napistu 0.1.0__py3-none-any.whl → 0.2.4.dev2__py3-none-any.whl

tests/test_net_propagation.py

@@ -0,0 +1,89 @@
+import pytest
+import igraph as ig
+import numpy as np
+from napistu.network.net_propagation import personalized_pagerank_by_attribute
+
+
+def test_personalized_pagerank_by_attribute_basic():
+    g = ig.Graph.Full(3)
+    g.vs["name"] = ["A", "B", "C"]
+    g.vs["score"] = [1, 0, 2]
+    df = personalized_pagerank_by_attribute(g, "score")
+    assert set(df.columns) == {
+        "name",
+        "pagerank_by_attribute",
+        "pagerank_uniform",
+        "score",
+    }
+    assert np.isclose(df["score"].sum(), 3)
+    assert np.isclose(df["pagerank_by_attribute"].sum(), 1)
+    assert np.isclose(df["pagerank_uniform"].sum(), 1)
+    # Uniform should only include A and C
+    assert df.loc[df["name"] == "B", "pagerank_uniform"].values[0] > 0
+
+
+def test_personalized_pagerank_by_attribute_no_uniform():
+    g = ig.Graph.Full(3)
+    g.vs["score"] = [1, 0, 2]
+    df = personalized_pagerank_by_attribute(g, "score", calculate_uniform_dist=False)
+    assert "pagerank_uniform" not in df.columns
+    assert np.isclose(df["pagerank_by_attribute"].sum(), 1)
+
+
+def test_personalized_pagerank_by_attribute_missing_and_negative():
+    g = ig.Graph.Full(3)
+    g.vs["score"] = [1, None, 2]
+    # None should be treated as 0
+    df = personalized_pagerank_by_attribute(g, "score")
+    assert np.isclose(df["score"].sum(), 3)
+    # Negative values should raise
+    g.vs["score"] = [1, -1, 2]
+    with pytest.raises(ValueError):
+        personalized_pagerank_by_attribute(g, "score")
+
+
+def test_personalized_pagerank_by_attribute_additional_args_directed():
+    # create an asymmetric directed graph to test whether additional_propagation_args is respected
+    g = ig.Graph(directed=True)
+    g.add_vertices(3)
+    g.add_edges([(0, 1), (1, 2)])
+    g.vs["score"] = [1, 0, 2]
+    # Run with directed=False, which should treat the graph as undirected
+    df_directed = personalized_pagerank_by_attribute(
+        g, "score", additional_propagation_args={"directed": True}
+    )
+    df_undirected = personalized_pagerank_by_attribute(
+        g, "score", additional_propagation_args={"directed": False}
+    )
+    # The results should differ for directed vs undirected
+    assert not np.allclose(
+        df_directed["pagerank_by_attribute"], df_undirected["pagerank_by_attribute"]
+    )
+    # Uniform should also be affected
+    assert not np.allclose(
+        df_directed["pagerank_uniform"], df_undirected["pagerank_uniform"]
+    )
+
+
+def test_personalized_pagerank_by_attribute_additional_args_invalid():
+    g = ig.Graph.Full(3)
+    g.vs["score"] = [1, 0, 2]
+    # Passing an invalid argument should raise ValueError
+    with pytest.raises(ValueError):
+        personalized_pagerank_by_attribute(
+            g, "score", additional_propagation_args={"not_a_real_arg": 123}
+        )
+
+
+def test_personalized_pagerank_by_attribute_all_missing():
+    g = ig.Graph.Full(3)
+    # No 'score' attribute at all
+    with pytest.raises(ValueError, match="missing for all vertices"):
+        personalized_pagerank_by_attribute(g, "score")
+
+
+def test_personalized_pagerank_by_attribute_all_zero():
+    g = ig.Graph.Full(3)
+    g.vs["score"] = [0, 0, 0]
+    with pytest.raises(ValueError, match="zero for all vertices"):
+        personalized_pagerank_by_attribute(g, "score")

tests/test_net_utils.py

@@ -3,6 +3,7 @@ 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
@@ -56,6 +57,85 @@ def test_validate_graph_attributes(sbml_dfs):
         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__
 ################################################
@@ -64,3 +144,6 @@ 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_sbml.py

