napistu 0.3.3__py3-none-any.whl → 0.3.5__py3-none-any.whl

napistu/source.py

@@ -223,7 +223,7 @@ def greedy_set_coverge_of_sources(
     Greedy Set Coverage of Sources
 
     Apply the greedy set coverge algorithm to find the minimal set of
-      sources which cover all entries
+    sources which cover all entries
 
     Parameters:
     source_df: pd.DataFrame

{napistu-0.3.3.dist-info → napistu-0.3.5.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: napistu
-Version: 0.3.3
+Version: 0.3.5
 Summary: Connecting high-dimensional data to curated pathways
 Home-page: https://github.com/napistu/napistu-py
 Author: Sean Hackett
@@ -19,7 +19,7 @@ Requires-Dist: Jinja2
 Requires-Dist: PyYAML<7.0.0,>=6.0.0
 Requires-Dist: click<9.0.0,>=8.0.0
 Requires-Dist: click-logging
-Requires-Dist: fs<3.0.0,>=2.4.0
+Requires-Dist: fs<3.0.0,>=2.4.16
 Requires-Dist: fs-gcsfs<2.0.0,>=1.5.0
 Requires-Dist: igraph
 Requires-Dist: matplotlib<4.0.0,>=3.5.0

{napistu-0.3.3.dist-info → napistu-0.3.5.dist-info}/RECORD

@@ -1,12 +1,12 @@
 napistu/__init__.py,sha256=dFXAhIqlTLJMwowS4BUDT08-Vy3Q0u1L0CMCErSZT1Y,239
 napistu/__main__.py,sha256=PbzIsFAoFHNQuSyi-ql-D7tQLEOuqgmTcgk0PY-OGeU,28636
 napistu/consensus.py,sha256=UbKKSLP1O46e3Rk8d_aqNlhRHeR3sZRztAgIm7-XK6Y,69960
-napistu/constants.py,sha256=M-zGc85bo1DDRe7uvyeEMUoD9Qf59Qz53nx4R6PwHvk,12483
+napistu/constants.py,sha256=XptXQa3OKmH5hPb6PK_3cLSNcETj6jqejJYY60GV9Zc,12384
 napistu/identifiers.py,sha256=wsVriQdvPllA5uvh5CiREklA2tYW2MIB14dV7CPaMVU,34003
 napistu/indices.py,sha256=E_djN1XWc6l1lrFw_QnQXfZTKYTaUv8-jFPP7cHkY5A,9780
-napistu/sbml_dfs_core.py,sha256=TUPp2nzaxRWkHKsXrbFzgp0_p5CzEGAmA5cg3dOUm84,91794
+napistu/sbml_dfs_core.py,sha256=us0Yz67ilav5dc2LY2TtXypaSdAQ7Kk55ZyGuyougzo,96605
 napistu/sbml_dfs_utils.py,sha256=LJo6WWTrmnE58ZLDuibeeHk88uCdfunWdja7XxdZpps,11525
-napistu/source.py,sha256=9uUJrkY4jHaKlzz5nNcQQ8wUAep2pfqhlHxHw1hmEkI,13648
+napistu/source.py,sha256=UGpN70bqbC9gnKmM0ivSdQYim9hfzgABeXoQKzRr9oU,13646
 napistu/utils.py,sha256=TcholWrFbRSu_sn9ODMA8y2YyAhekEKZjwf4S0WQNzI,33241
 napistu/context/__init__.py,sha256=LQBEqipcHKK0E5UlDEg1ct-ymCs93IlUrUaH8BCevf0,242
 napistu/context/discretize.py,sha256=Qq7zg46F_I-PvQIT2_pEDQV7YEtUQCxKoRvT5Gu9QsE,15052
@@ -60,14 +60,14 @@ napistu/modify/uncompartmentalize.py,sha256=U5X4Q7Z-YIkC8_711x3sU21vTVdv9rKfauwz
 napistu/network/__init__.py,sha256=dFXAhIqlTLJMwowS4BUDT08-Vy3Q0u1L0CMCErSZT1Y,239
 napistu/network/constants.py,sha256=fC1njZDu6in1JiaZ1-T1_fhmmkcc2HKSUUomDVyQ7Dw,5789
 napistu/network/data_handling.py,sha256=mxplWwyXNrjZRN-jjWWUI9IZOqX69k8qSMDIrL9h0Og,14736
-napistu/network/ig_utils.py,sha256=87vFuyLksYhfGoKBvjYeQt1yM_lg83m-14OaGbW64Wg,10478
