avoid redefined outer name errors, remove unneeded/redundant fixtures that didnt actually do anything

Author: ilaflott

fremorizer/tests/test_cli.py

@@ -335,7 +335,7 @@ def test_cli_fremor_config_case1(cli_sos_nc_file): # pylint: disable=redefined-o
     (mock_pp_dir / 'ocean' / 'ts' / 'annual').mkdir(parents=True, exist_ok=True)
 
     # symlink the test nc file into the mock tree
-    src_nc = INDIR / 'reduced_ocean_monthly_1x1deg.199301-199302.sos.nc'
+    src_nc = Path(cli_sos_nc_file)
     dst_nc = comp_ts_dir / src_nc.name
     if dst_nc.exists() or dst_nc.is_symlink():
         dst_nc.unlink()
@@ -412,16 +412,17 @@ def test_cli_fremor_varlist_opt_dne():
     assert result.exit_code == 2
 
 
-def test_cli_fremor_varlist_no_table_filter(cli_sos_nc_file, cli_sosv2_nc_file, tmp_path): # pylint: disable=redefined-outer-name
+def test_cli_fremor_varlist_no_table_filter(tmp_path, cli_sos_nc_file, cli_sosv2_nc_file): # pylint: disable=redefined-outer-name
     '''fremor varlist — no MIP table filter.
     Creates a variable list from the ocean_sos_var_file test data without a MIP table,
     so both sos and sosV2 should appear.'''
     output_varlist = tmp_path / 'test_varlist_no_filter.json'
+    assert Path(cli_sos_nc_file).parent == Path(cli_sosv2_nc_file).parent, 'something wrong with input nc files'
 
     result = runner.invoke(fremor, args=[
         "-v", "-v",
         "varlist",
-        "--dir_targ", str(INDIR),
+        "--dir_targ", str(Path(cli_sos_nc_file).parent),
         "--output_variable_list", str(output_varlist)
     ])
     assert result.exit_code == 0, f'varlist failed: {result.output}'
@@ -439,11 +440,12 @@ def test_cli_fremor_varlist_cmip6_table_filter(cli_sos_nc_file, cli_sosv2_nc_fil
     '''fremor varlist — with CMIP6 Omon MIP table filter.
     Only sos should survive; sosV2 is not in the CMIP6 Omon table.'''
     output_varlist = tmp_path / 'test_varlist_cmip6_filter.json'
+    assert Path(cli_sos_nc_file).parent == Path(cli_sosv2_nc_file).parent, 'something wrong with input nc files'
 
     result = runner.invoke(fremor, args=[
         "-v", "-v",
         "varlist",
-        "--dir_targ", str(INDIR),
+        "--dir_targ", str(Path(cli_sos_nc_file).parent),
         "--output_variable_list", str(output_varlist),
         "--mip_table", str(CMIP6_TABLE_CONFIG)
     ])
@@ -461,11 +463,12 @@ def test_cli_fremor_varlist_cmip7_table_filter(cli_sos_nc_file, cli_sosv2_nc_fil
     '''fremor varlist — with CMIP7 ocean MIP table filter.
     sos should survive (sos_tavg-u-hxy-sea splits to sos); sosV2 should not.'''
     output_varlist = tmp_path / 'test_varlist_cmip7_filter.json'
+    assert Path(cli_sos_nc_file).parent == Path(cli_sosv2_nc_file).parent, 'something wrong with input nc files'
 
     result = runner.invoke(fremor, args=[
         "-v", "-v",
         "varlist",
-        "--dir_targ", str(INDIR),
+        "--dir_targ", str(Path(cli_sos_nc_file).parent),
         "--output_variable_list", str(output_varlist),
         "--mip_table", str(CMIP7_TABLE_CONFIG)
     ])
@@ -580,7 +583,7 @@ def test_cli_fremor_run_with_logfile(cli_sos_nc_file, tmp_path): # pylint: disab
     result = runner.invoke(fremor, args=[
         '-vv', '-l', str(log_path),
         'run', '--run_one',
-        '--indir', str(INDIR),
+        '--indir', str(Path(cli_sos_nc_file).parent),
         '--varlist', str(VARLIST),
         '--table_config', str(CMIP6_TABLE_CONFIG),
         '--exp_config', str(EXP_CONFIG),
@@ -621,11 +624,12 @@ def test_cli_fremor_run_with_logfile_omission_case(cli_sos_nc_file, cli_sosv2_nc
     varlist_fd, varlist_path = tempfile.mkstemp(suffix='.json')
     with os.fdopen(varlist_fd, 'w') as f:
         json.dump(varlist_data, f)
+    assert Path(cli_sos_nc_file).parent == Path(cli_sosv2_nc_file).parent, "something wrong with input nc files"
 
