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

napistu/rpy2/netcontextr.py

@@ -91,10 +91,14 @@ def sbml_dfs_to_rcpr_string_graph(
     )
 
     # Perform validations
-    assert dat_gene["s_id"].is_unique
-    assert dat_gene["sc_id"].is_unique
-    assert dat_gene[COL_GENE].is_unique
-    assert dat_gene[COL_GENE].hasnans is False
+    if not dat_gene["s_id"].is_unique:
+        raise ValueError("dat_gene['s_id'] must be unique")
+    if not dat_gene["sc_id"].is_unique:
+        raise ValueError("dat_gene['sc_id'] must be unique")
+    if not dat_gene[COL_GENE].is_unique:
+        raise ValueError("dat_gene[COL_GENE] must be unique")
+    if dat_gene[COL_GENE].hasnans:
+        raise ValueError("dat_gene[COL_GENE] must not have NaNs")
 
     # Reshape into the correct format
     dat_reactions = dat_gene[["sc_id", COL_GENE]].merge(
@@ -102,9 +106,8 @@ def sbml_dfs_to_rcpr_string_graph(
     )[[COL_GENE, "r_id"]]
     # assert that this has the correct shape, ie 2x the shape of the number
     # of reactions
-    assert (
-        dat_reactions.shape[0] == 2 * sbml_dfs.reactions.shape[0]
-    ), "There should be exactly 2 reactants per reactions"
+    if dat_reactions.shape[0] != 2 * sbml_dfs.reactions.shape[0]:
+        raise ValueError("There should be exactly 2 reactants per reaction")
 
     # This is the fastest way I found to reshape this into the
     # Edgelist format

napistu/rpy2/rids.py

@@ -3,7 +3,6 @@ from __future__ import annotations
 import logging
 
 import pandas as pd
-from napistu import consensus
 from napistu import constants
 from napistu import identifiers
 from napistu import sbml_dfs_core
@@ -67,7 +66,8 @@ def expand_identifiers(
 
     # pull out all identifiers as a pd.DataFrame
     all_entity_identifiers = sbml_dfs.get_identifiers(id_type)
-    assert isinstance(all_entity_identifiers, pd.DataFrame)
+    if not isinstance(all_entity_identifiers, pd.DataFrame):
+        raise TypeError("all_entity_identifiers must be a pandas DataFrame")
 
     if id_type == "species":
         all_entity_identifiers = _check_species_identifiers_entrez_gene_ontology(
@@ -226,8 +226,10 @@ def create_bioconductor_mapping_tables(
 
     """
 
-    assert isinstance(mappings, set)
-    assert isinstance(species, str)
+    if not isinstance(mappings, set):
+        raise TypeError(f"mappings must be a set, but got {type(mappings).__name__}")
+    if not isinstance(species, str):
+        raise TypeError(f"species must be a str, but got {type(species).__name__}")
 
     logger.info(
         f"Creating mapping tables from entrez genes to/from {', '.join(mappings)}"
@@ -620,7 +622,7 @@ def connect_dogmatic_mappings(species: str, r_paths: str | None = None) -> dict:
     ]
 
     s_name_series = (
-        consensus._add_nameness_score(possible_names, IDENTIFIERS.IDENTIFIER)
+        utils._add_nameness_score(possible_names, IDENTIFIERS.IDENTIFIER)
         .sort_values(["ontology_preference", "nameness_score"])
         .groupby("cluster")
         .first()

napistu/sbml_dfs_core.py

@@ -8,7 +8,6 @@ from typing import Mapping
 from typing import MutableMapping
 from typing import TYPE_CHECKING
 
-import numpy as np
 import pandas as pd
 from napistu import identifiers
 from napistu import sbml_dfs_utils
@@ -171,7 +170,10 @@ class SBML_dfs:
             )
 
         if required_attributes is not None:
-            assert isinstance(required_attributes, set)
+            if not isinstance(required_attributes, set):
+                raise TypeError(
+                    f"required_attributes must be a set, but got {type(required_attributes).__name__}"
+                )
 
