Update code to pass pre-commit lint/format checks

pyproject.toml

@@ -75,6 +75,8 @@ exclude = [
     "site-packages",
     "venv",
 ]
+
+[tool.ruff.lint]
 # E402: module level import not at top of file
 # E501: line too long - let black worry about that
 ignore = [
@@ -93,8 +95,8 @@ select = [
     "UP",
 ]
 
-[tool.ruff.mccabe]
+[tool.ruff.lint.mccabe]
 max-complexity = 18
 
-[tool.ruff.isort]
+[tool.ruff.lint.isort]
 known-first-party = ["model_config_tests"]

src/model_config_tests/__main__.py

@@ -9,6 +9,7 @@
 
 def main():
     import pytest
+
     errcode = pytest.main([HERE] + sys.argv[1:])
     sys.exit(errcode)
 

src/model_config_tests/conftest.py

@@ -2,9 +2,9 @@
 # SPDX-License-Identifier: Apache-2.0
 
 import os
-import pytest
 from pathlib import Path
 
+import pytest
 import yaml
 from ruamel.yaml import YAML
 
@@ -14,19 +14,19 @@ def output_path(request):
     """Set the output path: This contains control and lab directories for each
     test and test output files - e.g. CHECKSUMS
     """
-    path = request.config.getoption('--output-path')
+    path = request.config.getoption("--output-path")
     if path is None:
         # Set default to /scratch/PROJECT/USER/test-model-repro/
-        project = os.environ.get('PROJECT')
-        user = os.environ.get('USER')
-        path = f'/scratch/{project}/{user}/test-model-repro'
+        project = os.environ.get("PROJECT")
+        user = os.environ.get("USER")
+        path = f"/scratch/{project}/{user}/test-model-repro"
     return Path(path)
 
 
 @pytest.fixture(scope="session")
 def control_path(request):
     """Set the path of the model configuration directory to test"""
-    path = request.config.getoption('--control-path')
+    path = request.config.getoption("--control-path")
     if path is None:
         # Set default to current working directory
         path = Path.cwd()
@@ -36,17 +36,17 @@ def control_path(request):
 @pytest.fixture(scope="session")
 def checksum_path(request, control_path):
     """Set the path of the model configuration directory to test"""
-    path = request.config.getoption('--checksum-path')
+    path = request.config.getoption("--checksum-path")
     if path is None:
         # Set default to checksum stored on model configuration
-        path = control_path / 'testing' / 'checksum' / 'historical-3hr-checksum.json'
+        path = control_path / "testing" / "checksum" / "historical-3hr-checksum.json"
     return Path(path)
 
 
 @pytest.fixture(scope="session")
 def metadata(control_path: Path):
     """Read the metadata file in the control directory"""
-    metadata_path = control_path / 'metadata.yaml'
+    metadata_path = control_path / "metadata.yaml"
     # Use ruamel.yaml as that is what is used to read metadata files in Payu
     # It also errors out if there are duplicate keys in metadata
     content = YAML().load(metadata_path)
@@ -56,7 +56,7 @@ def metadata(control_path: Path):
 @pytest.fixture(scope="session")
 def config(control_path: Path):
     """Read the config file in the control directory"""
-    config_path = control_path / 'config.yaml'
+    config_path = control_path / "config.yaml"
     with open(config_path) as f:
         config_content = yaml.safe_load(f)
     return config_content
@@ -67,27 +67,33 @@ def target_branch(request):
     """Set the target branch - i.e., the branch the configuration will be
     merged into. This used is to infer configuration information, if the
     configuration branches follow a common naming scheme (e.g. ACCESS-OM2)"""
-    return request.config.getoption('--target-branch')
+    return request.config.getoption("--target-branch")
 
