Merge pull request #237 from altheaden/lint-with-ruff

Switch to `ruff` for linting with `pre-commit`

Author: xylar

.flake8

@@ -9,12 +9,6 @@ repos:
       - id: trailing-whitespace
       - id: end-of-file-fixer
 
-  # Can run individually with `pre-commit run isort --all-files`
-  - repo: https://github.com/PyCQA/isort
-    rev: 6.0.0
-    hooks:
-      - id: isort
-
   # Can run individually with `flynt [file]` or `flynt [source]`
   - repo: https://github.com/ikamensh/flynt
     rev: '1.0.1'
@@ -23,16 +17,6 @@ repos:
         args: ["--fail-on-change", "--verbose"]
         require_serial: true
 
-  # Can run individually with `pre-commit run flake8 --all-files`
-  # Need to use flake8 GitHub mirror due to CentOS git issue with GitLab
-  # https://github.com/pre-commit/pre-commit/issues/1206
-  - repo: https://github.com/pycqa/flake8
-    rev: 7.1.2
-    hooks:
-      - id: flake8
-        args: ["--config=.flake8"]
-        additional_dependencies: [flake8-isort]
-
   # Can run individually with `pre-commit run mypy --all-files`
   - repo: https://github.com/pre-commit/mirrors-mypy
     rev: v1.15.0
@@ -42,7 +26,15 @@ repos:
         verbose: true
         additional_dependencies: ['types-requests', 'types-PyYAML']
 
-# https://pre-commit.ci/#configuration
-ci:
-  autofix_prs: false
-  autoupdate_schedule: weekly
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.9.7
+    hooks:
+      # Sort the imports
+      - id: ruff
+        name: ruff-sort-imports
+        args: [--select, I, --fix]
+      # Run the linter.
+      - id: ruff
+        args: [--fix]
+      # Run the formatter.
+      - id: ruff-format

.pre-commit-config.yaml

@@ -62,11 +62,11 @@ process until your commit is successful. Some changes need to be made manually,
 such as inconsistent variable types. When this happens, you must update the
 file to `pre-commit`'s standards, and then attempt to re-commit the file.
 
