tests: adjust to new warnings and errors

tests/integration/test_bracken_etl.py

@@ -71,6 +71,7 @@ def other_profile(data_dir: Path, request: pytest.FixtureRequest) -> Path:
         ),
     ],
 )
+@pytest.mark.filterwarnings("error")
 def test_bracken_etl(
     bracken_data_dir: Path,
     filename: str,

tests/integration/test_diamond_etl.py

@@ -22,6 +22,7 @@
 from pathlib import Path
 
 import pytest
+from pandas.errors import ParserError
 from pandera.errors import SchemaErrors
 
 from taxpasta.application.error import StandardisationError
@@ -60,11 +61,11 @@ def other_profile(data_dir: Path, request: pytest.FixtureRequest) -> Path:
         "diamond_valid_2.tsv",
         pytest.param(
             "diamond_invalid_1.tsv",
-            marks=pytest.mark.raises(exception=SchemaErrors),
+            marks=pytest.mark.raises(exception=ParserError),
         ),
         pytest.param(
             "diamond_invalid_2.tsv",
-            marks=pytest.mark.raises(exception=SchemaErrors),
+            marks=pytest.mark.raises(exception=ParserError),
         ),
     ],
 )

tests/integration/test_ganon_etl.py

@@ -59,7 +59,7 @@ def other_profile(data_dir: Path, request: pytest.FixtureRequest) -> Path:
         "2612_pe_ERR5766176_db1.ganon.tre",
         pytest.param(
             "invalid_2612_pe_ERR5766176_db1.ganon_missing_column.tre",
-            marks=pytest.mark.raises(exception=SchemaErrors),
+            marks=pytest.mark.raises(exception=ValueError),
         ),
     ],
 )

tests/integration/test_kaiju_etl.py

@@ -64,6 +64,7 @@ def other_profile(data_dir: Path, request: pytest.FixtureRequest) -> Path:
         ),
     ],
 )
+@pytest.mark.filterwarnings("error")
 def test_kaiju_etl(
     kaiju_data_dir: Path,
     filename: str,

tests/integration/test_kraken2_etl.py

@@ -71,6 +71,7 @@ def other_profile(data_dir: Path, request: pytest.FixtureRequest) -> Path:
         ),
     ],
 )
+@pytest.mark.filterwarnings("error")
 def test_kraken2_etl(
     kraken2_data_dir: Path,
     filename: str,

tests/integration/test_metaphlan_etl.py

@@ -86,6 +86,7 @@ def test_valid_profile_etl(
     )
 
 
+@pytest.mark.filterwarnings("error")
 def test_invalid_profile_etl(
     invalid_metaphlan_profile: Path,
 ):

tests/unit/infrastructure/application/bracken/test_bracken_profile.py

@@ -159,6 +159,7 @@ def test_column_presence(profile: pd.DataFrame):
         ),
     ],
 )
+@pytest.mark.filterwarnings("error")
 def test_fraction_total_reads(profile: pd.DataFrame):
     """Test that the fraction column is checked."""
     BrackenProfile.validate(profile)

tests/unit/infrastructure/application/centrifuge/test_centrifuge_profile.py

@@ -135,6 +135,7 @@ def test_column_presence(profile: pd.DataFrame):
         ),
     ],
 )
+@pytest.mark.filterwarnings("error")
 def test_percent(profile: pd.DataFrame):
     """Test that the percent column is checked."""
     CentrifugeProfile.validate(profile)

tests/unit/infrastructure/application/ganon/test_ganon_profile.py

@@ -128,7 +128,7 @@ def test_column_presence(profile: pd.DataFrame):
                 )
             ),
             marks=pytest.mark.raises(
-                exception=SchemaError, message="check_compositionality"
+                exception=SchemaError, message="<Check compositionality>"
             ),
         ),
         pytest.param(
@@ -148,11 +148,12 @@ def test_column_presence(profile: pd.DataFrame):
                 )
             ),
             marks=pytest.mark.raises(
-                exception=SchemaError, message="check_compositionality"
+                exception=SchemaError, message="<Check compositionality>"
             ),
         ),
     ],
 )
+@pytest.mark.filterwarnings("error")
 def test_percent(profile: pd.DataFrame):
     """Test that the percent column (percent_cumulative) is checked."""
     GanonProfile.validate(profile)

tests/unit/infrastructure/application/kaiju/test_kaiju_profile.py

@@ -143,6 +143,7 @@ def test_column_presence(profile: pd.DataFrame):
         ),
     ],
 )
+@pytest.mark.filterwarnings("error")
 def test_percent(profile: pd.DataFrame):
     """Test that the percent column is checked."""
     KaijuProfile.validate(profile)

tests/unit/infrastructure/application/kmcp/test_kmcp_profile.py

@@ -171,6 +171,7 @@ def test_column_presence(profile: pd.DataFrame):
         ),
     ],
 )
+@pytest.mark.filterwarnings("error")
 def test_percent(profile: pd.DataFrame):
     """Test that the percent column (percent_cumulative) is checked."""
     KMCPProfile.validate(profile)

tests/unit/infrastructure/application/kraken2/test_kraken2_profile.py

@@ -164,6 +164,7 @@ def test_column_presence(profile: pd.DataFrame):
         ),
     ],
 )
+@pytest.mark.filterwarnings("error")
 def test_percent(profile: pd.DataFrame):
     """Test that the percent column is checked."""
     Kraken2Profile.validate(profile)