Solve selected pylint issues

Co-Authored-By: Anna Kvashchuk kvashchuk.anna@gmail.com

Mostly by disable statements close to the offending line.
Some cleanup in unused fixtures

.pylintrc

@@ -54,19 +54,11 @@ confidence=
 # --disable=W"
 disable=
     duplicate-code,
-    import-outside-toplevel,
     invalid-name,
-    logging-format-interpolation,
     missing-class-docstring,
     missing-function-docstring,
     missing-module-docstring,
-    no-member,
-    no-self-use,
-    not-callable,
     redefined-outer-name,
-    too-many-arguments,
-    too-many-locals,
-    unused-argument,
     unspecified-encoding
 #
 # Enable the message, report, category or checker with the given id(s). You can

semeio/workflows/ahm_analysis/ahmanalysis.py

@@ -281,6 +281,7 @@ def run(
 def _run_ministep(
     ert, obs_group, data_parameters, prior_name, target_name, output_path
 ):
+    # pylint: disable=too-many-arguments
     update_step = {
         "name": "MINISTEP",
         "observations": obs_group,

semeio/workflows/csv_export2/csv_export2.py

@@ -93,6 +93,7 @@ def csv_exporter(runpathfile, time_index, outputfile, column_keys=None):
 
 class CsvExport2Job(ErtScript):  # pylint: disable=too-few-public-methods
     def run(self, *args):
+        # pylint: disable=no-self-use
         main(args)
 
 

semeio/workflows/localisation/local_script_lib.py

@@ -227,6 +227,7 @@ def apply_decay(
     tapering_range=None,
     calculate_qc_parameter=False,
 ):
+    # pylint: disable=too-many-arguments,too-many-locals
     """Calculates the scaling factor, assign it to ERT instance by row_scaling
     and returns a full sized grid parameter with scaling factors for active
     grid cells and 0 elsewhere to be used for QC purpose.
@@ -300,6 +301,7 @@ def apply_decay(
 
 
 def apply_from_file(row_scaling, data_size, grid, filename, param_name, log_level):
+    # pylint: disable=too-many-arguments
     debug_print(
         f"Read scaling factors as parameter {param_name}", LogLevel.LEVEL3, log_level
     )
@@ -348,7 +350,7 @@ def define_look_up_index(user_defined_active_region_list, max_region_number):
 def calculate_scaling_factors_in_regions(
     grid, region_parameter, active_segment_list, scaling_value_list, smooth_range_list
 ):
-    # pylint: disable=unused-argument
+    # pylint: disable=unused-argument,too-many-locals
     # ('grid' and 'smooth-range-list' are not currently used)
 
     min_region_number = region_parameter.min()
@@ -399,6 +401,7 @@ def smooth_parameter(
     active region and e.g 0 for all inactive regions and for inactive grid cells,
     then the smoothing will only appear on the border between active regions.
     """
+    # pylint: disable=too-many-locals
     nx = grid.get_nx()
     ny = grid.get_ny()
     nz = grid.get_nz()
@@ -439,6 +442,7 @@ def apply_segment(
     corr_name,
     log_level=LogLevel.OFF,
 ):
+    # pylint: disable=too-many-arguments,too-many-locals
     """
     Purpose: Use region numbers and list of scaling factors per region to
                    create scaling factors per active .
@@ -571,9 +575,9 @@ def add_ministeps(
     ert_ensemble_config,
     grid_for_field,
 ):
-    # pylint: disable-msg=too-many-branches
-    # pylint: disable-msg=too-many-statements
-    # pylint: disable-msg=too-many-nested-blocks
+    # pylint: disable=too-many-branches,too-many-statements
+    # pylint: disable=too-many-nested-blocks,too-many-locals
+
     debug_print("Add all ministeps:", LogLevel.LEVEL1, user_config.log_level)
     ScalingValues.initialize()
     # Read all region files used in correlation groups,
@@ -905,7 +909,7 @@ def __call__(self, data_index):
 
 
 class ScalingValues:
-    # pylint: disable=R0903
+    # pylint: disable=too-few-public-methods
     scaling_param_number = 1
     corr_name = None
 
