Cleanup tools folder

bin/bout-add-mod-path

@@ -104,8 +104,7 @@ def create_mod(modulepath, name, top, build):
     else:
         prereq = ""
     with open(filename, "w") as f:
-        f.write(
-            f"""#%Module 1.0
+        f.write(f"""#%Module 1.0
 #
 #  BOUT++ module for use with 'environment-modules' package
 #  Created by bout-add-mod-path v0.9
@@ -119,17 +118,14 @@ setenv        BOUT_TOP         {top}
 prepend-path  PATH             {top}/bin
 prepend-path  PYTHONPATH       {top}/tools/pylib
 prepend-path  IDL_PATH        +{top}/tools/idllib:'<IDL_DEFAULT>'
-"""
-        )
+""")
         if build != top:
-            f.write(
-                f"""#%Module 1.0
+            f.write(f"""#%Module 1.0
 setenv        BOUT_BUILD       {build}
 prepend-path  PATH             {build}/bin
 prepend-path  LD_LIBRARY_PATH  {build}/lib
 prepend-path  PYTHONPATH       {build}/tools/pylib
-"""
-            )
+""")
     print(f"created `{filename}`")
 
 

bin/bout-pylib-cmd-to-bin

@@ -126,8 +126,7 @@ def createwrapper(mod, func_name, func, name):
             out += end
             f.write(out)
 
-        fprint(
-            """#!/usr/bin/env python3
+        fprint("""#!/usr/bin/env python3
 # PYTHON_ARGCOMPLETE_OK
 
 import argparse
@@ -136,8 +135,7 @@ try:
 except ImportError:
     argcomplete=None
 
-"""
-        )
+""")
         doc = True
         para = False
         ret = False
@@ -183,19 +181,16 @@ except ImportError:
                         arg_help[curarg].append(esc(blas))
         # Print functions that are needed
         if "str_to_slice" in arg_type.values():
-            fprint(
-                """
+            fprint("""
 def str_to_slice(sstr):
     args=[]
     for s in sstr.split(','):
         args.append(int(s))
     print(args)
     return slice(*args)
-"""
-            )
+""")
         if "str_to_bool" in arg_type.values():
-            fprint(
-                """
+            fprint("""
 def str_to_bool(sstr):
     low=sstr.lower()
     # no or false
@@ -206,8 +201,7 @@ def str_to_bool(sstr):
         return True
     else:
         raise ArgumentTypeError("Cannot parse %s to bool type"%sstr)
-"""
-            )
+""")
         # Create the parser
         fprint("parser = argparse.ArgumentParser(%s)" % (esc(docs)))
         spec = inspect.signature(func)
@@ -247,24 +241,19 @@ def str_to_bool(sstr):
                     pre = "\n    "
             fprint(")")
 
-        fprint(
-            """
+        fprint("""
 if argcomplete:
     argcomplete.autocomplete(parser)
 
-# late import for faster auto-complete"""
-        )
+# late import for faster auto-complete""")
         fprint("from %s import %s" % (mod, func_name))
-        fprint(
-            """
+        fprint("""
 args = parser.parse_args()
 
 # Call the function %s, using command line arguments
 %s(**args.__dict__)
 
-"""
-            % (func_name, func_name)
-        )
+""" % (func_name, func_name))
     # alternative, but I think 0o755 is easier to read
     # import stat
     # os.chmod(filename,stat.S_IRWXU|stat.S_IRGRP|stat.S_IXGRP|stat.S_IROTH|stat.S_IXOTH)

bin/bout-v5-factory-upgrader.py

@@ -5,7 +5,6 @@
 import difflib
 import re
 
-
 # Dictionary of factory methods that may need updating
 factories = {
     "Interpolation": {
@@ -62,9 +61,7 @@ def find_factory_calls(factory, source):
         \s*=\s*
         {factory_name}::
         .*{create_method}.*
-        """.format(
-            **factory
-        ),
+        """.format(**factory),
         source,
         re.VERBOSE,
     )
@@ -75,9 +72,7 @@ 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,
     )
@@ -107,9 +102,7 @@ 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,
@@ -123,9 +116,7 @@ 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,
@@ -139,9 +130,7 @@ 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,

bin/bout-v5-format-upgrader.py

@@ -5,7 +5,6 @@
 import difflib
 import re
 
-
 format_replacements = {
     "c": "c",
     "d": "d",

bin/bout-v5-header-upgrader.py

@@ -9,7 +9,6 @@
 from typing import List
 from subprocess import run
 
-
 header_shim_sentinel = "// BOUT++ header shim"
 
 header_warning = f"""\
@@ -122,8 +121,7 @@ def create_patch(filename, original, modified):
 if __name__ == "__main__":
     parser = argparse.ArgumentParser(
         formatter_class=argparse.RawDescriptionHelpFormatter,
-        description=textwrap.dedent(
-            """\
+        description=textwrap.dedent("""\
             Fix deprecated header locations for BOUT++ v4 -> v5
 
             All BOUT++ headers are now under ``include/bout`` and
@@ -142,8 +140,7 @@ def create_patch(filename, original, modified):
             If you have staged changes, this tool will not work, so to
             avoid committing undesired or unrelated changes.
 
