risk-network 0.0.4b1__tar.gz → 0.0.4b2__tar.gz

{risk_network-0.0.4b1 → risk_network-0.0.4b2}/MANIFEST.in

@@ -5,6 +5,10 @@ recursive-include risk *.py
 include README.md
 include LICENSE
 
+# Exclude the tests directory
+exclude tests/
+exclude tests/*
+
 # Exclude compiled files or any other unwanted files
 exclude risk/**/*.c
 exclude risk/**/*.so

{risk_network-0.0.4b1 → risk_network-0.0.4b2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: risk-network
-Version: 0.0.4b1
+Version: 0.0.4b2
 Summary: A Python package for biological network analysis
 Author: Ira Horecka
 Author-email: Ira Horecka <ira89@icloud.com>

{risk_network-0.0.4b1 → risk_network-0.0.4b2}/risk/__init__.py

@@ -10,4 +10,4 @@ RISK: RISK Infers Spatial Kinship
 
 from risk.risk import RISK
 
-__version__ = "0.0.4-beta.1"
+__version__ = "0.0.4-beta.2"

{risk_network-0.0.4b1 → risk_network-0.0.4b2}/risk_network.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: risk-network
-Version: 0.0.4b1
+Version: 0.0.4b2
 Summary: A Python package for biological network analysis
 Author: Ira Horecka
 Author-email: Ira Horecka <ira89@icloud.com>

{risk_network-0.0.4b1 → risk_network-0.0.4b2}/risk_network.egg-info/SOURCES.txt

@@ -28,9 +28,4 @@ risk_network.egg-info/PKG-INFO
 risk_network.egg-info/SOURCES.txt
 risk_network.egg-info/dependency_links.txt
 risk_network.egg-info/requires.txt
-risk_network.egg-info/top_level.txt
-tests/test_load_annotations.py
-tests/test_load_graph.py
-tests/test_load_neighborhoods.py
-tests/test_load_network.py
-tests/test_load_plotter.py
+risk_network.egg-info/top_level.txt

risk_network-0.0.4b1/tests/test_load_annotations.py

@@ -1,75 +0,0 @@
-"""
-tests/test_load_annotations
-~~~~~~~~~~~~~~~~~~~~~~~~~~~
-"""
-
-def test_load_csv_annotation(risk_obj, network, data_path):
-    """Test loading a CSV annotation file and associating it with a network
-
-    Args:
-        risk_obj: The RISK object instance used for loading annotations
-        network: The network object to which annotations will be applied
-        data_path: The base path to the directory containing the annotation files
-
-    Returns:
-        None
-    """
-    annotation_file = data_path / "csv" / "annotations" / "go_biological_process.csv"
-    annotations = risk_obj.load_csv_annotation(filepath=str(annotation_file), network=network)
-
-    assert annotations is not None
-    assert len(annotations) > 0  # Check that annotations are loaded
-
-
-def test_load_json_annotation(risk_obj, network, data_path):
-    """Test loading a JSON annotation file and associating it with a network
-
-    Args:
-        risk_obj: The RISK object instance used for loading annotations
-        network: The network object to which annotations will be applied
-        data_path: The base path to the directory containing the annotation files
-
-    Returns:
-        None
-    """
-    annotation_file = data_path / "json" / "annotations" / "go_biological_process.json"
-    annotations = risk_obj.load_json_annotation(filepath=str(annotation_file), network=network)
-
-    assert annotations is not None
-    assert len(annotations) > 0  # Check that annotations are loaded
-
-
-def test_load_tsv_annotation(risk_obj, network, data_path):
-    """Test loading a TSV annotation file and associating it with a network
-
-    Args:
-        risk_obj: The RISK object instance used for loading annotations
-        network: The network object to which annotations will be applied
-        data_path: The base path to the directory containing the annotation files
-
-    Returns:
-        None
-    """
-    annotation_file = data_path / "tsv" / "annotations" / "go_biological_process.tsv"
-    annotations = risk_obj.load_tsv_annotation(filepath=str(annotation_file), network=network)
-
-    assert annotations is not None
-    assert len(annotations) > 0  # Check that annotations are loaded
-
-
-def test_load_excel_annotation(risk_obj, network, data_path):
-    """Test loading an Excel annotation file and associating it with a network
-
-    Args:
-        risk_obj: The RISK object instance used for loading annotations
-        network: The network object to which annotations will be applied
-        data_path: The base path to the directory containing the annotation files
-
-    Returns:
-        None
-    """
-    annotation_file = data_path / "excel" / "annotations" / "go_biological_process.xlsx"
-    annotations = risk_obj.load_excel_annotation(filepath=str(annotation_file), network=network)
-
-    assert annotations is not None
-    assert len(annotations) > 0  # Check that annotations are loaded