     result = runner.invoke(fremor, args=[
         '-vv', '-l', str(log_path),
         'run',
-        '--indir', str(INDIR),
+        '--indir', str(Path(cli_sos_nc_file).parent),
         '--varlist', varlist_path,
         '--table_config', str(CMIP6_TABLE_CONFIG),
         '--exp_config', str(EXP_CONFIG),

fremorizer/tests/test_cmor_find_subtool.py

@@ -4,32 +4,24 @@
 '''
 
 import json
-import tempfile
 from pathlib import Path
 
 import pytest
 
 from fremorizer.cmor_finder import make_simple_varlist, cmor_find_subtool
 
-@pytest.fixture
-def temp_dir():
-    ''' simple pytest fixture for providing temp directory '''
-    with tempfile.TemporaryDirectory() as tmpdir:
-        yield tmpdir
-
-
-def test_make_simple_varlist(temp_dir):
+def test_make_simple_varlist(tmp_path):
     '''
     quick tests of make_simple_varlist
     '''
     # Create some dummy netCDF files
     nc_files = ["test.20230101.var1.nc", "test.20230101.var2.nc", "test.20230101.var3.nc"]
-    assert Path(temp_dir).exists()
+    assert Path(tmp_path).exists()
     for nc_file in nc_files:
-        Path(temp_dir, nc_file).touch()
+        Path(tmp_path, nc_file).touch()
 
-    output_file = Path(temp_dir, "varlist.json")
-    make_simple_varlist(temp_dir, output_file)
+    output_file = Path(tmp_path, "varlist.json")
+    make_simple_varlist(tmp_path, output_file)
 
     # Check if the output file is created
     assert output_file.exists()
@@ -46,19 +38,19 @@ def test_make_simple_varlist(temp_dir):
     assert var_list == expected_var_list
 
 
-def test_find_subtool_no_json_dir_err(temp_dir):
+def test_find_subtool_no_json_dir_err(tmp_path):
     ''' test json_table_config_dir does not exist error '''
-    target_dir_dne = Path(temp_dir) / 'foo'
+    target_dir_dne = Path(tmp_path) / 'foo'
     assert not target_dir_dne.exists(), 'target dir should not exist for this test'
     with pytest.raises(OSError, match=f'ERROR directory {target_dir_dne} does not exist! exit.'):
         cmor_find_subtool(json_var_list=None,
                           json_table_config_dir=str(target_dir_dne),
                           opt_var_name=None)
 
 
-def test_find_subtool_no_json_files_in_dir_err(temp_dir):
+def test_find_subtool_no_json_files_in_dir_err(tmp_path):
     ''' test json_table_config_dir has no files in it error '''
-    target_dir = Path(temp_dir) / 'foo'
+    target_dir = Path(tmp_path) / 'foo'
     target_dir.mkdir(exist_ok=False)
     assert target_dir.is_dir() and target_dir.exists(), "temp dir directory creation failed, inspect code"
     with pytest.raises(OSError, match=f'ERROR directory {target_dir} contains no JSON files, exit.'):
@@ -67,7 +59,7 @@ def test_find_subtool_no_json_files_in_dir_err(temp_dir):
                           opt_var_name=None)
 
 
-def test_find_subtool_no_varlist_no_optvarname_err(temp_dir):
+def test_find_subtool_no_varlist_no_optvarname_err():
     ''' test no opt_var_name AND no varlist error '''    
     with pytest.raises(ValueError, match='ERROR: no opt_var_name given but also no content in variable list!!! exit!'):
         cmor_find_subtool(json_var_list=None,

fremorizer/tests/test_cmor_finder_make_simple_varlist.py

@@ -10,8 +10,8 @@
 from fremorizer.cmor_finder import make_simple_varlist
 
 
-@pytest.fixture
-def temp_netcdf_dir(tmp_path):
+@pytest.fixture(name='netcdf_dir_files')
+def temp_netcdf_dir_files(tmp_path):
     """
     Fixture to create a temporary directory with sample NetCDF files.
     """
@@ -29,8 +29,8 @@ def temp_netcdf_dir(tmp_path):
     return tmp_path
 
