Add bout_v6_coordinates_upgrader script

src/boutupgrader/__init__.py

@@ -9,6 +9,7 @@
 from .bout_v5_macro_upgrader import add_parser as add_macro_parser
 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
 
 try:
     # This gives the version if the boututils package was installed
@@ -52,19 +53,24 @@ def main():
     v4_subcommand = subcommand.add_parser(
         "v4", help="BOUT++ v4 upgrades"
     ).add_subparsers(title="v4 subcommands", required=True)
-    add_3to4_parser(v4_subcommand, common_args, files_args)
 
     v5_subcommand = subcommand.add_parser(
         "v5", help="BOUT++ v5 upgrades"
     ).add_subparsers(title="v5 subcommands", required=True)
 
+    v6_subcommand = subcommand.add_parser(
+        "v6", help="BOUT++ v6 upgrades"
+    ).add_subparsers(title="v6 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)
     add_header_parser(v5_subcommand, common_args)
     add_input_parser(v5_subcommand, common_args, files_args)
     add_macro_parser(v5_subcommand, common_args, files_args)
     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)
 
     args = parser.parse_args()
     args.func(args)

src/boutupgrader/bout_v6_coordinates_upgrader.py

@@ -0,0 +1,223 @@
+#!/usr/bin/env python3
+import argparse
+import copy
+import pathlib
+import re
+import textwrap
+
+from .common import apply_or_display_patch
+
+# find lines like: c->g_11 = x; and c.g_11 = x;
+SETTING_METRIC_COMPONENT_REGEX = re.compile(
+    r"(\b.+\-\>|\.)"  # arrow or dot (-> or .)
+    r"(g_?)(\d\d)"  # g12 or g_12, etc
+    r"\s?\=\s?"  # equals (maybe with spaces)
+    r"(.+)"  # anything
+    r"(?=;)"  # followed by ;
+)
+
+# c->g11, etc
+GETTING_METRIC_COMPONENT_REGEX = re.compile(
+    r"(\b\w+->|\.)"  # e.g. coord. or coord->
+    r"(?P<component>g_?\d\d)"  # g12 or g_12, etc
+)
+
+# find the string `geometry()`
+GEOMETRY_METHOD_CALL_REGEX = re.compile(r"geometry\(\)")
+
+
+def add_parser(subcommand, default_args, files_args):
+
+    help_text = textwrap.dedent(
+        """\
+            Upgrade files to use the refactored Coordinates class.
+
+            For example, changes coords->dx to coords->dx()
+            """
+    )
+    parser = subcommand.add_parser(
+        "v6_upgrader",
+        help=help_text,
+        formatter_class=argparse.RawDescriptionHelpFormatter,
+        description=help_text,
+        parents=[default_args, files_args],
+    )
+    parser.set_defaults(func=run)
+
+
+def run(args):
+    for filename in args.files:
+        try:
+            contents = pathlib.Path(filename).read_text()
+        except Exception as e:
+            error_message = textwrap.indent(f"{e}", " ")
+            print(f"Error reading {filename}:\n\n{error_message}")
+            continue
+
+        original = copy.deepcopy(contents)
+        modified_contents = modify(contents)
+
+        apply_or_display_patch(
+            filename,
+            original,
+            modified_contents,
+            args.patch_only,
+            args.quiet,
+            args.force,
+        )
+
+        return modified_contents
+
+
+def modify(original_string):
+    using_new_metric_accessor_methods = use_metric_accessors(original_string)
+    without_geometry_calls = remove_geometry_calls(using_new_metric_accessor_methods)
+    without_geometry_calls.append("")  # insert a blank line at the end of the file
+    lines_as_single_string = "\n".join(without_geometry_calls)
+    modified_contents = replace_one_line_cases(lines_as_single_string)
+    return modified_contents
+
+
+def indices_of_matching_lines(pattern, lines):
+    search_result_for_all_lines = [pattern.search(line) for line in lines]
+    matches = [x for x in search_result_for_all_lines if x is not None]
+    return [lines.index(match.string) for match in matches]
+
+
+def use_metric_accessors(original_string):
+
+    lines = original_string.splitlines()
+
+    line_matches = SETTING_METRIC_COMPONENT_REGEX.findall(original_string)
+
+    if len(line_matches) == 0:
+        return lines
+
+    metric_components = {match[1] + match[2]: match[3] for match in line_matches}
+    lines_to_remove = indices_of_matching_lines(SETTING_METRIC_COMPONENT_REGEX, lines)
+    lines_removed_count = 0
+    for line_index in lines_to_remove:
+        del lines[line_index - lines_removed_count]
+        lines_removed_count += 1
+    metric_components_with_value = {
+        key: value for key, value in metric_components.items() if value is not None
+    }
+    newline_inserted = False
+    for key, value in metric_components_with_value.items().__reversed__():
