tapadeep/pbgena

Parallelized Binary embedding GENerator for Attributed graphs

pbgena's Issues

Suggest to loosen the dependency on networkx

Hi, your project PBGENA requires "networkx==2.6.3" in its dependency. After analyzing the source code, we found that some other versions of networkx can also be suitable without affecting your project, i.e., networkx 2.6rc2, 2.6rc1, 2.6, 2.6.1, 2.6.2. Therefore, we suggest to loosen the dependency on networkx from "networkx==2.6.3" to "networkx>=2.6rc1,<=2.6.3" to avoid any possible conflict for importing more packages or for downstream projects that may use PBGENA.

May I pull a request to loosen the dependency on networkx?

By the way, could you please tell us whether such dependency analysis may be potentially helpful for maintaining dependencies easier during your development?

---

For your reference, here are details in our analysis.

Your project PBGENA(commit id: 35ec535) directly uses 3 APIs from package networkx.

networkx.classes.graph.Graph.__init__, networkx.classes.function.selfloop_edges, networkx.classes.function.create_empty_copy

From which, 4 functions are then indirectly called, including 3 networkx's internal APIs and 1 outsider APIs, as follows (neglecting some repeated function occurrences).

[/tapadeep/PBGENA]
+--networkx.classes.graph.Graph.__init__
|      +--networkx.convert.to_networkx_graph
|      |      +--networkx.convert.from_dict_of_dicts
|      |      +--networkx.convert.from_dict_of_lists
|      |      +--warnings.warn
|      |      +--networkx.convert.from_edgelist
+--networkx.classes.function.selfloop_edges
+--networkx.classes.function.create_empty_copy

We scan networkx's versions among [2.6rc2, 2.6rc1, 2.6, 2.6.1, 2.6.2] and 2.6.3, the changing functions (diffs being listed below) have none intersection with any function or API we mentioned above (either directly or indirectly called by this project).