@@ -1,6 +1,7 @@
 from __future__ import annotations
 
 import os
+import pytest
 
 import pandas as pd
 from napistu import sbml_dfs_core
@@ -19,6 +20,7 @@ def test_sbml_dfs(sbml_path):
     assert type(dfs.get_identifiers("species")) is pd.DataFrame
 
 
+@pytest.mark.skip_on_windows
 def test_adding_sbml_annotations(sbml_model):
     annotations = pd.DataFrame(
         [

tests/{test_sbml_dfs_create.py → test_sbml_dfs_core.py}

@@ -2,12 +2,17 @@ from __future__ import annotations
 
 import os
 
+import numpy as np
 import pandas as pd
 import pytest
 from napistu import sbml_dfs_core
 from napistu.ingestion import sbml
 from napistu.modify import pathwayannot
 
+from napistu import identifiers as napistu_identifiers
+from napistu.constants import SBML_DFS
+from napistu.sbml_dfs_core import SBML_dfs
+
 
 def test_drop_cofactors(sbml_dfs):
     starting_rscs = sbml_dfs.reaction_species.shape[0]
@@ -238,7 +243,7 @@ def test_read_sbml_with_invalid_ids():
 def test_stubbed_compartment():
     compartment = sbml_dfs_core._stub_compartments()
 
-    assert compartment["c_Identifiers"][0].ids[0] == {
+    assert compartment["c_Identifiers"].iloc[0].ids[0] == {
         "ontology": "go",
         "identifier": "GO:0005575",
         "url": "https://www.ebi.ac.uk/QuickGO/term/GO:0005575",
@@ -255,7 +260,7 @@ def test_get_table(sbml_dfs):
         sbml_dfs.get_table("foo", {"id"})
 
     # bad type
-    with pytest.raises(AssertionError):
+    with pytest.raises(TypeError):
         sbml_dfs.get_table("reaction_species", "id")
 
     # reaction species don't have ids
@@ -303,5 +308,64 @@ def test_species_status(sbml_dfs):
     )
 
 
-# if __name__ == "__main__":
-#   test_get_table()
+def test_get_identifiers_handles_missing_values():
+
+    # Minimal DataFrame with all types
+    df = pd.DataFrame(
+        {
+            SBML_DFS.S_NAME: ["A", "B", "C", "D"],
+            SBML_DFS.S_IDENTIFIERS: [
+                napistu_identifiers.Identifiers([]),
+                None,
+                np.nan,
+                pd.NA,
+            ],
+            SBML_DFS.S_SOURCE: [None, None, None, None],
+        },
+        index=["s1", "s2", "s3", "s4"],
+    )
+    df.index.name = SBML_DFS.S_ID
+
+    sbml_dict = {
+        SBML_DFS.COMPARTMENTS: pd.DataFrame(
+            {
+                SBML_DFS.C_NAME: ["cytosol"],
+                SBML_DFS.C_IDENTIFIERS: [None],
+                SBML_DFS.C_SOURCE: [None],
+            },
+            index=["c1"],
+        ),
+        SBML_DFS.SPECIES: df,
+        SBML_DFS.COMPARTMENTALIZED_SPECIES: pd.DataFrame(
+            {
+                SBML_DFS.SC_NAME: ["A [cytosol]"],
+                SBML_DFS.S_ID: ["s1"],
+                SBML_DFS.C_ID: ["c1"],
+                SBML_DFS.SC_SOURCE: [None],
+            },
+            index=["sc1"],
+        ),
+        SBML_DFS.REACTIONS: pd.DataFrame(
+            {
+                SBML_DFS.R_NAME: [],
+                SBML_DFS.R_IDENTIFIERS: [],
+                SBML_DFS.R_SOURCE: [],
+                SBML_DFS.R_ISREVERSIBLE: [],
+            },
+            index=[],
+        ),
+        SBML_DFS.REACTION_SPECIES: pd.DataFrame(
+            {
+                SBML_DFS.R_ID: [],
+                SBML_DFS.SC_ID: [],
+                SBML_DFS.STOICHIOMETRY: [],
+                SBML_DFS.SBO_TERM: [],
+            },
+            index=[],
+        ),
+    }
+    sbml = SBML_dfs(sbml_dict, validate=False)
+    result = sbml.get_identifiers(SBML_DFS.SPECIES)
+    assert result.shape[0] == 0 or all(
+        result[SBML_DFS.S_ID] == "s1"
+    ), "Only Identifiers objects should be returned."

