From 9b49c13d4e6918b515a182eef705431281209ad3 Mon Sep 17 00:00:00 2001
From: Ben Schroeter <benjschroeter@gmail.com>
Date: Tue, 13 Feb 2024 14:03:28 +1100
Subject: [PATCH] Black reapplied. #103

---
 benchcab/benchcab.py            | 14 +++++++-------
 benchcab/comparison.py          |  9 +++------
 benchcab/config.py              |  5 +++++
 benchcab/environment_modules.py |  4 ++++
 benchcab/fluxsite.py            |  4 +++-
 benchcab/main.py                |  1 +
 benchcab/model.py               |  1 +
 benchcab/utils/__init__.py      |  6 ++++--
 benchcab/utils/fs.py            |  1 +
 benchcab/utils/repo.py          | 11 +++++++++++
 benchcab/utils/subprocess.py    |  1 +
 tests/test_benchcab.py          |  1 +
 tests/test_config.py            |  2 +-
 13 files changed, 43 insertions(+), 17 deletions(-)

diff --git a/benchcab/benchcab.py b/benchcab/benchcab.py
index dc9e401..76ce38f 100644
--- a/benchcab/benchcab.py
+++ b/benchcab/benchcab.py
@@ -26,7 +26,7 @@
 from benchcab.utils import get_logger
 from benchcab.utils.fs import mkdir, next_path
 from benchcab.utils.pbs import render_job_script
-from benchcab.utils.repo import SVNRepo, create_repo
+from benchcab.utils.repo import create_repo
 from benchcab.utils.subprocess import SubprocessWrapper, SubprocessWrapperInterface
 from benchcab.workdir import setup_fluxsite_directory_tree
 
@@ -50,6 +50,7 @@ def __init__(
             Path to the executable.
         validate_env : bool, optional
             Validate the environment, by default True
+
         """
         self.benchcab_exe_path = benchcab_exe_path
         self.validate_env = validate_env
@@ -106,11 +107,10 @@ def _validate_environment(self, project: str, modules: list):
             paths = list(internal.MET_DIR.glob(f"{site_id}*"))
             if not paths:
                 self.logger.error(
-                    [
-                        f"Failed to infer met file for site id '{site_id}' in "
-                        f"{internal.MET_DIR}."
-                    ]
+                    f"Failed to infer met file for site id '{site_id}' in "
                 )
+                self.logger.error(f"{internal.MET_DIR}.")
+
                 sys.exit(1)
             if len(paths) > 1:
                 self.logger.error(
@@ -262,7 +262,7 @@ def fluxsite_run_tasks(self, config_path: str):
             ncpus = config.get("pbs", {}).get(
                 "ncpus", internal.FLUXSITE_DEFAULT_PBS["ncpus"]
             )
-            run_tasks_in_parallel(tasks, n_processes=ncpus, verbose=verbose)
+            run_tasks_in_parallel(tasks, n_processes=ncpus)
         else:
             run_tasks(tasks)
         self.logger.info("Successfully ran fluxsite tasks")
@@ -290,7 +290,7 @@ def fluxsite_bitwise_cmp(self, config_path: str):
                 ncpus = config["fluxsite"]["pbs"]["ncpus"]
             except KeyError:
                 ncpus = internal.FLUXSITE_DEFAULT_PBS["ncpus"]
-            run_comparisons_in_parallel(comparisons, n_processes=ncpus, verbose=verbose)
+            run_comparisons_in_parallel(comparisons, n_processes=ncpus)
         else:
             run_comparisons(comparisons)
         self.logger.info("Successfully ran comparison tasks")
diff --git a/benchcab/comparison.py b/benchcab/comparison.py
index 173ca02..495b9d7 100644
--- a/benchcab/comparison.py
+++ b/benchcab/comparison.py
@@ -32,6 +32,7 @@ def __init__(
             Files.
         task_name : str
             Name of the task.
+
         """
         self.files = files
         self.task_name = task_name
@@ -57,12 +58,8 @@ def run(self) -> None:
             with output_file.open("w", encoding="utf-8") as file:
                 file.write(exc.stdout)
 