diff: 2.6.3(original) 2.6rc2
['networkx.utils.mapped_queue._HeapElement.__getitem__', 'networkx.algorithms.minors.contraction.equivalence_classes', 'networkx.utils.tests.test_mapped_queue.TestMappedDict', 'networkx.utils.tests.test_mapped_queue.TestMappedQueue.test_push', 'networkx.utils.tests.test_mapped_queue.TestMappedQueue.test_siftup_right_child', 'networkx.utils.tests.test_mapped_queue.test_HeapElement_iter', 'networkx.algorithms.traversal.breadth_first_search.descendants_at_distance', 'networkx.algorithms.community.tests.test_modularity_max.test_modularity_communities_floating_point', 'networkx.utils.mapped_queue.MappedQueue.update', 'networkx.algorithms.assortativity.tests.base_test.BaseTestDegreeMixing.setup_class', 'networkx.algorithms.community.tests.test_modularity_max.test_n_communities_parameter', 'networkx.utils.mapped_queue.MappedQueue.__len__', 'networkx.utils.misc.arbitrary_element', 'networkx.algorithms.assortativity.tests.test_neighbor_degree.TestAverageNeighbor', 'networkx.utils.mapped_queue.MappedQueue._siftdown', 'networkx.classes.graph.Graph', 'networkx.conftest.set_warnings', 'networkx.utils.tests.test_mapped_queue.TestMappedQueue.test_update_root', 'networkx.algorithms.community.quality.performance', 'networkx.utils.mapped_queue._HeapElement.__lt__', 'networkx.utils.tests.test_mapped_queue.TestMappedQueue.test_pop', 'networkx.utils.tests.test_mapped_queue.TestMappedQueue.test_siftdown_single', 'networkx.algorithms.assortativity.tests.test_neighbor_degree.TestAverageNeighbor.test_degree_p4', 'networkx.readwrite.gml.read_gml', 'networkx.algorithms.community.modularity_max.naive_greedy_modularity_communities', 'networkx.utils.tests.test_mapped_queue.TestMappedQueue.test_remove_root', 'networkx.algorithms.assortativity.tests.test_correlation.TestDegreeMixingCorrelation.test_degree_assortativity_double_star', 'networkx.algorithms.community.quality.partition_quality', 'networkx.algorithms.assortativity.connectivity.k_nearest_neighbors', 'networkx.utils.tests.test_mapped_queue.TestMappedQueue.test_update_leaf', 'networkx.utils.mapped_queue._HeapElement.__iter__', 'networkx.algorithms.assortativity.tests.base_test.BaseTestDegreeMixing', 'networkx.utils.mapped_queue.MappedQueue._siftup', 'networkx.utils.mapped_queue._HeapElement.__eq__', 'networkx.algorithms.community.tests.test_modularity_max.test_modularity_communities_weighted', 'networkx.utils.tests.test_mapped_queue.TestMappedQueue._check_map', 'networkx.utils.tests.test_mapped_queue.TestMappedQueue.test_siftup_one_child', 'networkx.utils.tests.test_mapped_queue.TestMappedDict.test_push', 'networkx.utils.mapped_queue.MappedQueue.push', 'networkx.algorithms.community.tests.test_modularity_max.test_modularity_communities', 'networkx.utils.mapped_queue.MappedQueue.pop', 'networkx.utils.tests.test_mapped_queue.TestMappedQueue.test_remove_leaf', 'networkx.utils.tests.test_mapped_queue.TestMappedQueue.test_push_duplicate', 'networkx.algorithms.community.tests.test_modularity_max.test_modularity_communities_categorical_labels', 'networkx.algorithms.community.quality.inter_community_non_edges', 'networkx.algorithms.assortativity.tests.base_test.BaseTestNumericMixing', 'networkx.utils.tests.test_mapped_queue.TestMappedQueue._make_mapped_queue', 'networkx.utils.tests.test_mapped_queue.TestMappedDict.test_push_duplicate', 'networkx.utils.mapped_queue.MappedQueue', 'networkx.algorithms.approximation.tests.test_traveling_salesman.TestSimulatedAnnealingTSP', 'networkx.utils.tests.test_mapped_queue.test_HeapElement_eq', 'networkx.algorithms.community.tests.test_modularity_max.test_modularity_communities_directed_weighted', 'networkx.utils.tests.test_mapped_queue.TestMappedQueue.test_siftup_leaf', 'networkx.utils.mapped_queue._HeapElement.