tests/test_utils.py

@@ -16,6 +16,8 @@ from google.cloud import storage
 from pytest import fixture
 from testcontainers.core.container import DockerContainer
 
+from napistu.utils import drop_extra_cols
+
 
 @fixture(scope="session")
 def gcs_storage():
@@ -485,3 +487,82 @@ def test_click_str_to_list():
     assert utils.click_str_to_list("['foo', bar]") == ["foo", "bar"]
     with pytest.raises(ValueError):
         utils.click_str_to_list("foo")
+
+
+def test_drop_extra_cols():
+    """Test the _drop_extra_cols function for removing and reordering columns."""
+    # Setup test DataFrames
+    df_in = pd.DataFrame({"col1": [1, 2, 3], "col2": [4, 5, 6], "col3": [7, 8, 9]})
+
+    df_out = pd.DataFrame(
+        {
+            "col2": [10, 11, 12],
+            "col3": [13, 14, 15],
+            "col4": [16, 17, 18],  # Extra column that should be dropped
+            "col1": [19, 20, 21],  # Different order than df_in
+        }
+    )
+
+    # Test basic functionality without always_include
+    result = drop_extra_cols(df_in, df_out)
+
+    # Check that extra column was dropped
+    assert "col4" not in result.columns
+
+    # Check that columns are in the same order as df_in
+    assert list(result.columns) == list(df_in.columns)
+
+    # Check that values are preserved
+    pd.testing.assert_frame_equal(
+        result,
+        pd.DataFrame(
+            {"col1": [19, 20, 21], "col2": [10, 11, 12], "col3": [13, 14, 15]}
+        )[
+            list(df_in.columns)
+        ],  # Ensure same column order
+    )
+
+    # Test with always_include
+    result_with_include = drop_extra_cols(df_in, df_out, always_include=["col4"])
+
+    # Check that col4 is retained and appears at the end
+    assert list(result_with_include.columns) == list(df_in.columns) + ["col4"]
+    assert result_with_include["col4"].equals(df_out["col4"])
+
+    # Test with always_include containing non-existent column
+    result_non_existent = drop_extra_cols(
+        df_in, df_out, always_include=["col4", "col5"]
+    )
+    assert list(result_non_existent.columns) == list(df_in.columns) + ["col4"]
+
+    # Test with always_include containing column from df_in
+    result_overlap = drop_extra_cols(df_in, df_out, always_include=["col1", "col4"])
+    assert list(result_overlap.columns) == list(df_in.columns) + ["col4"]
+
+    # Test with no overlapping columns but some in always_include
+    df_out_no_overlap = pd.DataFrame({"col4": [1, 2, 3], "col5": [4, 5, 6]})
+    result_no_overlap = drop_extra_cols(df_in, df_out_no_overlap)
+    assert result_no_overlap.empty
+    assert list(result_no_overlap.columns) == []
+
+    result_no_overlap_with_include = drop_extra_cols(
+        df_in, df_out_no_overlap, always_include=["col4"]
+    )
+    assert list(result_no_overlap_with_include.columns) == ["col4"]
+    assert result_no_overlap_with_include["col4"].equals(df_out_no_overlap["col4"])
+
+    # Test with subset of columns
+    df_out_subset = pd.DataFrame(
+        {"col1": [1, 2, 3], "col3": [7, 8, 9], "col4": [10, 11, 12]}
+    )
+    result_subset = drop_extra_cols(df_in, df_out_subset)
+    assert list(result_subset.columns) == ["col1", "col3"]
+    pd.testing.assert_frame_equal(result_subset, df_out_subset[["col1", "col3"]])
+
+    result_subset_with_include = drop_extra_cols(
+        df_in, df_out_subset, always_include=["col4"]
+    )
+    assert list(result_subset_with_include.columns) == ["col1", "col3", "col4"]
+    pd.testing.assert_frame_equal(
+        result_subset_with_include, df_out_subset[["col1", "col3", "col4"]]
+    )

