fix test state leakage

src/seismometer/core/io.py

@@ -12,6 +12,8 @@
 
 Pathlike = str | Path
 
+logger = logging.getLogger("seismometer")
+
 
 def slugify(value: str) -> str:
     """
@@ -108,7 +110,7 @@ def resolve_filename(
     # Create pre-emptively
     if not basedir.is_dir():
         if not create:
-            logging.warning(f"No directory found for group: {basedir}")
+            logger.warning(f"No directory found for group: {basedir}")
         else:
             basedir.mkdir(parents=True, exist_ok=True)
     return basedir / filename
@@ -317,4 +319,4 @@ def _write(writer: Callable[[Any, "fileobject"], None], content: Any, file: Path
 
     with open(file, "w") as fo:
         writer(content, fo)
-    logging.info(f"File written: {file.resolve()}")
+    logger.info(f"File written: {file.resolve()}")

src/seismometer/data/loader/prediction.py

@@ -53,6 +53,7 @@ def _log_column_mismatch(actual_columns: list[str], desired_columns: list[str],
     """Logs warnings if the actual columns and desired columns are a mismatch."""
     if len(actual_columns) == len(desired_columns):
         return
+
     logger.warning(
         "Not all requested columns are present. " + f"Missing columns are {', '.join(desired_columns-present_columns)}"
     )

tests/configuration/test_model.py

@@ -78,7 +78,7 @@ def test_reduce_events_to_unique_names(self, caplog):
             undertest.Event(source="event2", display_name="Event 2"),
             undertest.Event(source="different source", display_name="Event 1"),
         ]
-        with caplog.at_level(logging.WARNING):
+        with caplog.at_level(logging.WARNING, logger="seismometer"):
             data_usage = undertest.DataUsage(events=events)
         assert "Duplicate" in caplog.text
 
@@ -93,7 +93,7 @@ def test_reduce_events_eliminates_source_display_collision(self, caplog):
             undertest.Event(source="event1"),
             undertest.Event(source="event2", display_name="event1"),
         ]
-        with caplog.at_level(logging.WARNING):
+        with caplog.at_level(logging.WARNING, logger="seismometer"):
             data_usage = undertest.DataUsage(events=events)
         assert "Duplicate" in caplog.text
 
@@ -107,7 +107,7 @@ def test_reduce_cohorts_to_unique_names(self, caplog):
             undertest.Cohort(source="cohort2", display_name="Cohort 2"),
             undertest.Cohort(source="different source", display_name="Cohort 1"),
         ]
-        with caplog.at_level(logging.WARNING):
+        with caplog.at_level(logging.WARNING, logger="seismometer"):
             data_usage = undertest.DataUsage(cohorts=cohorts)
         assert "Duplicate" in caplog.text
 
@@ -123,7 +123,7 @@ def test_reduce_cohorts_eliminates_source_display_collision(self, caplog):
             undertest.Cohort(source="cohort2", display_name="cohort1"),
         ]
 
-        with caplog.at_level(logging.WARNING):
+        with caplog.at_level(logging.WARNING, logger="seismometer"):
             data_usage = undertest.DataUsage(cohorts=cohorts)
         assert "Duplicate" in caplog.text
 

tests/core/test_decorators.py

@@ -8,11 +8,14 @@
 from seismometer.core.decorators import DiskCachedFunction, export
 
 
-def foo(arg1, kwarg1=None):
-    if kwarg1 is None:
-        return arg1 + 1
-    else:
-        return kwarg1 + 1
+def get_test_function():
+    def foo(arg1, kwarg1=None):
+        if kwarg1 is None:
+            return arg1 + 1
+        else:
+            return kwarg1 + 1
+
+    return foo
 
 
 class Test_Export:
@@ -26,14 +29,15 @@ def test_export(self):
         global __all__
         __all__ = []
 
-        new_fn = export(foo)
+        test_fn = get_test_function()
+        new_fn = export(test_fn)
 
         assert new_fn(1) == 2
         assert new_fn(1, 5) == 6
         assert __all__ == ["foo"]
 
         with pytest.raises(ImportError):
-            export(foo)
+            export(test_fn)
 
     def test_mod_none(self):
         """
@@ -45,8 +49,9 @@ def test_mod_none(self):
         global __all__
         __all__ = []
 
-        foo.__module__ = None
-        new_fn = export(foo)
+        test_fn = get_test_function()
+        test_fn.__module__ = None
+        new_fn = export(test_fn)
 
         assert new_fn(1) == 2
         assert new_fn(1, 5) == 6

tests/core/test_io.py

@@ -188,7 +188,7 @@ def test_write_new_file_in_nonexistent_directory(tmp_as_current):
 def test_write_logs_file_written(tmp_as_current, caplog):
     file = Path("new_file.txt")
 