risk_network-0.0.4b1/tests/test_load_graph.py

@@ -1,50 +0,0 @@
-"""
-tests/test_load_graph
-~~~~~~~~~~~~~~~~~~~~~
-"""
-
-def test_load_graph(risk_obj, network, annotations):
-    """Test loading a graph after generating neighborhoods with specific parameters
-
-    Args:
-        risk_obj: The RISK object instance used for loading neighborhoods and graphs
-        network: The network object to be used for neighborhood and graph generation
-        annotations: The annotations associated with the network
-
-    Returns:
-        None
-    """
-    # Load neighborhoods as a prerequisite
-    neighborhoods = risk_obj.load_neighborhoods(
-        network=network,
-        annotations=annotations,
-        distance_metric="louvain",
-        louvain_resolution=8,
-        edge_length_threshold=0.75,
-        score_metric="stdev",
-        null_distribution="network",
-        num_permutations=100,  # Perform 100 permutations
-        random_seed=887,
-        max_workers=4,  # Use 4 processes
-    )
-
-    # Load the graph with the specified parameters
-    graph = risk_obj.load_graph(
-        network=network,
-        annotations=annotations,
-        neighborhoods=neighborhoods,
-        tail="right",  # Right tail for enrichment
-        pval_cutoff=0.05,  # P-value cutoff of 0.05
-        fdr_cutoff=1.0,  # FDR cutoff
-        impute_depth=1,  # Set impute depth to 1
-        prune_threshold=0.1,  # Prune threshold set to 0.1
-        linkage_criterion="distance",  # Clustering based on distance
-        linkage_method="average",  # Set linkage method to average
-        linkage_metric="yule",  # Set linkage metric to yule
-        min_cluster_size=5,  # Minimum cluster size set to 5
-        max_cluster_size=1000,  # Maximum cluster size set to 1000
-    )
-
-    assert graph is not None
-    assert len(graph.network.nodes) > 0  # Ensure that the graph has nodes
-    assert len(graph.network.edges) > 0  # Ensure that the graph has edges

