Bring linting up to repo standards

src/subscript/fmuobs/fmuobs.py

@@ -363,7 +363,7 @@ def fmuobs(
                 "Please verify the output file"
             )
     logger.debug("After all the hard work, what is returned is this %s", dframe)
-    dump_results(dframe, csv, yml, resinsight, ertobs, Path(inputfile).parent)
+    dump_results(dframe, csv, yml, resinsight, ertobs, PosixPath(inputfile).parent)
 
 
 def dump_results(
@@ -372,7 +372,7 @@ def dump_results(
     yamlfile: Optional[str] = None,
     resinsightfile: Optional[str] = None,
     ertfile: Optional[str] = None,
-    parent_dir: Optional[PosixPath] = Path("."),
+    parent_dir: PosixPath = PosixPath("."),
 ) -> None:
     """Dump dataframe with ERT observations to CSV and/or YML
     format to disk. Writes to stdout if filenames are "-". Skips

src/subscript/fmuobs/gen_obs_writers.py

@@ -1,14 +1,12 @@
 """Read contents from simple text files"""
 import logging
-import warnings
 import re
+import warnings
 from datetime import datetime
-from pathlib import Path, PosixPath
-from subscript.fmuobs.util import (
-    ERT_ALT_DATE_FORMAT,
-    ERT_DATE_FORMAT,
-    ERT_ISO_DATE_FORMAT,
-)
+from pathlib import PosixPath
+from typing import Optional, Union, List, Tuple
+
+from subscript.fmuobs.util import ERT_DATE_FORMAT, ERT_ISO_DATE_FORMAT
 
 LOGGER = logging.getLogger("gen_obs_writers")
 
@@ -77,7 +75,7 @@ def ensure_correct_well_info_format(info):
     return info
 
 
-def find_well_file_path(folder_path: PosixPath) -> PosixPath:
+def find_well_file_path(folder_path: PosixPath) -> Optional[PosixPath]:
     """Find file with well information in folder
 
     Args:
@@ -182,7 +180,7 @@ def add_extra_well_data_if_rft(dict_to_change: dict, parent_dir, obs_folders):
     print("After modification dict is ", dict_to_change)
 
 
-def attach_spatial_data_if_exists(file_path: PosixPath, primary_content: dict) -> dict:
+def attach_spatial_data_if_exists(file_path: PosixPath, primary_content: dict):
     """Attach data from secondary file if it exists
 
     Args:
@@ -210,7 +208,8 @@ def attach_spatial_data_if_exists(file_path: PosixPath, primary_content: dict) -
 
 
 def dump_content_to_dict(
-    file_path: PosixPath, col_names: list = ("observations", "error")
+    file_path: PosixPath,
+    col_names: Union[List, Tuple] = ("observations", "error"),
 ) -> dict:
     """Read contents of file into list
 

src/subscript/fmuobs/writers.py

@@ -280,7 +280,7 @@ def summary_df2obsdict(smry_df: pd.DataFrame) -> List[dict]:
     return smry_obs_list
 
 
-def general_df2obsdict(general_df: pd.DataFrame, parent_dir: PosixPath) -> List[dict]:
+def general_df2obsdict(general_df: pd.DataFrame, parent_dir: PosixPath) -> dict:
     """Generate a dictionary structure suitable for yaml
     for general observations in dataframe representation
 
@@ -405,7 +405,7 @@ def block_df2obsdict(block_df: pd.DataFrame) -> List[dict]:
     return block_obs_list
 
 
-def df2obsdict(obs_df: pd.DataFrame, parent_dir: PosixPath = Path(".")) -> dict:
+def df2obsdict(obs_df: pd.DataFrame, parent_dir: PosixPath = PosixPath(".")) -> dict:
     """Generate a dictionary structure of all observations, this data structure
     is designed to look good in yaml, and is supported by WebViz and
     fmu-ensemble.