__repr__', 'networkx.algorithms.centrality.katz.katz_centrality_numpy', 'networkx.utils.mapped_queue._HeapElement', 'networkx.utils.mapped_queue.MappedQueue.remove', 'networkx.utils.mapped_queue._HeapElement.__gt__', 'networkx.algorithms.assortativity.tests.test_correlation.TestNumericMixingCorrelation', 'networkx.utils.mapped_queue.MappedQueue._heapify', 'networkx.algorithms.community.quality.modularity', 'networkx.algorithms.assortativity.tests.test_correlation.TestDegreeMixingCorrelation', 'networkx.utils.tests.test_mapped_queue.TestMappedDict.test_update_root', 'networkx.utils.tests.test_mapped_queue.TestMappedQueue', 'networkx.algorithms.assortativity.neighbor_degree.average_neighbor_degree', 'networkx.algorithms.assortativity.correlation.numeric_assortativity_coefficient', 'networkx.algorithms.assortativity.correlation.degree_assortativity_coefficient', 'networkx.algorithms.community.tests.test_modularity_max.test_greedy_modularity_communities_relabeled', 'networkx.algorithms.community.tests.test_modularity_max.test_greed_modularity_communities_multidigraph_weighted', 'networkx.algorithms.community.modularity_max.greedy_modularity_communities', 'networkx.utils.tests.test_mapped_queue.test_HeapElement_getitem', 'networkx.utils.tests.test_mapped_queue.TestMappedQueue.test_siftup_left_child', 'networkx.algorithms.assortativity.neighbor_degree._average_nbr_deg', 'networkx.utils.mapped_queue.MappedQueue.__init__', 'networkx.algorithms.community.tests.test_modularity_max.test_greedy_modularity_communities_multigraph_weighted', 'networkx.generators.trees.prefix_tree', 'networkx.utils.tests.test_mapped_queue.TestMappedQueue.test_siftdown_leaf', 'networkx.utils.mapped_queue._HeapElement.__init__', 'networkx.algorithms.link_analysis.hits_alg.hits_numpy', 'networkx.algorithms.assortativity.tests.base_test.BaseTestNumericMixing.setup_class', 'networkx.algorithms.community.quality.inter_community_edges', 'networkx.utils.tests.test_mapped_queue.test_HeapElement_gtlt', 'networkx.algorithms.assortativity.tests.test_neighbor_degree.TestAverageNeighbor.test_degree_p4_weighted', 'networkx.algorithms.community.tests.test_modularity_max.test_greedy_modularity_communities_directed', 'networkx.classes.graph.Graph.update', 'networkx.algorithms.community.tests.test_modularity_max.test_greed_modularity_communities_multidigraph', 'networkx.algorithms.community.tests.test_modularity_max.test_greedy_modularity_communities_multigraph', 'networkx.utils.tests.test_mapped_queue.TestMappedQueue.test_siftup_multiple', 'networkx.algorithms.assortativity.correlation.numeric_ac', 'networkx.utils.tests.test_mapped_queue.TestMappedQueue.test_siftdown_multiple', 'networkx.utils.tests.test_mapped_queue.TestMappedDict.test_update_leaf', 'networkx.algorithms.approximation.tests.test_traveling_salesman.TestSimulatedAnnealingTSP.test_error_on_input_order_mistake', 'networkx.utils.mapped_queue._HeapElement.__hash__', 'networkx.utils.tests.test_mapped_queue.TestMappedDict._make_mapped_queue', 'networkx.algorithms.assortativity.tests.test_correlation.TestNumericMixingCorrelation.test_numeric_assortativity_mixed']

