risk-network 0.0.9b4__tar.gz → 0.0.9b5__tar.gz

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Files changed (46) hide show
  1. {risk_network-0.0.9b4 → risk_network-0.0.9b5}/PKG-INFO +1 -1
  2. {risk_network-0.0.9b4 → risk_network-0.0.9b5}/risk/__init__.py +1 -1
  3. {risk_network-0.0.9b4 → risk_network-0.0.9b5}/risk/annotations/annotations.py +3 -2
  4. {risk_network-0.0.9b4 → risk_network-0.0.9b5}/risk_network.egg-info/PKG-INFO +1 -1
  5. {risk_network-0.0.9b4 → risk_network-0.0.9b5}/LICENSE +0 -0
  6. {risk_network-0.0.9b4 → risk_network-0.0.9b5}/MANIFEST.in +0 -0
  7. {risk_network-0.0.9b4 → risk_network-0.0.9b5}/README.md +0 -0
  8. {risk_network-0.0.9b4 → risk_network-0.0.9b5}/pyproject.toml +0 -0
  9. {risk_network-0.0.9b4 → risk_network-0.0.9b5}/risk/annotations/__init__.py +0 -0
  10. {risk_network-0.0.9b4 → risk_network-0.0.9b5}/risk/annotations/io.py +0 -0
  11. {risk_network-0.0.9b4 → risk_network-0.0.9b5}/risk/constants.py +0 -0
  12. {risk_network-0.0.9b4 → risk_network-0.0.9b5}/risk/log/__init__.py +0 -0
  13. {risk_network-0.0.9b4 → risk_network-0.0.9b5}/risk/log/console.py +0 -0
  14. {risk_network-0.0.9b4 → risk_network-0.0.9b5}/risk/log/parameters.py +0 -0
  15. {risk_network-0.0.9b4 → risk_network-0.0.9b5}/risk/neighborhoods/__init__.py +0 -0
  16. {risk_network-0.0.9b4 → risk_network-0.0.9b5}/risk/neighborhoods/community.py +0 -0
  17. {risk_network-0.0.9b4 → risk_network-0.0.9b5}/risk/neighborhoods/domains.py +0 -0
  18. {risk_network-0.0.9b4 → risk_network-0.0.9b5}/risk/neighborhoods/neighborhoods.py +0 -0
  19. {risk_network-0.0.9b4 → risk_network-0.0.9b5}/risk/network/__init__.py +0 -0
  20. {risk_network-0.0.9b4 → risk_network-0.0.9b5}/risk/network/geometry.py +0 -0
  21. {risk_network-0.0.9b4 → risk_network-0.0.9b5}/risk/network/graph/__init__.py +0 -0
  22. {risk_network-0.0.9b4 → risk_network-0.0.9b5}/risk/network/graph/network.py +0 -0
  23. {risk_network-0.0.9b4 → risk_network-0.0.9b5}/risk/network/graph/summary.py +0 -0
  24. {risk_network-0.0.9b4 → risk_network-0.0.9b5}/risk/network/io.py +0 -0
  25. {risk_network-0.0.9b4 → risk_network-0.0.9b5}/risk/network/plot/__init__.py +0 -0
  26. {risk_network-0.0.9b4 → risk_network-0.0.9b5}/risk/network/plot/canvas.py +0 -0
  27. {risk_network-0.0.9b4 → risk_network-0.0.9b5}/risk/network/plot/contour.py +0 -0
  28. {risk_network-0.0.9b4 → risk_network-0.0.9b5}/risk/network/plot/labels.py +0 -0
  29. {risk_network-0.0.9b4 → risk_network-0.0.9b5}/risk/network/plot/network.py +0 -0
  30. {risk_network-0.0.9b4 → risk_network-0.0.9b5}/risk/network/plot/plotter.py +0 -0
  31. {risk_network-0.0.9b4 → risk_network-0.0.9b5}/risk/network/plot/utils/color.py +0 -0
  32. {risk_network-0.0.9b4 → risk_network-0.0.9b5}/risk/network/plot/utils/layout.py +0 -0
  33. {risk_network-0.0.9b4 → risk_network-0.0.9b5}/risk/risk.py +0 -0
  34. {risk_network-0.0.9b4 → risk_network-0.0.9b5}/risk/stats/__init__.py +0 -0
  35. {risk_network-0.0.9b4 → risk_network-0.0.9b5}/risk/stats/hypergeom.py +0 -0
  36. {risk_network-0.0.9b4 → risk_network-0.0.9b5}/risk/stats/permutation/__init__.py +0 -0
  37. {risk_network-0.0.9b4 → risk_network-0.0.9b5}/risk/stats/permutation/permutation.py +0 -0
  38. {risk_network-0.0.9b4 → risk_network-0.0.9b5}/risk/stats/permutation/test_functions.py +0 -0
  39. {risk_network-0.0.9b4 → risk_network-0.0.9b5}/risk/stats/poisson.py +0 -0
  40. {risk_network-0.0.9b4 → risk_network-0.0.9b5}/risk/stats/stats.py +0 -0
  41. {risk_network-0.0.9b4 → risk_network-0.0.9b5}/risk_network.egg-info/SOURCES.txt +0 -0
  42. {risk_network-0.0.9b4 → risk_network-0.0.9b5}/risk_network.egg-info/dependency_links.txt +0 -0
  43. {risk_network-0.0.9b4 → risk_network-0.0.9b5}/risk_network.egg-info/requires.txt +0 -0
