Add bout-upgrader tool

pyproject.toml

@@ -50,6 +50,7 @@ docs = [
 
 [project.scripts]
 bout-squashoutput = "boutdata.scripts.bout_squashoutput:main"
+bout-upgrader = "boutupgrader:main"
 
 [tool.setuptools.dynamic]
 version = { attr = "setuptools_scm.get_version" }

src/boutupgrader/__init__.py

@@ -0,0 +1,70 @@
+import argparse
+from importlib.metadata import PackageNotFoundError, version
+
+from .bout_3to4 import add_parser as add_3to4_parser
+from .bout_v5_factory_upgrader import add_parser as add_factory_parser
+from .bout_v5_format_upgrader import add_parser as add_format_parser
+from .bout_v5_header_upgrader import add_parser as add_header_parser
+from .bout_v5_input_file_upgrader import add_parser as add_input_parser
+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
+
+try:
+    # This gives the version if the boututils package was installed
+    __version__ = version("boutdata")
+except PackageNotFoundError:
+    # This branch handles the case when boututils is used from the git repo
+    try:
+        from setuptools_scm import get_version
+
+        __version__ = get_version(root="..", relative_to=__file__)
+    except (ModuleNotFoundError, LookupError):
+        __version__ = "dev"
+
+
+def main():
+    # Parent parser that has arguments common to all subcommands
+    common_args = argparse.ArgumentParser(add_help=False)
+    common_args.add_argument(
+        "--quiet", "-q", action="store_true", help="Don't print patches"
+    )
+    force_or_patch_group = common_args.add_mutually_exclusive_group()
+    force_or_patch_group.add_argument(
+        "--force", "-f", action="store_true", help="Make changes without asking"
+    )
+    force_or_patch_group.add_argument(
+        "--patch-only", "-p", action="store_true", help="Print the patches and exit"
+    )
+
+    # Parent parser for commands that always take a list of files
+    files_args = argparse.ArgumentParser(add_help=False)
+    files_args.add_argument("files", action="store", nargs="+", help="Input files")
+
+    parser = argparse.ArgumentParser(
+        description="Upgrade BOUT++ source and input files to newer versions"
+    )
+    parser.add_argument(
+        "--version", action="version", version=f"%(prog)s {__version__}"
+    )
+    subcommand = parser.add_subparsers(title="subcommands", required=True)
+
+    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)
+
+    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)
+
+    args = parser.parse_args()
+    args.func(args)

