napistu 0.3.1__py3-none-any.whl → 0.3.2.dev1__py3-none-any.whl

napistu/__init__.py

@@ -3,10 +3,8 @@ from __future__ import annotations
 from importlib.metadata import PackageNotFoundError
 from importlib.metadata import version
 
-__version__ = "0.2.2"
-
 try:
-    __version__ = version("calicolabs-cpr")
+    __version__ = version("napistu")
 except PackageNotFoundError:
     # package is not installed
     pass

napistu/__main__.py

@@ -753,7 +753,7 @@ def export_precomputed_distances(
         weights_vars=weights_vars_list,
     )
 
-    utils.save_json(output_uri, precomputed_distances.to_json())
+    precompute.save_precomputed_distances(precomputed_distances, output_uri)
 
 
 @exporter.command(name="export_smbl_dfs_tables")

napistu/mcp/constants.py

@@ -104,7 +104,7 @@ REPOS_WITH_WIKI = [PACKAGE_DEFS.GITHUB_PROJECT_REPO]
 TUTORIAL_URLS = {
     "adding_data_to_graphs": "https://raw.githubusercontent.com/napistu/napistu/refs/heads/main/tutorials/adding_data_to_graphs.ipynb",
     "downloading_pathway_data": "https://raw.githubusercontent.com/napistu/napistu/refs/heads/main/tutorials/downloading_pathway_data.ipynb",
-    "formatting_sbml_dfs_as_napistu_graphs": "https://raw.githubusercontent.com/napistu/napistu/refs/heads/main/tutorials/formatting_sbml_dfs_as_napistu_graphs.ipynb",
+    "creating_a_napistu_graph": "https://raw.githubusercontent.com/napistu/napistu/refs/heads/main/tutorials/creating_a_napistu_graph.ipynb",
     "merging_models_into_a_consensus": "https://raw.githubusercontent.com/napistu/napistu/refs/heads/main/tutorials/merging_models_into_a_consensus.ipynb",
     "r_based_network_visualization": "https://raw.githubusercontent.com/napistu/napistu/refs/heads/main/tutorials/r_based_network_visualization.ipynb",
     "suggesting_mechanisms_with_networks": "https://raw.githubusercontent.com/napistu/napistu/refs/heads/main/tutorials/suggesting_mechanisms_with_networks.ipynb",

napistu/network/precompute.py

@@ -2,12 +2,16 @@ from __future__ import annotations
 
 import logging
 import math
+from pathlib import Path
+from typing import Union
 
 import numpy as np
 import pandas as pd
+from fs.errors import ResourceNotFound
 
 from napistu.network.napistu_graph_core import NapistuGraph
 from napistu.network.ig_utils import validate_edge_attributes
+from napistu.utils import load_json, save_json
 
 logger = logging.getLogger(__name__)
 
@@ -75,21 +79,17 @@ def precompute_distances(
     # interate through all partitions of "from" nodes and find their shortest and lowest weighted paths
     unique_partitions = vs_to_partition.index.unique().tolist()
 
-    precomputed_distances = (
-        pd.concat(
-            [
-                _calculate_distances_subset(
-                    napistu_graph,
-                    vs_to_partition,
-                    vs_to_partition.loc[uq_part],
-                    weights_vars=weights_vars,
-                )
-                for uq_part in unique_partitions
-            ]
-        )
-        .reset_index(drop=True)
-        .query("sc_id_origin != sc_id_dest")
-    )
+    precomputed_distances = pd.concat(
+        [
+            _calculate_distances_subset(
+                napistu_graph,
+                vs_to_partition,
+                vs_to_partition.loc[uq_part],
+                weights_vars=weights_vars,
+            )
+            for uq_part in unique_partitions
+        ]
+    ).query("sc_id_origin != sc_id_dest")
 
     # filter by path length and/or weight
     filtered_precomputed_distances = _filter_precomputed_distances(
@@ -97,11 +97,59 @@ def precompute_distances(
         max_steps=max_steps,
         max_score_q=max_score_q,
         path_weights_vars=["path_" + w for w in weights_vars],
-    )
+    ).reset_index(drop=True)
 