 
 # Set up command line options and default for directory paths
 def pytest_addoption(parser):
     """Attaches optional command line arguments"""
-    parser.addoption("--output-path",
-                     action="store",
-                     help="Specify the output directory path for test output")
-
-    parser.addoption("--control-path",
-                     action="store",
-                     help="Specify the model configuration path to test")
-
-    parser.addoption("--checksum-path",
-                     action="store",
-                     help="Specify the checksum file to compare against")
-
-    parser.addoption("--target-branch",
-                     action="store",
-                     help="Specify the target branch name")
+    parser.addoption(
+        "--output-path",
+        action="store",
+        help="Specify the output directory path for test output",
+    )
+
+    parser.addoption(
+        "--control-path",
+        action="store",
+        help="Specify the model configuration path to test",
+    )
+
+    parser.addoption(
+        "--checksum-path",
+        action="store",
+        help="Specify the checksum file to compare against",
+    )
+
+    parser.addoption(
+        "--target-branch", action="store", help="Specify the target branch name"
+    )
 
 
 def pytest_configure(config):

src/model_config_tests/exp_test_helper.py

@@ -1,31 +1,32 @@
 # Copyright 2024 ACCESS-NRI and contributors. See the top-level COPYRIGHT file for details.
 # SPDX-License-Identifier: Apache-2.0
 
-import subprocess as sp
-import shutil
-import re
+import glob
 import os
+import re
+import shutil
+import subprocess as sp
 import sys
-import glob
-import yaml
 from pathlib import Path
 
-from model_config_tests.util import wait_for_qsub
+import yaml
+
 from model_config_tests.models import index as model_index
+from model_config_tests.util import wait_for_qsub
 
 
-class ExpTestHelper(object):
+class ExpTestHelper:
 
     def __init__(self, control_path: Path, lab_path: Path):
 
         self.exp_name = control_path.name
         self.control_path = control_path
         self.lab_path = lab_path
-        self.config_path = control_path / 'config.yaml'
-        self.archive_path = lab_path / 'archive' / self.exp_name
-        self.work_path = lab_path / 'work' / self.exp_name
-        self.output000 = self.archive_path / 'output000'
-        self.output001 = self.archive_path / 'output001'
+        self.config_path = control_path / "config.yaml"
+        self.archive_path = lab_path / "archive" / self.exp_name
+        self.work_path = lab_path / "work" / self.exp_name
+        self.output000 = self.archive_path / "output000"
+        self.output001 = self.archive_path / "output001"
 
         with open(self.config_path) as f:
             self.config = yaml.safe_load(f)
@@ -35,13 +36,13 @@ def __init__(self, control_path: Path, lab_path: Path):
     def set_model(self):
         """Set model based on payu config. Currently only setting top-level
         model"""
-        self.model_name = self.config.get('model')
+        self.model_name = self.config.get("model")
         ModelType = model_index[self.model_name]
         self.model = ModelType(self)
 
-    def extract_checksums(self,
-                          output_directory: Path = None,
-                          schema_version: str = None):
+    def extract_checksums(
+        self, output_directory: Path = None, schema_version: str = None
+    ):
         """Use model subclass to extract checksums from output"""
         return self.model.extract_checksums(output_directory, schema_version)
 
@@ -61,17 +62,17 @@ def setup_for_test_run(self):
             doc = yaml.safe_load(f)
 
         # Disable git runlog
-        doc['runlog'] = False
+        doc["runlog"] = False
 
         # Disable metadata and set override experiment name for work/archive
         # directories
-        doc['metadata'] = {"enable": False}
-        doc['experiment'] = self.exp_name
+        doc["metadata"] = {"enable": False}
+        doc["experiment"] = self.exp_name
 
         # Set laboratory path
-        doc['laboratory'] = str(self.lab_path)
+        doc["laboratory"] = str(self.lab_path)
 
-        with open(self.config_path, 'w') as f:
+        with open(self.config_path, "w") as f:
             yaml.dump(doc, f)
 
