napistu 0.2.5.dev6__py3-none-any.whl → 0.3.1__py3-none-any.whl

tests/test_net_utils.py

@@ -1,149 +0,0 @@
-from __future__ import annotations
-
-import pytest
-
-import igraph as ig
-import numpy as np
-import pandas as pd
-from napistu.network import net_utils
-from napistu.network import net_create
-
-
-def test_safe_fill():
-    safe_fill_test = ["a_very_long stringggg", ""]
-    assert [net_utils.safe_fill(x) for x in safe_fill_test] == [
-        "a_very_long\nstringggg",
-        "",
-    ]
-
-
-def test_cpr_graph_to_pandas_dfs():
-    graph_data = [
-        (0, 1),
-        (0, 2),
-        (2, 3),
-        (3, 4),
-        (4, 2),
-        (2, 5),
-        (5, 0),
-        (6, 3),
-        (5, 6),
-    ]
-
-    g = ig.Graph(graph_data, directed=True)
-    vs, es = net_utils.cpr_graph_to_pandas_dfs(g)
-
-    assert all(vs["index"] == list(range(0, 7)))
-    assert (
-        pd.DataFrame(graph_data)
-        .rename({0: "source", 1: "target"}, axis=1)
-        .sort_values(["source", "target"])
-        .equals(es.sort_values(["source", "target"]))
-    )
-
-
-def test_validate_graph_attributes(sbml_dfs):
-
-    cpr_graph = net_create.process_cpr_graph(
-        sbml_dfs, directed=True, weighting_strategy="topology"
-    )
-
-    assert (
-        net_utils._validate_edge_attributes(cpr_graph, ["weights", "upstream_weights"])
-        is None
-    )
-    assert net_utils._validate_vertex_attributes(cpr_graph, "node_type") is None
-    with pytest.raises(ValueError):
-        net_utils._validate_vertex_attributes(cpr_graph, "baz")
-
-
-def test_pluck_entity_data_species_identity(sbml_dfs):
-    # Take first 10 species IDs
-    species_ids = sbml_dfs.species.index[:10]
-    # Create mock data with explicit dtype to ensure cross-platform consistency
-    # Fix for issue-42: Use explicit dtypes to avoid platform-specific dtype differences
-    # between Windows (int32) and macOS/Linux (int64)
-    mock_df = pd.DataFrame(
-        {
-            "string_col": [f"str_{i}" for i in range(10)],
-            "mixed_col": np.arange(-5, 5, dtype=np.int64),  # Explicitly use int64
-            "ones_col": np.ones(10, dtype=np.float64),  # Explicitly use float64
-            "squared_col": np.arange(10, dtype=np.int64),  # Explicitly use int64
-        },
-        index=species_ids,
-    )
-    # Assign to species_data
-    sbml_dfs.species_data["mock_table"] = mock_df
-
-    # Custom transformation: square
-    def square(x):
-        return x**2
-
-    custom_transformations = {"square": square}
-    # Create graph_attrs for species
-    graph_attrs = {
-        "species": {
-            "string_col": {
-                "table": "mock_table",
-                "variable": "string_col",
-                "trans": "identity",
-            },
-            "mixed_col": {
-                "table": "mock_table",
-                "variable": "mixed_col",
-                "trans": "identity",
-            },
-            "ones_col": {
-                "table": "mock_table",
-                "variable": "ones_col",
-                "trans": "identity",
-            },
-            "squared_col": {
-                "table": "mock_table",
-                "variable": "squared_col",
-                "trans": "square",
-            },
-        }
-    }
-    # Call pluck_entity_data with custom transformation
-    result = net_create.pluck_entity_data(
-        sbml_dfs, graph_attrs, "species", custom_transformations=custom_transformations
-    )
-    # Check output
-    assert isinstance(result, pd.DataFrame)
-    assert set(result.columns) == {"string_col", "mixed_col", "ones_col", "squared_col"}
-    assert list(result.index) == list(species_ids)
-    # Check values
-    pd.testing.assert_series_equal(result["string_col"], mock_df["string_col"])
-    pd.testing.assert_series_equal(result["mixed_col"], mock_df["mixed_col"])
-    pd.testing.assert_series_equal(result["ones_col"], mock_df["ones_col"])
-    pd.testing.assert_series_equal(
-        result["squared_col"], mock_df["squared_col"].apply(square)
-    )
-
-
-def test_pluck_entity_data_missing_species_key(sbml_dfs):
-    # graph_attrs does not contain 'species' key
-    graph_attrs = {}
-    result = net_create.pluck_entity_data(sbml_dfs, graph_attrs, "species")
-    assert result is None
-
-
-def test_pluck_entity_data_empty_species_dict(sbml_dfs):
-    # graph_attrs contains 'species' key but value is empty dict
-    graph_attrs = {"species": {}}
-    result = net_create.pluck_entity_data(sbml_dfs, graph_attrs, "species")
-    assert result is None
-
-
-################################################
-# __main__
-################################################
-
-if __name__ == "__main__":
-    test_safe_fill()
-    test_cpr_graph_to_pandas_dfs()
-    test_validate_graph_attributes()
-    test_pluck_entity_data_species_identity()
-    test_pluck_entity_data_missing_species_key()
-    test_pluck_entity_data_empty_species_dict()

