napistu 0.2.5.dev7__py3-none-any.whl → 0.3.1.dev1__py3-none-any.whl

tests/test_mechanism_matching.py

@@ -1,784 +0,0 @@
-from __future__ import annotations
-
-from datetime import datetime
-
-import numpy as np
-import pandas as pd
-import pytest
-
-from napistu import mechanism_matching
-from napistu.network import net_create
-from napistu.network import precompute
-from napistu.mechanism_matching import _validate_wide_ontologies
-from napistu.mechanism_matching import match_by_ontology_and_identifier
-from napistu.mechanism_matching import resolve_matches
-
-from napistu.constants import SBML_DFS
-from napistu.constants import IDENTIFIERS
-from napistu.constants import ONTOLOGIES
-from napistu.constants import RESOLVE_MATCHES_AGGREGATORS
-from napistu.constants import FEATURE_ID_VAR_DEFAULT
-
-
-def test_features_to_pathway_species(sbml_dfs):
-
-    species_identifiers = sbml_dfs.get_identifiers("species")
-    feature_identifiers = pd.DataFrame({"chebis": ["17627", "15379", "29105", "-1"]})
-
-    matching_df = (
-        mechanism_matching.features_to_pathway_species(
-            feature_identifiers, species_identifiers, {"chebi"}, "chebis"
-        )
-        .value_counts("identifier")
-        .sort_index()
-    )
-
-    assert matching_df.index.tolist() == ["15379", "17627", "29105"]
-    assert matching_df.tolist() == [2, 3, 2]
-
-
-def test_features_to_pathway_species_basic_and_expansion():
-
-    # Mock species_identifiers table
-    species_identifiers = pd.DataFrame(
-        {
-            "ontology": ["chebi", "chebi", "uniprot", "uniprot"],
-            "identifier": ["A", "B", "X", "Y"],
-            "s_id": [1, 2, 3, 4],
-            "s_name": ["foo", "bar", "baz", "qux"],
-            "bqb": ["BQB_IS", "BQB_IS", "BQB_IS", "BQB_IS"],
-        }
-    )
-    # Basic: no expansion, single identifier per row
-    features = pd.DataFrame({"my_id": ["A", "B", "X"], "other_col": [10, 20, 30]})
-    result = mechanism_matching.features_to_pathway_species(
-        feature_identifiers=features,
-        species_identifiers=species_identifiers,
-        ontologies={"chebi", "uniprot"},
-        feature_identifiers_var="my_id",
-        expand_identifiers=False,
-    )
-    # Should map all three
-    assert set(result["my_id"]) == {"A", "B", "X"}
-    assert set(result["identifier"]) == {"A", "B", "X"}
-    assert set(result["s_name"]) == {"foo", "bar", "baz"}
-    # Expansion: one row with multiple IDs
-    features2 = pd.DataFrame({"my_id": ["A / B / X", "Y"], "other_col": [100, 200]})
-    result2 = mechanism_matching.features_to_pathway_species(
-        feature_identifiers=features2,
-        species_identifiers=species_identifiers,
-        ontologies={"chebi", "uniprot"},
-        feature_identifiers_var="my_id",
-        expand_identifiers=True,
-        identifier_delimiter="/",
-    )
-    # Should expand to 4 rows (A, B, X, Y)
-    assert set(result2["identifier"]) == {"A", "B", "X", "Y"}
-    assert set(result2["s_name"]) == {"foo", "bar", "baz", "qux"}
-    # Whitespace trimming
-    features3 = pd.DataFrame({"my_id": ["  A  /  B  /X  ", " Y"], "other_col": [1, 2]})
-    result3 = mechanism_matching.features_to_pathway_species(
-        feature_identifiers=features3,
-        species_identifiers=species_identifiers,
-        ontologies={"chebi", "uniprot"},
-        feature_identifiers_var="my_id",
-        expand_identifiers=True,
-        identifier_delimiter="/",
-    )
-    # Should expand and trim whitespace
-    assert set(result3["identifier"]) == {"A", "B", "X", "Y"}
-    assert set(result3["s_name"]) == {"foo", "bar", "baz", "qux"}
-
-