     def run(self):
@@ -95,56 +96,56 @@ def force_qsub_run(self):
         owd = Path.cwd()
         try:
             os.chdir(self.control_path)
-            sp.check_output(['payu', 'sweep', '--lab', self.lab_path])
-            run_id = sp.check_output(['payu', 'run', '--lab', self.lab_path])
+            sp.check_output(["payu", "sweep", "--lab", self.lab_path])
+            run_id = sp.check_output(["payu", "run", "--lab", self.lab_path])
             run_id = run_id.decode().splitlines()[0]
-        except sp.CalledProcessError as err:
-            print('Error: call to payu run failed.', file=sys.stderr)
+        except sp.CalledProcessError:
+            print("Error: call to payu run failed.", file=sys.stderr)
             return 1, None, None, None
         finally:
             os.chdir(owd)
 
         wait_for_qsub(run_id)
-        run_id = run_id.split('.')[0]
+        run_id = run_id.split(".")[0]
 
         output_files = []
         # Read qsub stdout file
-        stdout_filename = glob.glob(str(self.control_path / f'*.o{run_id}'))
+        stdout_filename = glob.glob(str(self.control_path / f"*.o{run_id}"))
         print(stdout_filename)
         if len(stdout_filename) != 1:
-            print('Error: there are too many stdout files.', file=sys.stderr)
+            print("Error: there are too many stdout files.", file=sys.stderr)
             return 2, None, None, None
 
         stdout_filename = stdout_filename[0]
         output_files.append(stdout_filename)
-        stdout = ''
-        with open(stdout_filename, 'r') as f:
+        stdout = ""
+        with open(stdout_filename) as f:
             stdout = f.read()
 
         # Read qsub stderr file
-        stderr_filename = glob.glob(str(self.control_path / f'*.e{run_id}'))
-        stderr = ''
+        stderr_filename = glob.glob(str(self.control_path / f"*.e{run_id}"))
+        stderr = ""
         if len(stderr_filename) == 1:
             stderr_filename = stderr_filename[0]
             output_files.append(stderr_filename)
-            with open(stderr_filename, 'r') as f:
+            with open(stderr_filename) as f:
                 stderr = f.read()
 
         # TODO: Early return if not collating
 
         # Read the qsub id of the collate job from the stdout.
         # Payu puts this here.
-        m = re.search(r'(\d+.gadi-pbs)\n', stdout)
+        m = re.search(r"(\d+.gadi-pbs)\n", stdout)
         if m is None:
-            print('Error: qsub id of collate job.', file=sys.stderr)
+            print("Error: qsub id of collate job.", file=sys.stderr)
             return 3, stdout, stderr, output_files
 
         # Wait for the collate to complete.
         run_id = m.group(1)
         wait_for_qsub(run_id)
 
         # Return files created by qsub so caller can read or delete.
-        collate_files = self.control_path / f'*.[oe]{run_id}'
+        collate_files = self.control_path / f"*.[oe]{run_id}"
         output_files += glob.glob(str(collate_files))
 
         return 0, stdout, stderr, output_files
@@ -159,20 +160,19 @@ def setup_exp(control_path: Path, output_path: Path, exp_name: str):
     Create a exp by copying over base config
     """
     # Set experiment control path
-    if control_path.name != 'base-experiment':
-        exp_name = f'{control_path.name}-{exp_name}'
+    if control_path.name != "base-experiment":
+        exp_name = f"{control_path.name}-{exp_name}"
 
-    exp_control_path = output_path / 'control' / exp_name
+    exp_control_path = output_path / "control" / exp_name
 
     # Copy over base control directory (e.g. model configuration)
     if exp_control_path.exists():
         shutil.rmtree(exp_control_path)
     shutil.copytree(control_path, exp_control_path, symlinks=True)
 
-    exp_lab_path = output_path / 'lab'
+    exp_lab_path = output_path / "lab"
 
-    exp = ExpTestHelper(control_path=exp_control_path,
-                        lab_path=exp_lab_path)
+    exp = ExpTestHelper(control_path=exp_control_path, lab_path=exp_lab_path)
 
     # Remove any pre-existing archive or work directories for the experiment
     try:

src/model_config_tests/models/__init__.py

@@ -1,5 +1,3 @@
 from model_config_tests.models.accessom2 import AccessOm2
 
-index = {
-    'access-om2': AccessOm2
-}
+index = {"access-om2": AccessOm2}