             # determine whether required_attributes are appropriate
             VALID_REQUIRED_ATTRIBUTES = {"id", "source", "label"}
@@ -221,7 +223,11 @@ class SBML_dfs:
         ).assert_present()
 
         if ontologies is not None:
-            assert isinstance(ontologies, set)
+            if not isinstance(ontologies, set):
+                # for clarity this should not be reachable based on type hints
+                raise TypeError(
+                    f"ontologies must be a set, but got {type(ontologies).__name__}"
+                )
             ALL_VALID_ONTOLOGIES = identifiers_df["ontology"].unique()
             invalid_ontologies = ontologies.difference(ALL_VALID_ONTOLOGIES)
             if len(invalid_ontologies) > 0:
@@ -289,10 +295,7 @@ class SBML_dfs:
             self.compartmentalized_species.join(cspecies_n_connections)
             .join(cspecies_n_children)
             .join(cspecies_n_parents)
-            .fillna(0)
-            .astype(
-                {"sc_degree": "int32", "sc_children": "int32", "sc_parents": "int32"}
-            )
+            .fillna(int(0))  # Explicitly fill with int(0) to avoid downcasting warning
             .merge(species_features, left_on="s_id", right_index=True)
             .drop(columns=["sc_name", "s_id", "c_id"])
         )
@@ -307,13 +310,16 @@ class SBML_dfs:
 
             if isinstance(id_entry, identifiers.Identifiers):
                 identifiers_dict[sysid] = pd.DataFrame(id_entry.ids)
-            elif np.isnan(id_entry):
+            elif pd.isna(id_entry):
                 continue
             else:
                 raise ValueError(
                     f"id_entry was a {type(id_entry)} and must either be"
-                    " an identifiers.Identifiers object or NaN"
+                    " an identifiers.Identifiers object or a missing value (None, np.nan, pd.NA)"
                 )
+        if not identifiers_dict:
+            # Return empty DataFrame with expected columns if nothing found
+            return pd.DataFrame(columns=[schema[id_type]["pk"], "entry"])
         identifiers_tbl = pd.concat(identifiers_dict)
 
         identifiers_tbl.index.names = [schema[id_type]["pk"], "entry"]
@@ -362,7 +368,7 @@ class SBML_dfs:
         all_ids = pd.concat(
             [
                 sbml_dfs_utils._stub_ids(
-                    entity_table[schema[entity_type]["id"]][i].ids
+                    entity_table[schema[entity_type]["id"]].iloc[i].ids
                 ).assign(id=entity_table.index[i])
                 for i in range(0, entity_table.shape[0])
             ]
@@ -816,7 +822,10 @@ class SBML_dfs:
         _validate_matching_data(reactions_data_table, self.reactions)
 
     def _validate_reaction_species(self):
-        assert all(self.reaction_species[SBML_DFS.STOICHIOMETRY].notnull())
+        if not all(self.reaction_species[SBML_DFS.STOICHIOMETRY].notnull()):
+            raise ValueError(
+                "All reaction_species[SBML_DFS.STOICHIOMETRY] must be not null"
+            )
 
         # test for null SBO terms
         n_null_sbo_terms = sum(self.reaction_species[SBML_DFS.SBO_TERM].isnull())
@@ -963,7 +972,7 @@ def reaction_summary(r_id: str, sbml_dfs: SBML_dfs) -> pd.DataFrame:
                 augmented_matching_reaction_species, sbml_dfs.reactions, SBML_DFS.S_NAME
             )
             + " ["
-            + augmented_matching_reaction_species[SBML_DFS.C_NAME][0]
+            + augmented_matching_reaction_species[SBML_DFS.C_NAME].iloc[0]
             + "]"
         )
     else:
@@ -1118,9 +1127,14 @@ def construct_formula_string(
     ]
 
     rxn_reversible = bool(
-        reactions_df.loc[reaction_species_df[SBML_DFS.R_ID][0], SBML_DFS.R_ISREVERSIBLE]
+        reactions_df.loc[
+            reaction_species_df[SBML_DFS.R_ID].iloc[0], SBML_DFS.R_ISREVERSIBLE
+        ]
     )  # convert from a np.bool_ to bool if needed
-    assert isinstance(rxn_reversible, bool)
+    if not isinstance(rxn_reversible, bool):
+        raise TypeError(
+            f"rxn_reversible must be a bool, but got {type(rxn_reversible).__name__}"
+        )
 
