risk-network 0.0.16b0__py3-none-any.whl → 0.0.16b2__py3-none-any.whl

risk/_neighborhoods/_stats/_permutation/_test_functions.py

@@ -1,72 +0,0 @@
-"""
-risk/_neighborhoods/_stats/_permutation/_test_functions
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-"""
-
-import numpy as np
-from scipy.sparse import csr_matrix
-
-# NOTE: Cython optimizations provided minimal performance benefits.
-# The final version with Cython is archived in the `cython_permutation` branch.
-
-# DISPATCH_TEST_FUNCTIONS can be found at the end of the file.
-
-
-def compute_neighborhood_score_by_sum(
-    neighborhoods_matrix: csr_matrix, annotation_matrix: csr_matrix
-) -> np.ndarray:
-    """
-    Compute the sum of attribute values for each neighborhood using sparse matrices.
-
-    Args:
-        neighborhoods_matrix (csr_matrix): Sparse binary matrix representing neighborhoods.
-        annotation_matrix (csr_matrix): Sparse matrix representing annotation values.
-
-    Returns:
-        np.ndarray: Dense array of summed attribute values for each neighborhood.
-    """
-    # Calculate the neighborhood score as the dot product of neighborhoods and annotation
-    neighborhood_score = neighborhoods_matrix @ annotation_matrix  # Sparse matrix multiplication
-    # Convert the result to a dense array for downstream calculations
-    neighborhood_score_dense = neighborhood_score.toarray()
-    return neighborhood_score_dense
-
-
-def compute_neighborhood_score_by_stdev(
-    neighborhoods_matrix: csr_matrix, annotation_matrix: csr_matrix
-) -> np.ndarray:
-    """
-    Compute the standard deviation of neighborhood scores for sparse matrices.
-
-    Args:
-        neighborhoods_matrix (csr_matrix): Sparse binary matrix representing neighborhoods.
-        annotation_matrix (csr_matrix): Sparse matrix representing annotation values.
-
-    Returns:
-        np.ndarray: Standard deviation of the neighborhood scores.
-    """
-    # Calculate the neighborhood score as the dot product of neighborhoods and annotation
-    neighborhood_score = neighborhoods_matrix @ annotation_matrix  # Sparse matrix multiplication
-    # Calculate the number of elements in each neighborhood (sum of rows)
-    N = neighborhoods_matrix.sum(axis=1).A.flatten()  # Convert to 1D array
-    # Avoid division by zero by replacing zeros in N with np.nan temporarily
-    N[N == 0] = np.nan
-    # Compute the mean of the neighborhood scores
-    M = neighborhood_score.multiply(1 / N[:, None]).toarray()  # Sparse element-wise division
-    # Compute the mean of squares (EXX) directly using squared annotation matrix
-    annotation_squared = annotation_matrix.multiply(annotation_matrix)  # Element-wise squaring
-    EXX = (neighborhoods_matrix @ annotation_squared).multiply(1 / N[:, None]).toarray()
-    # Calculate variance as EXX - M^2
-    variance = EXX - np.power(M, 2)
-    # Compute the standard deviation as the square root of the variance
-    neighborhood_stdev = np.sqrt(variance)
-    # Replace np.nan back with zeros in case N was 0 (no elements in the neighborhood)
-    neighborhood_stdev[np.isnan(neighborhood_stdev)] = 0
-    return neighborhood_stdev
-
-
-# Dictionary to dispatch statistical test functions based on the score metric
-DISPATCH_TEST_FUNCTIONS = {
-    "sum": compute_neighborhood_score_by_sum,
-    "stdev": compute_neighborhood_score_by_stdev,
-}

risk/_network/__init__.py

@@ -1,8 +0,0 @@
-"""
-risk/_network
-~~~~~~~~~~~~~
-"""
-
-from ._graph import GraphAPI
-from ._io import NetworkAPI
-from ._plotter import PlotterAPI

risk/_network/_graph/__init__.py

@@ -1,7 +0,0 @@
-"""
-risk/_network/_graph
-~~~~~~~~~~~~~~~~~~~~
-"""
-
-from ._api import GraphAPI
-from ._graph import Graph

risk/_network/_plotter/__init__.py

@@ -1,6 +0,0 @@
-"""
-risk/_network/_plotter
-~~~~~~~~~~~~~~~~~~~~~~
-"""
-
-from ._api import PlotterAPI

risk/_network/_plotter/_utils/__init__.py

@@ -1,7 +0,0 @@
-"""
-risk/_network/_plotter/_utils
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-"""
-
-from ._colors import get_annotated_domain_colors, get_domain_colors, to_rgba
-from ._layout import calculate_bounding_box, calculate_centroids