 
-@pytest.fixture
-def temp_netcdf_dir_single_file(tmp_path):
+@pytest.fixture(name='netcdf_dir_file')
+def temp_netcdf_dir_file(tmp_path):
     """
     Fixture to create a temporary directory with a single NetCDF file.
     """
@@ -39,23 +39,18 @@ def temp_netcdf_dir_single_file(tmp_path):
     return tmp_path
 
 
-@pytest.fixture
-def empty_dir(tmp_path):
-    """
-    Fixture to create an empty temporary directory.
-    """
-    return tmp_path
 
 
-def test_make_simple_varlist_success(temp_netcdf_dir, tmp_path):
+
+def test_make_simple_varlist_success(netcdf_dir_files):
     """
     Test successful creation of variable list from NetCDF files.
     """
     # Arrange
-    output_file = tmp_path / "varlist.json"
+    output_file = netcdf_dir_files / "varlist.json"
 
     # Act
-    result = make_simple_varlist(str(temp_netcdf_dir), str(output_file))
+    result = make_simple_varlist(str(netcdf_dir_files), str(output_file))
 
     # Assert
     assert result is not None
@@ -74,12 +69,12 @@ def test_make_simple_varlist_success(temp_netcdf_dir, tmp_path):
         assert saved_data == result
 
 
-def test_make_simple_varlist_return_value_only(temp_netcdf_dir):
+def test_make_simple_varlist_return_value_only(netcdf_dir_files):
     """
     Test make_simple_varlist with output_variable_list=None returns var_list.
     """
     # Act
-    result = make_simple_varlist(str(temp_netcdf_dir), None)
+    result = make_simple_varlist(str(netcdf_dir_files), None)
 
     # Assert
     assert result is not None
@@ -89,15 +84,15 @@ def test_make_simple_varlist_return_value_only(temp_netcdf_dir):
     assert "velocity" in result
 
 
-def test_make_simple_varlist_single_file_warning(temp_netcdf_dir_single_file, tmp_path):
+def test_make_simple_varlist_single_file_warning(netcdf_dir_file):
     """
     Test warning when only one file is found.
     """
     # Arrange
-    output_file = tmp_path / "varlist.json"
+    output_file = netcdf_dir_file / "varlist.json"
 
     # Act
-    result = make_simple_varlist(str(temp_netcdf_dir_single_file), str(output_file))
+    result = make_simple_varlist(str(netcdf_dir_file), str(output_file))
 
     # Assert
     assert result is not None
@@ -106,18 +101,18 @@ def test_make_simple_varlist_single_file_warning(temp_netcdf_dir_single_file, tm
     assert result["temp"] == "temp"
 
 
-def test_make_simple_varlist_no_files(empty_dir):
+def test_make_simple_varlist_no_files(tmp_path):
     """
     Test behavior when no NetCDF files are found in directory.
     """
     # Act
-    result = make_simple_varlist(str(empty_dir), None)
+    result = make_simple_varlist(str(tmp_path), None)
 
     # Assert - function should return None when no files found
     assert result is None
 
 
-def test_make_simple_varlist_invalid_output_path(temp_netcdf_dir):
+def test_make_simple_varlist_invalid_output_path(netcdf_dir_file):
     """
     Test OSError when output file cannot be written.
     """
@@ -126,7 +121,7 @@ def test_make_simple_varlist_invalid_output_path(temp_netcdf_dir):
 
     # Act & Assert
     with pytest.raises(OSError, match="output variable list created but cannot be written"):
-        make_simple_varlist(str(temp_netcdf_dir), invalid_output_path)
+        make_simple_varlist(str(netcdf_dir_file), invalid_output_path)
 
 
 def test_make_simple_varlist_no_matching_pattern(tmp_path):

fremorizer/tests/test_cmor_helpers.py

@@ -239,7 +239,7 @@ def test_create_tmp_dir_with_exp_config(tmp_path):
     assert Path(result, 'CMIP7/output').is_dir()
 