diff: 2.6.3(original) 2.6rc1
['networkx.algorithms.assortativity.tests.test_correlation.TestNumericMixingCorrelation.test_numeric_assortativity_negative', 'networkx.utils.mapped_queue._HeapElement.__getitem__', 'networkx.algorithms.minors.contraction.equivalence_classes', 'networkx.algorithms.tests.test_lowest_common_ancestors.TestTreeLCA.test_not_implemented_for', 'networkx.utils.decorators._open_gz', 'networkx.readwrite.gml.parse_gml', 'networkx.algorithms.assortativity.tests.test_mixing.TestNumericMixingMatrix', 'networkx.classes.multigraph.MultiGraph.add_edge', 'networkx.algorithms.components.tests.test_attracting.TestAttractingComponents', 'networkx.utils.tests.test_mapped_queue.TestMappedDict', 'networkx.utils.tests.test_mapped_queue.TestMappedQueue.test_push', 'networkx.readwrite.graphml.write_graphml_lxml', 'networkx.utils.decorators.argmap._count', 'networkx.classes.tests.test_function.TestFunction.test_add_path', 'networkx.algorithms.components.tests.test_biconnected.test_biconnected_components1', 'networkx.utils.tests.test_mapped_queue.TestMappedQueue.test_siftup_right_child', 'networkx.utils.tests.test_decorators.TestArgmap.test_contextmanager_iterator', 'networkx.utils.tests.test_mapped_queue.test_HeapElement_iter', 'networkx.utils.tests.test_decorators.TestArgmap.test_actual_kwarg', 'networkx.algorithms.traversal.breadth_first_search.descendants_at_distance', 'networkx.readwrite.graphml.GraphMLReader.decode_data_elements', 'networkx.algorithms.tests.test_clique.TestCliques.test_directed', 'networkx.algorithms.assortativity.tests.test_mixing.TestDegreeMixingMatrix.test_degree_mixing_matrix_undirected', 'networkx.algorithms.community.tests.test_modularity_max.test_modularity_communities_floating_point', 'networkx.utils.tests.test_decorators.TestArgmap.test_indent', 'networkx.utils.mapped_queue.MappedQueue.update', 'networkx.generators.trees.random_tree', 'networkx.algorithms.isomorphism.tests.test_isomorphvf2.TestVF2GraphDB', 'networkx.utils.tests.test_decorators.TestArgmap.ArgmapError', 'networkx.algorithms.tests.test_lowest_common_ancestors.TestDAGLCA.test_all_pairs_lowest_common_ancestor10', 'networkx.utils.tests.test_decorators.TestArgmap.test_actual_vararg', 'networkx.algorithms.assortativity.tests.base_test.BaseTestDegreeMixing.setup_class', 'networkx.algorithms.community.tests.test_modularity_max.test_n_communities_parameter', 'networkx.classes.digraph.DiGraph.add_node', 'networkx.utils.mapped_queue.MappedQueue.__len__', 'networkx.algorithms.components.tests.test_strongly_connected.TestStronglyConnected', 'networkx.readwrite.gml.write_gml', 'networkx.algorithms.components.tests.test_connected.TestConnected', 'networkx.utils.misc.arbitrary_element', 'networkx.utils.tests.test_decorators.test_not_implemented_decorator', 'networkx.classes.multidigraph.MultiDiGraph', 'networkx.algorithms.assortativity.tests.test_neighbor_degree.TestAverageNeighbor', 'networkx.algorithms.bipartite.centrality.closeness_centrality', 'networkx.readwrite.graphml.GraphMLWriter.add_edges', 'networkx.utils.decorators.random_state', 'networkx.utils.mapped_queue.MappedQueue._siftdown', 'networkx.classes.tests.test_function.TestFunction', 'networkx.algorithms.centrality.current_flow_closeness.current_flow_closeness_centrality', 'networkx.classes.graph.Graph', 'networkx.classes.digraph.DiGraph.add_nodes_from', 'networkx.classes.tests.test_graph.BaseGraphTester.test_none_node', 'networkx.classes.digraph.DiGraph.add_edges_from', 'networkx.utils.decorators.argmap.assemble', 'networkx.conftest.set_warnings', 'networkx.algorithms.assortativity.tests.test_mixing.TestDegreeMixingDict', 'networkx.drawing.tests.test_pylab.test_draw_networkx_arrows_default_directed', 'networkx.utils.tests.test_mapped_queue.TestMappedQueue.test_update_root', 'networkx.algorithms.community.quality.performance', 'networkx.utils.mapped_queue._HeapElement.