risk_network-0.0.16b0.dist-info/RECORD

@@ -1,41 +0,0 @@
-risk/__init__.py,sha256=knyE98-BvAZ9sTJDMZ1TNr73YaAC-gqL_0Q1rKvwAHU,143
-risk/_risk.py,sha256=VULCdM41BlWKM1ou4Qc579ffZ9dMZkfhAwKYgbaEeKM,1054
-risk/_annotation/__init__.py,sha256=zr7w1DHkmvrkKFGKdPhrcvZHV-xsfd5TZOaWtFiP4Dc,164
-risk/_annotation/_annotation.py,sha256=psPRC7q4DjXIvpgmE3VLzHYElLarJTJhQpclesz2W0Q,15063
-risk/_annotation/_io.py,sha256=xic3dkEA54X82HbyWfCiXrUpAhPWFPBZ69R8jw31omQ,12457
-risk/_annotation/_nltk_setup.py,sha256=aHHnElLOKiouVDrZ3uON0CSFmBxvzmYfjYPi07v2rJM,3584
-risk/_log/__init__.py,sha256=LX6BsfcGOH0RbAdQaUmIU-LVMmArDdKwn0jFtj45FYo,205
-risk/_log/_console.py,sha256=1jSFzY3w0-vVqIBCgc-IhyJPNT6vRg8GSGxhyw_D9MI,4653
-risk/_log/_parameters.py,sha256=8FkeeBtULDFVw3UijLArK-G3OIjy6YXyRXmPPckK7fU,5893
-risk/_neighborhoods/__init__.py,sha256=eKwjpEUKSUmAirRZ_qPTVF7MLkvhCn_fulPVq158wM8,185
-risk/_neighborhoods/_api.py,sha256=kwCJo8fW1v11fNlCZmC_2XH4TG2ZrIL2j2PvBJrlyj8,18236
-risk/_neighborhoods/_community.py,sha256=Tr-EHO91EWbMmNr_z21UCngiqWOlWIqcjwBig_VXI8c,17850
-risk/_neighborhoods/_domains.py,sha256=Q3MUWW9KjuERpxs4H1dNFhalDjdatMkWSnB12BerUDU,16580
-risk/_neighborhoods/_neighborhoods.py,sha256=9hpQCYG0d9fZLYj-fVACgLJBtw3dW8C-0YbE2OWuX-M,21436
-risk/_neighborhoods/_stats/__init__.py,sha256=iu22scpdgTHm6N_hAN81iXIoZCRPFuFAxf71jYWwsUU,213
-risk/_neighborhoods/_stats/_tests.py,sha256=KWwNWyKJ3Rrb1cI5qJcKv9YhU1-7sJoI-yMR1RqvHOQ,7557
-risk/_neighborhoods/_stats/_permutation/__init__.py,sha256=nfTaW29CK8OZCdFnpMVlHnFaqr1E4AZp6mvhlUazHXM,140
-risk/_neighborhoods/_stats/_permutation/_permutation.py,sha256=e5qVuYWGhiAn5Jv8VILk-WYMOO4km48cGdRYTOl355M,10661
-risk/_neighborhoods/_stats/_permutation/_test_functions.py,sha256=lGI_MkdbW4UHI0jWN_T1OattRjXrq_qmzAmOfels670,3165
-risk/_network/__init__.py,sha256=YrAMfhL0CMWQb3sY-mn1VxK44zZAWeFAvHrBONH9I-A,127
-risk/_network/_io.py,sha256=wmokwNViz24Gv6o3OFRTYHftYYz4sN64VigGrdEGzy8,28057
-risk/_network/_graph/__init__.py,sha256=SFgxgxUiZK4vvw6bdQ04DSMXEr8xjMaQV-Wne6wAIqM,104
-risk/_network/_graph/_api.py,sha256=sp3_mLJDP_xQexYBjyM17iyzLb2oGmiC050kcw-jVho,8474
-risk/_network/_graph/_graph.py,sha256=x2EWT_ZVwxh7m9a01yG4WMdmAxBxiaxX3CvkqP9QAXE,12486
-risk/_network/_graph/_stats.py,sha256=6mxZkuL6LJlwKDsBbP22DAVkNUEhq-JZwYMKhFKD08k,7359
-risk/_network/_graph/_summary.py,sha256=RISQHy6Ur37e6F8ZM9X-IwNOit-hUiUxSCUZU_8-1Tw,10198
-risk/_network/_plotter/__init__.py,sha256=qFRtQKSBGIqmUGwmA7VPL7hTHBb9yvRIt0nLISXnwkY,84
-risk/_network/_plotter/_api.py,sha256=OaV1CCRGsz98wEEzyEhaq2CqEuZh6t2qS7g_rY6HJJs,1727
-risk/_network/_plotter/_canvas.py,sha256=H7rPz4Gv7ED3bDHMif4cf2usdU4ifmxzXeug5A_no68,13599
-risk/_network/_plotter/_contour.py,sha256=E3ILjlv-VBSbK3ClwObB84TvP1D48_B47ODXwtApjIE,15557
-risk/_network/_plotter/_labels.py,sha256=8JXzEOIBQefwr1ngF-2ZYCnYLZXs2Erz-R1c28NnsL0,46915
-risk/_network/_plotter/_network.py,sha256=W9eUUER9_qi1ubGaUfMp12gxAANZP-JNFKcG27I1nAk,14198
-risk/_network/_plotter/_plotter.py,sha256=F2hw-spUdsXjvuG36o0YFR3Pnd-CZOHYUq4vW0Qxzlk,6011
-risk/_network/_plotter/_utils/__init__.py,sha256=JXgjKiBWvXx0X2IeFnrOh5YZQGQoELbhJZ0Zh2mFEOo,211
-risk/_network/_plotter/_utils/_colors.py,sha256=JCliSvz8_-TsjilaRHSEsqdXFBUYlzhXKOSRGdCm9Kw,19177
-risk/_network/_plotter/_utils/_layout.py,sha256=GyGLc2U1WWUVL1Te9uPi_CLqlW_E4TImXRAL5TeA5D8,3633
-risk_network-0.0.16b0.dist-info/licenses/LICENSE,sha256=jOtLnuWt7d5Hsx6XXB2QxzrSe2sWWh3NgMfFRetluQM,35147
-risk_network-0.0.16b0.dist-info/METADATA,sha256=RyO3f1BZDQnREPp3my6tw6JI8Y4oFzY3gBDwEO10zL8,5390
-risk_network-0.0.16b0.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
-risk_network-0.0.16b0.dist-info/top_level.txt,sha256=NX7C2PFKTvC1JhVKv14DFlFAIFnKc6Lpsu1ZfxvQwVw,5
-risk_network-0.0.16b0.dist-info/RECORD,,