+        # Replace `c->g11` with `g11`, etc
+        new_value = GETTING_METRIC_COMPONENT_REGEX.sub(r"\g<component>", value)
+        if not key.startswith("g_") and not newline_inserted:
+            lines.insert(lines_to_remove[0], "")
+            newline_inserted = True
+        local_variable_line = rf"    const auto {key} = {new_value};"
+        lines.insert(lines_to_remove[0], local_variable_line)
+    # insert a blank line
+    lines.insert(lines_to_remove[0] + len(metric_components_with_value) + 1, "")
+    coordinates_name_and_arrow = line_matches[0][0]
+    new_metric_tensor_setter = (
+        f"    {coordinates_name_and_arrow}setMetricTensor(ContravariantMetricTensor(g11, g22, g33, g12, g13, g23),\n"
+        f"                           CovariantMetricTensor(g_11, g_22, g_33, g_12, g_13, g_23));"
+    )
+    lines.insert(
+        lines_to_remove[0] + len(metric_components_with_value) + 2,
+        new_metric_tensor_setter,
+    )
+    del lines[lines_to_remove[-1] + 3]
+    return lines
+
+
+def remove_geometry_calls(lines):
+    # Remove lines calling geometry()
+    lines_to_remove = indices_of_matching_lines(GEOMETRY_METHOD_CALL_REGEX, lines)
+    for line_index in lines_to_remove:
+        # If both the lines above and below are blank then remove one of them
+        if lines[line_index - 1].strip() == "" and lines[line_index + 1].strip() == "":
+            del lines[line_index + 1]
+        del lines[line_index]
+    return lines
+
+
+def assignment_regex_pairs(var):
+
+    arrow_or_dot = r"\b.+\-\>|\."
+    not_followed_by_equals = r"(?!\s?=)"
+    equals_something = r"\=\s?(.+)(?=;)"
+
+    def replacement_for_assignment(match):
+        coord_and_arrow_or_dot = match.groups()[0]
+        variable_name = match.groups()[1]
+        capitalised_name = variable_name[0].upper() + variable_name[1:]
+        value = match.groups()[2]
+        return rf"{coord_and_arrow_or_dot}set{capitalised_name}({value})"
+
+    def replacement_for_division_assignment(match):
+        coord_and_arrow_or_dot = match.groups()[0]
+        variable_name = match.groups()[1]
+        capitalised_name = variable_name[0].upper() + variable_name[1:]
+        value = match.groups()[2]
+        denominator = (
+            f"{value}" if value[0] == "(" and value[-1] == ")" else f"({value})"
+        )
+        return rf"{coord_and_arrow_or_dot}set{capitalised_name}({coord_and_arrow_or_dot}{variable_name} / {denominator})"
+
+    return [
+        # Replace `->var =` with `->setVar()`, etc
+        (rf"({arrow_or_dot})({var})\s?{equals_something}", replacement_for_assignment),
+        # Replace `foo->var /= bar` with `foo->setVar(foo->var() / (bar))`
+        (
+            rf"({arrow_or_dot})({var})\s?\/{equals_something}",
+            replacement_for_division_assignment,
+        ),
+        # Replace `c->var` with `c->var()` etc, but not if is assignment
+        (rf"({arrow_or_dot})({var})(?!\(){not_followed_by_equals}", r"\1\2()"),
+    ]
+
+
+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):
+        arrow_or_dot = match.groups()[0]
+        coords = match.groups()[1]
+        variable_name = match.groups()[3]
+        new_value = match.groups()[4]
+        capitalised_name = variable_name[0].upper() + variable_name[1:]
+        return rf"{coords}{arrow_or_dot}set{capitalised_name}(mesh->get({new_value}))"
+
+    arrow_or_dot = r"\-\>|\."
+
+    mesh_get_pattern_replacement = (
+        rf"mesh({arrow_or_dot})get\((\w+)({arrow_or_dot})(\w+)\(?\)?, (\"\w+\")\)",
+        replacement_for_assignment_with_mesh_get,
+    )
+    return mesh_get_pattern_replacement
+
+
+# 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]"
+
+    patterns_with_replacements = (
+        assignment_regex_pairs(metric_component)
+        + assignment_regex_pairs(mesh_spacing)
+        + assignment_regex_pairs("Bxy")
+        + assignment_regex_pairs("J")
+        + assignment_regex_pairs("IntShiftTorsion")
+        + assignment_regex_pairs("G1")
+        + assignment_regex_pairs("G2")
+        + assignment_regex_pairs("G3")
+    )
+
+    patterns_with_replacements.append(mesh_get_pattern_and_replacement())
+
+    for pattern, replacement in patterns_with_replacements:
+        compiled_pattern = re.compile(pattern)
+        MAX_OCCURRENCES = 12
+        count = 0
+        while compiled_pattern.search(modified) and count < MAX_OCCURRENCES:
+            count += 1
+            modified = compiled_pattern.sub(replacement, modified)
+    return modified