Partially solve pylint issues for semeio.

.pylintrc

@@ -13,7 +13,7 @@ ignore=CVS
 # regex matches against base names, not paths. Note that pre-commit runs
 # pylint on individual files, so if some patters should be ignored, put that
 # in .pre-commit-config.yaml
-ignore-patterns=
+ignore-patterns=version.py
 
 # Python code to execute, usually for sys.path manipulation such as
 # pygtk.require().
@@ -54,37 +54,21 @@ confidence=
 # --disable=W"
 disable=
     duplicate-code,
-    wrong-import-order,
-    unused-import,
+    import-outside-toplevel,
+    invalid-name,
+    logging-format-interpolation,
+    missing-class-docstring,
     missing-function-docstring,
     missing-module-docstring,
-    protected-access,
-    invalid-name,
-    redefined-outer-name,
-    unused-argument,
-    bad-continuation,
     no-member,
-    singleton-comparison,
-    import-outside-toplevel,
-    line-too-long,
-    too-many-arguments,
-    too-many-locals,
-    misplaced-comparison-constant,
-    missing-class-docstring,
-    no-else-return,
-    too-many-instance-attributes,
-    inconsistent-return-statements,
-    logging-format-interpolation,
-    useless-object-inheritance,
-    unused-variable,
     no-self-use,
-    consider-merging-isinstance,
-    consider-using-in,
-    deprecated-method,
-    method-hidden,
     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
 # either give multiple identifier separated by comma (,) or put this option
 # multiple time (only on the command line, not in the configuration file where
@@ -169,7 +153,7 @@ function-name-hint=(([a-z][a-z0-9_]{2,30})|(_[a-z0-9_]*))$
 function-rgx=(([a-z][a-z0-9_]{2,30})|(_[a-z0-9_]*))$
 
 # Good variable names which should always be accepted, separated by a comma
-good-names=i,j,k,ex,Run,_
+good-names=i,j,k,ex,Run,_,description,category,short_description,examples
 
 # Include a hint for the correct naming format with invalid-name
 include-naming-hint=no

semeio/_docs_utils/_json_schema_2_rst.py

@@ -2,13 +2,13 @@
 
 
 def _insert_ref(schema):
-    for k, v in schema.items():
-        if isinstance(v, dict):
-            _insert_ref(v)
-        elif isinstance(v, list):
-            for index, val in enumerate(v.copy()):
+    for value in schema.values():
+        if isinstance(value, dict):
+            _insert_ref(value)
+        elif isinstance(value, list):
+            for index, val in enumerate(value.copy()):
                 if "$ref" in val:
-                    v[index] = val["$ref"] + "_"
+                    value[index] = val["$ref"] + "_"
 
 
 def _remove_key(schema, del_key):

semeio/communication/reporter.py

@@ -2,7 +2,7 @@
 import os
 
 
-class FileReporter(object):
+class FileReporter:
     def __init__(self, output_dir):
         self._output_dir = output_dir
 
@@ -19,19 +19,19 @@ def publish(self, namespace, data):
         output_file = self._prepare_output_file(namespace) + ".json"
 
         if os.path.exists(output_file):
-            with open(output_file) as f:
-                all_data = json.load(f)
+            with open(output_file, encoding="utf-8") as f_handle:
+                all_data = json.load(f_handle)
         else:
             all_data = []
 
         all_data.append(data)
-        with open(output_file, "w") as f:
-            json.dump(all_data, f)
+        with open(output_file, "w", encoding="utf-8") as f_handle:
+            json.dump(all_data, f_handle)
 
     def publish_msg(self, namespace, msg):
         output_file = self._prepare_output_file(namespace)
-        with open(output_file, "a") as f:
-            f.write(f"{msg}\n")
+        with open(output_file, "a", encoding="utf-8") as f_handle:
+            f_handle.write(f"{msg}\n")
 
     def _prepare_output_file(self, namespace):
         if not os.path.exists(self._output_dir):

semeio/communication/semeio_script.py

@@ -13,7 +13,7 @@
 SEMEIOSCRIPT_LOG_FILE = "workflow-log.txt"
 
 
-class _LogHandlerContext(object):
+class _LogHandlerContext:
     def __init__(self, log, handler):
         self._log = log
         self._handler = handler
@@ -34,16 +34,17 @@ def __init__(self, output_dir, thread_id):
 
     def flush(self):
         for log_record in self.buffer:
-            self._reporter.publish_msg(self._namespace, self._format_record(log_record))
+            self._reporter.publish_msg(self._namespace, _format_record(log_record))
 
         super().flush()
 
-    def _format_record(self, log_record):
-        return (
-            f"{log_record.levelname} "
-            f"[{datetime.datetime.fromtimestamp(log_record.created)}]: "
-            f"{log_record.message}"
-        )
+
+def _format_record(log_record):
+    return (
+        f"{log_record.levelname} "
+        f"[{datetime.datetime.fromtimestamp(log_record.created)}]: "
+        f"{log_record.message}"
+    )
 
 
 class SemeioScript(ErtScript):  # pylint: disable=too-few-public-methods
@@ -93,10 +94,12 @@ def reporter(self):
 
     @property
     def _reports_dir(self):
+        # pylint: disable=protected-access
         return self.reporter._output_dir
 