-            self.logger.error(
-                [
-                    f"Failure: files {file_a.name} {file_b.name} differ. ",
-                    f"Results of diff have been written to {output_file}",
-                ]
-            )
+            self.logger.error(f"Failure: files {file_a.name} {file_b.name} differ. ")
+            self.logger.error(f"Results of diff have been written to {output_file}")
 
         sys.stdout.flush()
 
diff --git a/benchcab/config.py b/benchcab/config.py
index 25547d0..2cc5115 100644
--- a/benchcab/config.py
+++ b/benchcab/config.py
@@ -22,6 +22,7 @@ def __init__(self, validator: Validator):
         ----------
         validator: cerberus.Validator
             A validation object that has been used and has the errors attribute.
+
         """
         # Nicely format the errors.
         errors = [f"{k} = {v}" for k, v in validator.errors.items()]
@@ -51,6 +52,7 @@ def validate_config(config: dict) -> bool:
     ------
     ConfigValidationError
         Raised when the configuration file fails validation.
+
     """
     # Load the schema
     schema = bu.load_package_data("config-schema.yml")
@@ -81,6 +83,7 @@ def read_optional_key(config: dict):
     ----------
     config : dict
         The configuration file with with/without optional keys
+
     """
     if "project" not in config:
         config["project"] = os.environ.get("PROJECT", None)
@@ -118,6 +121,7 @@ def read_config_file(config_path: str) -> dict:
     -------
     dict
         Configuration dict
+
     """
     # Load the configuration file.
     with Path.open(Path(config_path), "r", encoding="utf-8") as file:
@@ -143,6 +147,7 @@ def read_config(config_path: str) -> dict:
     ------
     ConfigValidationError
         Raised when the configuration file fails validation.
+
     """
     # Read configuration file
     config = read_config_file(config_path)
diff --git a/benchcab/environment_modules.py b/benchcab/environment_modules.py
index 70546a5..fe845e8 100644
--- a/benchcab/environment_modules.py
+++ b/benchcab/environment_modules.py
@@ -72,6 +72,7 @@ def module_is_avail(self, *args: str) -> bool:
         -------
         bool
             True if available, False otherwise.
+
         """
         return module("is-avail", *args)
 
@@ -82,6 +83,7 @@ def module_is_loaded(self, *args: str) -> bool:
         -------
         bool
             True if loaded, False otherwise.
+
         """
         return module("is-loaded", *args)
 
@@ -92,6 +94,7 @@ def module_load(self, *args: str) -> None:
         ------
         EnvironmentModulesError
             Raised when module fails to load.
+
         """
         if not module("load", *args):
             raise EnvironmentModulesError("Failed to load modules: " + " ".join(args))
@@ -103,6 +106,7 @@ def module_unload(self, *args: str) -> None:
         ------
         EnvironmentModulesError
             Raised when module fails to unload.
+
         """
         if not module("unload", *args):
             raise EnvironmentModulesError("Failed to unload modules: " + " ".join(args))
diff --git a/benchcab/fluxsite.py b/benchcab/fluxsite.py
index bd3c41a..14ea70a 100644
--- a/benchcab/fluxsite.py
+++ b/benchcab/fluxsite.py
@@ -18,9 +18,9 @@
 from benchcab import __version__, internal
 from benchcab.comparison import ComparisonTask
 from benchcab.model import Model
+from benchcab.utils import get_logger
 from benchcab.utils.fs import chdir, mkdir
 from benchcab.utils.subprocess import SubprocessWrapper, SubprocessWrapperInterface
-from benchcab.utils import get_logger
 
 # fmt: off
 # ======================================================
@@ -44,6 +44,7 @@ def deep_update(mapping: Dict[KeyType, Any], *updating_mappings: Dict[KeyType, A
     -------
     Dict[KeyType, Any]
         Updated mapping.
+    
     """
     updated_mapping = mapping.copy()
     for updating_mapping in updating_mappings:
@@ -129,6 +130,7 @@ def __init__(
             Science configuration ID.
         sci_config : dict
             Science configuration.
+
         """
         self.model = model
         self.met_forcing_file = met_forcing_file
diff --git a/benchcab/main.py b/benchcab/main.py
index c935ebf..f7dc715 100644
--- a/benchcab/main.py
+++ b/benchcab/main.py
@@ -15,6 +15,7 @@ def parse_and_dispatch(parser):
     ----
     parser : argparse.ArgumentParser
         Parser object.
+
     """
     args = vars(parser.parse_args(sys.argv[1:] if sys.argv[1:] else ["-h"]))
 
diff --git a/benchcab/model.py b/benchcab/model.py
index 5642eec..1bbf014 100644
--- a/benchcab/model.py
+++ b/benchcab/model.py
@@ -49,6 +49,7 @@ def __init__(
             Build script, by default None
         model_id : Optional[int], optional
             Model ID, by default None
+
         """
         self.repo = repo
         self.name = name if name else repo.get_branch_name()
diff --git a/benchcab/utils/__init__.py b/benchcab/utils/__init__.py
index 9493886..aa09428 100644
--- a/benchcab/utils/__init__.py
+++ b/benchcab/utils/__init__.py
@@ -5,14 +5,14 @@
 
 """Top-level utilities."""
 import json
+import logging
 import os
 import pkgutil
+import sys
 from importlib import resources
 from pathlib import Path
 
 import yaml
-import logging
-import sys
 
 # List of one-argument decoding functions.
 PACKAGE_DATA_DECODERS = dict(json=json.loads, yml=yaml.safe_load)
@@ -25,6 +25,7 @@ def get_installed_root() -> Path:
     -------
     Path
         Path to the installed root.
+
     """
     return Path(resources.files("benchcab"))
 