+napistu/network/ig_utils.py,sha256=JSlf_sZtw3DiiSIiYJ2YqJFEP4hVJMwNRox2qYTA4zY,11470
 napistu/network/napistu_graph_core.py,sha256=2NbjiLcDcFWFyX1MuN17pobPDgoQFtcYWOwuPSFTT4g,10429
 napistu/network/neighborhoods.py,sha256=Q9HWUvf_J4a_4RQDKd7ywEy4cp3Wq2OPOfVsotDbEe0,56098
 napistu/network/net_create.py,sha256=2N5ocGmibdBxIUVtv3H36iFWwkbys9ECCERFRlByhLc,69407
 napistu/network/net_propagation.py,sha256=89ZR4p2mGpkCCIemofZ53XbUjQsuNABxIc6UmF8A5n8,4935
 napistu/network/ng_utils.py,sha256=ijWDa5MTuULJpdV6dcVFGmLmtB_xy87jaUG7F5nvC_k,15240
 napistu/network/paths.py,sha256=S4ZaV0yVmI-o8sXfom5eXA3yy2IEbleYUyXEvnmVw98,17468
-napistu/network/precompute.py,sha256=xDIHWxGWwDyEw1sF1bQKHVbunI8qmeJvo3Iv7wADUys,8960
+napistu/network/precompute.py,sha256=pIXCCE6Mf6HY8o-fiwUaOxvQ_9_mevK0vaC8fND4RZk,9141
 napistu/ontologies/__init__.py,sha256=dFXAhIqlTLJMwowS4BUDT08-Vy3Q0u1L0CMCErSZT1Y,239
 napistu/ontologies/constants.py,sha256=GyOFvezSxDK1VigATcruTKtNhjcYaid1ggulEf_HEtQ,4345
 napistu/ontologies/dogma.py,sha256=jGZS-J3d29AoUOow-HVjfVZQJ87lnqO5L1aozieN1ec,8825
@@ -81,7 +81,7 @@ napistu/rpy2/rids.py,sha256=AfXLTfTdonfspgAHYO0Ph7jSUWv8YuyT8x3fyLfAqc8,3413
 napistu/scverse/__init__.py,sha256=Lgxr3iMQAkTzXE9BNz93CndNP5djzerLvmHM-D0PU3I,357
 napistu/scverse/constants.py,sha256=0iAkhyJUIeFGHdLLU3fCaEU1O3Oix4qAsxr3CxGTjVs,653
 napistu/scverse/loading.py,sha256=jqiE71XB-wdV50GyZrauFNY0Lai4bX9Fm2Gv80VR8t8,27016
-napistu-0.3.3.dist-info/licenses/LICENSE,sha256=kW8wVT__JWoHjl2BbbJDAZInWa9AxzJeR_uv6-i5x1g,1063
+napistu-0.3.5.dist-info/licenses/LICENSE,sha256=kW8wVT__JWoHjl2BbbJDAZInWa9AxzJeR_uv6-i5x1g,1063
 tests/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 tests/conftest.py,sha256=XVkd0tQywhnf2cgab7fIjBo3NlaTVX3cO8HaRS2jIwM,3190
 tests/test_consensus.py,sha256=3dJvvPsPG7bHbw_FY4Pm647N_Gt_Ud9157OKYfPCUd4,9502
@@ -102,13 +102,13 @@ tests/test_mcp_config.py,sha256=GTu9vywqAHTYkolywdYS_BEIW3gBzs4A4qcneMSPpRk,7007
 tests/test_mcp_documentation_utils.py,sha256=OW0N2N_2IOktbYTcCWhhWz4bANi8IB60l1q3DJi8Ra4,810
 tests/test_mcp_server.py,sha256=bP3PWVQsEfX6-lAgXKP32njdg__o65n2WuLvkxTTHkQ,11215
 tests/test_network_data_handling.py,sha256=oBSZuB3IRG9bwmD6n8FY-UZLe2UqGzXpNSxVtkHRSvE,12605
-tests/test_network_ig_utils.py,sha256=uojDLtL7oT9S9NJrXL8kBEHHFq5DB1GnJQT0v-gHEBE,632
+tests/test_network_ig_utils.py,sha256=Buoh570mNm5pcac3Hf6f3pevCjWfBwPfKuD8IkDLg58,2120
 tests/test_network_neighborhoods.py,sha256=8BV17m5X1OUd5FwasTTYUOkNYUHDPUkxOKH_VZCsyBE,631
 tests/test_network_net_create.py,sha256=VNFZTwQawAZQPDnVk_qFevgZErx5KyQZ24bMoZF4T4w,16462
 tests/test_network_net_propagation.py,sha256=9pKkUdduWejH4iKNCJXKFzAkdNpCfrMbiUWySgI_LH4,3244