@@ -924,6 +928,7 @@ def write_qc_parameter(
         param_for_field,
         log_level=LogLevel.OFF,
     ):
+        # pylint: disable=too-many-arguments
         if param_for_field is None or field_scale is None:
             return
 

semeio/workflows/localisation/localisation_config.py

@@ -1,4 +1,4 @@
-# pylint: disable=E0213
+# pylint: disable=no-self-argument
 import itertools
 import pathlib
 
@@ -54,7 +54,7 @@ def check_for_duplicated_correlation_specifications(correlations):
 
 
 class BaseModel(PydanticBaseModel):
-    # pylint: disable=R0903
+    # pylint: disable=too-few-public-methods
     class Config:
         extra = Extra.forbid
 
@@ -79,18 +79,21 @@ class ObsConfig(BaseModel):
 
     @validator("add")
     def validate_add(cls, add):
+        # pylint: disable=no-self-use
         if isinstance(add, str):
             add = [add]
         return add
 
     @validator("remove")
     def validate_remove(cls, remove):
+        # pylint: disable=no-self-use
         if isinstance(remove, str):
             remove = [remove]
         return remove
 
     @validator("result_items", always=True)
     def expanded_items(cls, _, values):
+        # pylint: disable=no-self-use
         add, remove = values["add"], values.get("remove", None)
         result = _check_specification(add, remove, values["context"])
         if len(result) == 0:
@@ -220,6 +223,7 @@ class ScalingForSegmentsConfig(BaseModel):
 
     @validator("scalingfactors")
     def check_length_consistency(cls, v, values):
+        # pylint: disable=no-self-use
         # Ensure that active segment list and scaling factor lists are of equal length.
         scalingfactors = v
         active_segment_list = values.get("active_segments", None)
@@ -285,12 +289,14 @@ class CorrelationConfig(BaseModel):
 
     @root_validator(pre=True)
     def inject_context(cls, values: Dict) -> Dict:
+        # pylint: disable=no-self-use
         values["obs_group"]["context"] = values["obs_context"]
         values["param_group"]["context"] = values["params_context"]
         return values
 
     @validator("field_scale", pre=True)
     def validate_field_scale(cls, value):
+        # pylint: disable=no-self-use
         """
         To improve the user feedback we explicitly check
         which method is configured and bypass the Union
@@ -316,6 +322,7 @@ def validate_field_scale(cls, value):
 
     @validator("surface_scale", pre=True)
     def validate_surface_scale(cls, value):
+        # pylint: disable=no-self-use
         """
         To improve the user feedback we explicitly check
         which method is configured and bypass the Union
@@ -372,19 +379,22 @@ class LocalisationConfig(BaseModel):
 
     @validator("log_level")
     def validate_log_level(cls, level):
+        # pylint: disable=no-self-use
         if not isinstance(level, int):
             level = LogLevel.OFF
         return level
 
     @root_validator(pre=True)
     def inject_context(cls, values: Dict) -> Dict:
+        # pylint: disable=no-self-use
         for correlation in values["correlations"]:
             correlation["obs_context"] = values["observations"]
             correlation["params_context"] = values["parameters"]
         return values
 
     @validator("correlations")
     def validate_correlations(cls, correlations):
+        # pylint: disable=no-self-use
         duplicates = check_for_duplicated_correlation_specifications(correlations)
         if len(duplicates) > 0:
             error_msgs = "\n".join(duplicates)

semeio/workflows/misfit_preprocessor/hierarchical_config.py

@@ -41,6 +41,7 @@ class BaseFclusterConfig(BaseMisfitPreprocessorConfig):
 