tests/_common_fmuobs.py

@@ -1,4 +1,5 @@
 from pathlib import Path
+
 import yaml
 
 TEST_DATA = TEST_DATA = "testdata_fmuobs/"
@@ -74,10 +75,16 @@ def assert_equal_length(to_be_tested, correct, key):
     if to_be_tested_len != correct_len:
         if to_be_tested_len > correct_len:
             diff_set = to_be_tested_set.difference(correct_set)
-            mess = f"{key}: Produced keys are {to_be_tested_len - correct_len} more than they should ({diff_set})"
+            mess = (
+                f"{key}: Produced keys are {to_be_tested_len - correct_len} "
+                f"more than they should ({diff_set})"
+            )
         else:
             diff_set = correct_set.difference(to_be_tested_set)
-            mess = f"{key}: Produced keys are {correct_len - to_be_tested_len} less than they should ({diff_set})"
+            mess = (
+                f"{key}: Produced keys are {correct_len - to_be_tested_len} "
+                f"less than they should ({diff_set})"
+            )
         raise AssertionError(mess)
 
 

tests/test_fmuobs_functions_4_general_obs_w_drogon.py

@@ -1,12 +1,13 @@
 """Test functions with drogon data"""
 import pandas as pd
 import pytest
-from subscript.fmuobs.parsers import ertobs2df
+
 from subscript.fmuobs.writers import general_df2obsdict
+
 from ._common_fmuobs import (
-    _find_observation_file,
     _assert_compulsories_are_correct,
     _compare_to_results_in_file,
+    _find_observation_file,
 )
 
 
@@ -81,13 +82,6 @@ def _fix_drogon_full_file():
     return _find_observation_file("drogon_wbhp_rft_wct_gor_tracer_4d_plt.obs")
 
 
-# def test_ertobs2df(drogon_full_obs_file):
-# input_str = drogon_full_obs_file.read_text()
-# print(input_str)
-# full_df = ertobs2df(input_str)
-# print(full_df)
-
-
 @pytest.mark.parametrize(
     "fixture_name",
     ["ert-doc_df", "drogon_tracer_df", "drogon_seismic_df", "drogon_rft_df"],
@@ -117,16 +111,6 @@ def test_general_df2obsdict(fixture_name, drogon_full_obs_file, request):
     stream.close()
     _assert_compulsories_are_correct(results)
     if fixture_name != "ert-doc_df":
-        # Comparison with file not done for ert-doc, the ert-doc file is for
+        # Comparison with file not done for ert-doc, the ert-doc file is
         # not just for general_obs
         _compare_to_results_in_file(results, correct_result_file, where)
-
-
-def test_general_df2obsdict_rft(drogon_full_obs_file, request):
-    fixture_name = "drogon_rft_df"
-    results = general_df2obsdict(
-        request.getfixturevalue(fixture_name), drogon_full_obs_file.parent
-    )
-    # _assert_compulsories_are_correct(results)
-
-    # _compare_to_results_in_file(results, fixture_name)

tests/test_fmuobs_gen_obs_writers.py

@@ -1,8 +1,10 @@
-import re
+"""Unit tests for gen_obs_writers"""
 from pathlib import Path
-from subscript.fmuobs import gen_obs_writers
+
 import pytest
 
+from subscript.fmuobs import gen_obs_writers
+
 TEST_DATA = "testdata_fmuobs"
 RFT_FOLDERS = ["drogon/rft/", "somewhere/completely/different/rft_ERT_use_MDadjusted/"]
 
@@ -118,8 +120,3 @@ def test_tidy_general_obs_keys():
         "tracer_jungle",
         "magic_seismic_data",
     }
-
-
-# def test_add_extra_well_data_if_rft(dict_to_change: dict, parent_dir):
-# def test_attach_spatial_data_if_exists(file_path: PosixPath, primary_content: dict) -> dict:
-# def test_dump_content_to_dict(

tests/test_fmuobs_make_dictionaries.py

@@ -1,15 +1,10 @@
-import re
-from pathlib import Path
-import yaml
-from subscript.fmuobs.fmuobs import autoparse_file, df2obsdict
-from pandas import DataFrame
 import pytest
+from pandas import DataFrame
+
+from subscript.fmuobs.fmuobs import autoparse_file, df2obsdict
+
+from ._common_fmuobs import _find_observation_file
 
-from ._common_fmuobs import (
-    _find_observation_file,
-    _assert_compulsories_are_correct,
-    _compare_to_results_in_file,
-)
 
 TEST_DATA = "testdata_fmuobs/"