STY: Apply more linting rules

This implements some additional linting rules and prepares a few others.
It also adds the `--cov --cov-report term-missing` coverage report to be
emitted at the end of test runs, which may be noisier but still useful
to see. The test runs install the package with `-e` now so that the code
lines missing test coverage are visible.

.github/workflows/ci-fmudataio.yml

@@ -26,7 +26,7 @@ jobs:
       - name: Install fmu-dataio
         run: |
           pip install pip -U
-          pip install .[dev]
+          pip install -e .[dev]
 
       - name: Install fmu-sumo-uploader for Python 3.8
         if: matrix.python-version == '3.8'

docs/ext/pydantic_autosummary/generate.py

@@ -516,9 +516,8 @@ def _get_modules(
         if public_members is not None:
             if modname in public_members:
                 public.append(fullname)
-        else:
-            if not modname.startswith("_"):
-                public.append(fullname)
+        elif not modname.startswith("_"):
+            public.append(fullname)
     return public, items
 
 

examples/s/d/nn/xcase/realization-0/iter-0/any/bin/export_grid3d.py

@@ -5,7 +5,7 @@
 
 import xtgeo
 
-import fmu.dataio as dataio
+from fmu import dataio
 from fmu.config import utilities as ut
 
 logging.basicConfig(level=logging.DEBUG)

examples/s/d/nn/xcase/realization-0/iter-0/rms/bin/export_a_surface.py

@@ -10,7 +10,7 @@
 
 import xtgeo
 
-import fmu.dataio as dataio
+from fmu import dataio
 from fmu.config import utilities as ut
 
 logger = logging.getLogger(__name__)

examples/s/d/nn/xcase/realization-0/iter-0/rms/bin/export_faultpolygons.py

@@ -5,7 +5,7 @@
 
 import xtgeo
 
-import fmu.dataio as dataio
+from fmu import dataio
 from fmu.config import utilities as utils
 
 logger = logging.getLogger(__name__)

examples/s/d/nn/xcase/realization-0/iter-0/rms/bin/export_faultroom_surfaces.py

@@ -3,7 +3,7 @@
 import logging
 from pathlib import Path
 
-import fmu.dataio as dataio
+from fmu import dataio
 from fmu.config import utilities as utils
 
 logger = logging.getLogger(__name__)

examples/s/d/nn/xcase/realization-0/iter-0/rms/bin/export_propmaps.py

@@ -16,7 +16,7 @@
 
 import xtgeo
 
-import fmu.dataio as dataio
+from fmu import dataio
 from fmu.config import utilities as ut
 
 logger = logging.getLogger(__name__)

examples/s/d/nn/xcase/realization-1/iter-0/rms/bin/export_a_surface.py

@@ -10,7 +10,7 @@
 
 import xtgeo
 
-import fmu.dataio as dataio
+from fmu import dataio
 from fmu.config import utilities as ut
 
 logger = logging.getLogger(__name__)

examples/s/d/nn/xcase/realization-9/iter-0/rms/bin/export_a_surface.py

@@ -10,7 +10,7 @@
 
 import xtgeo
 
-import fmu.dataio as dataio
+from fmu import dataio
 from fmu.config import utilities as ut
 
 logger = logging.getLogger(__name__)

pyproject.toml

@@ -89,31 +89,49 @@ write_to = "src/fmu/dataio/version.py"
 minversion = "6.0"
 testpaths = "tests"
 
+[tool.coverage.run]
+omit = [
+    "version.py",
+    "tests/**",
+]
+
 [tool.pydocstyle]
 convention = "google"
 match = '(?!(test_|_)).*\.py'
 
 [tool.ruff]
 line-length = 88
 exclude = ["version.py"]
+
 [tool.ruff.lint]
-ignore = ["C901"]
+ignore = [
+    "B028",  # No explicit `stacklevel` keyword argument found
+    "C901",  # mccabe complex-structure
+]
 select = [
-    "C",
-    "E",
-    "F",
-    "I",
-    "PIE",
-    "Q",
-    "RET",
-    "RSE",
-    "SIM",
-    "W",
-    # "C90",
-    # "NPY",
-    # "PD",
-    # "PL",
+    "B",  # flake-8-bugbear
+    "C",  # pylint-convention
+    "C90",  # mccabe
+    "E",  # pycodestyle-error
+    "F",  # pyflakes
+    "I",  # isort
+    "NPY",  # numpy
+    # "PD",  # pandas-vet
+    "PIE",  # flake8-pie
+    # "PL",  # pylint
+    "Q",  # flake8-quotes
+    "RET",  # flake8-return
+    "RSE",  # flake8-raise
+    "SIM",  # flake8-simplify
+    # "TCH",  # flake8-type-checking
+    # "TID",  # flake8-tidy-imports
+    # "UP",  # pyupgrade
+    "W",  # pylint-warnings
 ]
+
+[tool.ruff.lint.pydocstyle]
+convention = "google"
+
 [tool.ruff.lint.isort]
 combine-as-imports = true
 