-    with caplog.at_level(logging.INFO):
+    with caplog.at_level(logging.INFO, logger="seismometer"):
         undertest._write(lambda content, fo: fo.write(content), "test content", file, overwrite=False)
 
     assert f"File written: {file.resolve()}" in caplog.text
@@ -227,7 +227,7 @@ def test_create_makesdir_on_none(self, tmp_path, caplog):
         filename = "new_file"
         expected = Path("output/attr") / "age1_0-3_0-self+strip" / filename
 
-        with caplog.at_level(30):
+        with caplog.at_level(30, logger="seismometer"):
             _ = undertest.resolve_filename("new_file", attribute, subgroups)
 
         assert not caplog.text
@@ -239,7 +239,7 @@ def test_no_create_warns_on_nonexistent(self, caplog):
         filename = "new_file"
         expected = Path("output/attr") / "age1_0-3_0-self+strip" / filename
 
-        with caplog.at_level(30):
+        with caplog.at_level(30, logger="seismometer"):
             _ = undertest.resolve_filename("new_file", attribute, subgroups, create=False)
 
         assert "No directory" in caplog.text
@@ -252,7 +252,7 @@ def test_no_create_existent_does_not_warn(self, caplog):
         expected = Path("output/attr") / "gg" / filename
 
         expected.parent.mkdir(parents=True, exist_ok=False)
-        with caplog.at_level(30):
+        with caplog.at_level(30, logger="seismometer"):
             _ = undertest.resolve_filename("new_file", attribute, subgroups, create=False)
 
         assert not caplog.text

tests/data/loaders/test_load_events.py

@@ -68,7 +68,7 @@ def test_nofile_warns_and_returns_empty(self, setup_fn, load_fn, caplog):
         config = setup_fn()
         config.event_path = "not_a_file.parquet"
 
-        with caplog.at_level(logging.DEBUG):
+        with caplog.at_level(logging.DEBUG, logger="seismometer"):
             actual = load_fn(config)
         print(caplog.text)
         assert "No events found" in caplog.text
@@ -144,7 +144,7 @@ def test_merge_info_logged(self, event, str_inclusions, caplog):
             }
         )
 
-        with caplog.at_level(logging.DEBUG):
+        with caplog.at_level(logging.DEBUG, logger="seismometer"):
             _ = undertest.merge_onto_predictions(config, event_df, predictions)
 
         for pattern in str_inclusions:
@@ -166,7 +166,7 @@ def test_imputation_on_target(self, caplog):
             }
         )
 
-        with caplog.at_level(logging.WARNING):
+        with caplog.at_level(logging.WARNING, logger="seismometer"):
             _ = undertest.merge_onto_predictions(config, event_df, predictions)
 
         assert "Event a specified impute" in caplog.text

tests/data/loaders/test_load_pipeline.py

@@ -71,7 +71,7 @@ def test_loading_can_log_location(self, fake_config, caplog):
         input = "INPUT"
 
         loader = undertest.SeismogramLoader(fake_config)
-        with caplog.at_level("INFO"):
+        with caplog.at_level("INFO", logger="seismometer"):
             _ = loader.load_data(input)
 
         assert "Configuration speficies" in caplog.text

tests/data/loaders/test_load_predictions.py

@@ -140,7 +140,7 @@ def test_column_mismatch_logs_warning(
         config = setup_fn()
         config.features = desired_columns
 
-        with caplog.at_level(log_level):
+        with caplog.at_level(log_level, logger="seismometer"):
             _ = load_fn(config)
 
         assert ("Not all requested columns are present" in caplog.text) == warning_present

tests/html/test_templates.py

@@ -29,7 +29,7 @@ def cohort_summaries_template(res):
 
 class Test_Templates:
     def test_nonexistent_template(self, caplog):
-        with caplog.at_level(logging.WARNING):
+        with caplog.at_level(logging.WARNING, logger="seismometer"):
             undertest.render_into_template("unknown")
         assert "HTML template unknown not found" in caplog.text
 

tests/test_startup.py

@@ -10,7 +10,7 @@
 from seismometer.seismogram import Seismogram
 
 
-def fake_load_config(self, *args):
+def fake_load_config(self, *args, definitions=None):
     mock_config = Mock(autospec=ConfigProvider)
     mock_config.output_dir.return_value
     self.config = mock_config
@@ -19,7 +19,7 @@ def fake_load_config(self, *args):
 
 
 # TODO: update this to create testing Loader and have factory return it
-def fake_load_data(self, *args):
+def fake_load_data(self, predictions=None, events=None, reset=False):
     self.dataframe = pd.DataFrame()