     if rxn_reversible:
         arrow_type = " <-> "
@@ -1265,6 +1279,7 @@ def filter_to_characteristic_species_ids(
         data=[True] * len(promiscuous_component_identifiers_index),
         index=promiscuous_component_identifiers_index,
         name="is_shared_component",
+        dtype=bool,
     )
 
     if len(promiscuous_component_identifiers) == 0:
@@ -1476,7 +1491,10 @@ def infer_sbo_terms(sbml_dfs: SBML_dfs) -> SBML_dfs:
         ~sbml_dfs.reaction_species[SBML_DFS.SBO_TERM].isin(MINI_SBO_TO_NAME.keys())
     ]
 
-    assert all(sbml_dfs.reaction_species[SBML_DFS.SBO_TERM].notnull())
+    if not all(sbml_dfs.reaction_species[SBML_DFS.SBO_TERM].notnull()):
+        raise ValueError(
+            "All sbml_dfs.reaction_species[SBML_DFS.SBO_TERM] must be not null"
+        )
     if invalid_sbo_terms.shape[0] == 0:
         logger.info("All sbo_terms were valid; returning input sbml_dfs")
         return sbml_dfs
@@ -1485,22 +1503,25 @@ def infer_sbo_terms(sbml_dfs: SBML_dfs) -> SBML_dfs:
 
     # add missing/invalid terms based on stoichiometry
     invalid_sbo_terms.loc[
-        invalid_sbo_terms[sbml_dfs.STOICHIOMETRY] < 0, SBML_DFS.SBO_TERM
+        invalid_sbo_terms[SBML_DFS.STOICHIOMETRY] < 0, SBML_DFS.SBO_TERM
     ] = MINI_SBO_FROM_NAME[SBOTERM_NAMES.REACTANT]
 
     invalid_sbo_terms.loc[
-        invalid_sbo_terms[sbml_dfs.STOICHIOMETRY] > 0, SBML_DFS.SBO_TERM
+        invalid_sbo_terms[SBML_DFS.STOICHIOMETRY] > 0, SBML_DFS.SBO_TERM
     ] = MINI_SBO_FROM_NAME[SBOTERM_NAMES.PRODUCT]
 
     invalid_sbo_terms.loc[
-        invalid_sbo_terms[sbml_dfs.STOICHIOMETRY] == 0, SBML_DFS.SBO_TERM
+        invalid_sbo_terms[SBML_DFS.STOICHIOMETRY] == 0, SBML_DFS.SBO_TERM
     ] = MINI_SBO_FROM_NAME[SBOTERM_NAMES.STIMULATOR]
 
     updated_reaction_species = pd.concat(
         [valid_sbo_terms, invalid_sbo_terms]
     ).sort_index()
 
-    assert sbml_dfs.reaction_species.shape[0] == updated_reaction_species.shape[0]
+    if sbml_dfs.reaction_species.shape[0] != updated_reaction_species.shape[0]:
+        raise ValueError(
+            f"Trying to overwrite {sbml_dfs.reaction_species.shape[0]} reaction_species with {updated_reaction_species.shape[0]}"
+        )
     sbml_dfs.reaction_species = updated_reaction_species
 
     return sbml_dfs
@@ -1583,15 +1604,11 @@ def export_sbml_dfs(
         raise TypeError(
             f"sbml_dfs was a {type(sbml_dfs)} and must" " be an sbml.SBML_dfs"
         )
-    # select valid BQB attributes based on dogmatic flag
-    defining_biological_qualifiers = sbml_dfs_utils._dogmatic_to_defining_bqbs(dogmatic)
-
-    # pre-summarize ontologies
-    species_identifiers = sbml_dfs.get_identifiers(SBML_DFS.SPECIES)
-    # drop some BQB_HAS_PART annotations
-    species_identifiers = filter_to_characteristic_species_ids(
-        species_identifiers,
-        defining_biological_qualifiers=defining_biological_qualifiers,
+
+    # filter to identifiers which make sense when mapping from ids -> species
+    species_identifiers = sbml_dfs_utils.get_characteristic_species_ids(
+        sbml_dfs,
+        dogmatic=dogmatic,
     )
 