__lt__', 'networkx.utils.tests.test_decorators.TestArgmap.test_contextmanager', 'networkx.utils.tests.test_mapped_queue.TestMappedQueue.test_pop', 'networkx.utils.tests.test_mapped_queue.TestMappedQueue.test_siftdown_single', 'networkx.algorithms.assortativity.tests.test_neighbor_degree.TestAverageNeighbor.test_degree_p4', 'networkx.readwrite.gml.read_gml', 'networkx.algorithms.tests.test_lowest_common_ancestors.TestDAGLCA', 'networkx.algorithms.community.modularity_max.naive_greedy_modularity_communities', 'networkx.utils.tests.test_mapped_queue.TestMappedQueue.test_remove_root', 'networkx.algorithms.assortativity.tests.test_correlation.TestDegreeMixingCorrelation.test_degree_assortativity_double_star', 'networkx.algorithms.community.quality.partition_quality', 'networkx.algorithms.connectivity.tests.test_edge_kcomponents.test_not_implemented', 'networkx.readwrite.tests.test_graphml.TestWriteGraphML.test_write_generate_edge_id_from_attribute', 'networkx.algorithms.assortativity.tests.test_mixing.TestDegreeMixingMatrix.test_degree_mixing_matrix_weighted', 'networkx.utils.tests.test_decorators.TestArgmap.test_signature_destroying_intermediate_decorator', 'networkx.utils.tests.test_mapped_queue.TestMappedQueue.test_update_leaf', 'networkx.utils.mapped_queue._HeapElement.__iter__', 'networkx.algorithms.assortativity.connectivity.k_nearest_neighbors', 'networkx.algorithms.assortativity.tests.base_test.BaseTestDegreeMixing', 'networkx.utils.mapped_queue.MappedQueue._siftup', 'networkx.utils.mapped_queue._HeapElement.__eq__', 'networkx.algorithms.community.tests.test_modularity_max.test_modularity_communities_weighted', 'networkx.algorithms.assortativity.tests.test_mixing.TestNumericMixingMatrix.test_numeric_mixing_matrix_negative', 'networkx.utils.tests.test_mapped_queue.TestMappedQueue._check_map', 'networkx.utils.tests.test_mapped_queue.TestMappedQueue.test_siftup_one_child', 'networkx.utils.tests.test_mapped_queue.TestMappedDict.test_push', 'networkx.algorithms.connectivity.edge_augmentation._minimum_rooted_branching', 'networkx.algorithms.connectivity.tests.test_cuts.test_white_harary_paper', 'networkx.utils.mapped_queue.MappedQueue.push', 'networkx.utils.decorators.nodes_or_number', 'networkx.utils.decorators.argmap.signature', 'networkx.classes.tests.test_graph.BaseGraphTester', 'networkx.readwrite.tests.test_graphml.TestWriteGraphML', 'networkx.algorithms.community.tests.test_modularity_max.test_modularity_communities', 'networkx.utils.mapped_queue.MappedQueue.pop', 'networkx.utils.tests.test_mapped_queue.TestMappedQueue.test_remove_leaf', 'networkx.utils.decorators._open_bz2', 'networkx.readwrite.gexf.write_gexf', 'networkx.algorithms.smallworld.lattice_reference', 'networkx.classes.tests.test_graph.BaseAttrGraphTester.test_to_undirected_as_view', 'networkx.utils.tests.test_mapped_queue.TestMappedQueue.test_push_duplicate', 'networkx.algorithms.assortativity.tests.test_mixing.TestDegreeMixingMatrix', 'networkx.utils.decorators.argmap.compile', 'networkx.algorithms.community.tests.test_modularity_max.test_modularity_communities_categorical_labels', 'networkx.algorithms.assortativity.tests.test_correlation.TestDegreeMixingCorrelation.test_degree_assortativity_weighted', 'networkx.algorithms.community.quality.inter_community_non_edges', 'networkx.algorithms.assortativity.tests.base_test.BaseTestNumericMixing', 'networkx.algorithms.bipartite.centrality.degree_centrality', 'networkx.utils.decorators.open_file', 'networkx.algorithms.community.quality.require_partition', 'networkx.classes.digraph.DiGraph', 'networkx.utils.tests.test_decorators.TestArgmap', 'networkx.algorithms.connectivity.utils.build_auxiliary_node_connectivity', 'networkx.utils.tests.test_mapped_queue.TestMappedQueue._make_mapped_queue', 'networkx.algorithms.tests.test_lowest_common_ancestors.TestTreeLCA', 