tests/test_netcontextr.py

@@ -1,105 +0,0 @@
-from __future__ import annotations
-
-import pandas as pd
-import pytest
-from napistu import sbml_dfs_core
-from napistu.identifiers import Identifiers
-from napistu.rpy2 import netcontextr
-from napistu.source import Source
-
-
-@pytest.fixture
-def sbml_dfs_one_reaction():
-    """An sbml_dfs with one reaction and one annotated reactant"""
-    interaction_edgelist = pd.DataFrame(
-        {
-            "upstream_name": ["a"],
-            "downstream_name": ["b"],
-            "upstream_compartment": ["nucleoplasm"],
-            "downstream_compartment": ["nucleoplasm"],
-            "r_name": ["a b of a"],
-            "sbo_term": ["SBO:0000010"],
-            "r_Identifiers": Identifiers([]),
-            "r_isreversible": False,
-        }
-    )
-    species = pd.DataFrame(
-        {
-            "s_name": ["a", "b"],
-            "s_Identifiers": [
-                Identifiers([{"ontology": "ensembl_gene", "identifier": "test"}]),
-                Identifiers([]),
-            ],
-        }
-    )
-    compartments = pd.DataFrame(
-        {"c_name": ["nucleoplasm"], "c_Identifiers": Identifiers([])}
-    )
-    interaction_source = Source(init=True)
-    sbml_dfs = sbml_dfs_core.sbml_dfs_from_edgelist(
-        interaction_edgelist, species, compartments, interaction_source
-    )
-    return sbml_dfs
-
-
-@pytest.fixture
-def sbml_dfs_one_reaction_duplicated_identifiers():
-    """
-    An sbml_dfs with one reactions and one annotated reactant
-    that has two identifiers
-    """
-    interaction_edgelist = pd.DataFrame(
-        {
-            "upstream_name": ["a"],
-            "downstream_name": ["b"],
-            "upstream_compartment": ["nucleoplasm"],
-            "downstream_compartment": ["nucleoplasm"],
-            "r_name": ["a b of a"],
-            "sbo_term": ["SBO:0000010"],
-            "r_Identifiers": Identifiers([]),
-            "r_isreversible": False,
-        }
-    )
-    species = pd.DataFrame(
-        {
-            "s_name": ["a", "b"],
-            "s_Identifiers": [
-                Identifiers(
-                    [
-                        {"ontology": "ensembl_gene", "identifier": "test"},
-                        {"ontology": "ensembl_gene", "identifier": "test2"},
-                    ]
-                ),
-                Identifiers([]),
-            ],
-        }
-    )
-    compartments = pd.DataFrame(
-        {"c_name": ["nucleoplasm"], "c_Identifiers": Identifiers([])}
-    )
-    interaction_source = Source(init=True)
-    sbml_dfs = sbml_dfs_core.sbml_dfs_from_edgelist(
-        interaction_edgelist, species, compartments, interaction_source
-    )
-    return sbml_dfs
-
-
-def test_get_reactions_one_reaction(sbml_dfs_one_reaction):
-    reactions = netcontextr._get_reactions(sbml_dfs_one_reaction)
-    assert not reactions[netcontextr.COL_GENE].isna().any()
-    assert reactions.shape[0] == 1
-
-
-def test_get_reactions_outcols(sbml_dfs_one_reaction):
-    reactions = netcontextr._get_reactions(sbml_dfs_one_reaction)
-    assert netcontextr.COL_GENE in reactions.columns
-    assert netcontextr.COL_REACTION_ID in reactions.columns
-    assert netcontextr.COL_ROLE in reactions.columns
-
-
-def test_get_reactions_one_reaction_duplicated_ids(
-    sbml_dfs_one_reaction_duplicated_identifiers,
-):
-    reactions = netcontextr._get_reactions(sbml_dfs_one_reaction_duplicated_identifiers)
-    assert not reactions[netcontextr.COL_GENE].isna().any()
-    assert reactions.shape[0] == 2

tests/test_rpy2.py

@@ -1,61 +0,0 @@
-from __future__ import annotations
-
-import sys
-from importlib import reload
-from unittest.mock import Mock
-from unittest.mock import patch
-
-import pytest
-
-
-# Patch rpy2_arrow.arrow to avoid ImportError
-# if the R env is not properly set up during testing
-sys.modules["rpy2_arrow.arrow"] = Mock()
-import napistu.rpy2.callr  # noqa: E402
-import napistu.rpy2.rids  # noqa: E402
-
-
-def test_rpy2_has_rpy2_false():
-    with patch.dict("sys.modules", {"rpy2": None}):
-        reload(napistu.rpy2)
-        assert napistu.rpy2.has_rpy2 is False
-        # Test if other napistu.rpy2 modules can be
-        # loaded without rpy2 installed
-        reload(napistu.rpy2.callr)
-        reload(napistu.rpy2.rids)
-
-
-# def test_rpy2_has_rpy2_true():
-#    with patch.dict("sys.modules", {"rpy2": "pytest"}):
-#        reload(napistu.rpy2)
-#        assert napistu.rpy2.has_rpy2 is True
-
-
-@patch("napistu.rpy2.has_rpy2", False)
-def test_warn_if_no_rpy2_false():
-    @napistu.rpy2.warn_if_no_rpy2
-    def test_func():
-        pass
-
-    with pytest.raises(ImportError):
-        test_func()
-
-
-@patch("napistu.rpy2.has_rpy2", True)
-def test_warn_if_no_rpy2_true():
-    @napistu.rpy2.warn_if_no_rpy2
-    def test_func():
-        pass
-
-    test_func()
-
-
-################################################
-# __main__
-################################################
-
-if __name__ == "__main__":
-    test_rpy2_has_rpy2_false()
-    # test_rpy2_has_rpy2_true()
-    test_warn_if_no_rpy2_false()
-    test_warn_if_no_rpy2_true()