     try:
@@ -2000,7 +2017,7 @@ def find_underspecified_reactions(
             ),
             how="left",
         )
-        .fillna(False)[SBML_DFS.R_ID]
+        .fillna(False)[SBML_DFS.R_ID]  # Fill boolean column with False
         .tolist()
     )
 

napistu/sbml_dfs_utils.py

@@ -13,6 +13,7 @@ import pandas as pd
 from napistu import utils
 from napistu import indices
 
+from napistu import sbml_dfs_core
 from napistu.constants import SBML_DFS
 from napistu.constants import IDENTIFIERS
 from napistu.constants import BQB_DEFINING_ATTRS
@@ -151,7 +152,6 @@ def adapt_pw_index(
 
 
 def _dogmatic_to_defining_bqbs(dogmatic: bool = False) -> str:
-    assert isinstance(dogmatic, bool)
     if dogmatic:
         logger.info(
             "Running in dogmatic mode - differences genes, transcripts, and proteins will "
@@ -268,6 +268,42 @@ def check_entity_data_index_matching(sbml_dfs, table):
     return sbml_dfs
 
 
+def get_characteristic_species_ids(
+    sbml_dfs: sbml_dfs_core.SBML_dfs, dogmatic: bool = True
+) -> pd.DataFrame:
+    """
+    Get Characteristic Species IDs
+
+    List the systematic identifiers which are characteristic of molecular species, e.g., excluding subcomponents, and optionally, treating proteins, transcripts, and genes equiavlently.
+
+    Parameters
+    ----------
+    sbml_dfs : sbml_dfs_core.SBML_dfs
+        The SBML_dfs object.
+    dogmatic : bool, default=True
+        Whether to use the dogmatic flag to determine which BQB attributes are valid.
+
+    Returns
+    -------
+    pd.DataFrame
+        A DataFrame containing the systematic identifiers which are characteristic of molecular species.
+    """
+
+    # select valid BQB attributes based on dogmatic flag
+    defining_biological_qualifiers = _dogmatic_to_defining_bqbs(dogmatic)
+
+    # pre-summarize ontologies
+    species_identifiers = sbml_dfs.get_identifiers(SBML_DFS.SPECIES)
+
+    # drop some BQB_HAS_PART annotations
+    species_identifiers = sbml_dfs_core.filter_to_characteristic_species_ids(
+        species_identifiers,
+        defining_biological_qualifiers=defining_biological_qualifiers,
+    )
+
+    return species_identifiers
+
+
 def _dogmatic_to_defining_bqbs(dogmatic: bool = False) -> str:
     assert isinstance(dogmatic, bool)
     if dogmatic:

napistu/source.py

@@ -191,7 +191,10 @@ def unnest_sources(
         # check that the entries of sourcevar are Source objects
         source_value = source_table[source_var].iloc[i]
 
-        assert isinstance(source_value, Source)
+        if not isinstance(source_value, Source):
+            raise TypeError(
+                f"source_value must be a Source, but got {type(source_value).__name__}"
+            )
 
         if source_value.source is None:
             print("Some sources were only missing - returning None")
@@ -310,7 +313,10 @@ def _deduplicate_source_df(source_df: pd.DataFrame, table_schema: dict) -> pd.Da
     )
 
     category_index = membership_categories.index.unique()
-    assert isinstance(category_index, pd.core.indexes.base.Index)
+    if not isinstance(category_index, pd.core.indexes.base.Index):
+        raise TypeError(
+            f"category_index must be a pandas Index, but got {type(category_index).__name__}"
+        )
 
     merged_sources = pd.concat(
         [

napistu/utils.py

@@ -14,6 +14,8 @@ from contextlib import closing
 from itertools import starmap
 from typing import Any
 from typing import Union
+from typing import Optional
+from typing import List
 from urllib.parse import urlparse
 
 import igraph as ig
@@ -729,6 +731,62 @@ def ensure_pd_df(pd_df_or_series: pd.DataFrame | pd.Series) -> pd.DataFrame:
         )
 