 
-def test_create_tmp_dir_oserror(tmp_path):
+def test_create_tmp_dir_oserror():
     ''' create_tmp_dir should raise OSError when directory creation fails '''
     # /dev/null is not a directory; we can't mkdir inside it
     with pytest.raises(OSError, match='problem creating tmp output directory'):

fremorizer/tests/test_cmor_helpers_update_grid_label.py

@@ -17,7 +17,7 @@
     "other_field": "some_value"
 }
 
-@pytest.fixture
+@pytest.fixture(name='test_json_file')
 def temp_json_file(tmp_path):
     """
     Fixture to create a temporary JSON file for testing.
@@ -33,7 +33,7 @@ def temp_json_file(tmp_path):
         json.dump(TEST_JSON_CONTENT, file, indent=4)
     return json_file
 
-def test_update_grid_label_and_grid_success(temp_json_file):
+def test_update_grid_label_and_grid_success(test_json_file):
     """
     Test successful update of 'grid_label' and 'grid' fields.
     """
@@ -43,22 +43,22 @@ def test_update_grid_label_and_grid_success(temp_json_file):
     new_nom_res = "updated_nom_res"
 
     # Act
-    update_grid_and_label(temp_json_file, new_grid_label, new_grid, new_nom_res)
+    update_grid_and_label(test_json_file, new_grid_label, new_grid, new_nom_res)
 
     # Assert
-    with open(temp_json_file, "r", encoding="utf-8") as file:
+    with open(test_json_file, "r", encoding="utf-8") as file:
         data = json.load(file)
         assert data["grid"] == new_grid
         assert data["grid_label"] == new_grid_label
         assert data["nominal_resolution"] == new_nom_res
         assert data["other_field"] == "some_value"  # Ensure other fields are untouched
 
-def test_missing_nom_res_field(temp_json_file):
+def test_missing_nom_res_field(test_json_file):
     """
     Test behavior when the 'nominal_resolution' field is missing in the JSON file.
     """
     # Arrange
-    with open(temp_json_file, "r+", encoding="utf-8") as file:
+    with open(test_json_file, "r+", encoding="utf-8") as file:
         data = json.load(file)
         del data["nominal_resolution"]  # Remove the 'nominal_resolution' field
         file.seek(0)
@@ -74,14 +74,14 @@ def test_missing_nom_res_field(temp_json_file):
         KeyError,
         match='"Error updating \'nominal_resolution\'. Ensure the field exists and is modifiable."'
     ):
-        update_grid_and_label(temp_json_file, new_grid_label, new_grid, new_nom_res)
+        update_grid_and_label(test_json_file, new_grid_label, new_grid, new_nom_res)
 
-def test_missing_grid_label_field(temp_json_file):
+def test_missing_grid_label_field(test_json_file):
     """
     Test behavior when the 'grid_label' field is missing in the JSON file.
     """
     # Arrange
-    with open(temp_json_file, "r+", encoding="utf-8") as file:
+    with open(test_json_file, "r+", encoding="utf-8") as file:
         data = json.load(file)
         del data["grid_label"]  # Remove the 'grid_label' field
         file.seek(0)
@@ -94,14 +94,14 @@ def test_missing_grid_label_field(temp_json_file):
 
     # Act & Assert
     with pytest.raises(KeyError, match="Error while updating 'grid_label'"):
-        update_grid_and_label(temp_json_file, new_grid_label, new_grid, new_nom_res)
+        update_grid_and_label(test_json_file, new_grid_label, new_grid, new_nom_res)
 
-def test_missing_grid_field(temp_json_file):
+def test_missing_grid_field(test_json_file):
     """
     Test behavior when the 'grid' field is missing in the JSON file.
     """
     # Arrange
-    with open(temp_json_file, "r+", encoding="utf-8") as file:
+    with open(test_json_file, "r+", encoding="utf-8") as file:
         data = json.load(file)
         del data["grid"]  # Remove the 'grid' field
         file.seek(0)
@@ -114,7 +114,7 @@ def test_missing_grid_field(temp_json_file):
 
     # Act & Assert
     with pytest.raises(KeyError, match="Error while updating 'grid'"):
-        update_grid_and_label(temp_json_file, new_grid_label, new_grid, new_nom_res)
+        update_grid_and_label(test_json_file, new_grid_label, new_grid, new_nom_res)
 
 def test_invalid_json_file(tmp_path):
     """