Update pre-commit dependencies (#627)

* Update pre-commit dependencies

* Update pre-commit deps in `conda/dev.yml`

* Fix `black` formatting errors

* Fix `flake8` programming errors

.pre-commit-config.yaml

@@ -4,7 +4,7 @@ fail_fast: true
 
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.3.0
+    rev: v5.0.0
     hooks:
       - id: trailing-whitespace
       - id: end-of-file-fixer
@@ -13,29 +13,34 @@ repos:
 
   # Can run individually with `pre-commit run black --all-files`
   - repo: https://github.com/psf/black
-    rev: 22.8.0
+    rev: 24.10.0
     hooks:
       - id: black
 
   # Can run individually with `pre-commit run isort --all-files`
   - repo: https://github.com/PyCQA/isort
-    rev: 5.12.0
+    rev: 5.13.2
     hooks:
       - id: isort
 
   # 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: 5.0.4
+    rev: 7.1.1
     hooks:
       - id: flake8
         args: ["--config=setup.cfg"]
-        additional_dependencies: [flake8-isort]
+        additional_dependencies: [flake8-isort==6.1.1]
 
   # Can run individually with `pre-commit run mypy --all-files`
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v0.982
+    rev: v1.11.2
     hooks:
       - id: mypy
         args: ["--config=setup.cfg"]
+
+# https://pre-commit.ci/#configuration
+ci:
+  autofix_prs: false
+  autoupdate_schedule: monthly

conda/dev.yml

@@ -15,12 +15,12 @@ dependencies:
   # Developer Tools
   # =================
   # If versions are updated, also update 'rev' in `.pre-commit-config.yaml`
-  - black=22.8.0        # version from https://anaconda.org/conda-forge/black
-  - flake8=5.0.4        # version from https://anaconda.org/conda-forge/flake8
+  - black=24.10.0        # version from https://anaconda.org/conda-forge/black
+  - flake8=7.1.1         # version from https://anaconda.org/conda-forge/flake8
   # This line also implicitly installs isort
-  - flake8-isort=4.2.0  # version from https://anaconda.org/conda-forge/flake8-isort
-  - mypy=0.982          # version from https://anaconda.org/conda-forge/mypy
-  - pre-commit=2.20.0   # version from https://anaconda.org/conda-forge/pre-commit
+  - flake8-isort=6.1.1  # version from https://anaconda.org/conda-forge/flake8-isort
+  - mypy=1.11.2         # version from https://anaconda.org/conda-forge/mypy
+  - pre-commit=4.0.1    # version from https://anaconda.org/conda-forge/pre-commit
   - tbump=6.9.0
   # Documentation
   # If versions are updated, also update in `.github/workflows/build_workflow.yml`

setup.py

@@ -7,7 +7,7 @@
 def package_files(directory, prefixes, extensions):
     """based on https://stackoverflow.com/a/36693250/7728169"""
     paths = []
-    for (path, directories, filenames) in os.walk(directory):
+    for path, directories, filenames in os.walk(directory):
         for filename in filenames:
             parts = filename.split(".")
             prefix = parts[0]

tests/test_sections.py

@@ -21,7 +21,7 @@ def compare(tester, actual, expected):
             tester.assertEqual(only_in_expected, set())
         incorrect_values = []
         for key in actual_keys:
-            if type(actual[key]) == Section:
+            if isinstance(actual[key], Section):
                 print("Calling `compare` again on {}".format(key))
                 compare(tester, actual[key], expected[key])
             elif actual[key] != expected[key]:

zppy/e3sm_diags.py

@@ -200,9 +200,9 @@ def check_and_define_parameters(c: Dict[str, Any]) -> None:
         if ("tc_analysis" in c["sets"]) and (c["reference_data_path_tc"] == ""):
             # We have to guess parameters here,
             # because multiple year sets are defined in a single subtask.
-            c[
-                "reference_data_path_tc"
-            ] = f"{reference_data_path}/atm/tc-analysis_{c['ref_year1']}_{c['ref_year2']}"
+            c["reference_data_path_tc"] = (
+                f"{reference_data_path}/atm/tc-analysis_{c['ref_year1']}_{c['ref_year2']}"
+            )
         if set(["enso_diags", "qbo", "area_mean_time_series"]) & set(c["sets"]):
             define_or_guess2(
                 c,

zppy/mpas_analysis.py

@@ -60,7 +60,9 @@ def mpas_analysis(config: ConfigObj, script_dir: str, existing_bundles, job_ids_
             if ("last_year" in c.keys()) and (c["enso_year2"] > c["last_year"]):
                 continue  # Skip this year set
             c["scriptDir"] = script_dir
-            prefix_suffix: str = f"_ts_{c['ts_year1']:04d}-{c['ts_year2']:04d}_climo_{c['climo_year1']:04d}-{c['climo_year2']:04d}"
+            prefix_suffix: str = (
+                f"_ts_{c['ts_year1']:04d}-{c['ts_year2']:04d}_climo_{c['climo_year1']:04d}-{c['climo_year2']:04d}"
+            )
             prefix: str
             if c["subsection"]:
                 prefix = f"mpas_analysis_{c['subsection']}{prefix_suffix}"

zppy/templates/coupled_global.py

@@ -156,6 +156,7 @@ def get_ylim(standard_range, extreme_values):
 # -----------------------------------------------------------------------------
 # Plotting functions
 