 
+def drop_extra_cols(
+    df_in: pd.DataFrame,
+    df_out: pd.DataFrame,
+    always_include: Optional[List[str]] = None,
+) -> pd.DataFrame:
+    """Remove columns in df_out that are not in df_in, except those specified in always_include.
+
+    Parameters
+    ----------
+    df_in : pd.DataFrame
+        Reference DataFrame whose columns determine what to keep
+    df_out : pd.DataFrame
+        DataFrame to filter columns from
+    always_include : Optional[List[str]], optional
+        List of column names to always include in output, even if not in df_in
+
+    Returns
+    -------
+    pd.DataFrame
+        DataFrame with columns filtered to match df_in plus any always_include columns.
+        Column order follows df_in, with always_include columns appended at the end.
+
+    Examples
+    --------
+    >>> df_in = pd.DataFrame({'a': [1], 'b': [2]})
+    >>> df_out = pd.DataFrame({'a': [3], 'c': [4], 'd': [5]})
+    >>> _drop_extra_cols(df_in, df_out)
+    # Returns DataFrame with just column 'a'
+
+    >>> _drop_extra_cols(df_in, df_out, always_include=['d'])
+    # Returns DataFrame with columns ['a', 'd']
+    """
+    # Handle None case for always_include
+    if always_include is None:
+        always_include = []
+
+    # Get columns to retain: intersection with df_in plus always_include
+    retained_cols = df_in.columns.intersection(df_out.columns).union(always_include)
+
+    # Filter to only columns that exist in df_out
+    retained_cols = retained_cols.intersection(df_out.columns)
+
+    # Order columns: first those matching df_in's order, then any remaining always_include
+    ordered_cols = []
+    # Add columns that are in df_in in their original order
+    for col in df_in.columns:
+        if col in retained_cols:
+            ordered_cols.append(col)
+    # Add any remaining always_include columns that weren't in df_in
+    for col in always_include:
+        if col in retained_cols and col not in ordered_cols:
+            ordered_cols.append(col)
+
+    return df_out.loc[:, ordered_cols]
+
+
 def format_identifiers_as_edgelist(
     df: pd.DataFrame, defining_vars: list[str]
 ) -> pd.DataFrame:
@@ -750,14 +808,14 @@ def format_identifiers_as_edgelist(
             values of the index and defining_vars
     """
 
-    assert isinstance(df, pd.DataFrame)
     # requires a named index by convention
     if None in df.index.names:
         raise ValueError(
             "df did not have a named index. A named index or multindex is expected"
         )
 
-    assert isinstance(defining_vars, list)
+    if not isinstance(defining_vars, list):
+        raise TypeError("defining_vars must be a list")
 
     logger.info(
         f"creating an edgelist linking index levels {', '.join(df.index.names)} and linking it "
@@ -783,14 +841,15 @@ def format_identifiers_as_edgelist(
     return df
 
 
-def find_weakly_connected_subgraphs(edgelist):
+def find_weakly_connected_subgraphs(edgelist: pd.DataFrame) -> pd.DataFrame:
     """Find all cliques of loosly connected components."""
 
-    assert isinstance(edgelist, pd.DataFrame)
-    assert edgelist.shape[1] == 2
-    assert edgelist.columns.tolist() == ["ind", "id"]
-    # at least some entries in ind should start with ind because this is how we'll pull them out
-    assert any(edgelist["ind"].str.startswith("ind"))
+    if edgelist.shape[1] != 2:
+        raise ValueError("edgelist must have exactly 2 columns")
+    if edgelist.columns.tolist() != ["ind", "id"]:
+        raise ValueError("edgelist columns must be ['ind', 'id']")
+    if not any(edgelist["ind"].str.startswith("ind")):
+        raise ValueError("At least some entries in 'ind' must start with 'ind'")
 
     id_graph = ig.Graph.TupleList(edgelist.itertuples(index=False))
 