-Internally, `pre-commit`  uses [flake8](https://flake8.pycqa.org/en/latest/) to
-check PEP8 compliance, [isort](https://pycqa.github.io/isort/) to sort, check
-and format imports, [flynt](https://github.com/ikamensh/flynt) to change any
-format strings to f-strings, and [mypy](https://mypy-lang.org/) to check for
-consistent variable types. An example error might be:
+Internally, `pre-commit`  uses [ruff](https://docs.astral.sh/ruff/) to check 
+PEP8 compliance, as well as sort, check and format imports, 
+[flynt](https://github.com/ikamensh/flynt) to change any format strings to 
+f-strings, and [mypy](https://mypy-lang.org/) to check for consistent variable 
+types. An example error might be:
 
 ```bash
 example.py:77:1: E302 expected 2 blank lines, found 1

docs/developers_guide/quick_start.md

@@ -1,3 +1,4 @@
-from mache.discover import discover_machine
-from mache.machine_info import MachineInfo
-from mache.version import __version__, __version_info__
+from mache.discover import discover_machine as discover_machine
+from mache.machine_info import MachineInfo as MachineInfo
+from mache.version import __version__ as __version__
+from mache.version import __version_info__ as __version_info__

mache/__init__.py

@@ -11,20 +11,24 @@ def main():
     """
 
     parser = argparse.ArgumentParser(
-        description="Perform mache commands",
-        usage='''
+        description='Perform mache commands',
+        usage="""
 mache <command> [<args>]
 The available mache commands are:
     sync    Sync files between supported machines
  To get help on an individual command, run:
     mache <command> --help
-    ''')
+    """,
+    )
 
     parser.add_argument('command', help='command to run')
-    parser.add_argument('-v', '--version',
-                        action='version',
-                        version=f'mache {mache.version.__version__}',
-                        help="Show version number and exit")
+    parser.add_argument(
+        '-v',
+        '--version',
+        action='version',
+        version=f'mache {mache.version.__version__}',
+        help='Show version number and exit',
+    )
     if len(sys.argv) == 1:
         parser.print_help()
         sys.exit(0)

mache/__main__.py

@@ -59,14 +59,16 @@ def discover_machine(quiet=False):
                 'either delete or \n'
                 'edit that file so it no longer defines $NERSC_HOST, log out, '
                 'log back in, \n'
-                'and try again.')
+                'and try again.'
+            )
 
     # As a last resort (e.g. on a compute node), try getting the machine from
     # a file created on install
     if machine is None and 'CONDA_PREFIX' in os.environ:
         prefix = os.environ['CONDA_PREFIX']
         machine_filename = os.path.join(
-            prefix, 'share', 'mache', 'machine.txt')
+            prefix, 'share', 'mache', 'machine.txt'
+        )
         if os.path.exists(machine_filename):
             with open(machine_filename) as fp:
                 machine = fp.read().replace('\n', '').strip()

mache/discover.py

@@ -114,69 +114,57 @@ def __str__(self):
             The contents as a string for printing to the terminal
         """
 
-        info = \
-            f'Machine: {self.machine}\n' \
+        info = (
+            f'Machine: {self.machine}\n'
             f'  E3SM Supported Machine: {self.e3sm_supported}'
-
-        if self.e3sm_supported and self.compilers is not None and \
-                self.mpilibs is not None and self.os is not None:
-            info = \
-                f'{info}\n' \
-                f'  Compilers: {", ".join(self.compilers)}\n' \
-                f'  MPI libraries: {", ".join(self.mpilibs)}\n' \
+        )
+
+        if (
+            self.e3sm_supported
+            and self.compilers is not None
+            and self.mpilibs is not None
+            and self.os is not None
+        ):
+            info = (
+                f'{info}\n'
+                f'  Compilers: {", ".join(self.compilers)}\n'
+                f'  MPI libraries: {", ".join(self.mpilibs)}\n'
                 f'  OS: {self.os}'
+            )
 
         info = f'{info}\n'
 
-        print_unified = (self.e3sm_unified_activation is not None or
-                         self.e3sm_unified_base is not None or
-                         self.e3sm_unified_mpi is not None)
+        print_unified = (
+            self.e3sm_unified_activation is not None
+            or self.e3sm_unified_base is not None
+            or self.e3sm_unified_mpi is not None
+        )
         if print_unified:
-            info = \
-                f'{info}\n' \
-                f'E3SM-Unified: '
+            info = f'{info}\nE3SM-Unified: '
 
             if self.e3sm_unified_activation is None:
-                info = \
-                    f'{info}\n' \
-                    f'  E3SM-Unified is not currently loaded'
+                info = f'{info}\n  E3SM-Unified is not currently loaded'
             else:
-                info = \
-                    f'{info}\n' \
-                    f'  Activation: {self.e3sm_unified_activation}'
+                info = f'{info}\n  Activation: {self.e3sm_unified_activation}'
             if self.e3sm_unified_base is not None:
-                info = \
-                    f'{info}\n' \
-                    f'  Base path: {self.e3sm_unified_base}'
+                info = f'{info}\n  Base path: {self.e3sm_unified_base}'
             if self.e3sm_unified_mpi is not None:
-                info = \
-                    f'{info}\n' \
-                    f'  MPI type: {self.e3sm_unified_mpi}'
+                info = f'{info}\n  MPI type: {self.e3sm_unified_mpi}'
             info = f'{info}\n'
 
         print_diags = self.diagnostics_base is not None
         if print_diags:
-            info = \
-                f'{info}\n' \
-                f'Diagnostics: '
+            info = f'{info}\nDiagnostics: '
 
             if self.diagnostics_base is not None:
-                info = \
-                    f'{info}\n' \
-                    f'  Base path: {self.diagnostics_base}'
+                info = f'{info}\n  Base path: {self.diagnostics_base}'
             info = f'{info}\n'
 
-        info = \
-            f'{info}\n' \
-            f'Config options: '
+        info = f'{info}\nConfig options: '
         for section in self.config.sections():
-            info = \
-                f'{info}\n' \
-                f'  [{section}]'
+            info = f'{info}\n  [{section}]'
             for key, value in self.config.items(section):
-                info = \
-                    f'{info}\n' \
-                    f'    {key} = {value}'
+                info = f'{info}\n    {key} = {value}'
             info = f'{info}\n'
         return info
 
@@ -232,30 +220,35 @@ def get_account_defaults(self):
         return account, partition, constraint, qos
 
     def _get_config(self):
-        """ get a parser for config options """
+        """get a parser for config options"""
 
         config = configparser.ConfigParser(
-            interpolation=configparser.ExtendedInterpolation())
+            interpolation=configparser.ExtendedInterpolation()
+        )
 
         machine = self.machine
         try:
-            cfg_path = \
+            cfg_path = (
                 importlib_resources.files('mache.machines') / f'{machine}.cfg'
+            )
             config.read(str(cfg_path))
         except FileNotFoundError:
             # this isn't a known machine so use the default
-            cfg_path = \
+            cfg_path = (
                 importlib_resources.files('mache.machines') / 'default.cfg'
+            )
             config.read(str(cfg_path))
 
         return config
 
     def _parse_compilers_and_mpi(self):
-        """ Parse the compilers and mpi modules from XML config files """
+        """Parse the compilers and mpi modules from XML config files"""
         machine = self.machine
 
-        xml_path = (importlib_resources.files('mache.cime_machine_config') /
-                    'config_machines.xml')
+        xml_path = (
+            importlib_resources.files('mache.cime_machine_config')
+            / 'config_machines.xml'
+        )
 
         root = etree.parse(str(xml_path))
 
@@ -299,11 +292,12 @@ def _parse_compilers_and_mpi(self):
         self.os = machine_os
 
     def _detect_e3sm_unified(self):
-        """ Read E3SM-Unified base path and detect whether it is running """
+        """Read E3SM-Unified base path and detect whether it is running"""
         config = self.config
 
-        if config is not None and \
-                config.has_option('e3sm_unified', 'base_path'):
+        if config is not None and config.has_option(
+            'e3sm_unified', 'base_path'
+        ):
             self.e3sm_unified_base = config.get('e3sm_unified', 'base_path')
 
         if 'E3SMU_SCRIPT' in os.environ:
@@ -313,10 +307,11 @@ def _detect_e3sm_unified(self):
             self.e3sm_unified_mpi = os.environ['E3SMU_MPI'].lower()
 
     def _get_diagnostics_info(self):
-        """ Get config options related to diagnostics data """
+        """Get config options related to diagnostics data"""
 
         config = self.config
 
-        if config is not None and \
-                config.has_option('diagnostics', 'base_path'):
+        if config is not None and config.has_option(
+            'diagnostics', 'base_path'
+        ):
             self.diagnostics_base = config.get('diagnostics', 'base_path')