 tests/test_network_ng_utils.py,sha256=CwDw4MKTPhVZXz2HA2XU2QjjBv8CXc1_yQ0drvkBkFw,724
 tests/test_network_paths.py,sha256=TWZnxY5bF3m6gahcxcYJGrBIawh2-_vUcec1LyPmXV8,1686
-tests/test_network_precompute.py,sha256=W1tuHM-dd90nk0vUUNP_xZ7EhCKSjigI5ndm8oq8l0c,8869
+tests/test_network_precompute.py,sha256=xMGmZI9DxcWhJxuP7GCZEqtmcOvDRNK2LSia0x94v0U,9018
 tests/test_ontologies_genodexito.py,sha256=hBlunyEPiKskqagjWKW5Z6DJwKvpueYHJLwbfyeeAdo,2256
 tests/test_ontologies_mygene.py,sha256=BuBLm8VatzpK39-Ew_fFTK9ueLE4eqmKIDS5UKE59n8,1541
 tests/test_ontologies_renaming.py,sha256=k7bQzP24zG7W3fpULwk1me2sOWEWlxylr4Mhx1_gJJY,3740
@@ -116,8 +116,8 @@ tests/test_pathwayannot.py,sha256=bceosccNy9tgxQei_7j7ATBSSvBSxOngJvK-mAzR_K0,33
 tests/test_rpy2_callr.py,sha256=UVzXMvYN3wcc-ikDIjH2sA4BqkbwiNbMm561BcbnbD4,2936
 tests/test_rpy2_init.py,sha256=APrNt9GEQV9va3vU5k250TxFplAoWFc-FJRFhM2GcDk,5927
 tests/test_sbml.py,sha256=f25zj1NogYrmLluvBDboLameTuCiQ309433Qn3iPvhg,1483
-tests/test_sbml_dfs_core.py,sha256=z2dYl5-3ZvIsEeK_sHxm8VtWSdL81Eljz_9aeedlM6U,16806
-tests/test_sbml_dfs_utils.py,sha256=onFWdhrTix30XR1-CMrMXld37BYxEGi6TZrweugLDzI,505
+tests/test_sbml_dfs_core.py,sha256=MtmQp9EZD4OFmk-5tWUSb9hUjcGfRKTFbSBymiE_Qzo,23628
+tests/test_sbml_dfs_utils.py,sha256=5lNzZ1NLOnFb_sZ0YWTgLzXy28yGNCtS_H8Q-W-T6Bw,2022
 tests/test_sbo.py,sha256=x_PENFaXYsrZIzOZu9cj_Wrej7i7SNGxgBYYvcigLs0,308
 tests/test_scverse_loading.py,sha256=bnU1lQSYYWhOAs0IIBoi4ZohqPokDQJ0n_rtkAfEyMU,29948
 tests/test_set_coverage.py,sha256=J-6m6LuOjcQa9pxRuWglSfJk4Ltm7kt_eOrn_Q-7P6Q,1604
@@ -126,8 +126,8 @@ tests/test_uncompartmentalize.py,sha256=nAk5kfAVLU9a2VWe2x2HYVcKqj-EnwmwddERIPRa
 tests/test_utils.py,sha256=JRJFmjDNZpjG59a-73JkTyGqa_a7Z8d0fE2cZt0CRII,22580
 tests/utils.py,sha256=SoWQ_5roJteFGcMaOeEiQ5ucwq3Z2Fa3AAs9iXHTsJY,749
 tests/test_data/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-napistu-0.3.3.dist-info/METADATA,sha256=Y5HCnBOuVO0Rvc1S-P3llVgWJSeBR1hes6UTt0cyhB4,3413
-napistu-0.3.3.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
-napistu-0.3.3.dist-info/entry_points.txt,sha256=_QnaPOvJNA3IltxmZgWIiBoen-L1bPYX18YQfC7oJgQ,41
-napistu-0.3.3.dist-info/top_level.txt,sha256=Gpvk0a_PjrtqhYcQ9IDr3zR5LqpZ-uIHidQMIpjlvhY,14
-napistu-0.3.3.dist-info/RECORD,,
+napistu-0.3.5.dist-info/METADATA,sha256=Dla6z2cQaQt3eR7HeUfSNOcqOn4uWY3vYtYp3gKEBl4,3414
+napistu-0.3.5.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
+napistu-0.3.5.dist-info/entry_points.txt,sha256=_QnaPOvJNA3IltxmZgWIiBoen-L1bPYX18YQfC7oJgQ,41
+napistu-0.3.5.dist-info/top_level.txt,sha256=Gpvk0a_PjrtqhYcQ9IDr3zR5LqpZ-uIHidQMIpjlvhY,14
+napistu-0.3.5.dist-info/RECORD,,