risk_network-0.0.4b1/tests/test_load_neighborhoods.py

@@ -1,61 +0,0 @@
-"""
-tests/test_load_neighborhoods
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-"""
-
-def test_load_neighborhoods_single_process(risk_obj, network, annotations):
-    """Test loading neighborhoods using a single process
-
-    Args:
-        risk_obj: The RISK object instance used for loading neighborhoods
-        network: The network object to be used for neighborhood generation
-        annotations: The annotations associated with the network
-
-    Returns:
-        None
-    """
-    # Load neighborhoods with 1 process
-    neighborhoods = risk_obj.load_neighborhoods(
-        network=network,
-        annotations=annotations,
-        distance_metric="markov_clustering",
-        louvain_resolution=0.01,
-        edge_length_threshold=0.25,
-        score_metric="stdev",
-        null_distribution="network",
-        num_permutations=10,  # Set to 10 permutations as requested
-        random_seed=887,
-        max_workers=1,  # Single process
-    )
-
-    assert neighborhoods is not None
-    assert len(neighborhoods) > 0  # Ensure neighborhoods are loaded
-
-
-def test_load_neighborhoods_multi_process(risk_obj, network, annotations):
-    """Test loading neighborhoods using multiple processes
-
-    Args:
-        risk_obj: The RISK object instance used for loading neighborhoods
-        network: The network object to be used for neighborhood generation
-        annotations: The annotations associated with the network
-
-    Returns:
-        None
-    """
-    # Load neighborhoods with 4 processes
-    neighborhoods = risk_obj.load_neighborhoods(
-        network=network,
-        annotations=annotations,
-        distance_metric="markov_clustering",
-        louvain_resolution=0.01,
-        edge_length_threshold=0.25,
-        score_metric="stdev",
-        null_distribution="network",
-        num_permutations=10,  # Set to 10 permutations as requested
-        random_seed=887,
-        max_workers=4,  # Four processes
-    )
-
-    assert neighborhoods is not None
-    assert len(neighborhoods) > 0  # Ensure neighborhoods are loaded

risk_network-0.0.4b1/tests/test_load_network.py

@@ -1,74 +0,0 @@
-"""
-tests/test_load_network
-~~~~~~~~~~~~~~~~~~~~~~~
-"""
-
-def test_load_cytoscape_network(risk_obj, data_path):
-    """Test loading a Cytoscape network from a .cys file
-
-    Args:
-        risk_obj: The RISK object instance used for loading the network
-        data_path: The base path to the directory containing the Cytoscape file
-
-    Returns:
-        None
-    """
-    cys_file = data_path / "cytoscape" / "michaelis_2023.cys"
-    network = risk_obj.load_cytoscape_network(
-        filepath=str(cys_file), source_label="source", target_label="target", view_name=""
-    )
-
-    assert network is not None
-    assert len(network.nodes) > 0  # Check that the network has nodes
-    assert len(network.edges) > 0  # Check that the network has edges
-
-
-def test_load_cytoscape_json_network(risk_obj, data_path):
-    """Test loading a Cytoscape JSON network from a .cyjs file
-
-    Args:
-        risk_obj: The RISK object instance used for loading the network
-        data_path: The base path to the directory containing the Cytoscape JSON file
-
-    Returns:
-        None
-    """
-    cyjs_file = data_path / "cyjs" / "michaelis_2023.cyjs"
-    network = risk_obj.load_cytoscape_json_network(
-        filepath=str(cyjs_file), source_label="source", target_label="target"
-    )
-
-    assert network is not None
-    assert len(network.nodes) > 0  # Check that the network has nodes
-    assert len(network.edges) > 0  # Check that the network has edges
-
-
-def test_load_gpickle_network(risk_obj, data_path):
-    """Test loading a network from a .gpickle file
-
-    Args:
-        risk_obj: The RISK object instance used for loading the network
-        data_path: The base path to the directory containing the gpickle file
-
-    Returns:
-        None
-    """
-    gpickle_file = data_path / "gpickle" / "michaelis_2023.gpickle"
-    network = risk_obj.load_gpickle_network(filepath=str(gpickle_file))
-
-    assert network is not None
-    assert len(network.nodes) > 0  # Check that the network has nodes
-    assert len(network.edges) > 0  # Check that the network has edges
-
-
-def test_load_networkx_network(risk_obj, network):
-    """Test loading a network from a NetworkX graph object
-
-    Args:
-        risk_obj: The RISK object instance used for loading the network
-        network: The NetworkX graph object to be loaded into the RISK network
-
-    Returns:
-        None
-    """
-    network = risk_obj.load_networkx