@@ -36,6 +37,7 @@ def load_package_data(filename: str) -> dict:
     ----------
     filename : str
         Filename of the file to load out of the data directory.
+
     """
     # Work out the encoding of requested file.
     ext = filename.split(".")[-1]
diff --git a/benchcab/utils/fs.py b/benchcab/utils/fs.py
index 78bc63c..2be838f 100644
--- a/benchcab/utils/fs.py
+++ b/benchcab/utils/fs.py
@@ -67,6 +67,7 @@ def mkdir(new_path: Path, **kwargs):
         Path to the directory to be created.
     **kwargs : dict, optional
         Additional options for `pathlib.Path.mkdir()`
+
     """
     get_logger().debug(f"Creating {new_path} directory")
     new_path.mkdir(**kwargs)
diff --git a/benchcab/utils/repo.py b/benchcab/utils/repo.py
index f7025be..2f89172 100644
--- a/benchcab/utils/repo.py
+++ b/benchcab/utils/repo.py
@@ -31,6 +31,7 @@ def get_revision(self) -> str:
         -------
         str
             Human readable string describing the latest revision.
+
         """
 
     @abstractmethod
@@ -41,6 +42,7 @@ def get_branch_name(self) -> str:
         -------
         str
             Branch name of the source code.
+
         """
 
 
@@ -51,6 +53,7 @@ class GitRepo(Repo):
     ----------
     subprocess_handler: SubprocessWrapper
         Object for handling subprocess calls.
+
     """
 
     subprocess_handler = SubprocessWrapper()
@@ -73,6 +76,7 @@ def __init__(
         commit: str, optional
             Commit hash (long). When specified the repository will reset to this
             commit when cloning.
+
         """
         self.url = url
         self.branch = branch
@@ -103,6 +107,7 @@ def get_revision(self) -> str:
         -------
         str
             Human readable string describing the latest revision.
+
         """
         repo = git.Repo(self.path)
         return f"commit {repo.head.commit.hexsha}"
@@ -114,6 +119,7 @@ def get_branch_name(self) -> str:
         -------
         str
             Branch name of the source code.
+
         """
         return self.branch
 
@@ -125,6 +131,7 @@ class SVNRepo(Repo):
     ----------
     subprocess_handler: SubprocessWrapper
         Object for handling subprocess calls.
+
     """
 
     subprocess_handler: SubprocessWrapperInterface = SubprocessWrapper()
@@ -152,6 +159,7 @@ def __init__(
         revision: int, optional
             SVN revision number. When specified the branch will be set to this
             revision on checkout.
+
         """
         self.svn_root = svn_root
         self.branch_path = branch_path
@@ -181,6 +189,7 @@ def get_revision(self) -> str:
         -------
         str
             Human readable string describing the latest revision.
+
         """
         proc = self.subprocess_handler.run_cmd(
             f"svn info --show-item last-changed-revision {self.path}",
@@ -195,6 +204,7 @@ def get_branch_name(self) -> str:
         -------
         str
             Branch name of the source code.
+
         """
         return Path(self.branch_path).name
 
@@ -218,6 +228,7 @@ def create_repo(spec: dict, path: Path) -> Repo:
     -------
     Repo
         A subclass instance of `Repo`.
+
     """
     if "git" in spec:
         if "url" not in spec["git"]:
diff --git a/benchcab/utils/subprocess.py b/benchcab/utils/subprocess.py
index 7734141..8951c19 100644
--- a/benchcab/utils/subprocess.py
+++ b/benchcab/utils/subprocess.py
@@ -60,6 +60,7 @@ def run_cmd(
         -------
         subprocess.CompletedProcess
             _description_
+
         """
         # Use the logging level (10 = Debug) to determine verbosity.
         verbose = get_logger().getEffectiveLevel() == DEBUG_LEVEL
diff --git a/tests/test_benchcab.py b/tests/test_benchcab.py
index 5fdc370..12b5c69 100644
--- a/tests/test_benchcab.py
+++ b/tests/test_benchcab.py
@@ -1,4 +1,5 @@
 """`pytest` tests for `benchcab.py`."""
+
 import re
 from contextlib import nullcontext as does_not_raise
 from unittest import mock
diff --git a/tests/test_config.py b/tests/test_config.py
index 1e98eeb..dcf306b 100644
--- a/tests/test_config.py
+++ b/tests/test_config.py
@@ -1,6 +1,6 @@
 """`pytest` tests for config.py."""
+
 import os
-import re
 from contextlib import nullcontext as does_not_raise
 from pathlib import Path
 from pprint import pformat