  44. {risk_network-0.0.9b4 → risk_network-0.0.9b5}/risk_network.egg-info/top_level.txt +0 -0
  45. {risk_network-0.0.9b4 → risk_network-0.0.9b5}/setup.cfg +0 -0
  46. {risk_network-0.0.9b4 → risk_network-0.0.9b5}/setup.py +0 -0
{risk_network-0.0.9b4 → risk_network-0.0.9b5}/PKG-INFO RENAMED
@@ -1,6 +1,6 @@
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  Metadata-Version: 2.1
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  Name: risk-network
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- Version: 0.0.9b4
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+ Version: 0.0.9b5
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  Summary: A Python package for biological network analysis
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  Author: Ira Horecka
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  Author-email: Ira Horecka <ira89@icloud.com>
{risk_network-0.0.9b4 → risk_network-0.0.9b5}/risk/__init__.py RENAMED
@@ -7,4 +7,4 @@ RISK: RISK Infers Spatial Kinships
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  from risk.risk import RISK
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- __version__ = "0.0.9-beta.4"
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+ __version__ = "0.0.9-beta.5"
{risk_network-0.0.9b4 → risk_network-0.0.9b5}/risk/annotations/annotations.py RENAMED
@@ -65,8 +65,9 @@ def load_annotations(network: nx.Graph, annotations_input: Dict[str, Any]) -> Di
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  "No annotations found in the annotations file for the nodes in the network."
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  )
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- # Remove columns with all zeros to improve performance
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- annotations_pivot = annotations_pivot.loc[:, annotations_pivot.sum(axis=0) != 0]
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+ # Remove columns with all zeros and those with only a single '1' to improve statistical performance
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+ # (i.e., it's unreliable to compute the significance of an annotation in a node cluster based on a single occurrence).
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+ annotations_pivot = annotations_pivot.loc[:, (annotations_pivot.sum(axis=0) > 1)]
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  # Extract ordered nodes and annotations
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  ordered_nodes = tuple(annotations_pivot.index)
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  ordered_annotations = tuple(annotations_pivot.columns)
{risk_network-0.0.9b4 → risk_network-0.0.9b5}/risk_network.egg-info/PKG-INFO RENAMED
@@ -1,6 +1,6 @@
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  Metadata-Version: 2.1
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  Name: risk-network
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- Version: 0.0.9b4
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+ Version: 0.0.9b5
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  Summary: A Python package for biological network analysis
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  Author: Ira Horecka
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  Author-email: Ira Horecka <ira89@icloud.com>
{risk_network-0.0.9b4 → risk_network-0.0.9b5}/LICENSE RENAMED
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{risk_network-0.0.9b4 → risk_network-0.0.9b5}/README.md RENAMED
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{risk_network-0.0.9b4 → risk_network-0.0.9b5}/setup.cfg RENAMED
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{risk_network-0.0.9b4 → risk_network-0.0.9b5}/setup.py RENAMED
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