tests/test_network_ig_utils.py

@@ -6,6 +6,15 @@ from napistu.network import ig_utils
 from napistu.network import net_create
 
 
+@pytest.fixture
+def multi_component_graph() -> ig_utils.ig.Graph:
+    """Creates a graph with multiple disconnected components of different sizes."""
+    g1 = ig_utils.ig.Graph.Ring(5)  # 5 vertices, 5 edges
+    g2 = ig_utils.ig.Graph.Tree(3, 2)  # 3 vertices, 2 edges
+    g3 = ig_utils.ig.Graph.Full(2)  # 2 vertices, 1 edge
+    return ig_utils.ig.disjoint_union([g1, g2, g3])
+
+
 def test_validate_graph_attributes(sbml_dfs):
 
     napistu_graph = net_create.process_napistu_graph(
@@ -21,3 +30,30 @@ def test_validate_graph_attributes(sbml_dfs):
     assert ig_utils.validate_vertex_attributes(napistu_graph, "node_type") is None
     with pytest.raises(ValueError):
         ig_utils.validate_vertex_attributes(napistu_graph, "baz")
+
+
+def test_filter_to_largest_subgraph(multi_component_graph):
+    """Tests that the function returns only the single largest component."""
+    largest = ig_utils.filter_to_largest_subgraph(multi_component_graph)
+    assert isinstance(largest, ig_utils.ig.Graph)
+    assert largest.vcount() == 5
+    assert largest.ecount() == 5
+
+
+def test_filter_to_largest_subgraphs(multi_component_graph):
+    """Tests that the function returns the top K largest components."""
+    # Test getting the top 2
+    top_2 = ig_utils.filter_to_largest_subgraphs(multi_component_graph, top_k=2)
+    assert isinstance(top_2, list)
+    assert len(top_2) == 2
+    assert all(isinstance(g, ig_utils.ig.Graph) for g in top_2)
+    assert [g.vcount() for g in top_2] == [5, 3]
+
+    # Test getting more than the total number of components
+    top_5 = ig_utils.filter_to_largest_subgraphs(multi_component_graph, top_k=5)
+    assert len(top_5) == 3
+    assert [g.vcount() for g in top_5] == [5, 3, 2]
+
+    # Test invalid top_k
+    with pytest.raises(ValueError):
+        ig_utils.filter_to_largest_subgraphs(multi_component_graph, top_k=0)