-def test_edgelist_to_pathway_species(sbml_dfs):
-
-    edgelist = pd.DataFrame(
-        [
-            {"identifier_upstream": "17996", "identifier_downstream": "16526"},
-            {"identifier_upstream": "15377", "identifier_downstream": "17544"},
-            {"identifier_upstream": "15378", "identifier_downstream": "57945"},
-            {"identifier_upstream": "57540", "identifier_downstream": "17996"},
-        ]
-    )
-    species_identifiers = sbml_dfs.get_identifiers("species").query("bqb == 'BQB_IS'")
-
-    edgelist_w_sids = mechanism_matching.edgelist_to_pathway_species(
-        edgelist, species_identifiers, ontologies={"chebi", "uniprot"}
-    )
-    assert edgelist_w_sids.shape == (4, 4)
-
-    egelist_w_scids = mechanism_matching.edgelist_to_scids(
-        edgelist, sbml_dfs, species_identifiers, ontologies={"chebi"}
-    )
-
-    assert egelist_w_scids.shape == (12, 6)
-
-    direct_interactions = mechanism_matching.filter_to_direct_mechanistic_interactions(
-        edgelist, sbml_dfs, species_identifiers, ontologies={"chebi"}
-    )
-
-    assert direct_interactions.shape == (2, 10)
-
-
-def test_direct_and_indirect_mechanism_matching(sbml_dfs_glucose_metabolism):
-
-    cpr_graph = net_create.process_cpr_graph(sbml_dfs_glucose_metabolism)
-
-    edgelist = pd.DataFrame(
-        [
-            {
-                "identifier_upstream": "17925",
-                "identifier_downstream": "32966",
-            },  # glu, fbp
-            {
-                "identifier_upstream": "57634",
-                "identifier_downstream": "32966",
-            },  # f6p, fbp
-            {
-                "identifier_upstream": "32966",
-                "identifier_downstream": "57642",
-            },  # fbp, dhap
-            {
-                "identifier_upstream": "17925",
-                "identifier_downstream": "15361",
-            },  # glu, pyr
-        ]
-    )
-
-    species_identifiers = sbml_dfs_glucose_metabolism.get_identifiers("species")
-
-    direct_interactions = mechanism_matching.filter_to_direct_mechanistic_interactions(
-        formatted_edgelist=edgelist,
-        sbml_dfs=sbml_dfs_glucose_metabolism,
-        species_identifiers=species_identifiers,
-        ontologies={"chebi"},
-    )
-
-    assert direct_interactions.shape == (2, 10)
-
-    indirect_interactions = (
-        mechanism_matching.filter_to_indirect_mechanistic_interactions(
-            formatted_edgelist=edgelist,
-            sbml_dfs=sbml_dfs_glucose_metabolism,
-            species_identifiers=species_identifiers,
-            cpr_graph=cpr_graph,
-            ontologies={"chebi"},
-            precomputed_distances=None,
-            max_path_length=10,
-        )
-    )
-
-    assert indirect_interactions.shape == (6, 12)
-
-    # confirm that we get the same thing even when using precomputed distances
-    precomputed_distances = precompute.precompute_distances(
-        cpr_graph, weights_vars=["weights"]
-    )
-
-    indirect_interactions_w_precompute = (
-        mechanism_matching.filter_to_indirect_mechanistic_interactions(
-            formatted_edgelist=edgelist,
-            sbml_dfs=sbml_dfs_glucose_metabolism,
-            species_identifiers=species_identifiers,
-            cpr_graph=cpr_graph,
-            ontologies={"chebi"},
-            precomputed_distances=precomputed_distances,
-            max_path_length=10,
-        )
-    )
-
-    assert all(
-        indirect_interactions["weight"] == indirect_interactions_w_precompute["weight"]
-    )
-
-
-def test_validate_wide_ontologies():
-    """Test the _validate_wide_ontologies function with various input types and error cases."""