     return filtered_precomputed_distances
 
 
+def save_precomputed_distances(
+    precomputed_distances: pd.DataFrame, uri: Union[str, Path]
+) -> None:
+    """
+    Save a precomputed distances DataFrame to a JSON file.
+
+    Parameters
+    ----------
+    precomputed_distances : pd.DataFrame
+        The precomputed distances DataFrame to save
+    uri : Union[str, Path]
+        Path where to save the JSON file. Can be a local path or a GCS URI.
+
+    Raises
+    ------
+    OSError
+        If the file cannot be written to (permission issues, etc.)
+    """
+    save_json(str(uri), precomputed_distances.to_dict(orient="index"))
+
+
+def load_precomputed_distances(uri: Union[str, Path]) -> pd.DataFrame:
+    """
+    Load a precomputed distances DataFrame from a JSON file.
+
+    Parameters
+    ----------
+    uri : Union[str, Path]
+        Path to the JSON file to load
+
+    Returns
+    -------
+    pd.DataFrame
+        The reconstructed precomputed distances DataFrame
+
+    Raises
+    ------
+    FileNotFoundError
+        If the specified file does not exist
+    """
+    try:
+        data_dict = load_json(str(uri))
+    except ResourceNotFound as e:
+        raise FileNotFoundError(f"File not found: {uri}") from e
+
+    return pd.DataFrame.from_dict(data_dict, orient="index").rename(index=int)
+
+
 def _calculate_distances_subset(
     napistu_graph: NapistuGraph,
     vs_to_partition: pd.DataFrame,

{napistu-0.3.1.dist-info → napistu-0.3.2.dev1.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: napistu
-Version: 0.3.1
+Version: 0.3.2.dev1
 Summary: Connecting high-dimensional data to curated pathways
 Home-page: https://github.com/napistu/napistu-py
 Author: Sean Hackett

{napistu-0.3.1.dist-info → napistu-0.3.2.dev1.dist-info}/RECORD

@@ -1,5 +1,5 @@
-napistu/__init__.py,sha256=HEXcB6w8PCTD-tm4rq7AoFi7ufZNDuoG3EoM0kz9aPY,269
-napistu/__main__.py,sha256=1O_ZyCqNeHcyuL4rbbz6R7_jnPOAamKtTNXZ68gSA7U,28624
+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=Wb1eir8DKSAjukNPknNkKTS4kQSqZjTcTjFaOYNyrC8,15317
 napistu/identifiers.py,sha256=wsVriQdvPllA5uvh5CiREklA2tYW2MIB14dV7CPaMVU,34003
@@ -41,7 +41,7 @@ napistu/mcp/codebase.py,sha256=q3L76xzpIalcw1ZBy2Zt59G22rX1knila__QdQMh-OA,7950
 napistu/mcp/codebase_utils.py,sha256=r1nbDmGzq-NaH9cT11jC53mEjszQpwQ0uZUJkMHvgVs,10567
 napistu/mcp/component_base.py,sha256=nTa8RMW2rRBpFXfhUSHMgaA0sUS2Vy-ERZe__OB-R6Y,4461
 napistu/mcp/config.py,sha256=2CMUlcYhS0TMziAHFfmwQXpR1jx1qxSnZoP7UcNKYBk,7149
-napistu/mcp/constants.py,sha256=XlU5P9uY3LfRPjpSbe9xU35LkcBShP-oRNk_iQ2CqQk,3945
+napistu/mcp/constants.py,sha256=XJuWS-ORCOFU0xi80lRfWo0-MO4CIWYvmrUM7UwwGCs,3919
 napistu/mcp/documentation.py,sha256=BduopA2YiJQ43Gz_EtK3JGAE2HvFhuknj_pB1KaLBnQ,10738
 napistu/mcp/documentation_utils.py,sha256=dxzyu2pNxqlvCWJ2Au87_Q1BlmKrVnOo3qyTctoSogc,5873
 napistu/mcp/execution.py,sha256=ATwMNhrZTZHQCvWPAwmC95B-Yj9QjMyVR_1kqop5dak,16049
@@ -67,7 +67,7 @@ napistu/network/net_create.py,sha256=2N5ocGmibdBxIUVtv3H36iFWwkbys9ECCERFRlByhLc
 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=aEynTDdKK_WJbEqBd6Q8iihXzuk3rheurkPcnh9bYqQ,7651
+napistu/network/precompute.py,sha256=xDIHWxGWwDyEw1sF1bQKHVbunI8qmeJvo3Iv7wADUys,8960
 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-0.3.1.dist-info/licenses/LICENSE,sha256=kW8wVT__JWoHjl2BbbJDAZInWa9AxzJeR_uv6-i5x1g,1063
+napistu-0.3.2.dev1.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
@@ -101,14 +101,14 @@ tests/test_matching_species.py,sha256=OuUWp0-X3WYXkc-g51XyOqhp4MgO8cJvUSqt8ZvqRa
 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_net_propagation.py,sha256=9pKkUdduWejH4iKNCJXKFzAkdNpCfrMbiUWySgI_LH4,3244
 tests/test_network_data_handling.py,sha256=oBSZuB3IRG9bwmD6n8FY-UZLe2UqGzXpNSxVtkHRSvE,12605
 tests/test_network_ig_utils.py,sha256=uojDLtL7oT9S9NJrXL8kBEHHFq5DB1GnJQT0v-gHEBE,632
 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=iyqvxdlt_LQdAoFr8x-NZUbq5VH4Xo64fTg3gyXiWEg,7245
+tests/test_network_precompute.py,sha256=W1tuHM-dd90nk0vUUNP_xZ7EhCKSjigI5ndm8oq8l0c,8869
 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
@@ -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-0.3.1.dist-info/METADATA,sha256=Dy28usEPYFT-rbmyJSn2lvcNhc7tU2kcCZsj8oTlRWQ,3413
-napistu-0.3.1.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
-napistu-0.3.1.dist-info/entry_points.txt,sha256=_QnaPOvJNA3IltxmZgWIiBoen-L1bPYX18YQfC7oJgQ,41
-napistu-0.3.1.dist-info/top_level.txt,sha256=Gpvk0a_PjrtqhYcQ9IDr3zR5LqpZ-uIHidQMIpjlvhY,14
-napistu-0.3.1.dist-info/RECORD,,
+napistu-0.3.2.dev1.dist-info/METADATA,sha256=go09DE0iiD9UQmhyGSTdq2iGLGgODt84uZ9vKbridIg,3418
+napistu-0.3.2.dev1.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
+napistu-0.3.2.dev1.dist-info/entry_points.txt,sha256=_QnaPOvJNA3IltxmZgWIiBoen-L1bPYX18YQfC7oJgQ,41
+napistu-0.3.2.dev1.dist-info/top_level.txt,sha256=Gpvk0a_PjrtqhYcQ9IDr3zR5LqpZ-uIHidQMIpjlvhY,14
+napistu-0.3.2.dev1.dist-info/RECORD,,