tests/test_network_precompute.py

@@ -179,8 +179,11 @@ def test_precomputed_distances_neighborhoods():
                 right_on=join_key,
                 how="outer",
             )
-            .fillna(False)
         )
+        for col in ["in_precompute", "in_otf"]:
+            neighbor_comparison[col] = (
+                neighbor_comparison[col].astype("boolean").fillna(False)
+            )
         comparison_l.append(neighbor_comparison.assign(focal_sc_id=key))
 
     comparison_df = pd.concat(comparison_l)

tests/test_sbml_dfs_core.py

@@ -6,14 +6,83 @@ import numpy as np
 import pandas as pd
 import pytest
 from napistu import sbml_dfs_core
+from napistu.source import Source
 from napistu.ingestion import sbml
 from napistu.modify import pathwayannot
+from napistu.sbml_dfs_utils import _stub_ids
 
 from napistu import identifiers as napistu_identifiers
-from napistu.constants import SBML_DFS, SBOTERM_NAMES
+from napistu.constants import (
+    SBML_DFS,
+    SBOTERM_NAMES,
+    BQB_DEFINING_ATTRS,
+    BQB_DEFINING_ATTRS_LOOSE,
+    BQB,
+    IDENTIFIERS,
+)
 from napistu.sbml_dfs_core import SBML_dfs
 
 
+@pytest.fixture
+def test_data():
+    """Create test data for SBML integration tests."""
+
+    # Test compartments
+    compartments_df = pd.DataFrame(
+        [
+            {"c_name": "nucleus", "c_Identifiers": _stub_ids([])},
+            {"c_name": "cytoplasm", "c_Identifiers": _stub_ids([])},
+        ]
+    )
+
+    # Test species with extra data
+    species_df = pd.DataFrame(
+        [
+            {
+                "s_name": "TP53",
+                "s_Identifiers": _stub_ids([]),
+                "gene_type": "tumor_suppressor",
+            },
+            {"s_name": "MDM2", "s_Identifiers": _stub_ids([]), "gene_type": "oncogene"},
+            {
+                "s_name": "CDKN1A",
+                "s_Identifiers": _stub_ids([]),
+                "gene_type": "cell_cycle",
+            },
+        ]
+    )
+
+    # Test interactions with extra data
+    interaction_edgelist = pd.DataFrame(
+        [
+            {
+                "upstream_name": "TP53",
+                "downstream_name": "CDKN1A",
+                "upstream_compartment": "nucleus",
+                "downstream_compartment": "nucleus",
+                "r_name": "TP53_activates_CDKN1A",
+                "sbo_term": "SBO:0000459",
+                "r_Identifiers": _stub_ids([]),
+                "r_isreversible": False,
+                "confidence": 0.95,
+            },
+            {
+                "upstream_name": "MDM2",
+                "downstream_name": "TP53",
+                "upstream_compartment": "cytoplasm",
+                "downstream_compartment": "nucleus",
+                "r_name": "MDM2_inhibits_TP53",
+                "sbo_term": "SBO:0000020",
+                "r_Identifiers": _stub_ids([]),
+                "r_isreversible": False,
+                "confidence": 0.87,
+            },
+        ]
+    )
+
+    return [interaction_edgelist, species_df, compartments_df, Source(init=True)]
+
+
 def test_drop_cofactors(sbml_dfs):
     starting_rscs = sbml_dfs.reaction_species.shape[0]
     reduced_dfs = pathwayannot.drop_cofactors(sbml_dfs)
@@ -493,3 +562,153 @@ def test_remove_entity_data_nonexistent(sbml_dfs_w_data, caplog):
 