-    # Setup test data
-    example_data_wide = pd.DataFrame(
-        {
-            "results": [-1.0, 0.0, 1.0],
-            "chebi": ["15377", "16810", "17925"],
-            "uniprot": ["P12345", "Q67890", "O43826"],
-        }
-    )
-
-    # Test auto-detection of ontology columns
-    assert _validate_wide_ontologies(example_data_wide) == {"chebi", "uniprot"}
-
-    # Test string input
-    assert _validate_wide_ontologies(example_data_wide, ontologies="chebi") == {"chebi"}
-
-    # Test set input
-    assert _validate_wide_ontologies(example_data_wide, ontologies={"chebi"}) == {
-        "chebi"
-    }
-    assert _validate_wide_ontologies(
-        example_data_wide, ontologies={"chebi", "uniprot"}
-    ) == {"chebi", "uniprot"}
-
-    # Test dictionary mapping for renaming
-    assert _validate_wide_ontologies(
-        example_data_wide, ontologies={"chebi": "reactome", "uniprot": "ensembl_gene"}
-    ) == {"reactome", "ensembl_gene"}
-
-    # Test error cases
-
-    # Missing column in set input (checks existence first)
-    with pytest.raises(
-        ValueError, match="Specified ontology columns not found in DataFrame:.*"
-    ):
-        _validate_wide_ontologies(example_data_wide, ontologies={"invalid_ontology"})
-
-    # Valid column name but invalid ontology
-    df_with_invalid = pd.DataFrame(
-        {
-            "results": [-1.0, 0.0, 1.0],
-            "invalid_ontology": ["a", "b", "c"],
-        }
-    )
-    with pytest.raises(ValueError, match="Invalid ontologies in set:.*"):
-        _validate_wide_ontologies(df_with_invalid, ontologies={"invalid_ontology"})
-
-    # Missing source column in mapping
-    with pytest.raises(ValueError, match="Source columns not found in DataFrame:.*"):
-        _validate_wide_ontologies(
-            example_data_wide, ontologies={"missing_column": "reactome"}
-        )
-
-    # Invalid target ontology in mapping
-    with pytest.raises(ValueError, match="Invalid ontologies in mapping:.*"):
-        _validate_wide_ontologies(
-            example_data_wide, ontologies={"chebi": "invalid_ontology"}
-        )
-
-    # DataFrame with no valid ontology columns
-    invalid_df = pd.DataFrame(
-        {"results": [-1.0, 0.0, 1.0], "col1": ["a", "b", "c"], "col2": ["d", "e", "f"]}
-    )
-    with pytest.raises(
-        ValueError, match="No valid ontology columns found in DataFrame.*"
-    ):
-        _validate_wide_ontologies(invalid_df)
-
-
-def test_ensure_feature_id_var():
-    """Test the _ensure_feature_id_var function with various input cases."""
-    from napistu.mechanism_matching import _ensure_feature_id_var
-    from napistu.constants import FEATURE_ID_VAR_DEFAULT
-
-    # Test case 1: DataFrame already has feature_id column
-    df1 = pd.DataFrame({"feature_id": [100, 200, 300], "data": ["a", "b", "c"]})
-    result1 = _ensure_feature_id_var(df1)
-    # Should return unchanged DataFrame
-    pd.testing.assert_frame_equal(df1, result1)
-
-    # Test case 2: DataFrame missing feature_id column
-    df2 = pd.DataFrame({"data": ["x", "y", "z"]})
-    result2 = _ensure_feature_id_var(df2)
-    # Should add feature_id column with sequential integers
-    assert FEATURE_ID_VAR_DEFAULT in result2.columns
-    assert list(result2[FEATURE_ID_VAR_DEFAULT]) == [0, 1, 2]
-    assert list(result2["data"]) == ["x", "y", "z"]  # Original data preserved
-
-    # Test case 3: Custom feature_id column name
-    df3 = pd.DataFrame({"data": ["p", "q", "r"]})
-    custom_id = "custom_feature_id"
-    result3 = _ensure_feature_id_var(df3, feature_id_var=custom_id)
-    # Should add custom named feature_id column
-    assert custom_id in result3.columns
-    assert list(result3[custom_id]) == [0, 1, 2]
-    assert list(result3["data"]) == ["p", "q", "r"]  # Original data preserved
-
-    # Test case 4: Empty DataFrame
-    df4 = pd.DataFrame()
-    result4 = _ensure_feature_id_var(df4)
-    # Should handle empty DataFrame gracefully
-    assert FEATURE_ID_VAR_DEFAULT in result4.columns
-    assert len(result4) == 0
-
-
-def test_match_by_ontology_and_identifier():
-    """Test the match_by_ontology_and_identifier function with various input types."""