     @validator("depth", pre=True)
     def constrained_int(cls, depth):
+        # pylint: disable=no-self-use
         if isinstance(depth, float):
             raise ValueError("Depth must be int")
         return depth
@@ -55,6 +56,7 @@ class FclusterConfig(BaseFclusterConfig):
 
     @root_validator(pre=True)
     def validate_threshold(cls, values):
+        # pylint: disable=no-self-use
         criterion = values.get("criterion")
         threshold = values.get("threshold")
         if criterion in ("maxclust", "maxclust_monocrit") and "threshold" not in values:
@@ -68,6 +70,7 @@ def validate_threshold(cls, values):
 
     @validator("threshold")
     def t_larger_than_zero(cls, threshold):
+        # pylint: disable=no-self-use
         if threshold <= 0:
             raise ValueError(f"threshold must be larger than zero, is {threshold}")
         return threshold

semeio/workflows/misfit_preprocessor/workflow_config.py

@@ -60,6 +60,7 @@ class MisfitConfig(BaseMisfitPreprocessorConfig):
 
     @validator("workflow", pre=True)
     def validate_workflow(cls, value):
+        # pylint: disable=no-self-use
         """
         To improve the user feedback we explicitly check if the type of workflow
         is configured, and if it is, we bypass the Union. If it has not been given

semeio/workflows/spearman_correlation_job/cluster_analysis.py

@@ -10,6 +10,7 @@ def fcluster_analysis(
     method="single",
     metric="euclidean",
 ):
+    # pylint: disable=too-many-arguments
     a = linkage(correlation_matrix, method, metric)
     return fcluster(a, threshold, criterion=criterion, depth=depth)
 
@@ -22,6 +23,7 @@ def kmeans_analysis(
     max_iter=300,
     random_state=None,
 ):
+    # pylint: disable=too-many-arguments
     kmeans = KMeans(
         init=init,
         n_clusters=n_clusters,

semeio/workflows/spearman_correlation_job/spearman_correlation.py

@@ -42,7 +42,7 @@ def run(self, *args):
 
 
 def spearman_job_parser():
-    description = """
+    description = """R
     A module that calculates the Spearman correlation in simulated data
     and clusters
     """

tests/communication/test-data/logging_test_workflow_job.py

@@ -7,6 +7,7 @@
 class TestWorkflowJob(SemeioScript):
     # pylint: disable=method-hidden
     def run(self, *args):
+        # pylint: disable=unused-argument
         self.reporter.publish("test_data", list(range(10)))
 
         # The mission of this code is to simulate that something outside the

tests/communication/unit/test_semeio_script.py

@@ -8,7 +8,7 @@
 
 from semeio.communication import SEMEIOSCRIPT_LOG_FILE, SemeioScript
 
-# pylint: disable=method-hidden
+# pylint: disable=method-hidden,no-self-use
 
 
 def _ert_mock(ensemble_path="storage", user_case_name="case_name"):
@@ -33,6 +33,7 @@ def test_semeio_script_publish(tmpdir):
 
     class MySuperScript(SemeioScript):
         def run(self, *args):
+            # pylint: disable=unused-argument
             self.reporter.publish(namespace, data)
 
     my_super_script = MySuperScript(ert)
@@ -61,6 +62,7 @@ def test_semeio_script_logging(tmpdir):
 
     class MySuperScript(SemeioScript):
         def run(self, *args):
+            # pylint: disable=unused-argument
             logging.error(msg)
 
     my_super_script = MySuperScript(ert)
@@ -105,6 +107,7 @@ def test_semeio_script_multiple_logging(messages, tmpdir):
 
     class MySuperScript(SemeioScript):
         def run(self, *args):
+            # pylint: disable=unused-argument
             posted_messages = []
             for msg in messages:
                 logging.error(msg)
@@ -133,6 +136,7 @@ def test_semeio_script_post_logging(tmpdir):
 
     class MySuperScript(SemeioScript):
         def run(self, *args):
+            # pylint: disable=unused-argument
             logging.error("A message from MySuperScript")
 