     # Validate the model is still valid
     sbml_dfs_w_data.validate()
+
+
+def test_filter_to_characteristic_species_ids():
+
+    species_ids_dict = {
+        SBML_DFS.S_ID: ["large_complex"] * 6
+        + ["small_complex"] * 2
+        + ["proteinA", "proteinB"]
+        + ["proteinC"] * 3
+        + [
+            "promiscuous_complexA",
+            "promiscuous_complexB",
+            "promiscuous_complexC",
+            "promiscuous_complexD",
+            "promiscuous_complexE",
+        ],
+        IDENTIFIERS.ONTOLOGY: ["complexportal"]
+        + ["HGNC"] * 7
+        + ["GO"] * 2
+        + ["ENSG", "ENSP", "pubmed"]
+        + ["HGNC"] * 5,
+        IDENTIFIERS.IDENTIFIER: [
+            "CPX-BIG",
+            "mem1",
+            "mem2",
+            "mem3",
+            "mem4",
+            "mem5",
+            "part1",
+            "part2",
+            "GO:1",
+            "GO:2",
+            "dna_seq",
+            "protein_seq",
+            "my_cool_pub",
+        ]
+        + ["promiscuous_complex"] * 5,
+        IDENTIFIERS.BQB: [BQB.IS]
+        + [BQB.HAS_PART] * 7
+        + [BQB.IS] * 2
+        + [
+            # these are retained if BQB_DEFINING_ATTRS_LOOSE is used
+            BQB.ENCODES,
+            BQB.IS_ENCODED_BY,
+            # this should always be removed
+            BQB.IS_DESCRIBED_BY,
+        ]
+        + [BQB.HAS_PART] * 5,
+    }
+
+    species_ids = pd.DataFrame(species_ids_dict)
+
+    characteristic_ids_narrow = sbml_dfs_core.filter_to_characteristic_species_ids(
+        species_ids,
+        defining_biological_qualifiers=BQB_DEFINING_ATTRS,
+        max_complex_size=4,
+        max_promiscuity=4,
+    )
+
+    EXPECTED_IDS = ["CPX-BIG", "GO:1", "GO:2", "part1", "part2"]
+    assert characteristic_ids_narrow[IDENTIFIERS.IDENTIFIER].tolist() == EXPECTED_IDS
+
+    characteristic_ids_loose = sbml_dfs_core.filter_to_characteristic_species_ids(
+        species_ids,
+        # include encodes and is_encoded_by as equivalent to is
+        defining_biological_qualifiers=BQB_DEFINING_ATTRS_LOOSE,
+        max_complex_size=4,
+        # expand promiscuity to default value
+        max_promiscuity=20,
+    )
+
+    EXPECTED_IDS = [
+        "CPX-BIG",
+        "GO:1",
+        "GO:2",
+        "dna_seq",
+        "protein_seq",
+        "part1",
+        "part2",
+    ] + ["promiscuous_complex"] * 5
+    assert characteristic_ids_loose[IDENTIFIERS.IDENTIFIER].tolist() == EXPECTED_IDS
+
+
+def test_sbml_basic_functionality(test_data):
+    """Test basic SBML_dfs creation from edgelist."""
+    interaction_edgelist, species_df, compartments_df, interaction_source = test_data
+
+    result = sbml_dfs_core.sbml_dfs_from_edgelist(
+        interaction_edgelist, species_df, compartments_df, interaction_source
+    )
+
+    assert isinstance(result, SBML_dfs)
+    assert len(result.species) == 3
+    assert len(result.compartments) == 2
+    assert len(result.reactions) == 2
+    assert (
+        len(result.compartmentalized_species) == 3
+    )  # TP53[nucleus], CDKN1A[nucleus], MDM2[cytoplasm]
+    assert len(result.reaction_species) == 4  # 2 reactions * 2 species each
+
+
+def test_sbml_extra_data_preservation(test_data):
+    """Test that extra columns are preserved when requested."""
+    interaction_edgelist, species_df, compartments_df, interaction_source = test_data
+
+    result = sbml_dfs_core.sbml_dfs_from_edgelist(
+        interaction_edgelist,
+        species_df,
+        compartments_df,
+        interaction_source,
+        keep_species_data=True,
+        keep_reactions_data="experiment",
+    )
+
+    assert hasattr(result, "species_data")
+    assert hasattr(result, "reactions_data")
+    assert "gene_type" in result.species_data["source"].columns
+    assert "confidence" in result.reactions_data["experiment"].columns
+
+
+def test_sbml_compartmentalized_naming(test_data):
+    """Test compartmentalized species naming convention."""
+    interaction_edgelist, species_df, compartments_df, interaction_source = test_data
+
+    result = sbml_dfs_core.sbml_dfs_from_edgelist(
+        interaction_edgelist, species_df, compartments_df, interaction_source
+    )
+
+    comp_names = result.compartmentalized_species["sc_name"].tolist()
+    assert "TP53 [nucleus]" in comp_names
+    assert "MDM2 [cytoplasm]" in comp_names
+    assert "CDKN1A [nucleus]" in comp_names
+
+
+def test_sbml_custom_stoichiometry(test_data):
+    """Test custom stoichiometry parameters."""
+    interaction_edgelist, species_df, compartments_df, interaction_source = test_data
+
+    result = sbml_dfs_core.sbml_dfs_from_edgelist(
+        interaction_edgelist,
+        species_df,
+        compartments_df,
+        interaction_source,
+        upstream_stoichiometry=2,
+        downstream_stoichiometry=3,
+    )
+
+    stoichiometries = result.reaction_species["stoichiometry"].unique()
+    assert 2 in stoichiometries  # upstream
+    assert 3 in stoichiometries  # downstream

