+                         "--detail",
+                         action="store_true",
+                         default=False,
+                         help="Show detailed action/check options" )
 
-    parser.add_argument("-i", "--info", action="store_true", default=False, help="Info on various topics")
+    parser.add_argument( "-i", "--info", action="store_true", default=False, help="Info on various topics" )
 
-    parser.add_argument("-r",
-                        "--restartCheckOverrides",
-                        nargs='+',
-                        action='append',
-                        help='Restart check parameter override (name value)',
-                        default=[])
+    parser.add_argument( "-r",
+                         "--restartCheckOverrides",
+                         nargs='+',
+                         action='append',
+                         help='Restart check parameter override (name value)',
+                         default=[] )
 
-    parser.add_argument("--salloc",
-                        default=True,
-                        help="Used by the chaosM machine to first allocate nodes with salloc, before running the tests")
+    parser.add_argument(
+        "--salloc",
+        default=True,
+        help="Used by the chaosM machine to first allocate nodes with salloc, before running the tests" )
 
     parser.add_argument(
         "--sallocoptions",
         type=str,
         default="",
-        help="Used to override all command-line options for salloc. No other options with be used or added.")
+        help="Used to override all command-line options for salloc. No other options with be used or added." )
 
-    parser.add_argument("--ats", nargs='+', default=[], action="append", help="pass arguments to ats")
+    parser.add_argument( "--ats", nargs='+', default=[], action="append", help="pass arguments to ats" )
 
-    parser.add_argument("--machine", default=None, help="name of the machine")
+    parser.add_argument( "--machine", default=None, help="name of the machine" )
 
-    parser.add_argument("--machine-dir", default=None, help="Search path for machine definitions")
+    parser.add_argument( "--machine-dir", default=None, help="Search path for machine definitions" )
 
-    parser.add_argument("-l", "--logs", type=str, default=None)
+    parser.add_argument( "-l", "--logs", type=str, default=None )
 
     parser.add_argument(
         "--failIfTestsFail",
@@ -87,14 +96,14 @@ def build_command_line_parser():
         help="geos_ats normally exits with 0. This will cause it to exit with an error code if there was a failed test."
     )
 
-    parser.add_argument("-n", "-N", "--numNodes", type=int, default="2")
+    parser.add_argument( "-n", "-N", "--numNodes", type=int, default="2" )
 
-    parser.add_argument("ats_targets", type=str, nargs='*', help="ats files or directories.")
+    parser.add_argument( "ats_targets", type=str, nargs='*', help="ats files or directories." )
 
     return parser
 
 
-def parse_command_line_arguments(args):
+def parse_command_line_arguments( args ):
     parser = build_command_line_parser()
     options, unkown_args = parser.parse_known_args()
     exit_flag = False
@@ -103,7 +112,7 @@ def parse_command_line_arguments(args):
     check = options.check
     if check not in check_options:
         print(
-            f"Selected check option ({check}) not recognized.  Try running with --help/--details for more information")
+            f"Selected check option ({check}) not recognized.  Try running with --help/--details for more information" )
         exit_flag = True
 
     action = options.action
@@ -115,15 +124,15 @@ def parse_command_line_arguments(args):
 
     verbose = options.verbose
     if verbose not in verbose_options:
-        print(f"Selected verbose option ({verbose}) not recognized")
+        print( f"Selected verbose option ({verbose}) not recognized" )
         exit_flag = True
 
     # Print detailed information
     if options.detail:
-        for option_type, details in zip(['action', 'check'], [action_options, check_options]):
-            print(f'\nAvailable {option_type} options:')
+        for option_type, details in zip( [ 'action', 'check' ], [ action_options, check_options ] ):
+            print( f'\nAvailable {option_type} options:' )
             for k, v in details.items():
-                print(f'    {k}:  {v}')
+                print( f'    {k}:  {v}' )
         exit_flag = True
 
     if exit_flag:
@@ -132,20 +141,20 @@ def parse_command_line_arguments(args):
     return options
 
 
-def patch_parser(parser):
+def patch_parser( parser ):
 
-    def add_option_patch(*xargs, **kwargs):
+    def add_option_patch( *xargs, **kwargs ):
         """
         Convert type string to actual type instance
         """
-        tmp = kwargs.get('type', str)
-        type_map = {'string': str}
-        if isinstance(tmp, str):
+        tmp = kwargs.get( 'type', str )
+        type_map = { 'string': str }
+        if isinstance( tmp, str ):
             if tmp in type_map:
-                tmp = type_map[tmp]
+                tmp = type_map[ tmp ]
             else:
-                tmp = locate(tmp)
-        kwargs['type'] = tmp
-        parser.add_argument(*xargs, **kwargs)
+                tmp = locate( tmp )
+        kwargs[ 'type' ] = tmp
+        parser.add_argument( *xargs, **kwargs )
 
     parser.add_option = add_option_patch