Add tool to upgrade collisions/closure in Hermes-3

src/boutupgrader/__init__.py

@@ -11,6 +11,7 @@
 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
+from .hermes_collisions_input_file_upgrader import add_parser as add_hermes_input_parser
 
 try:
     # This gives the version if the boututils package was installed
@@ -63,6 +64,10 @@ def main():
         "v6", help="BOUT++ v6 upgrades"
     ).add_subparsers(title="v6 subcommands", required=True)
 
+    hermes_subcommand = subcommand.add_parser(
+        "hermes", help="Hermes-3 subcommands"
+    ).add_subparsers(title="hermes subcommands", required=True)
+
     add_3to4_parser(v4_subcommand, common_args, files_args)
     add_factory_parser(v5_subcommand, common_args, files_args)
     add_format_parser(v5_subcommand, common_args, files_args)
@@ -73,6 +78,7 @@ def main():
     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)
+    add_hermes_input_parser(hermes_subcommand, common_args, files_args)
 
     args = parser.parse_args()
     args.func(args)

src/boutupgrader/bout_v5_input_file_upgrader.py

@@ -203,7 +203,7 @@ def remove_deleted(deleted, options_file):
             del options_file[key]
 
 
-def apply_fixes(replacements, deleted, options_file):
+def apply_fixes(replacements, deleted, options_file, additional_modifications):
     """Apply all fixes in this module"""
 
     modified = copy.deepcopy(options_file)
@@ -212,6 +212,8 @@ def apply_fixes(replacements, deleted, options_file):
 
     remove_deleted(deleted, modified)
 
+    additional_modifications(modified)
+
     return modified
 
 
@@ -236,14 +238,14 @@ def possibly_apply_patch(patch, options_file, quiet=False, force=False):
     return make_change
 
 
-def add_parser_general(subcommand, default_args, files_args, run):
+def add_parser_general(subcommand, default_args, files_args, run, name):
     parser = subcommand.add_parser(
         "input",
         formatter_class=argparse.RawDescriptionHelpFormatter,
         help="Fix input files",
         description=textwrap.dedent(
-            """\
-            Fix input files for BOUT++ v5+
+            f"""\
+            Fix input files for {name}
 
             Please note that this will only fix input options in sections with
             standard or default names. You may also need to fix options in custom
@@ -290,7 +292,7 @@ def add_parser_general(subcommand, default_args, files_args, run):
     parser.set_defaults(func=run)
 
 
-def run_general(REPLACEMENTS, DELETED, args):
+def run_general(REPLACEMENTS, DELETED, args, *, additional_modifications=None):
     from boutdata.data import BoutOptions, BoutOptionsFile
 
     # Monkey-patch BoutOptions to make sure it's case sensitive
@@ -324,7 +326,9 @@ def run_general(REPLACEMENTS, DELETED, args):
             continue
 
         try:
-            modified = apply_fixes(REPLACEMENTS, DELETED, original)
+            modified = apply_fixes(
+                REPLACEMENTS, DELETED, original, additional_modifications
+            )
         except RuntimeError as e:
             print(e)
             continue
@@ -347,4 +351,4 @@ def run(args):
 
 
 def add_parser(subcommand, default_args, files_args):
-    return add_parser_general(subcommand, default_args, files_args, run)
+    return add_parser_general(subcommand, default_args, files_args, run, "BOUT++ v5+")

src/boutupgrader/bout_v6_input_file_upgrader.py

@@ -19,4 +19,4 @@ def run(args):
 
 
 def add_parser(subcommand, default_args, files_args):
-    return add_parser_general(subcommand, default_args, files_args, run)
+    return add_parser_general(subcommand, default_args, files_args, run, "BOUT++ v6+")

