Linter CI part 1

.github/CODEOWNERS

@@ -0,0 +1,4 @@
+# Default owners of the repository
+* @metoffice/ssdteam
+
+# Add component owners as appropriate

.github/linters/.isort.cfg

@@ -0,0 +1,3 @@
+[settings]
+profile=black
+src_paths=.

.github/linters/.perlcriticrc

@@ -0,0 +1,5 @@
+# Report slightly less severe violations (severity >= 4)
+severity = 4
+# Verbosity format
+# filename:line:column [severity policy] message near 'string of source code that caused the violation'
+verbose  = %f:%l:%c [%s %p] %m near '%r'\n

.github/linters/.python-lint

@@ -0,0 +1,20 @@
+[MASTER]
+# Use multiple processes to speed up Pylint.
+jobs=2
+
+[MESSAGES CONTROL]
+# C0114: Missing module docstring (missing-module-docstring)
+# C0116: Missing function or method docstring (missing-function-docstring)
+# C0103: Constant name doesn't conform to UPPER_CASE naming style (invalid-name)
+# C0209: Formatting a regular string which could be an f-string (consider-using-f-string)
+# E0401: Unable to import module (import-error)
+# W0611: Unused import sphinx_rtd_theme (unused-import)
+# W0622: Redefining built-in 'copyright' (redefined-builtin)
+# R0801: Similar lines in 2 files
+disable=C0114,C0116,C0103,C0209,E0401,W0611,W0622,R0801,
+
+[SIMILARITIES]
+# Minimum lines number of a similarity.
+min-similarity-lines=4
+ignore-comments=yes
+ignore-docstrings=yes

.github/linters/.ruff.toml

@@ -0,0 +1,13 @@
+cache-dir = "/tmp/.ruff_cache"
+line-length = 80
+
+
+# Allow unused variables when underscore-prefixed.
+dummy-variable-rgx = "^(_+|(_+[a-zA-Z0-9_]*[a-zA-Z0-9]+?))$"
+
+[format]
+# Like Black, indent with spaces, rather than tabs.
+indent-style = "space"
+
+# Like Black, respect magic trailing commas.
+skip-magic-trailing-comma = false

.github/linters/.shellcheckrc

@@ -0,0 +1 @@
+source-path=SCRIPTDIR

.github/pull_request_template.md

@@ -0,0 +1,32 @@
+# Description
+
+## Summary
+
+_Briefly describe the feature being introduced._
+
+## Changes
+
+_List the major changes made in this pull request._
+
+## Dependency
+
+_List dependent changes. Can use build-group logic here._
+
+## Impact
+
+_Discuss any potential impacts this feature may have on existing functionalities._
+
+## Issues addressed
+
+Resolves
+
+_List issue(s) related to this PR._
+
+## Coordinated merge
+
+_Specify any coordinated merges here._
+
+
+## Checklist
+
+- [ ] I have performed a self-review of my own changes

.github/workflows/lint.yml

@@ -0,0 +1,58 @@
+---
+# Lint/analyse code with Super-Linter.
+name: Checks
+
+on:
+  pull_request:
+    branches: [main]
+  push:
+    branches: [main, 'releases/**']
+  workflow_dispatch:
+
+concurrency:
+  group: ${{ github.ref }}
+  cancel-in-progress:  ${{ github.ref != 'refs/heads/main' }}
+
+permissions: read-all
+
+jobs:
+  check:
+    name: Lint
+    runs-on: ubuntu-latest
+    strategy:
+      max-parallel: 4
+      fail-fast: false
+      matrix:
+        python-version: ["3.9", "3.10", "3.11", "3.12"]
+
+    permissions:
+        contents: read
+        packages: read
+        statuses: write
+
+    steps:
+      - name: Checkout current
+        uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+
+      - name: Super-Linter
+        uses: super-linter/super-linter/slim@v7.2.1
+        env:
+          FILTER_REGEX_EXCLUDE: (.*[.]conf.py|pull_request_template.md|/linters/)
+          IGNORE_GITIGNORED_FILES: true
+          VALIDATE_BASH_EXEC: false
+          VALIDATE_JAVASCRIPT_STANDARD: false
+          VALIDATE_JSCPD: false
+          VALIDATE_MARKDOWN_PRETTIER: false
+          VALIDATE_PYTHON_FLAKE8: false
+          VALIDATE_PYTHON_MYPY: false
+          VALIDATE_PYTHON_PYINK: false
+          VALIDATE_PYTHON_PYLINT: false
+          VALIDATE_PYTHON_RUFF: false
+          VALIDATE_SHELL_SHFMT: false
+          VALIDATE_YAML_PRETTIER: false
+          VALIDATE_YAML: false
+          # To report GitHub Actions status checks
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+...