risk_network-0.0.4b1/tests/test_load_plotter.py

@@ -1,317 +0,0 @@
-"""
-tests/test_load_plotter
-~~~~~~~~~~~~~~~~~~~~~~~
-"""
-
-def test_initialize_plotter(risk_obj, graph):
-    """Test initializing the plotter object with a graph
-
-    Args:
-        risk_obj: The RISK object instance used for initializing the plotter
-        graph: The graph object to be plotted
-
-    Returns:
-        None
-    """
-    plotter = initialize_plotter(risk_obj, graph)
-
-    assert plotter is not None  # Ensure the plotter is initialized
-    assert hasattr(plotter, "graph")  # Check that the plotter has a graph attribute
-
-
-def test_plot_network(risk_obj, graph):
-    """Test plotting the full network using the plotter
-
-    Args:
-        risk_obj: The RISK object instance used for plotting
-        graph: The graph object to be plotted
-
-    Returns:
-        None
-    """
-    plotter = initialize_plotter(risk_obj, graph)
-    plot_network(plotter)
-
-    assert plotter is not None  # Ensure the plotter is initialized
-
-
-def test_plot_subnetwork(risk_obj, graph):
-    """Test plotting a subnetwork using the plotter
-
-    Args:
-        risk_obj: The RISK object instance used for plotting
-        graph: The graph object containing the subnetwork to be plotted
-
-    Returns:
-        None
-    """
-    plotter = initialize_plotter(risk_obj, graph)
-    plot_subnetwork(plotter)
-
-    assert plotter is not None  # Ensure the plotter is initialized
-
-
-def test_plot_contours(risk_obj, graph):
-    """Test plotting contours on the network using the plotter
-
-    Args:
-        risk_obj: The RISK object instance used for plotting
-        graph: The graph object on which contours will be plotted
-
-    Returns:
-        None
-    """
-    plotter = initialize_plotter(risk_obj, graph)
-    plot_contours(plotter)
-
-    assert plotter is not None  # Ensure the plotter is initialized
-
-
-def test_plot_subcontour(risk_obj, graph):
-    """Test plotting subcontours on the network using the plotter
-
-    Args:
-        risk_obj: The RISK object instance used for plotting
-        graph: The graph object on which subcontours will be plotted
-
-    Returns:
-        None
-    """
-    plotter = initialize_plotter(risk_obj, graph)
-    plot_subcontour(plotter)
-
-    assert plotter is not None  # Ensure the plotter is initialized
-
-
-def test_plot_labels(risk_obj, graph):
-    """Test plotting labels on the network using the plotter
-
-    Args:
-        risk_obj: The RISK object instance used for plotting
-        graph: The graph object on which labels will be plotted
-
-    Returns:
-        None
-    """
-    plotter = initialize_plotter(risk_obj, graph)
-    plot_labels(plotter)
-
-    assert plotter is not None  # Ensure the plotter is initialized
-
-
-def test_plot_sublabel(risk_obj, graph):
-    """Test plotting a sublabel on the network using the plotter
-
-    Args:
-        risk_obj: The RISK object instance used for plotting
-        graph: The graph object on which the sublabel will be plotted
-
-    Returns:
-        None
-    """
-    plotter = initialize_plotter(risk_obj, graph)
-    plot_sublabel(plotter)
-
-    assert plotter is not None  # Ensure the plotter is initialized
-
-
-def test_display_plot(risk_obj, graph):
-    """Test displaying the plot using the plotter
-
-    Args:
-        risk_obj: The RISK object instance used for plotting
-        graph: The graph object to be displayed
-
-    Returns:
-        None
-    """
-    plotter = initialize_plotter(risk_obj, graph)
-    display_plot(plotter)
-
-    assert plotter is not None  # Ensure the plotter is initialized
-
-
-def initialize_plotter(risk, graph):
-    """Initialize the plotter with specified settings
-
-    Args:
-        risk: The RISK object instance used for plotting
-        graph: The graph object to be plotted
-
-    Returns:
-        Plotter: The initialized plotter object
-    """
-    return risk.load_plotter(
-        graph=graph,
-        figsize=(15, 15),
-        background_color="black",
-        plot_outline=True,
-        outline_color="white",
-        outline_scale=1.05,
-    )
-
-
-def plot_network(plotter):
-    """Plot the full network using the plotter
-
-    Args:
-        plotter: The initialized plotter object
-
-    Returns:
-        None
-    """
-    plotter.plot_network(
-        node_size=plotter.get_annotated_node_sizes(enriched_nodesize=100, nonenriched_nodesize=10),
-        edge_width=0.0,
-        node_color=plotter.get_annotated_node_colors(
-            cmap="gist_rainbow",
-            min_scale=0.5,
-            max_scale=1.0,
-            nonenriched_color="white",
-            random_seed=887,
-        ),
-        node_edgecolor="black",
-        edge_color="white",
-        node_shape="o",
-    )
-
-
-def plot_subnetwork(plotter):
-    """Plot a specific subnetwork using the plotter
-
-    Args:
-        plotter: The initialized plotter object
-
-    Returns:
-        None
-    """
-    plotter.plot_subnetwork(
-        nodes=[
-            "LSM1",
-            "LSM2",
-            "LSM3",
-            "LSM4",
-            "LSM5",
-            "LSM6",
-            "LSM7",
-            "PAT1",
-        ],
-        node_size=250,
-        edge_width=0.0,
-        node_color="white",
-        node_edgecolor="black",
-        edge_color="white",
-        node_shape="^",
-    )
-
-
-def plot_contours(plotter):
-    """Plot contours on the network using the plotter
-
-    Args:
-        plotter: The initialized plotter object
-
-    Returns:
-        None
-    """
-    plotter.plot_contours(
-        levels=5,
-        bandwidth=0.8,
-        grid_size=250,
-        alpha=0.2,
-        color=plotter.get_annotated_contour_colors(cmap="gist_rainbow", random_seed=887),
-    )
-
-
-def plot_subcontour(plotter):
-    """Plot subcontours on a specific subnetwork using the plotter
-
-    Args:
-        plotter: The initialized plotter object
-
-    Returns:
-        None
-    """
-    plotter.plot_subcontour(
-        nodes=[
-            "LSM1",
-            "LSM2",
-            "LSM3",
-            "LSM4",
-            "LSM5",
-            "LSM6",
-            "LSM7",
-            "PAT1",
-        ],
-        levels=5,
-        bandwidth=0.8,
-        grid_size=250,
-        alpha=0.2,
-        color="white",
-    )
-
-
-def plot_labels(plotter):
-    """Plot labels on the network using the plotter
-
-    Args:
-        plotter: The initialized plotter object
-
-    Returns:
-        None
-    """
-    plotter.plot_labels(
-        perimeter_scale=1.25,
-        offset=0.10,
-        font="Arial",
-        fontsize=10,
-        fontcolor=plotter.get_annotated_label_colors(cmap="gist_rainbow", random_seed=887),
-        arrow_linewidth=1,
-        arrow_color=plotter.get_annotated_label_colors(cmap="gist_rainbow", random_seed=887),
-        max_words=4,
-        min_words=2,
-    )
-
-
-def plot_sublabel(plotter):
-    """Plot a specific sublabel on the network using the plotter
-
-    Args:
-        plotter: The initialized plotter object
-
-    Returns:
-        None
-    """
-    plotter.plot_sublabel(
-        nodes=[
-            "LSM1",
-            "LSM2",
-            "LSM3",
-            "LSM4",
-            "LSM5",
-            "LSM6",
-            "LSM7",
-            "PAT1",
-        ],
-        label="LSM1-7-PAT1 Complex",
-        radial_position=73,
-        perimeter_scale=1.6,
-        offset=0.10,
-        font="Arial",
-        fontsize=14,
-        fontcolor="white",
-        arrow_linewidth=1.5,
-        arrow_color="white",
-    )
-
-
-def display_plot(plotter):
-    """Display the plot using the plotter
-
-    Args:
-        plotter: The initialized plotter object
-
-    Returns:
-        None
-    """
-    plotter.show()