src/fmu/dataio/aggregation.py

@@ -226,9 +226,8 @@ def _set_metadata(
 
         if self.aggregation_id is None:
             self.aggregation_id = self._generate_aggr_uuid(uuids)
-        else:
-            if not isinstance(self.aggregation_id, str):
-                raise ValueError("aggregation_id must be a string")
+        elif not isinstance(self.aggregation_id, str):
+            raise ValueError("aggregation_id must be a string")
 
         if not self.operation:
             raise ValueError("The 'operation' key has no value")
@@ -346,8 +345,10 @@ def generate_metadata(
             try:
                 rid = conf["fmu"]["realization"]["id"]
                 xuuid = conf["fmu"]["realization"]["uuid"]
-            except Exception as error:
-                raise ValidationError(f"Seems that input config are not valid: {error}")
+            except Exception as e:
+                raise ValidationError(
+                    f"Seems that input config are not valid: {e}"
+                ) from e
 
             real_ids.append(rid)
             uuids.append(xuuid)

src/fmu/dataio/export/rms/_conditional_rms_imports.py

@@ -19,7 +19,7 @@ def import_rms_package() -> tuple[Any, Any]:
     """
     try:
         import rmsapi
-        import rmsapi.jobs as jobs
+        from rmsapi import jobs
 
     except ImportError:
         try:
@@ -28,13 +28,13 @@ def import_rms_package() -> tuple[Any, Any]:
                     "ignore", category=DeprecationWarning, module="roxar"
                 )
                 import roxar as rmsapi
-                import roxar.jobs as jobs
+                from roxar import jobs
 
-        except ImportError:
+        except ImportError as e:
             raise ImportError(
                 "Neither 'roxar' nor 'rmsapi' are available. You have to be inside "
                 "RMS to use this function."
-            )
+            ) from e
 
     return (rmsapi, jobs)
 

src/fmu/dataio/providers/objectdata/_base.py

@@ -265,8 +265,8 @@ def _validate_get_ext(fmt: str, validator: ValidFormats) -> str:
         """Validate that fmt (file format) matches data and return legal extension."""
         try:
             return validator.value[fmt]
-        except KeyError:
+        except KeyError as e:
             raise ConfigurationError(
                 f"The file format {fmt} is not supported. ",
                 f"Valid formats are: {list(validator.value.keys())}",
-            )
+            ) from e

tests/test_export_rms/test_export_rms_volumetrics.py

@@ -1,7 +1,7 @@
 """Test the dataio running RMS spesici utility function for volumetrics"""
 
-import unittest.mock as mock
 from pathlib import Path
+from unittest import mock
 
 import jsonschema
 import numpy as np
@@ -10,7 +10,7 @@
 import pytest
 from pydantic import ValidationError
 
-import fmu.dataio as dataio
+from fmu import dataio
 from fmu.dataio._logging import null_logger
 from fmu.dataio._products.inplace_volumes import (
     InplaceVolumesResult,

tests/test_integration/test_wf_copy_preprocessed_data.py

@@ -2,7 +2,7 @@
 import pytest
 import yaml
 
-import fmu.dataio as dataio
+from fmu import dataio
 
 from .ert_config_utils import (
     add_copy_preprocessed_workflow,

tests/test_units/test_aggregated_surfaces.py

@@ -7,7 +7,7 @@
 import xtgeo
 
 import fmu.dataio._utils as utils
-import fmu.dataio.dataio as dataio
+from fmu.dataio import dataio
 
 logger = logging.getLogger(__name__)
 

tests/test_units/test_checksum_md5.py

@@ -1,6 +1,6 @@
 from pathlib import Path
 
-import fmu.dataio.readers as readers
+from fmu.dataio import readers
 from fmu.dataio._utils import md5sum
 from fmu.dataio.dataio import ExportData, read_metadata
 

tests/test_units/test_dataio.py

@@ -714,7 +714,7 @@ def test_global_config_from_env(monkeypatch, global_config2_path, globalconfig1)
     monkeypatch.setenv("FMU_GLOBAL_CONFIG", str(global_config2_path))
 
     edata = ExportData(content="depth")  # the env variable will override this
-    assert getattr(edata.config.masterdata, "smda")
+    assert edata.config.masterdata.smda
     assert edata.config.model.name == "ff"
 