src/boutupgrader/bout_3to4.py

@@ -0,0 +1,230 @@
+#!/usr/bin/env python3
+
+import fileinput
+import re
+import sys
+
+nonmembers = {
+    "DC": ["DC", 1],
+    "slice": ["sliceXZ", 2],
+}
+
+coordinates = [
+    "outputVars",
+    "dx",
+    "dy",
+    "dz",
+    "non_uniform",
+    "d1_dx",
+    "d1_dy",
+    "J",
+    "Bxy",
+    "g11",
+    "g22",
+    "g33",
+    "g12",
+    "g13",
+    "g23",
+    "g_11",
+    "g_22",
+    "g_33",
+    "g_12",
+    "g_13",
+    "g_23",
+    "G1_11",
+    "G1_22",
+    "G1_33",
+    "G1_12",
+    "G1_13",
+    "G2_11",
+    "G2_22",
+    "G2_33",
+    "G2_12",
+    "G2_23",
+    "G3_11",
+    "G3_22",
+    "G3_33",
+    "G3_13",
+    "G3_23",
+    "G1",
+    "G2",
+    "G3",
+    "ShiftTorsion",
+    "IntShiftTorsion",
+    "geometry",
+    "calcCovariant",
+    "calcContravariant",
+    "jacobian",
+]
+
+local_mesh = [
+    ("ngx", "LocalNx"),
+    ("ngy", "LocalNy"),
+]
+
+warnings = [
+    (r"\^", "Use pow(a,b) instead of a^b"),
+    (r"\.max\(", "Use max(a) instead of a.max()"),
+    (
+        "ngz",
+        (
+            "ngz is changed to LocalNz in v4."
+            " The extra point in z has been removed."
+            " Change ngz -> LocalNz, and ensure that"
+            " the number of points are correct"
+        ),
+    ),
+]
+
+
+def fix_nonmembers(line_text, filename, line_num, replace=False):
+    """Replace member functions with nonmembers"""
+
+    old_line_text = line_text
+
+    for old, (new, num_args) in nonmembers.items():
+        pattern = re.compile(rf"(\w*)\.{old}\(")
+        matches = re.findall(pattern, line_text)
+        for match in matches:
+            replacement = f"{new}({match}"
+            if num_args > 1:
+                replacement += ", "
+            line_text = re.sub(pattern, replacement, line_text)
+            if not replace:
+                name_num = f"{filename}:{line_num}:"
+                print(f"{name_num}{old_line_text}", end="")
+                print(" " * len(name_num) + line_text)
+    if replace:
+        return line_text
+
+
+def fix_subscripts(line_text, filename, line_num, replace=False):
+    """Replace triple square brackets with round brackets
+
+    Should also check that the variable is a Field3D/Field2D - but doesn't
+    """
+
+    old_line_text = line_text
+    # Catch both 2D and 3D arrays
+    pattern = re.compile(r"\[([^[]*)\]\[([^[]*)\](?:\[([^[]*)\])?")
+    matches = re.findall(pattern, line_text)
+    for match in matches:
+        # If the last group is non-empty, then it was a 3D array
+        if len(match[2]):
+            replacement = r"(\1, \2, \3)"
+        else:
+            replacement = r"(\1, \2)"
+        line_text = re.sub(pattern, replacement, line_text)
+        if not replace:
+            name_num = f"{filename}:{line_num}:"
+            print(f"{name_num}{old_line_text}", end="")
+            print(" " * len(name_num) + line_text)
+    if replace:
+        return line_text
+
+
+def fix_coordinates(line_text, filename, line_num, replace=False):
+    """Fix variables that have moved from mesh to coordinates"""
+
+    old_line_text = line_text
+
+    for var in coordinates:
+        pattern = re.compile(f"mesh->{var}")
+        matches = re.findall(pattern, line_text)
+        for match in matches:
+            line_text = re.sub(pattern, f"mesh->coordinates()->{var}", line_text)
+            if not replace:
+                name_num = f"{filename}:{line_num}:"
+                print(
+                    f"{name_num}{old_line_text}",
+                    end="",
+                )
+                print(" " * len(name_num) + line_text)
+    if replace:
+        return line_text
+
+
+def fix_local_mesh_size(line_text, filename, line_num, replace=False):
+    """Replaces ng@ with LocalNg@, where @ is in {x,y,z}"""
+
+    old_line_text = line_text
+
+    for lm in local_mesh:
+        pattern = re.compile(lm[0])
+        matches = re.findall(pattern, line_text)
+        for match in matches:
+            line_text = re.sub(pattern, lm[1], line_text)
+            if not replace:
+                name_num = f"{filename}:{line_num}:"
+                print(
+                    f"{name_num}{old_line_text}",
+                    end="",
+                )
+                print(" " * len(name_num) + line_text)
+    if replace:
+        return line_text
+
+
+def throw_warnings(line_text, filename, line_num):
+    """Throws a warning for ^, .max() and ngz"""
+
+    for warn in warnings:
+        pattern = re.compile(warn[0])
+        matches = re.findall(pattern, line_text)
+        for match in matches:
+            name_num = f"{filename}:{line_num}:"
+            # stdout is redirected to the file if --replace is given,
+            # therefore use stderr
+            sys.stderr.write(f"{name_num}{line_text}")
+            # Coloring with \033[91m, end coloring with \033[0m\n
+            sys.stderr.write(
+                " " * len(name_num) + f"\033[91m!!!WARNING: {warn[1]}\033[0m\n\n"
+            )
+
+
+def add_parser(subcommand, default_args, files_args):
+    epilog = """
+    Currently bout_3to4 can detect the following transformations are needed:
+        - Triple square brackets instead of round brackets for subscripts
+        - Field member functions that are now non-members
+        - Variables/functions that have moved from Mesh to Coordinates
+
+    Note that in the latter case of transformations, you will still need to manually add
+        Coordinates *coords = mesh->coordinates();
+    to the correct scopes
+    """
+
+    parser = subcommand.add_parser(
+        "3to4",
+        help="A little helper for upgrading from BOUT++ version 3 to version 4",
+        description="A little helper for upgrading from BOUT++ version 3 to version 4",
+        parents=[default_args, files_args],
+        epilog=epilog,
+    )
+    parser.set_defaults(func=run)
+
+
+def run(args):
+    # Loops over all lines across all files
+    for line in fileinput.input(files=args.files, inplace=args.replace):
+        filename = fileinput.filename()
+        line_num = fileinput.filelineno()
+
+        # Apply the transformations and then update the line if we're doing a replacement
+        new_line = fix_nonmembers(line, filename, line_num, args.replace)
+        line = new_line if args.replace else line
+
+        new_line = fix_subscripts(line, filename, line_num, args.replace)
+        line = new_line if args.replace else line
+
+        new_line = fix_coordinates(line, filename, line_num, args.replace)
+        line = new_line if args.replace else line
+
+        new_line = fix_local_mesh_size(line, filename, line_num, args.replace)
+        line = new_line if args.replace else line
+
+        new_line = throw_warnings(line, filename, line_num)
+
+        # If we're doing a replacement, then we need to print all lines, without a newline
+        if args.replace:
+            print(line, end="")