src/boutupgrader/hermes_collisions_input_file_upgrader.py

@@ -0,0 +1,145 @@
+from itertools import chain
+from typing import TypedDict
+from warnings import warn
+
+from boutdata.data import BoutOptionsFile
+
+from .bout_v5_input_file_upgrader import add_parser_general, run_general
+
+
+class Replacement(TypedDict):
+    old: str
+    new: str
+
+
+REPLACEMENTS = []
+DELETED = []
+
+NEW_NAMES: dict[str, str | dict[str, list[str]]] = {
+    "collisions": {
+        "braginskii_collisions": [
+            "electron_electron",
+            "electron_ion",
+            "electron_neutral",
+            "ion_ion",
+            "ion_neutral",
+            "neutral_neutral",
+            "ei_multiplier",
+            "diagnose",
+        ],
+        "braginskii_friction": ["frictional_heating", "diagnose"],
+        "braginskii_heat_exchange": ["diagnose"],
+    },
+    "electron_viscosity": "braginskii_electron_viscosity",
+    "ion_viscosity": "braginskii_ion_viscosity",
+    "thermal_force": "braginskii_thermal_force",
+}
+
+# If name in `components` and type not given then change the name in components and heading; if a multi-replacement, duplicate the section
+# If type is same as name, duplicate section
+# If name in type of any component, change it there (don't duplicate)
+
+
+def split_list_string(list_string: str) -> tuple[list[str], bool]:
+    result = [tname.strip() for tname in list_string.split(",")]
+    open_paren = result[0][0] == "("
+    close_paren = result[-1][-1] == ")"
+    if open_paren != close_paren:
+        warn(f'Unmatched parentheses around "{list_string}"')
+    if open_paren:
+        result[0] = result[0][1:]
+    if close_paren:
+        result[-1] = result[-1][:-1]
+    return result, open_paren and close_paren
+
+
+def rename_simple_component(
+    options_file: BoutOptionsFile, section_name: str
+) -> list[str]:
+    """Rename a component when its type is the same as its name."""
+    if section_name in NEW_NAMES:
+        new_names = NEW_NAMES[section_name]
+        if isinstance(new_names, dict):
+            old_section = options_file.getSection(section_name)
+            new_components = []
+            for new_name, configs in new_names.items():
+                new_components.append(new_name)
+                new_section = options_file.getSection(new_name)
+                for conf in configs:
+                    if conf in old_section:
+                        new_section[conf] = old_section[conf]
+            return new_components
+        else:
+            options_file.rename(section_name, new_names)
+            return [new_names]
+    return [section_name]
+
+
+def update_component_names(options_file: BoutOptionsFile) -> None:
+    """Change the names of closure-related components to reflect the refactor"""
+    has_collisions = False
+    recycling_component = ""
+    old_components, has_parens = split_list_string(options_file["hermes:components"])
+    new_components = []
+    for section_name in old_components:
+        section = options_file.getSection(section_name)
+        # Component type is set explicitly
+        if "type" in section:
+            old_types, types_have_parens = split_list_string(section["type"])
+            # If component name and type match, treat similarly to if no type were given (see below)
+            if len(old_types) == 1 and old_types[0] == section_name:
+                has_collisions = has_collisions or section_name == "collisions"
+                new_types = rename_simple_component(options_file, section_name)
+                for t in new_types:
+                    options_file[f"{t}:type"] = (
+                        ("(" if types_have_parens else "")
+                        + t
+                        + (")" if types_have_parens else "")
+                    )
+                new_components.extend(new_types)
+            # Otherwise simply replace any type-names that need changing
+            else:
+                has_collisions = has_collisions or section_name in old_types
+                new_types = list(
+                    chain.from_iterable(
+                        [nt] if isinstance((nt := NEW_NAMES.get(t, t)), str) else nt
+                        for t in old_types
+                    )
+                )
+                if new_types != old_types:
+                    section["type"] = (
+                        ("(" if types_have_parens else "")
+                        + ", ".join(new_types)
+                        + (")" if types_have_parens else "")
+                    )
+                new_components.append(section_name)
+        # Component type is same as component name
+        else:
+            has_collisions = has_collisions or section_name == "collisions"
+            new_types = rename_simple_component(options_file, section_name)
+            new_components.extend(new_types)
+        if "recycling" in new_types:
+            recycling_component = section_name
+    # Add braginskii_conduction to the end of the list of components
+    if has_collisions:
+        new_components.append("braginskii_conduction")
+        # Make sure recycling is evaluated after conduction
+        if recycling_component != "":
+            new_components.remove(recycling_component)
+            new_components.append(recycling_component)
+    if new_components != old_components:
+        options_file["hermes:components"] = (
+            ("(" if has_parens else "")
+            + ", ".join(new_components)
+            + (")" if has_parens else "")
+        )
+
+
+def run(args) -> None:
+    run_general(
+        REPLACEMENTS, DELETED, args, additional_modifications=update_component_names
+    )
+
+
+def add_parser(subcommand, default_args, files_args):
+    return add_parser_general(subcommand, default_args, files_args, run, "Hermes-3")