     # do not use global config from environment when explicitly given

tests/test_units/test_dunder_methods.py

@@ -39,18 +39,18 @@ def _fixture_testdata_stratigraphy() -> Stratigraphy:
 def test_stratigraphy_dunder_iter(testdata_stratigraphy):
     try:
         count = 0
-        for item in testdata_stratigraphy:
+        for _ in testdata_stratigraphy:
             count += 1
         assert count == 3
     except Exception:
-        assert False, "Stratigraphy class does not have __iter__()"
+        pytest.fail("Stratigraphy class does not have __iter__()")
 
 
 def test_stratigraphy_dunder_getitem(testdata_stratigraphy):
     try:
         testdata_stratigraphy["TopStratUnit2"]
     except Exception:
-        assert False, "Stratigraphy class does not have __getitem__()"
+        pytest.fail("Stratigraphy class does not have __getitem__()")
 
 
 # --------------------------------------------------------------------------------------
@@ -80,15 +80,15 @@ def _fixture_testdata_parameters() -> Parameters:
 def test_parameters_dunder_iter(testdata_parameters):
     try:
         count = 0
-        for item in testdata_parameters:
+        for _ in testdata_parameters:
             count += 1
         assert count == 3
     except Exception:
-        assert False, "Parameters class does not have __iter__()"
+        pytest.fail("Parameters class does not have __iter__()")
 
 
 def test_parameters_dunder_getitem(testdata_parameters):
     try:
         testdata_parameters["p2"]
     except Exception:
-        assert False, "Parameters class does not have __getitem__()"
+        pytest.fail("Parameters class does not have __getitem__()")

tests/test_units/test_ert_context.py

@@ -14,7 +14,7 @@
 import pytest
 import yaml
 
-import fmu.dataio.dataio as dataio
+from fmu.dataio import dataio
 from fmu.dataio._utils import prettyprint_dict
 
 logger = logging.getLogger(__name__)

tests/test_units/test_fmuprovider_class.py

@@ -7,7 +7,7 @@
 import pydantic
 import pytest
 
-import fmu.dataio as dataio
+from fmu import dataio
 
 # from conftest import pretend_ert_env_run1
 from fmu.dataio._model.enums import ErtSimulationMode, FMUContext

tests/test_units/test_objectdataprovider_class.py

@@ -6,7 +6,7 @@
 import pytest
 import yaml
 
-import fmu.dataio as dataio
+from fmu import dataio
 from fmu.dataio._definitions import ConfigurationError, ValidFormats
 from fmu.dataio._model.specification import FaultRoomSurfaceSpecification
 from fmu.dataio.providers.objectdata._faultroom import FaultRoomSurfaceProvider

tests/test_units/test_preprocessed.py

@@ -6,7 +6,7 @@
 import pytest
 import yaml
 
-import fmu.dataio as dataio
+from fmu import dataio
 from fmu.dataio import _utils as utils
 from fmu.dataio.exceptions import InvalidMetadataError
 from fmu.dataio.providers._fmu import ERT_RELATIVE_CASE_METADATA_FILE

tests/test_units/test_prerealization_surfaces.py

@@ -15,7 +15,7 @@
 
 import pytest
 
-import fmu.dataio as dataio
+from fmu import dataio
 from fmu.dataio import _utils as utils
 
 from ..conftest import remove_ert_env, set_ert_env_prehook

tests/test_units/test_rms_context.py

@@ -14,8 +14,7 @@
 import xtgeo
 import yaml
 
-import fmu.dataio.dataio as dataio
-import fmu.dataio.readers as readers
+from fmu.dataio import dataio, readers
 from fmu.dataio._utils import prettyprint_dict
 from fmu.dataio.dataio import ValidationError