     @_reports_dir.setter
     def _reports_dir(self, output_dir):
+        # pylint: disable=protected-access
         output_dir = Path(output_dir)
         if not output_dir.is_absolute():
             res_config = self.ert().resConfig()

semeio/hook_implementations/jobs.py

@@ -20,14 +20,15 @@ def _get_jobs_from_directory(directory):
         for f in os.listdir(resource_directory)
         if os.path.isfile(os.path.join(resource_directory, f))
     ]
-    # libres will look for an executable in the same folder as the job configuration
-    # file is located. If the name of the config is the same as the name of the executable,
-    # libres will be confused. The usual standard in ERT would be to capitalize the config
-    # file. On OSX systems, which are case-insensitive, this isn't viable. The job config
-    # files are therefore appended with "_CONFIG".
-    # The jobs will be installed as JOB_NAME JOB_NAME_CONFIG, and the JOB_NAME_CONFIG will
-    # point to an executable named job_name - which we install with entry-points. The user
-    # can use the forward model job as normal:
+    # libres will look for an executable in the same folder as the job
+    # configuration file is located. If the name of the config is the same as
+    # the name of the executable, libres will be confused. The usual standard in
+    # ERT would be to capitalize the config file. On OSX systems, which are
+    # case-insensitive, this isn't viable. The job config files are therefore
+    # appended with "_CONFIG".  The jobs will be installed as JOB_NAME
+    # JOB_NAME_CONFIG, and the JOB_NAME_CONFIG will point to an executable named
+    # job_name - which we install with entry-points. The user can use the
+    # forward model job as normal:
     # SIMULATION_JOB JOB_NAME
     return {
         _remove_suffix(os.path.basename(path), "_CONFIG"): path for path in all_files
@@ -62,18 +63,16 @@ def job_documentation(job_name):
         insert = verb == "insert"
         return {
             "description": (
-                "{} NOSIM {} the ECLIPSE data file. "  # pylint: disable=consider-using-f-string
-                "This will {} simulation in ECLIPSE. NB: the job does not currently work on osx systems"
-            ).format(
-                verb.capitalize(),
-                "into" if insert else "from",
-                "disable" if insert else "enable",
+                f"{verb.capitalize()} NOSIM "
+                f"{'into' if insert else 'from'} the ECLIPSE data file. "
+                f"This will {'disable' if insert else 'enable'} simulation in ECLIPSE. "
+                "NB: the job does not currently work on osx systems"
             ),
             "examples": "",
             "category": "utility.eclipse",
         }
 
-    if job_name == "STEA" or job_name == "PYSCAL":
+    if job_name in ["STEA", "PYSCAL"]:
         module_name = f"semeio.jobs.scripts.fm_{job_name.lower()}"
     elif job_name == "OTS":
         module_name = "semeio.jobs.scripts.overburden_timeshift"

semeio/jobs/design2params/design2params.py

@@ -34,6 +34,7 @@ def run(
     parametersfilename="parameters.txt",
     log_level=None,
 ):
+    # pylint: disable=too-many-arguments
     """
     Reads out all file content from different files and create dataframes
     """
@@ -73,6 +74,7 @@ def run(
 def _complete_parameters_file(
     realization, parameters, parametersfilename, design_matrix_sheet, default_sheet
 ):
+    # pylint: disable=too-many-locals
     """
     Pick key / values from choosen realization in design matrix
     Append those key / values if not present into parameters.txt
@@ -176,7 +178,7 @@ def _complete_parameters_file(
     )
 
     # if all ok - write the ok file
-    with open(_TARGET_FILE_TXT, "w") as target_file:
+    with open(_TARGET_FILE_TXT, "w", encoding="utf-8") as target_file:
         target_file.write("OK\n")
 
 
@@ -188,7 +190,7 @@ def _read_excel(file_name, sheet_name, header=0, usecols=None, engine=None):
     :raises: SystemExit if file not loaded correctly
     """
     try:
-        df = pd.read_excel(
+        dframe = pd.read_excel(
             file_name,
             sheet_name,
             header=header,
@@ -214,13 +216,13 @@ def _read_excel(file_name, sheet_name, header=0, usecols=None, engine=None):
             )
         ) from err
 
-    p = Path(file_name)
-    if p.suffix == ".xls":
+    file_path = Path(file_name)
+    if file_path.suffix == ".xls":
         warnings.warn(
             "Support for XLS files is deprecated. Use XLSX", DeprecationWarning
         )
 
-    return df.dropna(axis=1, how="all")
+    return dframe.dropna(axis=1, how="all")
 
 
 def _validate_design_matrix_header(design_matrix):

semeio/jobs/design_kw/design_kw.py

@@ -26,18 +26,18 @@ def run(
 
     valid = True
 
-    with open(parameters_file_name) as parameters_file:
+    with open(parameters_file_name, encoding="utf-8") as parameters_file:
         parameters = parameters_file.readlines()
 
     key_vals = extract_key_value(parameters)
 
     key_vals.update(rm_genkw_prefix(key_vals))
 
-    with open(template_file_name, "r") as template_file:
+    with open(template_file_name, "r", encoding="utf-8") as template_file:
         template = template_file.readlines()
 
     if valid:
-        with open(result_file_name, "w") as result_file:
+        with open(result_file_name, "w", encoding="utf-8") as result_file:
             for line in template:
                 if not is_comment(line):
                     for key, value in key_vals.items():
@@ -49,7 +49,7 @@ def run(
                 result_file.write(line)
 
     if valid:
-        with open(_STATUS_FILE_NAME, "w") as status_file:
+        with open(_STATUS_FILE_NAME, "w", encoding="utf-8") as status_file:
             status_file.write("DESIGN_KW OK\n")
 
 
@@ -90,8 +90,7 @@ def unmatched_templates(line):
     bracketpattern = re.compile("<.+?>")
     if bracketpattern.search(line):
         return bracketpattern.findall(line)
-    else:
-        return []
+    return []
 
 
 def is_comment(line):