-    # Setup test data
-    feature_identifiers = pd.DataFrame(
-        {
-            "ontology": ["chebi", "chebi", "uniprot", "uniprot", "reactome"],
-            "identifier": ["15377", "16810", "P12345", "Q67890", "R12345"],
-            "results": [1.0, 2.0, -1.0, -2.0, 0.5],
-        }
-    )
-
-    species_identifiers = pd.DataFrame(
-        {
-            "ontology": ["chebi", "chebi", "uniprot", "uniprot", "ensembl_gene"],
-            "identifier": ["15377", "17925", "P12345", "O43826", "ENSG123"],
-            "s_id": ["s1", "s2", "s3", "s4", "s5"],
-            "s_name": ["compound1", "compound2", "protein1", "protein2", "gene1"],
-            "bqb": ["BQB_IS"] * 5,  # Add required bqb column with BQB_IS values
-        }
-    )
-
-    # Test with single ontology (string)
-    result = match_by_ontology_and_identifier(
-        feature_identifiers=feature_identifiers,
-        species_identifiers=species_identifiers,
-        ontologies="chebi",
-    )
-    assert len(result) == 1  # Only one matching chebi identifier
-    assert result.iloc[0]["identifier"] == "15377"
-    assert result.iloc[0]["results"] == 1.0
-    assert result.iloc[0]["ontology"] == "chebi"  # From species_identifiers
-    assert result.iloc[0]["s_name"] == "compound1"  # Verify join worked correctly
-    assert result.iloc[0]["bqb"] == "BQB_IS"  # Verify bqb column is preserved
-
-    # Test with multiple ontologies (set)
-    result = match_by_ontology_and_identifier(
-        feature_identifiers=feature_identifiers,
-        species_identifiers=species_identifiers,
-        ontologies={"chebi", "uniprot"},
-    )
-    assert len(result) == 2  # One chebi and one uniprot match
-    assert set(result["ontology"]) == {"chebi", "uniprot"}  # From species_identifiers
-    assert set(result["identifier"]) == {"15377", "P12345"}
-    # Verify results are correctly matched
-    chebi_row = result[result["ontology"] == "chebi"].iloc[0]
-    uniprot_row = result[result["ontology"] == "uniprot"].iloc[0]
-    assert chebi_row["results"] == 1.0
-    assert uniprot_row["results"] == -1.0
-    assert chebi_row["s_name"] == "compound1"
-    assert uniprot_row["s_name"] == "protein1"
-    assert chebi_row["bqb"] == "BQB_IS"
-    assert uniprot_row["bqb"] == "BQB_IS"
-
-    # Test with list of ontologies
-    result = match_by_ontology_and_identifier(
-        feature_identifiers=feature_identifiers,
-        species_identifiers=species_identifiers,
-        ontologies=["chebi", "uniprot"],
-    )
-    assert len(result) == 2
-    assert set(result["ontology"]) == {"chebi", "uniprot"}  # From species_identifiers
-
-    # Test with no matches
-    no_match_features = pd.DataFrame(
-        {"ontology": ["chebi"], "identifier": ["99999"], "results": [1.0]}
-    )
-    result = match_by_ontology_and_identifier(
-        feature_identifiers=no_match_features,
-        species_identifiers=species_identifiers,
-        ontologies="chebi",
-    )
-    assert len(result) == 0
-
-    # Test with empty features
-    empty_features = pd.DataFrame({"ontology": [], "identifier": [], "results": []})
-    result = match_by_ontology_and_identifier(
-        feature_identifiers=empty_features,
-        species_identifiers=species_identifiers,
-        ontologies={"chebi", "uniprot"},
-    )
-    assert len(result) == 0
-
-    # Test with invalid ontology
-    with pytest.raises(ValueError, match="Invalid ontologies specified:.*"):
-        match_by_ontology_and_identifier(
-            feature_identifiers=feature_identifiers,
-            species_identifiers=species_identifiers,
-            ontologies="invalid_ontology",
-        )
-
