Deprecate options that only use as default for other options

src/boutupgrader/__init__.py

@@ -10,6 +10,7 @@
 from .bout_v5_physics_model_upgrader import add_parser as add_model_parser
 from .bout_v5_xzinterpolation_upgrader import add_parser as add_xzinterp_parser
 from .bout_v6_coordinates_upgrader import add_parser as add_v6_coordinates_parser
+from .bout_v6_input_file_upgrader import add_parser as add_v6_input_parser
 
 try:
     # This gives the version if the boututils package was installed
@@ -71,6 +72,7 @@ def main():
     add_model_parser(v5_subcommand, common_args, files_args)
     add_xzinterp_parser(v5_subcommand, common_args, files_args)
     add_v6_coordinates_parser(v6_subcommand, common_args, files_args)
+    add_v6_input_parser(v6_subcommand, common_args, files_args)
 
     args = parser.parse_args()
     args.func(args)

src/boutupgrader/bout_v5_factory_upgrader.py

@@ -59,9 +59,7 @@ def find_factory_calls(factory, source):
         \s*=\s*
         {factory_name}::
         .*{create_method}.*
-        """.format(
-            **factory
-        ),
+        """.format(**factory),
         source,
         re.VERBOSE,
     )
@@ -72,9 +70,7 @@ def find_type_pointers(factory, source):
         r"""
         \b{type_name}\s*\*\s*   # Type name and pointer
         ([\w_]+)\s*;            # Variable name
-        """.format(
-            **factory
-        ),
+        """.format(**factory),
         source,
         re.VERBOSE,
     )
@@ -104,9 +100,7 @@ def fix_declarations(factory, variables, source):
             (.*?)(class\s*)?         # optional "class" keyword
             \b({type_name})\s*\*\s*  # Type-pointer
             ({variable_name})\s*;    # Variable
-            """.format(
-                type_name=factory["type_name"], variable_name=variable
-            ),
+            """.format(type_name=factory["type_name"], variable_name=variable),
             r"\1std::unique_ptr<\3> \4{nullptr};",
             source,
             flags=re.VERBOSE,
@@ -120,9 +114,7 @@ def fix_declarations(factory, variables, source):
             ({variable_name})\s*   # Variable
             =\s*                   # Assignment from factory
             ({factory_name}::.*{create_method}.*);
-            """.format(
-                variable_name=variable, **factory
-            ),
+            """.format(variable_name=variable, **factory),
             r"\1auto \4 = \5;",
             source,
             flags=re.VERBOSE,
@@ -136,9 +128,7 @@ def fix_declarations(factory, variables, source):
             ({variable_name})\s*   # Variable
             =\s*                   # Assignment
             (0|nullptr|NULL);
-            """.format(
-                variable_name=variable, **factory
-            ),
+            """.format(variable_name=variable, **factory),
             r"\1std::unique_ptr<\2> \3{nullptr};",
             source,
             flags=re.VERBOSE,

src/boutupgrader/bout_v5_input_file_upgrader.py

@@ -236,7 +236,7 @@ def possibly_apply_patch(patch, options_file, quiet=False, force=False):
     return make_change
 
 
-def add_parser(subcommand, default_args, files_args):
+def add_parser_general(subcommand, default_args, files_args, run):
     parser = subcommand.add_parser(
         "input",
         formatter_class=argparse.RawDescriptionHelpFormatter,
@@ -290,7 +290,7 @@ def add_parser(subcommand, default_args, files_args):
     parser.set_defaults(func=run)
 
 
-def run(args):
+def run_general(REPLACEMENTS, DELETED, args):
     from boutdata.data import BoutOptions, BoutOptionsFile
 
     # Monkey-patch BoutOptions to make sure it's case sensitive
@@ -340,3 +340,11 @@ def run(args):
             continue
 
         possibly_apply_patch(patch, modified, args.quiet, args.force)
+
+
+def run(args):
+    return run_general(REPLACEMENTS, DELETED, args)
+
+
+def add_parser(subcommand, default_args, files_args):
+    return add_parser_general(subcommand, default_args, files_args, run)

src/boutupgrader/bout_v6_coordinates_upgrader.py

@@ -27,7 +27,6 @@
 
 
 def add_parser(subcommand, default_args, files_args):
-
     help_text = textwrap.dedent(
         """\
             Upgrade files to use the refactored Coordinates class.
@@ -85,7 +84,6 @@ def indices_of_matching_lines(pattern, lines):
 
 
 def use_metric_accessors(original_string):
-
     lines = original_string.splitlines()
 
     line_matches = SETTING_METRIC_COMPONENT_REGEX.findall(original_string)
@@ -138,7 +136,6 @@ def remove_geometry_calls(lines):
 
 
 def assignment_regex_pairs(var):
-
     arrow_or_dot = r"\b.+\-\>|\."
     not_followed_by_equals = r"(?!\s?=)"
     equals_something = r"\=\s?(.+)(?=;)"
@@ -174,7 +171,6 @@ def replacement_for_division_assignment(match):
 
 
 def mesh_get_pattern_and_replacement():
-
     # Convert `mesh->get(coord->dx(), "dx")` to `coord->setDx(mesh->get("dx"));`, etc
 
     def replacement_for_assignment_with_mesh_get(match):
@@ -196,7 +192,6 @@ def replacement_for_assignment_with_mesh_get(match):
 
 # Deal with the basic find-and-replace cases that do not involve multiple lines
 def replace_one_line_cases(modified):
-
     metric_component = r"g_?\d\d"
     mesh_spacing = r"d[xyz]"
 

src/boutupgrader/bout_v6_input_file_upgrader.py

@@ -0,0 +1,22 @@
+from .bout_v5_input_file_upgrader import add_parser_general, run_general
+
+# This should be a list of dicts, each containing "old", "new" and optionally "new_values".
+# The values of "old"/"new" keys should be the old/new names of input file values or
+# sections. The value of "new_values" is a dict containing replacements for values of the
+# option. "old_type" optionally specifies the type of the old value of the option; for
+# example this is needed for special handling of boolean values.
+REPLACEMENTS = [
+    {"old": "timestep", "new": "solver:output_step"},
+    {"old": "nout", "new": "solver:nout"},
+    {"old": "grid", "new": "mesh:file"},
+]
+
+DELETED = []
+
+
+def run(args):
+    return run_general(REPLACEMENTS, DELETED, args)
+
+
+def add_parser(subcommand, default_args, files_args):
+    return add_parser_general(subcommand, default_args, files_args, run)