+
 # 1
 def plot_net_toa_flux_restom(ax, xlim, exps, rgn):
     print("Plot 1: plot_net_toa_flux_restom")
@@ -748,24 +749,36 @@ def run(parameters, rgn):  # noqa: C901
     use_ocn = plots_ocn or (not atmosphere_only and has_original_ocn_plots)
     exps: List[Dict[str, Any]] = [
         {
-            "atmos": f"{case_dir}/post/atm/glb/ts/monthly/{ts_num_years}yr/"
-            if use_atmos
-            else None,
-            "ice": f"{case_dir}/post/ice/glb/ts/monthly/{ts_num_years}yr/"
-            if plots_ice
-            else None,
-            "land": f"{case_dir}/post/lnd/glb/ts/monthly/{ts_num_years}yr/"
-            if plots_lnd
-            else None,
-            "ocean": f"{case_dir}/post/ocn/glb/ts/monthly/{ts_num_years}yr/"
-            if use_ocn
-            else None,
-            "moc": f"{case_dir}/post/ocn/glb/ts/monthly/{ts_num_years}yr/"
-            if use_ocn
-            else None,
-            "vol": f"{case_dir}/post/ocn/glb/ts/monthly/{ts_num_years}yr/"
-            if use_ocn
-            else None,
+            "atmos": (
+                f"{case_dir}/post/atm/glb/ts/monthly/{ts_num_years}yr/"
+                if use_atmos
+                else None
+            ),
+            "ice": (
+                f"{case_dir}/post/ice/glb/ts/monthly/{ts_num_years}yr/"
+                if plots_ice
+                else None
+            ),
+            "land": (
+                f"{case_dir}/post/lnd/glb/ts/monthly/{ts_num_years}yr/"
+                if plots_lnd
+                else None
+            ),
+            "ocean": (
+                f"{case_dir}/post/ocn/glb/ts/monthly/{ts_num_years}yr/"
+                if use_ocn
+                else None
+            ),
+            "moc": (
+                f"{case_dir}/post/ocn/glb/ts/monthly/{ts_num_years}yr/"
+                if use_ocn
+                else None
+            ),
+            "vol": (
+                f"{case_dir}/post/ocn/glb/ts/monthly/{ts_num_years}yr/"
+                if use_ocn
+                else None
+            ),
             "name": experiment_name,
             "yoffset": 0.0,
             "yr": ([year1, year2],),

zppy/utils.py

@@ -32,9 +32,9 @@ class DependencySkipError(RuntimeError):
 
 def get_active_status(task: Dict[str, Any]) -> bool:
     active: Any = task["active"]
-    if type(active) == bool:
+    if isinstance(active, bool):
         return active
-    elif type(active) == str:
+    elif isinstance(active, str):
         active_lower_case: str = active.lower()
         if active_lower_case == "true":
             return True
@@ -73,6 +73,7 @@ def get_url_message(c: Dict[str, Any], task: str) -> str:
 
 # Beginning steps #############################################################
 
+
 # TODO: determine return type
 def initialize_template(config: ConfigObj, template_name: str) -> Tuple[Any, Any]:
     # --- Initialize jinja2 template engine ---
@@ -87,6 +88,7 @@ def initialize_template(config: ConfigObj, template_name: str) -> Tuple[Any, Any
 # TODO: type aliases require python 3.12 or higher
 # type TaskDict = Dict[str, Any]
 
+
 # Process specified section and its sub-sections to build the list of tasks.
 # If the section includes sub-sections, one task will be created for each
 # sub-section and no task will be created for the main section.
@@ -149,7 +151,7 @@ def get_tasks(config: ConfigObj, section_name: str) -> List[Dict[str, Any]]:
     username = os.environ.get("USER")
     for c in tasks:
         for key in c:
-            if (type(c[key]) == str) and ("$USER" in c[key]):
+            if (isinstance(c[key], str)) and ("$USER" in c[key]):
                 c[key] = c[key].replace("$USER", username)
 
     return tasks
@@ -240,7 +242,7 @@ def check_required_parameters(
 # "year_begin-year_end"
 def get_years(years_input) -> List[Tuple[int, int]]:
     years_list: List[str]
-    if type(years_input) == str:
+    if isinstance(years_input, str):
         # This will be the case if years_list is missing a trailing comma
         years_list = [years_input]
     else:
@@ -272,6 +274,7 @@ def get_years(years_input) -> List[Tuple[int, int]]:
 
 # `for s in year_sets` steps ##################################################
 
+
 # This returns a value
 def define_or_guess(
     c: Dict[str, Any],