     my_super_script = MySuperScript(ert)
@@ -161,6 +165,7 @@ def test_semeio_script_pre_logging(tmpdir):
 
     class MySuperScript(SemeioScript):
         def run(self, *args):
+            # pylint: disable=unused-argument
             logging.error("A message from MySuperScript")
 
     my_super_script = MySuperScript(ert)
@@ -190,6 +195,7 @@ def test_semeio_script_concurrent_logging(tmpdir):
 
     class MySuperScript(SemeioScript):
         def run(self, *args):
+            # pylint: disable=unused-argument
             logging.error("A message from MySuperScript")
             thread = Thread(target=lambda: logging.error("External event."))
             thread.start()
@@ -218,6 +224,7 @@ def test_semeio_script_post_logging_exception(tmpdir):
 
     class MySuperScript(SemeioScript):
         def run(self, *args):
+            # pylint: disable=unused-argument
             logging.error("A message from MySuperScript")
             raise AssertionError("Bazinga")
 

tests/jobs/ahm_analysis/test_integration.py

@@ -25,6 +25,7 @@ def test_ahmanalysis_run(test_data_root):
     res_config.convertToCReference(None)
     ert = EnKFMain(res_config)
 
+    # pylint: disable=not-callable
     ahmanalysis.AhmAnalysisJob(ert).run(prior_name="default_0")
 
     # assert that this returns/generates a KS csv file
@@ -82,6 +83,7 @@ def test_ahmanalysis_run_field(test_data_root, grid_prop):
     res_config.convertToCReference(None)
     ert = EnKFMain(res_config)
 
+    # pylint: disable=not-callable
     ahmanalysis.AhmAnalysisJob(ert).run(prior_name="default")
 
     # assert that this returns/generates the delta field parameter
@@ -121,4 +123,5 @@ def test_no_prior(test_data_root):
     expected_msg = "Empty prior ensemble"
     # check that it fails
     with pytest.raises(ValidationError, match=expected_msg):
+        # pylint: disable=not-callable
         ahmanalysis.AhmAnalysisJob(ert).run(prior_name="default")

tests/jobs/correlated_observations_scaling/test_integration.py

@@ -1,3 +1,4 @@
+# pylint: disable=not-callable
 import json
 import os
 import shutil
@@ -24,7 +25,7 @@ def get_std_from_obs_vector(vector):
     return result
 
 
-def test_installed_python_version_of_enkf_scaling_job(setup_ert, monkeypatch):
+def test_installed_python_version_of_enkf_scaling_job(setup_ert):
 
     pm = ErtPluginManager(
         plugins=[
@@ -143,7 +144,7 @@ def test_main_entry_point_gen_data(setup_ert):
         assert reported_scalefactor == pytest.approx(1.224744871391589, 0.1)
 
 
-def test_main_entry_point_summary_data_calc(setup_ert, monkeypatch):
+def test_main_entry_point_summary_data_calc(setup_ert):
     cos_config = {
         "CALCULATE_KEYS": {"keys": [{"key": "WOPR_OP1_108"}, {"key": "WOPR_OP1_144"}]}
     }
@@ -180,9 +181,7 @@ def test_main_entry_point_summary_data_calc(setup_ert, monkeypatch):
         ),
     ],
 )
-def test_main_entry_point_history_data_calc(
-    setup_ert, monkeypatch, config, expected_result
-):
+def test_main_entry_point_history_data_calc(setup_ert, config, expected_result):
 
     res_config = setup_ert
 
@@ -196,7 +195,7 @@ def test_main_entry_point_history_data_calc(
     assert result == [expected_result] * 200
 
 
-def test_main_entry_point_history_data_calc_subset(setup_ert, monkeypatch):
+def test_main_entry_point_history_data_calc_subset(setup_ert):
     config = {"CALCULATE_KEYS": {"keys": [{"key": "FOPR", "index": [10, 20]}]}}
     res_config = setup_ert