napistu-0.1.0.dist-info/METADATA

@@ -1,56 +0,0 @@
-Metadata-Version: 2.4
-Name: napistu
-Version: 0.1.0
-Summary: Connecting high-dimensional data to curated pathways
-Home-page: https://github.com/napistu/napistu-py
-Author: Sean Hackett
-Author-email: seanmchackett@gmail.com
-Project-URL: Bug Tracker, https://github.com/napistu/napistu-py/issues
-Classifier: License :: OSI Approved :: MIT License
-Classifier: Operating System :: OS Independent
-Classifier: Programming Language :: Python :: 3
-Classifier: Programming Language :: Python :: 3 :: Only
-Requires-Python: >=3.11
-Description-Content-Type: text/markdown
-License-File: LICENSE
-Requires-Dist: Jinja2
-Requires-Dist: PyYAML==6.*
-Requires-Dist: click==8.*
-Requires-Dist: click-logging
-Requires-Dist: fs==2.4.*
-Requires-Dist: fs-gcsfs==1.5.*
-Requires-Dist: igraph
-Requires-Dist: matplotlib==3.*
-Requires-Dist: numpy==1.26.*
-Requires-Dist: pandas==1.5.*
-Requires-Dist: pydantic==2.*
-Requires-Dist: python-libsbml
-Requires-Dist: requests>=2
-Requires-Dist: scipy==1.14.*
-Requires-Dist: tqdm
-Requires-Dist: zeep==3.*
-Provides-Extra: dev
-Requires-Dist: black==25.*; extra == "dev"
-Requires-Dist: ipykernel; extra == "dev"
-Requires-Dist: pre-commit==3.3.*; extra == "dev"
-Requires-Dist: pytest==7.*; extra == "dev"
-Requires-Dist: pytest-cov; extra == "dev"
-Requires-Dist: ruff; extra == "dev"
-Requires-Dist: testcontainers; extra == "dev"
-Provides-Extra: rpy2
-Requires-Dist: pyarrow==18.0.0; extra == "rpy2"
-Requires-Dist: rpy2==3.5.*; extra == "rpy2"
-Requires-Dist: rpy2-arrow==0.1.1; extra == "rpy2"
-Dynamic: license-file
-
-# Napistu Python Library
-
-This Python package hosts the majority of the algorithmic code for the [Napistu project](https://github.com/napistu/napistu).
-
-## Setup
-
-Currently the only way to use this repository is to clone the repo and perform a local install. e.g., from this directory:
-
-```bash
-pip install .
-```