-    # Test with ontology not in feature_identifiers
-    result = match_by_ontology_and_identifier(
-        feature_identifiers=feature_identifiers,
-        species_identifiers=species_identifiers,
-        ontologies={"ensembl_gene"},  # Only in species_identifiers
-    )
-    assert len(result) == 0
-
-    # Test with custom feature_identifiers_var
-    feature_identifiers_custom = feature_identifiers.rename(
-        columns={"identifier": "custom_id"}
-    )
-    result = match_by_ontology_and_identifier(
-        feature_identifiers=feature_identifiers_custom,
-        species_identifiers=species_identifiers,
-        ontologies={"chebi"},
-        feature_identifiers_var="custom_id",
-    )
-    assert len(result) == 1
-    assert result.iloc[0]["custom_id"] == "15377"
-    assert result.iloc[0]["ontology"] == "chebi"  # From species_identifiers
-    assert result.iloc[0]["s_name"] == "compound1"
-    assert result.iloc[0]["bqb"] == "BQB_IS"
-
-
-def test_match_features_to_wide_pathway_species(sbml_dfs_glucose_metabolism):
-
-    def compare_frame_contents(df1, df2):
-        """
-        Compare if two DataFrames have the same content, ignoring index and column ordering.
-
-        Parameters
-        ----------
-        df1 : pd.DataFrame
-            First DataFrame to compare
-        df2 : pd.DataFrame
-            Second DataFrame to compare
-
-        Returns
-        -------
-        None
-        """
-        df1_sorted = (
-            df1.reindex(columns=sorted(df1.columns))
-            .sort_values(sorted(df1.columns))
-            .reset_index(drop=True)
-        )
-
-        df2_sorted = (
-            df2.reindex(columns=sorted(df2.columns))
-            .sort_values(sorted(df2.columns))
-            .reset_index(drop=True)
-        )
-
-        pd.testing.assert_frame_equal(df1_sorted, df2_sorted, check_like=True)
-
-        return None
-
-    species_identifiers = (
-        sbml_dfs_glucose_metabolism.get_identifiers("species")
-        .query("bqb == 'BQB_IS'")
-        .query("ontology != 'reactome'")
-    )
-
-    # create a table whose index is s_ids and columns are faux-measurements
-    example_data = species_identifiers.groupby("ontology").head(10)[
-        ["ontology", "identifier"]
-    ]
-
-    example_data["results_a"] = np.random.randn(len(example_data))
-    example_data["results_b"] = np.random.randn(len(example_data))
-    # add a feature_id column to the example_data which tracks the row of the original data
-    example_data["feature_id"] = range(0, len(example_data))
-
-    # pivot (identifier, ontology) to columns for each ontology
-    example_data_wide = (
-        example_data.pivot(
-            columns="ontology",
-            values="identifier",
-            index=["feature_id", "results_a", "results_b"],
-        )
-        .reset_index()
-        .rename_axis(None, axis=1)
-    )
-
-    # options, for matching
-    # 1. match by identifier and a set of ontologies (provided by arg).
-    matched_s_ids = mechanism_matching.features_to_pathway_species(
-        feature_identifiers=example_data.drop(columns="ontology"),
-        species_identifiers=species_identifiers,
-        ontologies={"uniprot", "chebi"},
-        feature_identifiers_var="identifier",
-    )
-
-    # 2. match by identifier and ontology.
-    matched_s_ids_w_ontologies = mechanism_matching.match_by_ontology_and_identifier(
-        feature_identifiers=example_data,
-        species_identifiers=species_identifiers,
-        ontologies={"uniprot", "chebi"},
-        feature_identifiers_var="identifier",
-    )
-
-    # 3. format wide identifier sets into a table with a single identifier column and apply strategy #2.
