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

napistu/utils.py

@@ -12,17 +12,19 @@ import urllib.request as request
 import zipfile
 from contextlib import closing
 from itertools import starmap
+from textwrap import fill
 from typing import Any
 from typing import Union
 from typing import Optional
 from typing import List
 from urllib.parse import urlparse
+import requests
+from requests.adapters import HTTPAdapter
+from requests.adapters import Retry
 
 import igraph as ig
+import numpy as np
 import pandas as pd
-import requests
-from napistu.constants import FILE_EXT_GZ
-from napistu.constants import FILE_EXT_ZIP
 from fs import open_fs
 from fs.copy import copy_dir
 from fs.copy import copy_file
@@ -32,8 +34,9 @@ from fs.errors import ResourceNotFound
 from fs.tarfs import TarFS
 from fs.tempfs import TempFS
 from fs.zipfs import ZipFS
-from requests.adapters import HTTPAdapter
-from requests.adapters import Retry
+
+from napistu.constants import FILE_EXT_GZ
+from napistu.constants import FILE_EXT_ZIP
 
 logger = logging.getLogger(__name__)
 
@@ -261,22 +264,42 @@ def write_file_contents_to_path(path: str, contents) -> None:
 
 
 def download_wget(
-    url: str, path, target_filename: str = None, verify: bool = True
+    url: str,
+    path,
+    target_filename: str = None,
+    verify: bool = True,
+    timeout: int = 30,
+    max_retries: int = 3,
 ) -> None:
-    """Downloades file / archive with wget
+    """Downloads file / archive with wget
 
     Args:
         url (str): url
         path (FilePath | WriteBuffer): file path or buffer
         target_filename (str): specific file to extract from ZIP if URL is a ZIP file
         verify (bool): verify argument to pass to requests.get
+        timeout (int): timeout in seconds for the request
+        max_retries (int): number of times to retry the download if it fails
 
     Returns:
         None
     """
-    r = requests.get(url, allow_redirects=True, verify=verify)
-    # throw an exception if one was generated
-    r.raise_for_status()
+    session = requests.Session()
+    retry_strategy = Retry(
+        total=max_retries,
+        backoff_factor=1,
+        status_forcelist=[429, 500, 502, 503, 504],
+    )
+    adapter = HTTPAdapter(max_retries=retry_strategy)
+    session.mount("http://", adapter)
+    session.mount("https://", adapter)
+
+    try:
+        r = session.get(url, allow_redirects=True, verify=verify, timeout=timeout)
+        r.raise_for_status()
+    except (requests.exceptions.Timeout, requests.exceptions.ConnectionError) as e:
+        logger.error(f"Failed to download {url} after {max_retries} retries: {str(e)}")
+        raise
 
     # check if the content is a ZIP file
     if (
@@ -787,6 +810,52 @@ def drop_extra_cols(
     return df_out.loc[:, ordered_cols]
 
 
+def _merge_and_log_overwrites(
+    left_df: pd.DataFrame, right_df: pd.DataFrame, merge_context: str, **merge_kwargs
+) -> pd.DataFrame:
+    """
+    Merge two DataFrames and log any column overwrites.
+
+    Parameters
+    ----------
+    left_df : pd.DataFrame
+        Left DataFrame for merge
+    right_df : pd.DataFrame
+        Right DataFrame for merge
+    merge_context : str
+        Description of the merge operation for logging
+    **merge_kwargs : dict
+        Additional keyword arguments passed to pd.merge
+
+    Returns
+    -------
+    pd.DataFrame
+        Merged DataFrame with overwritten columns removed
+    """
+    # Track original columns
+    original_cols = left_df.columns.tolist()
+
+    # Ensure we're using the correct suffixes
+    merge_kwargs["suffixes"] = ("_old", "")
+
+    # Perform merge
+    merged_df = pd.merge(left_df, right_df, **merge_kwargs)
+
+    # Check for and log any overwritten columns
+    new_cols = merged_df.columns.tolist()
+    overwritten_cols = [col for col in original_cols if col + "_old" in new_cols]
+    if overwritten_cols:
+        logger.warning(
+            f"The following columns were overwritten during {merge_context} merge and their original values "
+            f"have been suffixed with '_old': {', '.join(overwritten_cols)}"
+        )
+        # Drop the old columns
+        cols_to_drop = [col + "_old" for col in overwritten_cols]
+        merged_df = merged_df.drop(columns=cols_to_drop)
+
+    return merged_df
+
+
 def format_identifiers_as_edgelist(
     df: pd.DataFrame, defining_vars: list[str]
 ) -> pd.DataFrame:
@@ -841,6 +910,20 @@ def format_identifiers_as_edgelist(
     return df
 
 
+def matrix_to_edgelist(matrix, row_labels=None, col_labels=None):
+    rows, cols = np.where(~np.isnan(matrix))
+
+    edgelist = pd.DataFrame(
+        {
+            "row": rows if row_labels is None else [row_labels[i] for i in rows],
+            "column": cols if col_labels is None else [col_labels[i] for i in cols],
+            "value": matrix[rows, cols],
+        }
+    )
+
+    return edgelist
+
+
 def find_weakly_connected_subgraphs(edgelist: pd.DataFrame) -> pd.DataFrame:
     """Find all cliques of loosly connected components."""
 