tests/test_sbml_dfs_utils.py

@@ -1,6 +1,9 @@
 from __future__ import annotations
 
+import pandas as pd
+
 from napistu import sbml_dfs_utils
+from napistu.constants import BQB, BQB_DEFINING_ATTRS, BQB_DEFINING_ATTRS_LOOSE
 
 
 def test_id_formatter():
@@ -14,9 +17,47 @@ def test_id_formatter():
     assert list(input_vals) == inv_ids
 
 
-################################################
-# __main__
-################################################
-
-if __name__ == "__main__":
-    test_id_formatter()
+def test_get_characteristic_species_ids():
+    """
+    Test get_characteristic_species_ids function with both dogmatic and non-dogmatic cases.
+    """
+    # Create mock species identifiers data
+    mock_species_ids = pd.DataFrame(
+        {
+            "s_id": ["s1", "s2", "s3", "s4", "s5"],
+            "identifier": ["P12345", "CHEBI:15377", "GO:12345", "P67890", "P67890"],
+            "ontology": ["uniprot", "chebi", "go", "uniprot", "chebi"],
+            "bqb": [
+                "BQB_IS",
+                "BQB_IS",
+                "BQB_HAS_PART",
+                "BQB_HAS_VERSION",
+                "BQB_ENCODES",
+            ],
+        }
+    )
+
+    # Create mock SBML_dfs object
+    class MockSBML_dfs:
+        def get_identifiers(self, entity_type):
+            return mock_species_ids
+
+    mock_sbml = MockSBML_dfs()
+
+    # Test dogmatic case (default)
+    expected_bqbs = BQB_DEFINING_ATTRS + [BQB.HAS_PART]  # noqa: F841
+    dogmatic_result = sbml_dfs_utils.get_characteristic_species_ids(mock_sbml)
+    expected_dogmatic = mock_species_ids.query("bqb in @expected_bqbs")
+
+    pd.testing.assert_frame_equal(dogmatic_result, expected_dogmatic, check_like=True)
+
+    # Test non-dogmatic case
+    expected_bqbs = BQB_DEFINING_ATTRS_LOOSE + [BQB.HAS_PART]  # noqa: F841
+    non_dogmatic_result = sbml_dfs_utils.get_characteristic_species_ids(
+        mock_sbml, dogmatic=False
+    )
+    expected_non_dogmatic = mock_species_ids.query("bqb in @expected_bqbs")
+
+    pd.testing.assert_frame_equal(
+        non_dogmatic_result, expected_non_dogmatic, check_like=True
+    )