-    matched_s_ids_from_wide = mechanism_matching.match_features_to_wide_pathway_species(
-        example_data_wide,
-        species_identifiers,
-        ontologies={"uniprot", "chebi"},
-        feature_identifiers_var="identifier",
-    )
-
-    compare_frame_contents(
-        matched_s_ids.drop(columns="s_Source"),
-        matched_s_ids_w_ontologies.drop(columns="s_Source"),
-    )
-    compare_frame_contents(
-        matched_s_ids.drop(columns="s_Source"),
-        matched_s_ids_from_wide.drop(columns="s_Source"),
-    )
-
-
-def test_resolve_matches_with_example_data():
-    """Test resolve_matches function with example data for all aggregation methods."""
-    # Setup example data with overlapping 1-to-many and many-to-1 cases
-    example_data = pd.DataFrame(
-        {
-            FEATURE_ID_VAR_DEFAULT: ["A", "B", "C", "D", "D", "E", "B", "B", "C"],
-            SBML_DFS.S_ID: [
-                "s_id_1",
-                "s_id_1",
-                "s_id_1",
-                "s_id_4",
-                "s_id_5",
-                "s_id_6",
-                "s_id_2",
-                "s_id_3",
-                "s_id_3",
-            ],
-            "results_a": [1, 2, 3, 0.4, 5, 6, 0.7, 0.8, 9],
-            "results_b": [
-                "foo",
-                "foo",
-                "bar",
-                "bar",
-                "baz",
-                "baz",
-                "not",
-                "not",
-                "not",
-            ],
-        }
-    )
-
-    # Test that missing feature_id raises KeyError
-    data_no_id = pd.DataFrame(
-        {
-            SBML_DFS.S_ID: ["s_id_1", "s_id_1", "s_id_2"],
-            "results_a": [1, 2, 3],
-            "results_b": ["foo", "bar", "baz"],
-        }
-    )
-    with pytest.raises(KeyError, match=FEATURE_ID_VAR_DEFAULT):
-        resolve_matches(data_no_id)
-
-    # Test with keep_id_col=True (default)
-    result_with_id = resolve_matches(
-        example_data, keep_id_col=True, numeric_agg=RESOLVE_MATCHES_AGGREGATORS.MEAN
-    )
-
-    # Verify feature_id column is present and correctly aggregated
-    assert FEATURE_ID_VAR_DEFAULT in result_with_id.columns
-    assert result_with_id.loc["s_id_1", FEATURE_ID_VAR_DEFAULT] == "A,B,C"
-    assert result_with_id.loc["s_id_3", FEATURE_ID_VAR_DEFAULT] == "B,C"
-
-    # Test with keep_id_col=False
-    result_without_id = resolve_matches(
-        example_data, keep_id_col=False, numeric_agg=RESOLVE_MATCHES_AGGREGATORS.MEAN
-    )
-
-    # Verify feature_id column is not in output
-    assert FEATURE_ID_VAR_DEFAULT not in result_without_id.columns
-
-    # Verify other columns are still present and correctly aggregated
-    assert "results_a" in result_without_id.columns
-    assert "results_b" in result_without_id.columns
-    assert "feature_id_match_count" in result_without_id.columns
-
-    # Verify numeric aggregation still works
-    actual_mean = result_without_id.loc["s_id_1", "results_a"]
-    expected_mean = 2.0  # (1 + 2 + 3) / 3
-    assert (
-        actual_mean == expected_mean
-    ), f"Expected mean {expected_mean}, but got {actual_mean}"
-
-    # Verify string aggregation still works
-    assert result_without_id.loc["s_id_1", "results_b"] == "bar,foo"
-
-    # Verify match counts are still present
-    assert result_without_id.loc["s_id_1", "feature_id_match_count"] == 3
-    assert result_without_id.loc["s_id_3", "feature_id_match_count"] == 2
-
-    # Test maximum aggregation
-    max_result = resolve_matches(
-        example_data, numeric_agg=RESOLVE_MATCHES_AGGREGATORS.MAX
-    )
-
-    # Verify maximum values are correct
-    assert max_result.loc["s_id_1", "results_a"] == 3.0  # max of [1, 2, 3]