@@ -983,6 +1066,31 @@ def click_str_to_list(string: str) -> list[str]:
         )
 
 
+def safe_fill(x: str, fill_width: int = 15) -> str:
+    """
+    Safely wrap a string to a specified width.
+
+    Parameters
+    ----------
+    x : str
+        The string to wrap.
+    fill_width : int, optional
+        The width to wrap the string to. Default is 15.
+
+    Returns
+    -------
+    str
+        The wrapped string.
+    """
+
+    # TODO - move to non-network utils
+
+    if x == "":
+        return ""
+    else:
+        return fill(x, fill_width)
+
+
 def _add_nameness_score_wrapper(df, name_var, table_schema):
     """Call _add_nameness_score with default value."""
 

{napistu-0.2.5.dev6.dist-info → napistu-0.3.1.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: napistu
-Version: 0.2.5.dev6
+Version: 0.3.1
 Summary: Connecting high-dimensional data to curated pathways
 Home-page: https://github.com/napistu/napistu-py
 Author: Sean Hackett
@@ -23,6 +23,7 @@ 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: mygene<4.0.0,>=3.0.0
 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
@@ -32,6 +33,7 @@ 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: napistu[mcp,scverse]; 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"
@@ -52,6 +54,9 @@ 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"
+Provides-Extra: scverse
+Requires-Dist: anndata; extra == "scverse"
+Requires-Dist: mudata; extra == "scverse"
 Dynamic: license-file
 
 # Napistu Python Library
@@ -75,8 +80,8 @@ pip install .
 ```
 
 ## Documentation
-📘 **Full Documentation**: [https://napistu.readthedocs.io](https://napistu.readthedocs.io)
-** Wiki **: [napistu/wiki](https://github.com/napistu/napistu/wiki)
+- 📘 **Library Documentation**: [napistu.readthedocs.io](https://napistu.readthedocs.io)
+- 🚸 **Project Documentation**: [napistu/wiki](https://github.com/napistu/napistu/wiki)
 
 ### Quick Links
 - [Installation Guide](https://napistu.readthedocs.io/en/latest/installation.html)

napistu-0.3.1.dist-info/RECORD

@@ -0,0 +1,133 @@
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tests/conftest.py

@@ -3,10 +3,12 @@ from __future__ import annotations
 import os
 import sys
 
+
 from napistu import consensus
 from napistu import indices
 from napistu import sbml_dfs_core
 from napistu.ingestion import sbml
+from napistu.network import net_create
 from pytest import fixture
 from pytest import skip
 
@@ -57,6 +59,26 @@ def sbml_dfs_glucose_metabolism():
     return sbml_dfs
 
 
+@fixture
+def napistu_graph(sbml_dfs):
+    """
+    Pytest fixture to create a NapistuGraph from sbml_dfs with directed=True and topology weighting.
+    """
+    return net_create.process_napistu_graph(
+        sbml_dfs, directed=True, weighting_strategy="topology"
+    )
+
+
+@fixture
+def napistu_graph_undirected(sbml_dfs):
+    """
+    Pytest fixture to create a NapistuGraph from sbml_dfs with directed=False and topology weighting.
+    """
+    return net_create.process_napistu_graph(
+        sbml_dfs, directed=False, weighting_strategy="topology"
+    )
+
+
 # Define custom markers for platforms
 def pytest_configure(config):
     config.addinivalue_line("markers", "skip_on_windows: mark test to skip on Windows")

tests/test_context_discretize.py

@@ -0,0 +1,56 @@
+import numpy as np
+
+from napistu.context import discretize
+
+
+def test_peak_selector():
+
+    # Test Case 0: No peaks (flat/monotonic)
+    x0 = np.linspace(-5, 5, 100)
+    y0 = np.exp(-x0)  # Monotonic decreasing
+    peaks0 = discretize.PeakSelector().find_peaks(y0, x0)
+
+    assert peaks0.major == -5
+    assert peaks0.minor is None
+    assert peaks0.other is None
+
+    # Test Case 2: Single peak (Gaussian)
+    x1 = np.linspace(-5, 5, 100)
+    y1 = np.exp(-0.5 * x1**2)  # Single Gaussian peak
+    peaks1 = discretize.PeakSelector().find_peaks(y1, x1)
+
+    assert abs(peaks1.major - -0.05) < 0.01
+    assert peaks1.minor is None
+    assert peaks1.other is None
+
+    # Test Case 3: Two peaks (bimodal)
+    x2 = np.linspace(-5, 5, 100)
+    y2 = 0.6 * np.exp(-0.5 * (x2 + 1.5) ** 2) + 0.4 * np.exp(-0.5 * (x2 - 1.5) ** 2)
+    peaks2 = discretize.PeakSelector().find_peaks(y2, x2)
+
+    assert abs(peaks2.major - 1.46) < 0.01
+    assert abs(peaks2.minor - -1.46) < 0.01
+    assert peaks2.other is None
+
+    # Test Case 4: Three peaks (trimodal)
+    x3 = np.linspace(-8, 8, 100)
+    y3 = (
+        0.4 * np.exp(-0.5 * (x3 + 4) ** 2)
+        + 0.5 * np.exp(-0.5 * x3**2)
+        + 0.3 * np.exp(-0.5 * (x3 - 4) ** 2)
+    )
+    peaks3 = discretize.PeakSelector().find_peaks(y3, x3)
+
+    assert abs(peaks3.major - 3.95) < 0.01
+    assert abs(peaks3.minor - -0.08) < 0.01
+    assert abs(peaks3.other[0] - -3.95) < 0.01
+
+
+def test_zfpkm():
+
+    fpkm_df = discretize.generate_simple_test_data()
+    zfpkm_df = discretize.zfpkm(fpkm_df)
+
+    assert zfpkm_df.shape == fpkm_df.shape
+    assert zfpkm_df.index.equals(fpkm_df.index)
+    assert zfpkm_df.columns.equals(fpkm_df.columns)