.gitignore

@@ -1,2 +1,6 @@
+*.sublime-workspace
+*.code-workspace
+.vscode
 __pycache__/
-
+*.pyc
+*~

README.md

@@ -1,7 +1,11 @@
-# SimSys Scripts
+# Simulation Systems Scripts
 
-This repository contains support scripts that are common across the many simulation and modelling codes owned by the Met Office.
-Particularily those owned and maintained by the SSD team.
+[![Checks](https://github.com/MetOffice/SimSys_Scripts/actions/workflows/lint.yml/badge.svg)](https://github.com/MetOffice/SimSys_Scripts/actions/workflows/lint.yml)
+[![CodeQL](https://github.com/MetOffice/SimSys_Scripts/actions/workflows/github-code-scanning/codeql/badge.svg)](https://github.com/MetOffice/SimSys_Scripts/actions/workflows/github-code-scanning/codeql)
 
-Also contains a copy of script_updater.sh which is intended to live in the fcm repositories to pull from
-this repo.
+This repository contains support scripts that are common across the many
+simulation and modelling codes owned by the Met Office. Particularly those
+owned and maintained by the Simulation Systems and Deployment (SSD) team.
+
+Also contains a copy of `script_updater.sh` which is intended to live in the
+fcm repositories to pull from this repository.

fcm_bdiff.py

@@ -9,8 +9,9 @@
 run tests on based on the branch-difference (to allow checking of only files
 which a developer has actually modified on their branch)
 """
-import re
+
 import os
+import re
 import subprocess
 import time
 
@@ -20,10 +21,11 @@ class FCMError(Exception):
     """
     Exception class for FCM commands
     """
+
     def __str__(self):
-        return ("\nFCM command: \"{0:s}\""
-                "\nFailed with error: \"{1:s}\""
-                .format(" ".join(self.args[0]), self.args[1].strip()))
+        return '\nFCM command: "{0:s}"\nFailed with error: "{1:s}"'.format(
+            " ".join(self.args[0]), self.args[1].strip()
+        )
 
 
 # ------------------------------------------------------------------------------
@@ -32,16 +34,20 @@ def is_trunk(url):
     Given an FCM url, returns True if it appears to be pointing to the
     UM main trunk
     """
-    search = re.search(r"""
+    search = re.search(
+        r"""
                        (svn://fcm\d+/\w+_svn/\w+/trunk|
                        .*/svn/[\w\.]+/\w+/trunk|
                        ..*_svn/\w+/trunk)
-                       """, url, flags=re.VERBOSE)
+                       """,
+        url,
+        flags=re.VERBOSE,
+    )
     return search is not None
 
 
 # ------------------------------------------------------------------------------
-def text_decoder(bytes_type_string, codecs=['utf8', 'cp1252']):
+def text_decoder(bytes_type_string, codecs=["utf8", "cp1252"]):
     """
     Given a bytes type string variable, attempt to decode it using the codecs
     listed.
@@ -127,18 +133,20 @@ def get_branch_diff_filenames(branch=".", path_override=None):
     # Strip whitespace, and remove blank lines while turning the output into
     # a list of strings.
     bdiff_files = [x.strip() for x in bdiff.split("\n") if x.strip()]
-    bdiff_files = [bfile.split()[1] for bfile in bdiff_files
-                   if bfile.split()[0].strip() == "M" or
-                   bfile.split()[0].strip() == "A"]
+    bdiff_files = [
+        bfile.split()[1]
+        for bfile in bdiff_files
+        if bfile.split()[0].strip() == "M" or bfile.split()[0].strip() == "A"
+    ]
 
     # Convert the file paths to be relative to the current URL; to do this
     # construct the base path of the trunk URL and compare it to the results
     # of the bdiff command above
     repos_root = get_repository_root(info)
-    relative_paths = [os.path.relpath(bfile,
-                                      os.path.join(repos_root,
-                                                   "main", "trunk"))
-                      for bfile in bdiff_files]
+    relative_paths = [
+        os.path.relpath(bfile, os.path.join(repos_root, "main", "trunk"))
+        for bfile in bdiff_files
+    ]
 
     # These relative paths can be joined to an appropriate base to complete
     # the filenames to return
@@ -169,9 +177,9 @@ def run_fcm_command(command, max_retries, snooze):
     """
     retries = 0
     while True:
-        output = subprocess.Popen(command,
-                                  stdout=subprocess.PIPE,
-                                  stderr=subprocess.PIPE)
+        output = subprocess.Popen(
+            command, stdout=subprocess.PIPE, stderr=subprocess.PIPE
+        )
         _ = output.wait()
         if output.returncode == 0:
             return text_decoder(output.stdout.read())
@@ -198,8 +206,7 @@ def use_mirror(branch):
     if mirror_key in os.environ:
         branch = os.environ[mirror_key]
         retries = 2
-        print("[INFO] Switching branch used for fcm command to : {0:}".format(
-            branch))
+        print(f"[INFO] Switching branch used for fcm command to: {branch}")
     else:
         retries = 0
     return branch, retries
@@ -211,8 +218,9 @@ def get_repository_root(branch_info):
     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*$",
-                           branch_info, flags=re.MULTILINE)
+    repos_root = re.search(
+        r"^Repository Root:\s*(?P<url>.*)\s*$", branch_info, flags=re.MULTILINE
+    )
     if repos_root:
         repos_root = repos_root.group("url")
     else:
@@ -226,8 +234,9 @@ def get_branch_parent(branch_info):
     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>.*)$", branch_info,
-                       flags=re.MULTILINE)
+    parent = re.search(
+        r"^Branch Parent:\s*(?P<parent>.*)$", branch_info, flags=re.MULTILINE
+    )
     if parent:
         parent = parent.group("parent")
     else: