try removing fix_

.github/linters/.ruff.toml

@@ -1,5 +1,6 @@
 cache-dir = "/tmp/.ruff_cache"
 line-length = 88
+output-format = "grouped"
 
 [lint]
 # Allow unused variables when underscore-prefixed.

.github/workflows/lint.yml

@@ -42,8 +42,6 @@ jobs:
           # Once the codebase is perfectly linted/formatted, switch to validating only changed files
           # VALIDATE_ALL_CODEBASE: false  # lint and format new or changed files only
           FILTER_REGEX_EXCLUDE: (.*[.]conf.py|pull_request_template.md)
-          FIX_PYTHON_RUFF_FORMAT: true
-          FIX_PYTHON_RUFF: true
           IGNORE_GITIGNORED_FILES: true
           VALIDATE_BASH: true
           VALIDATE_CHECKOV: true

fcm_bdiff/fcm_bdiff.py

@@ -39,7 +39,7 @@ class FCMBase:
     Note that the version for Git has a small handful of methods, mostly
     internal and some propeties. These are kept as close as possible to
     version in git_bdiff.py.
-    
+
     Attributes used to navigate the horros of FCM and thus used in this
     package are therefore preceded with an '_' and shouldn't be what is
     being referred to outwith this class. Nor should the original
@@ -60,7 +60,7 @@ def __init__(self, parent=None, repo=None):
         kind of 'discovery' that was necessary for FCM that is hoped to
         become outdated with Git.
         """
-        
+
         # use_mirror checks for SOURCE_UM_MIRROR env var, and if set
         # redirects the branch to that value and sets retries.
         # Otherwise it returns the branch unchanged and retries=0
@@ -88,7 +88,7 @@ def get_branch_name(self):
         For now, define it to be the contants of the URL after .*/main/ has been
         stripped off. i.e. it will start with trunk/... or branches/...
         """
-        
+
         pattern = rf"{self.get_repository_root()}/main/(.*)$"
         match = re.match(pattern, self._branch_url)
         if match:
@@ -101,7 +101,7 @@ def run_fcm_command(self, command, max_retries, snooze):
         """
         Run an fcm command, optionally retrying on failure.
         """
-        
+
         retries = 0
         while True:
             result = subprocess.run(
@@ -156,7 +156,7 @@ def get_branch_parent(self):
         Given the raw output from an fcm binfo command - which can be retrieved by
         calling get_branch_info() - returns the Branch Parent Field
         """
-        
+
         parent = re.search(
             r"^Branch Parent:\s*(?P<parent>.*)$",
             self._branch_info,
@@ -182,7 +182,7 @@ def get_url(self):
         Given the raw output from an fcm binfo command - which can be retrieved
         by calling get_branch_info() - returns the URL field
         """
-        
+
         url = re.search(r"^URL:\s*(?P<url>.*)$", self._branch_info, flags=re.MULTILINE)
         if url:
             url = url.group("url")
@@ -195,7 +195,7 @@ def is_trunk_test(self, url):
         Given an FCM url, returns True if it appears to be pointing to the
         UM main trunk
         """
-        
+
         search = re.search(
             r"""
                         (svn://fcm\d+/\w+_svn/\w+/trunk|
@@ -212,7 +212,7 @@ def get_repository_root(self):
         Given the raw output from an fcm binfo command - which can be retrieved by
         calling get_branch_info() - returns the Repository Root field
         """
-        
+
         repos_root = re.search(
             r"^Repository Root:\s*(?P<url>.*)\s*$",
             self._branch_info,
@@ -229,7 +229,7 @@ def get_latest_commit(self):
         Given the raw output from an fcm binfo command - which can be retrieved by
         calling get_branch_info() - returns the Last Changed Rev
         """
-        
+
         repos_rev = re.search(
             r"^Last Changed Rev:\s*(?P<rev>.*)\s*$",
             self._branch_info,
@@ -263,7 +263,7 @@ def has_diverged(self):
         Bit vague here, so we're going to check to see if 'parent' had
         an '@' in it denoting it's a branch of <something>
         """
-        
+
         match = re.match(r".*@(\d+)$", self.parent)
         if match:
             return True
@@ -272,7 +272,7 @@ def has_diverged(self):
 
     def files(self):
         """Iterate over files changed on the branch."""
-        
+
         dem_danged_files = self._get_files()
         for line in dem_danged_files:
             if line != "":
@@ -335,7 +335,7 @@ def get_bdiff_summarize(self, snooze=300, retries=0):
         (if the branch is the mirror, allow for a few retries in case
         it hasn't picked up the latest commit yet)
         """
-        
+
         command = ["fcm", "bdiff", "--summarize", self._branch]
         return self.run_fcm_command(command, retries, snooze)
 