-            """
-        ),
+            """),
     )
 
     parser.add_argument(

bin/bout-v5-input-file-upgrader.py

@@ -271,8 +271,7 @@ def possibly_apply_patch(patch, options_file, quiet=False, force=False):
 if __name__ == "__main__":
     parser = argparse.ArgumentParser(
         formatter_class=argparse.RawDescriptionHelpFormatter,
-        description=textwrap.dedent(
-            """\
+        description=textwrap.dedent("""\
             Fix input files for BOUT++ v5+
 
             Please note that this will only fix input options in sections with
@@ -300,8 +299,7 @@ def possibly_apply_patch(patch, options_file, quiet=False, force=False):
 
             Files that change in this way will have the "canonicalisation" patch
             presented first. If you choose not to apply this patch, the "upgrade
-            fixer" patch will still include it."""
-        ),
+            fixer" patch will still include it."""),
     )
 
     parser.add_argument("files", action="store", nargs="+", help="Input files")

bin/bout-v5-macro-upgrader.py

@@ -342,8 +342,7 @@ def create_patch(filename, original, modified):
 if __name__ == "__main__":
     parser = argparse.ArgumentParser(
         formatter_class=argparse.RawDescriptionHelpFormatter,
-        description=textwrap.dedent(
-            """\
+        description=textwrap.dedent("""\
             Fix macro defines for BOUT++ v4 -> v5
 
             Please note that this is only slightly better than dumb text replacement. It
@@ -359,8 +358,7 @@ def create_patch(filename, original, modified):
             still replace them in strings or comments.
 
             Please check the diff output carefully!
-            """
-        ),
+            """),
     )
 
     parser.add_argument("files", action="store", nargs="+", help="Input files")

bin/bout-v5-physics-model-upgrader.py

@@ -8,7 +8,6 @@
 import textwrap
 import warnings
 
-
 PHYSICS_MODEL_INCLUDE = '#include "bout/physicsmodel.hxx"'
 
 PHYSICS_MODEL_SKELETON = """
@@ -213,13 +212,11 @@ def fix_bout_constrain(source, error_on_warning):
             "\n  ".join(["{}:{}".format(i, source_lines[i]) for i in line_range])
         )
 
-    message = textwrap.dedent(
-        """\
+    message = textwrap.dedent("""\
         Some uses of `bout_constrain` remain, but we could not automatically
         convert them to use `Solver::constraint`. Please fix them before
         continuing:
-        """
-    )
+        """)
     message += "  " + "\n  ".join(lines_context)
 
     if error_on_warning:
@@ -389,8 +386,7 @@ def create_patch(filename, original, modified):
 if __name__ == "__main__":
     parser = argparse.ArgumentParser(
         formatter_class=argparse.RawDescriptionHelpFormatter,
-        description=textwrap.dedent(
-            """\
+        description=textwrap.dedent("""\
             Upgrade legacy physics models to use the PhysicsModel class
 
             This will do the bare minimum required to compile, and
@@ -403,8 +399,7 @@ def create_patch(filename, original, modified):
             By default, this will use the file name stripped of file
             extensions as the name of the new class. Use '--name=<new
             name>' to give a different name.
-            """
-        ),
+            """),
     )
 
     parser.add_argument("files", action="store", nargs="+", help="Files to fix")

bin/bout-v5-xzinterpolation-upgrader.py

@@ -54,9 +54,7 @@ def fix_header_includes(old_header, new_header, source):
         (<|")
         ({header})              # Header name
         (>|")
-        """.format(
-            header=old_header
-        ),
+        """.format(header=old_header),
         r"\1\2{header}\4".format(header=new_header),
         source,
         flags=re.VERBOSE,
@@ -67,9 +65,7 @@ def fix_interpolations(old_interpolation, new_interpolation, source):
     return re.sub(
         r"""
         \b{}\b
-        """.format(
-            old_interpolation
-        ),
+        """.format(old_interpolation),
         r"{}".format(new_interpolation),
         source,
         flags=re.VERBOSE,
@@ -120,9 +116,7 @@ def fix_factories(old_factory, new_factory, source):
     return re.sub(
         r"""
         \b{}\b
-        """.format(
-            old_factory
-        ),
+        """.format(old_factory),
         r"{}".format(new_factory),
         source,
         flags=re.VERBOSE,

bin/update_version_number_in_files.py

@@ -158,8 +158,7 @@ def create_patch(filename, original, modified):
 if __name__ == "__main__":
     parser = argparse.ArgumentParser(
         formatter_class=argparse.RawDescriptionHelpFormatter,
-        description=textwrap.dedent(
-            """\
+        description=textwrap.dedent("""\
             Update the software version number to the specified version, 
             to be given in the form major.minor.patch, 
             e.g. 5.10.3
@@ -172,8 +171,7 @@ def create_patch(filename, original, modified):
             the 'minor' version number of the provided version will be incremented by 1, 
             e.g. 5.10.3 -> 5.11.3
 
-            """
-        ),
+            """),
     )
 
     parser.add_argument(

src/field/gen_fieldops.py

@@ -11,7 +11,6 @@
 
 """
 
-
 from __future__ import print_function
 
 from builtins import object

tests/MMS/GBS/runtest-slab2d

@@ -11,7 +11,6 @@ from boutdata.collect import collect
 
 from numpy import sqrt, max, abs, mean, array, log, concatenate
 
-
 build_and_log("MMS test")
 
 

tests/MMS/GBS/runtest-slab3d

@@ -14,7 +14,6 @@ from numpy import sqrt, max, abs, mean, array, log, concatenate
 
 import pickle
 
-
 build_and_log("MMS test")
 
 # List of NX values to use

tests/MMS/advection/runtest

@@ -20,7 +20,6 @@ import pickle
 
 import time
 
-
 if __name__ == "__main__":
     build_and_log("MMS advection")
 

tests/MMS/diffusion/runtest

@@ -15,7 +15,6 @@ from boutdata.collect import collect
 
 from numpy import sqrt, max, abs, mean, array, log
 
-
 build_and_log("MMS diffusion test")
 
 # List of NX values to use

tests/MMS/diffusion2/Z/plot_error.py

@@ -4,6 +4,7 @@
 
 @author: yolen
 """
+
 import boutdata
 import matplotlib.pyplot as plt