napistu-0.1.0.dist-info/RECORD

@@ -1,77 +0,0 @@
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-napistu/__main__.py,sha256=i1OyReHD58GjyGYShXmMuBfA0VoGBF9dirg2nA4JCa8,28334
-napistu/consensus.py,sha256=p8GjWFzq1cvBB-H-LVSatWL_9fxbdYq2wsF4-JZnc_M,54641
-napistu/constants.py,sha256=hQ1OLH07xFTxMukJLCptzqqHk22vgrByej8lvMb2qbc,14702
-napistu/identifiers.py,sha256=wque0qsMZK2AMsAhkF1ERSMrEF7h6b5SMp3iqVu8e1o,28796
-napistu/indices.py,sha256=UeJjjsYs0sGvZIKz1y4ZQ6aUkABn-6TCUDZ2VCVT9JI,7534
-napistu/mechanism_matching.py,sha256=CPhtM6GERmGlBK8zH1cEvSpsasa0mG7ojLKDOze3dyE,21704
-napistu/sbml_dfs_core.py,sha256=iSng-3cpJVpVMb340YGM6s0pFBTA9SyYCdYvHdZRSMA,79387
-napistu/sbml_dfs_utils.py,sha256=j6Bu3acqOFSEbyVzASXhlnV8hQvi4k-vdMYzVMPzz5A,10318
-napistu/source.py,sha256=oBgw2OZLVBETQG8Mwoc5ZUe-6cg_Yt6Mxsto3fCdw1k,13386
-napistu/utils.py,sha256=G4IfG_WBSxkn5RBdPPn9sAkzrz2BdKgXlFFmMsB9wsA,28038
-napistu/gcs/__init__.py,sha256=1kqmRHlEyI7VpILzurZb1URwC_UIc1PTMEBHQnjXW6s,246
-napistu/gcs/constants.py,sha256=rc-oQBh6pdu7cjqTCerHG_fDub-FQcEjzWh2ic715cs,2844
-napistu/gcs/downloads.py,sha256=EiOxLW1MMexdPTSiakWknTB-BGY1y__s2n1z9Sd8VYM,5033
-napistu/ingestion/__init__.py,sha256=1kqmRHlEyI7VpILzurZb1URwC_UIc1PTMEBHQnjXW6s,246
-napistu/ingestion/bigg.py,sha256=XPJZv64mrIMCuKe1mjQfS5QPR9tmengGvndSjc3QFLA,5559
-napistu/ingestion/constants.py,sha256=TYATiVNrLyuQ1AvLVt35F1xQ8pQ3U19o_N6ZSkdW3PA,9941
-napistu/ingestion/cpr_edgelist.py,sha256=eVT9M7gmdBuGHcAYlvkD_zzvTtyzXufKWjwDiT8OxF4,3572
-napistu/ingestion/identifiers_etl.py,sha256=6ppDUA6lEZurdmVbiFLOUzphYbr-hndMhtqsQnq_yAc,5009
-napistu/ingestion/obo.py,sha256=pszLLfImZxDYjL3WQUCow2hQFURROGHqIq3qbgVtzAM,8836
-napistu/ingestion/psi_mi.py,sha256=Icj73EK75ytFPBw-TH2B6yW1ZWAmckmn5mtPl9pIxuA,9389
-napistu/ingestion/reactome.py,sha256=-Q3GsAsfVkTD7cDD1fLEEnWQbI6vs7nxsdYInk7ZvVE,7907
-napistu/ingestion/sbml.py,sha256=gK6_jHgo6oaiG16WlrbBSvxq_0VzFR4a5fG9IQrp5bU,24153
-napistu/ingestion/string.py,sha256=tsaHrjppgFbl9NnRcB2DytpoontqrpfQL65zD9HPgEM,11668
-napistu/ingestion/trrust.py,sha256=ccjZc_eF3PdxxurnukiEo_e0-aKc_3z22NYbaJBtHdY,9774
-napistu/ingestion/yeast.py,sha256=bwFBNxRq-dLDaddgBL1hpfZj0eQ56nBXyR_9n0NZT9Y,5233
-napistu/modify/__init__.py,sha256=1kqmRHlEyI7VpILzurZb1URwC_UIc1PTMEBHQnjXW6s,246
-napistu/modify/constants.py,sha256=KHigix_8A8kCLWYVGR9_6_n34UNDcq2guDLC1KLeNZ4,2648
-napistu/modify/curation.py,sha256=UNeAfJ26XDFvSwkPL8WHCAP0FQYiVUrSvJn3UIt5jy8,21607
-napistu/modify/gaps.py,sha256=XqwfvzgJywA7ws5hzDlj22xs5tRGc4xOdbQ2v51UJqc,23983
-napistu/modify/pathwayannot.py,sha256=onbQy9YNYPbeOih8fSxymxUQJc1jXjRIQOABv3xkvng,47183
-napistu/modify/uncompartmentalize.py,sha256=U5X4Q7Z-YIkC8_711x3sU21vTVdv9rKfauwz4JNzl6c,9690
-napistu/network/__init__.py,sha256=1kqmRHlEyI7VpILzurZb1URwC_UIc1PTMEBHQnjXW6s,246
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