napistu-0.2.4.dev2.dist-info/METADATA

@@ -0,0 +1,84 @@
+Metadata-Version: 2.4
+Name: napistu
+Version: 0.2.4.dev2
+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: Documentation, https://napistu.readthedocs.io
+Project-URL: Source, https://github.com/napistu/napistu-py
+Project-URL: 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<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-gcsfs<2.0.0,>=1.5.0
+Requires-Dist: igraph
+Requires-Dist: matplotlib<4.0.0,>=3.5.0
+Requires-Dist: numpy<3.0.0,>=1.24.0
+Requires-Dist: pandas<3.0.0,>=1.5.0
+Requires-Dist: pydantic<3.0.0,>=2.0.0
+Requires-Dist: python-libsbml
+Requires-Dist: requests>=2.25.0
+Requires-Dist: scipy<2.0.0,>=1.10.0
+Requires-Dist: tqdm
+Requires-Dist: zeep<4.0.0,>=3.0.0
+Provides-Extra: dev
+Requires-Dist: black>=24.0.0; extra == "dev"
+Requires-Dist: ipykernel; extra == "dev"
+Requires-Dist: pre-commit<4.0.0,>=3.0.0; extra == "dev"
+Requires-Dist: pytest<8.0.0,>=7.0.0; extra == "dev"
+Requires-Dist: pytest-asyncio; extra == "dev"
+Requires-Dist: pytest-cov; extra == "dev"
+Requires-Dist: ruff; extra == "dev"
+Requires-Dist: testcontainers; extra == "dev"
+Provides-Extra: mcp
+Requires-Dist: fastmcp<3.0.0,>=2.0.0; extra == "mcp"
+Requires-Dist: mcp<2.0.0,>=1.0.0; extra == "mcp"
+Requires-Dist: httpx>=0.24.0; extra == "mcp"
+Requires-Dist: beautifulsoup4<5.0.0,>=4.11.0; extra == "mcp"
+Requires-Dist: markdown>=3.4.0; extra == "mcp"
+Requires-Dist: jupyter-client>=7.0.0; extra == "mcp"
+Requires-Dist: nbformat>=5.0.0; extra == "mcp"
+Provides-Extra: rpy2
+Requires-Dist: pyarrow<19.0.0,>=15.0.0; extra == "rpy2"
+Requires-Dist: rpy2<4.0.0,>=3.5.0; extra == "rpy2"
+Requires-Dist: rpy2-arrow<1.0.0,>=0.1.0; extra == "rpy2"
+Dynamic: license-file
+
+# Napistu Python Library
+
+[![Documentation Status](https://readthedocs.org/projects/napistu/badge/?version=latest)](https://napistu.readthedocs.io/en/latest/?badge=latest)
+
+This Python package hosts the majority of the algorithmic code for the [Napistu project](https://github.com/napistu/napistu).
+
+## Setup
+
+Napistu is available on [PyPI](https://pypi.org/project/napistu) so the recommended way to use it is just to pip install with:
+
+```bash
+pip install napistu
+```
+
+Alternatively, you can clone this repository and perform a local install. e.g., from this directory:
+
+```bash
+pip install .
+```
+
+## Documentation
+📘 **Full Documentation**: [https://napistu.readthedocs.io](https://napistu.readthedocs.io)
+** Wiki **: [napistu/wiki](https://github.com/napistu/napistu/wiki)
+
+### Quick Links
+- [Installation Guide](https://napistu.readthedocs.io/en/latest/installation.html)
+- [API Reference](https://napistu.readthedocs.io/en/latest/api.html)
+- [Usage Examples](https://napistu.readthedocs.io/en/latest/usage.html)

napistu-0.2.4.dev2.dist-info/RECORD

@@ -0,0 +1,95 @@
+napistu/__init__.py,sha256=HEXcB6w8PCTD-tm4rq7AoFi7ufZNDuoG3EoM0kz9aPY,269
+napistu/__main__.py,sha256=i1OyReHD58GjyGYShXmMuBfA0VoGBF9dirg2nA4JCa8,28334
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