-    assert max_result.loc["s_id_3", "results_a"] == 9.0  # max of [0.8, 9]
-    assert max_result.loc["s_id_4", "results_a"] == 0.4  # single value
-    assert max_result.loc["s_id_5", "results_a"] == 5.0  # single value
-    assert max_result.loc["s_id_6", "results_a"] == 6.0  # single value
-
-    # Test weighted mean (feature_id is used for weights regardless of keep_id_col)
-    weighted_result = resolve_matches(
-        example_data,
-        numeric_agg=RESOLVE_MATCHES_AGGREGATORS.WEIGHTED_MEAN,
-        keep_id_col=True,
-    )
-
-    # For s_id_1:
-    # A appears once in total (weight = 1/1)
-    # B appears three times in total (weight = 1/3)
-    # C appears twice in total (weight = 1/2)
-    # Sum of unnormalized weights = 1 + 1/3 + 1/2 = 1.833
-    # Normalized weights:
-    # A: (1/1)/1.833 = 0.545
-    # B: (1/3)/1.833 = 0.182
-    # C: (1/2)/1.833 = 0.273
-    # Weighted mean = 1×0.545 + 2×0.182 + 3×0.273 = 1.73
-    actual_weighted_mean_1 = weighted_result.loc["s_id_1", "results_a"]
-    expected_weighted_mean_1 = 1.73
-    assert (
-        abs(actual_weighted_mean_1 - expected_weighted_mean_1) < 0.01
-    ), f"s_id_1 weighted mean: expected {expected_weighted_mean_1:.3f}, but got {actual_weighted_mean_1:.3f}"
-
-    # For s_id_3:
-    # B appears three times in total (weight = 1/3)
-    # C appears twice in total (weight = 1/2)
-    # Sum of unnormalized weights = 1/3 + 1/2 = 0.833
-    # Normalized weights:
-    # B: (1/3)/0.833 = 0.4
-    # C: (1/2)/0.833 = 0.6
-    # Weighted mean = 0.8×0.4 + 9×0.6 = 5.72
-    actual_weighted_mean_3 = weighted_result.loc["s_id_3", "results_a"]
-    expected_weighted_mean_3 = 5.72
-    assert (
-        abs(actual_weighted_mean_3 - expected_weighted_mean_3) < 0.01
-    ), f"s_id_3 weighted mean: expected {expected_weighted_mean_3:.3f}, but got {actual_weighted_mean_3:.3f}"
-
-    # Test weighted mean with keep_id_col=False (weights still use feature_id)
-    weighted_result_no_id = resolve_matches(
-        example_data,
-        numeric_agg=RESOLVE_MATCHES_AGGREGATORS.WEIGHTED_MEAN,
-        keep_id_col=False,
-    )
-
-    # Verify weighted means are the same regardless of keep_id_col
-    assert (
-        abs(weighted_result_no_id.loc["s_id_1", "results_a"] - expected_weighted_mean_1)
-        < 0.01
-    ), "Weighted mean should be the same regardless of keep_id_col"
-    assert (
-        abs(weighted_result_no_id.loc["s_id_3", "results_a"] - expected_weighted_mean_3)
-        < 0.01
-    ), "Weighted mean should be the same regardless of keep_id_col"
-
-    # Test that both versions preserve the same index structure
-    expected_index = pd.Index(
-        ["s_id_1", "s_id_2", "s_id_3", "s_id_4", "s_id_5", "s_id_6"], name="s_id"
-    )
-    pd.testing.assert_index_equal(result_with_id.index, expected_index)
-    pd.testing.assert_index_equal(result_without_id.index, expected_index)
-
-
-def test_resolve_matches_invalid_dtypes():
-    """Test that resolve_matches raises an error for unsupported dtypes."""
-    # Setup data with boolean and datetime columns
-    data = pd.DataFrame(
-        {
-            FEATURE_ID_VAR_DEFAULT: ["A", "B", "B", "C"],
-            "bool_col": [True, False, True, False],
-            "datetime_col": [
-                datetime(2024, 1, 1),
-                datetime(2024, 1, 2),
-                datetime(2024, 1, 3),
-                datetime(2024, 1, 4),
-            ],
-            "s_id": ["s1", "s1", "s2", "s2"],
-        }
-    )
-
-    # Should raise TypeError for unsupported dtypes
-    with pytest.raises(TypeError, match="Unsupported data types"):
-        resolve_matches(data)
-
-
-def test_resolve_matches_first_method():
-    """Test resolve_matches with first method."""
