Bump some dependencies

.github/workflows/black-fix.yml

@@ -20,7 +20,7 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-    - uses: actions/checkout@v5
+    - uses: actions/checkout@v6
       with:
         ref: ${{ github.head_ref }}
 

.github/workflows/clang-format.yml

@@ -13,7 +13,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       # Checkout the pull request branch, also include all history
-      - uses: actions/checkout@v5
+      - uses: actions/checkout@v6
         with:
           ref: ${{ github.head_ref }}
           fetch-depth: 0

.github/workflows/clang-tidy-review.yml

@@ -16,12 +16,12 @@ jobs:
     if: ${{ !endsWith(github.head_ref, '-rc') }}
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v5
+      - uses: actions/checkout@v6
         with:
           submodules: true
 
       - name: Run clang-tidy
-        uses: ZedThree/clang-tidy-review@v0.21.0
+        uses: ZedThree/clang-tidy-review@v0.23.0
         id: review
         with:
           build_dir: build
@@ -46,4 +46,4 @@ jobs:
                              -DBOUT_UPDATE_GIT_SUBMODULE=OFF
 
       - name: Upload clang-tidy fixes
-        uses: ZedThree/clang-tidy-review/upload@v0.21.0
+        uses: ZedThree/clang-tidy-review/upload@v0.23.0

.github/workflows/docker.yml

@@ -52,7 +52,7 @@ jobs:
 
     steps:
       - name: Checkout repository
-        uses: actions/checkout@v5
+        uses: actions/checkout@v6
 
       - name: Log in to the Container registry
         uses: docker/login-action@master

.github/workflows/python-package.yml

@@ -17,7 +17,7 @@ jobs:
     if: always()
 
     steps:
-    - uses: actions/checkout@v5
+    - uses: actions/checkout@v6
       with:
         fetch-depth: 0
         submodules: true
@@ -57,7 +57,7 @@ jobs:
     if: always()
 
     steps:
-    - uses: actions/checkout@v5
+    - uses: actions/checkout@v6
       with:
         fetch-depth: 0
         submodules: true
@@ -106,7 +106,7 @@ jobs:
     if: always()
 
     steps:
-    - uses: actions/checkout@v5
+    - uses: actions/checkout@v6
       with:
         fetch-depth: 0
         submodules: true

.github/workflows/tests.yml

@@ -168,7 +168,7 @@ jobs:
                  libparpack2-dev
                  libhypre-dev
 
-      - uses: actions/checkout@v5
+      - uses: actions/checkout@v6
         with:
           submodules: true
 
@@ -182,7 +182,7 @@ jobs:
           python -m pip install -r requirements.txt
 
       - name: Cache SUNDIALS build
-        uses: actions/cache@v4
+        uses: actions/cache@v5
         with:
           path: /home/runner/local
           key: bout-sundials-${{ matrix.config.os }}${{ matrix.config.build_petsc }}
@@ -205,7 +205,7 @@ jobs:
     timeout-minutes: 120
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v5
+      - uses: actions/checkout@v6
         with:
           submodules: true
       - name: Build Fedora
@@ -219,7 +219,7 @@ jobs:
     container: ghcr.io/ggeorgakoudis/boutdev-cuda:latest
 
     steps:
-      - uses: actions/checkout@v5
+      - uses: actions/checkout@v6
         with:
           submodules: true
       - name: Build minimal CUDA 12.2 @ GCC9.4.0 @ Ubuntu 20.04

CMakeLists.txt

@@ -741,7 +741,7 @@ endif()
 
 option(BOUT_BUILD_DOCS "Build the documentation" OFF)
 if (BOUT_BUILD_DOCS)
-  add_subdirectory(manual EXCLUDE_FROM_ALL)
+  add_subdirectory(manual)
 endif()
 
 

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")