tests/test_network_precompute.py

@@ -1,6 +1,8 @@
 from __future__ import annotations
 
+import pytest
 import os
+import tempfile
 
 import numpy as np
 import pandas as pd
@@ -214,11 +216,59 @@ def test_precomputed_distances_neighborhoods():
     assert upstream_disagreement_w_precompute.shape[0] == 0
 
 
-################################################
-# __main__
-################################################
-
-if __name__ == "__main__":
-    test_precomputed_distances()
-    test_precomputed_distances_shortest_paths()
-    test_precomputed_distances_neighborhoods()
+@pytest.mark.skip_on_windows
+def test_precomputed_distances_serialization():
+    """
+    Test that validates the serialization -> deserialization approach works correctly.
+
+    Notes
+    -----
+    This function creates a sample DataFrame with the structure of precomputed
+    distances data, saves it to a temporary JSON file, loads it back, and
+    validates that all data is preserved correctly through the serialization
+    round-trip.
+    """
+    # Create a sample DataFrame that mimics the precomputed distances structure
+    sample_data = {
+        "sc_id_origin": {
+            1: "SC00000000",
+            3: "SC00000003",
+            4: "SC00000004",
+            5: "SC00000005",
+            6: "SC00000011",
+        },
+        "sc_id_dest": {
+            1: "SC00000001",
+            3: "SC00000001",
+            4: "SC00000001",
+            5: "SC00000001",
+            6: "SC00000001",
+        },
+        "path_length": {1: 1.0, 3: 4.0, 4: 6.0, 5: 6.0, 6: 1.0},
+        "path_upstream_weights": {1: 1.0, 3: 4.0, 4: 6.0, 5: 6.0, 6: 1.0},
+        "path_weights": {1: 1.0, 3: 4.0, 4: 6.0, 5: 6.0, 6: 1.0},
+    }
+
+    # Create original DataFrame
+    original_df = pd.DataFrame(sample_data)
+
+    # Create a temporary file path
+    with tempfile.NamedTemporaryFile(
+        mode="w", suffix=".json", delete=False
+    ) as tmp_file:
+        temp_path = tmp_file.name
+
+    try:
+        # Test serialization
+        precompute.save_precomputed_distances(original_df, temp_path)
+
+        # Test deserialization
+        loaded_df = precompute.load_precomputed_distances(temp_path)
+
+        # Validate that the loaded DataFrame is identical to the original
+        pd.testing.assert_frame_equal(original_df, loaded_df, check_like=True)
+
+    finally:
+        # Clean up the temporary file
+        if os.path.exists(temp_path):
+            os.remove(temp_path)