-    # Setup data with known order
-    data = pd.DataFrame(
-        {
-            FEATURE_ID_VAR_DEFAULT: ["A", "C", "B", "B", "A"],
-            SBML_DFS.S_ID: ["s1", "s1", "s1", "s2", "s2"],
-            "value": [1, 2, 3, 4, 5],
-        }
-    )
-
-    result = resolve_matches(data, numeric_agg=RESOLVE_MATCHES_AGGREGATORS.FIRST)
-
-    # Should take first value after sorting by feature_id
-    assert result.loc["s1", "value"] == 1  # A comes first
-    assert result.loc["s2", "value"] == 5  # A comes first
-
-
-def test_resolve_matches_deduplicate_feature_id_within_sid():
-    """Test that only the first value for each (s_id, feature_id) is used in mean aggregation."""
-    data = pd.DataFrame(
-        {
-            FEATURE_ID_VAR_DEFAULT: ["A", "A", "B"],
-            SBML_DFS.S_ID: ["s1", "s1", "s1"],
-            "value": [
-                1,
-                1,
-                2,
-            ],  # average should be 1.5 because the two A's are redundant
-        }
-    )
-
-    result = resolve_matches(data, numeric_agg=RESOLVE_MATCHES_AGGREGATORS.MEAN)
-    assert result.loc["s1", "value"] == 1.5
-
-
-def test_bind_wide_results(sbml_dfs_glucose_metabolism):
-    """
-    Test that bind_wide_results correctly matches identifiers and adds results to species data.
-    """
-    # Get species identifiers, excluding reactome
-    species_identifiers = (
-        sbml_dfs_glucose_metabolism.get_identifiers(SBML_DFS.SPECIES)
-        .query("bqb == 'BQB_IS'")
-        .query("ontology != 'reactome'")
-    )
-
-    # Create example data with identifiers and results
-    example_data = species_identifiers.groupby("ontology").head(10)[
-        [IDENTIFIERS.ONTOLOGY, IDENTIFIERS.IDENTIFIER]
-    ]
-    example_data["results_a"] = np.random.randn(len(example_data))
-    example_data["results_b"] = np.random.randn(len(example_data))
-    example_data[FEATURE_ID_VAR_DEFAULT] = range(0, len(example_data))
-
-    # Create wide format data
-    example_data_wide = (
-        example_data.pivot(
-            columns=IDENTIFIERS.ONTOLOGY,
-            values=IDENTIFIERS.IDENTIFIER,
-            index=[FEATURE_ID_VAR_DEFAULT, "results_a", "results_b"],
-        )
-        .reset_index()
-        .rename_axis(None, axis=1)
-    )
-
-    # Call bind_wide_results
-    results_name = "test_results"
-    sbml_dfs_result = mechanism_matching.bind_wide_results(
-        sbml_dfs=sbml_dfs_glucose_metabolism,
-        results_df=example_data_wide,
-        results_name=results_name,
-        ontologies={ONTOLOGIES.UNIPROT, ONTOLOGIES.CHEBI},
-        dogmatic=False,
-        species_identifiers=None,
-        feature_id_var=FEATURE_ID_VAR_DEFAULT,
-        verbose=True,
-    )
-
-    # Verify the results were added correctly
-    assert (
-        results_name in sbml_dfs_result.species_data
-    ), f"{results_name} not found in species_data"
-
-    # Get the bound results
-    bound_results = sbml_dfs_result.species_data[results_name]
-
-    # columns are feature_id, results_a, results_b
-    assert set(bound_results.columns) == {
-        FEATURE_ID_VAR_DEFAULT,
-        "results_a",
-        "results_b",
-    }
-
-    assert bound_results.shape == (23, 3)
-    assert bound_results.loc["S00000056", "feature_id"] == "18,19"
-    assert bound_results.loc["S00000057", "feature_id"] == "18"
-    assert bound_results.loc["S00000010", "feature_id"] == "9"