@@ -352,5 +352,5 @@ def __init__(self, branch_info: str):
 
     def is_main(self) -> bool:
         """Return True if the branch is the main trunk."""
-        
+
         return self.is_trunk_test(self._branch_url)

gh_review_project/cr_deadline.py

@@ -37,8 +37,7 @@ def parse_args():
     testfile_path = Path(__file__).parent / "test"
 
     parser = argparse.ArgumentParser(
-        "Changes to the Simulation System projects required at the code"
-        "review deadline."
+        "Changes to the Simulation System projects required at the codereview deadline."
     )
 
     parser.add_argument("--milestone", help="Milestone being released")
@@ -79,7 +78,6 @@ def parse_args():
 def main(
     milestone: str, test: bool, capture_project: bool, file: Path, dry: bool
 ) -> None:
-
     # Get milestone data
     if test:
         issue_data = ProjectData.from_file(ISSUE_ID, file / "issue.json")

gh_review_project/finish_milestone.py

@@ -13,6 +13,7 @@
         * Remaining open PRs and issues against this milestone
         * Closed PRs against this milestone
 """
+
 from pathlib import Path
 import argparse
 from review_project import ProjectData, REVIEW_ID, ISSUE_ID
@@ -186,7 +187,6 @@ def parse_args():
 def main(
     milestone: str, test: bool, capture_project: bool, file: Path, dry: bool
 ) -> None:
-
     # Get milestone data
     if test:
         review_data = ProjectData.from_file(REVIEW_ID, file / "pr.json")

gh_review_project/review_project.py

@@ -8,6 +8,7 @@
 Classes and functions for interacting with the Simulation Systems Review Tracker
 Project.
 """
+
 from __future__ import annotations
 
 import json
@@ -248,7 +249,6 @@ def get_milestone(self, milestone: str, status: str = "all") -> dict:
                 or (status == "open" and item.status in item.open_states)
                 or (status == "closed" and item.status not in item.open_states)
             ):
-
                 milestone_data[item.repo].append(item)
         return milestone_data
 
@@ -357,7 +357,7 @@ def modify_milestone(self, milestone: str, dry_run: bool = False) -> None:
         if milestone:
             command += f" --milestone='{milestone}'"
         else:
-            command += f" --remove-milestone"
+            command += " --remove-milestone"
 
         message = f"Changing milestone for #{self.number} in {self.repo}"
 

gh_review_project/workload.py

@@ -202,7 +202,6 @@ def parse_args():
 
 
 def main(total: bool, test: bool, capture_project: bool, file: Path):
-
     # Extract data from github about the reviews and team members.
     if test:
         data = ProjectData.from_file(REVIEW_ID, file)

kgo_updates/kgo_update/kgo_update.py

@@ -31,6 +31,7 @@
 
 
 """
+
 import argparse
 import os
 import re
@@ -208,7 +209,6 @@ def group_comparisons_by_dir(comparisons, skip=False):
     """
     kgo_dirs = defaultdict(dict)
     for _, kgo_file, suite_file, status, _ in comparisons:
-
         # If the kgo_file isn't set, move on (in some cases the test is not
         # comparing two files at all
         if kgo_file is None:
@@ -237,17 +237,13 @@ def group_comparisons_by_dir(comparisons, skip=False):
         # If the above goes wrong it will eventually hit root; if this happens
         # we cannot continue as something is seriously not right
         if basedir == "/":
-            msg = (
-                "Problem locating KGO directory - "
-                "is this actually a KGO file?\n  {0}"
-            )
+            msg = "Problem locating KGO directory - is this actually a KGO file?\n  {0}"
             sys.exit(msg.format(kgo_file))
 
         # Otherwise add the result to the list - for each entry we store the
         # relative path to the KGO file and the full path to the file in the
         # suite which should be used to update it (if it needs updating)
         if status.strip() in UPDATE_CRITERIA:
-
             # Here we could check if this update has already been lodged,
             # and if it has perhaps we can do some additional checking
             # (for instance, are the changes in answers the same?)
@@ -501,7 +497,7 @@ def _split_lines(self, text, width):
         "-E",
         "--extension",
         default=".cylc",
-        help="The extension of the variables file, either .rc " "or .cylc",
+        help="The extension of the variables file, either .rc or .cylc",
     )
 
     args = parser.parse_args()
@@ -607,8 +603,7 @@ def _split_lines(self, text, width):
     # Open the file for viewing in user's editor
     if interactive:
         print(
-            f"\n\nOpening {script_path}\nHit Return to Step through, "
-            "q to print all\n\n"
+            f"\n\nOpening {script_path}\nHit Return to Step through, q to print all\n\n"
         )
         with open(script_path, "r") as f:
             line_count = 0

lfric_macros/files/template_versions.py

@@ -1,6 +1,7 @@
 import sys
 
-from metomi.rose.upgrade import MacroUpgrade
+
+from metomi.rose.upgrade import MacroUpgrade  # noqa: F401
 
 
 class UpgradeError(Exception):

lfric_macros/tests/test_lfric_apps_dir/test_read_python_imports.py

@@ -1,4 +1,4 @@
-import os
-from shlex import split
-from pathlib import Path, PurePath
-import networkx as nx
+import os  # noqa: F401
+from shlex import split  # noqa: F401
+from pathlib import Path, PurePath  # noqa: F401
+import networkx as nx  # noqa: F401

lfric_styling/styling_keywords.py

@@ -9,6 +9,7 @@
 """
 Newer keywords used during physics forking.
 """
+
 NEW_KEYWORDS = [
     "abort",
     "abs",

script_copyright_checker/bin/copyright_checker.py

@@ -8,6 +8,7 @@
 Script which tests code files within the UM repository to ensure they contain a
 recognised copyright notice.
 """
+
 import argparse
 import os
 import re
@@ -208,9 +209,7 @@ def parse_options():
         "--full_trunk",
         action="store_true",
         default=False,
-        help=(
-            "run on use the full file list when trunk, " "else run on fcm branch-diff"
-        ),
+        help=("run on use the full file list when trunk, else run on fcm branch-diff"),
     )
     excl_group.add_argument(
         "files",