'networkx.algorithms.centrality.betweenness.edge_betweenness_centrality', 'networkx.algorithms.assortativity.mixing.attribute_mixing_matrix', 'networkx.utils.tests.test_decorators.TestArgmap.test_trivial_iterator', 'networkx.utils.tests.test_mapped_queue.TestMappedDict.test_push_duplicate', 'networkx.classes.multigraph.MultiGraph', 'networkx.utils.tests.test_decorators.TestArgmap.test_nested_tuple', 'networkx.algorithms.components.tests.test_strongly_connected.TestStronglyConnected.test_connected_raise', 'networkx.readwrite.tests.test_graphml.TestWriteGraphML.test_multigraph_write_generate_edge_id_from_attribute', 'networkx.readwrite.graphml.GraphMLWriter.__init__', 'networkx.algorithms.approximation.tests.test_traveling_salesman.TestSimulatedAnnealingTSP', 'networkx.utils.mapped_queue.MappedQueue', 'networkx.classes.graph.Graph.add_nodes_from', 'networkx.utils.decorators.argmap.__call__', 'networkx.utils.tests.test_mapped_queue.test_HeapElement_eq', 'networkx.algorithms.community.tests.test_modularity_max.test_modularity_communities_directed_weighted', 'networkx.utils.tests.test_mapped_queue.TestMappedQueue.test_siftup_leaf', 'networkx.utils.decorators.argmap.__init__', 'networkx.algorithms.traversal.breadth_first_search.bfs_edges', 'networkx.readwrite.gml.generate_gml', 'networkx.algorithms.tests.test_smallworld.test_random_reference', 'networkx.utils.tests.test_decorators.TestArgmap.test_flatten', 'networkx.utils.decorators.py_random_state', 'networkx.algorithms.community.quality._require_partition', 'networkx.readwrite.tests.test_graphml.TestReadGraphML.test_node_default_attribute_graphml', 'networkx.algorithms.centrality.group.group_closeness_centrality', 'networkx.classes.graph.Graph.add_edge', 'networkx.algorithms.components.tests.test_connected.TestConnected.test_connected_raise', 'networkx.drawing.nx_pylab.draw_networkx', 'networkx.utils.mapped_queue._HeapElement.__repr__', 'networkx.algorithms.components.tests.test_weakly_connected.TestWeaklyConnected.test_null_graph', 'networkx.utils.decorators.not_implemented_for', 'networkx.algorithms.assortativity.tests.test_mixing.TestNumericMixingMatrix.test_numeric_mixing_matrix_float', 'networkx.algorithms.assortativity.tests.test_mixing.TestDegreeMixingMatrix.test_degree_mixing_matrix_multigraph', 'networkx.algorithms.triads.triad_type', 'networkx.algorithms.assortativity.tests.test_mixing.TestDegreeMixingDict.test_degree_mixing_dict_weighted', 'networkx.algorithms.centrality.katz.katz_centrality_numpy', 'networkx.utils.mapped_queue._HeapElement', 'networkx.utils.mapped_queue.MappedQueue.remove', 'networkx.algorithms.centrality.load.newman_betweenness_centrality', 'networkx.readwrite.graphml.GraphMLReader.find_graphml_keys', 'networkx.algorithms.tests.test_lowest_common_ancestors.TestTreeLCA.test_tree_all_pairs_lowest_common_ancestor11', 'networkx.utils.mapped_queue._HeapElement.__gt__', 'networkx.algorithms.assortativity.mixing.numeric_mixing_matrix', 'networkx.algorithms.assortativity.tests.test_correlation.TestNumericMixingCorrelation', 'networkx.algorithms.isomorphism.isomorph.is_isomorphic', 'networkx.utils.mapped_queue.MappedQueue._heapify', 'networkx.algorithms.approximation.kcomponents.k_components', 'networkx.utils.decorators.argmap._lazy_compile', 'networkx.algorithms.community.quality.modularity', 'networkx.algorithms.assortativity.tests.test_correlation.TestDegreeMixingCorrelation', 'networkx.utils.tests.test_mapped_queue.TestMappedDict.test_update_root', 'networkx.classes.tests.test_graph.BaseAttrGraphTester.test_directed_class', 'networkx.utils.tests.test_mapped_queue.TestMappedQueue', 'networkx.algorithms.components.tests.test_attracting.TestAttractingComponents.test_connected_raise', 'networkx.classes.graph.Graph.add_edges_from', 'networkx.algorithms.assortativity.neighbor_degree.average_neighbor_degree', 'networkx.algorithms.assortativity.correlation.numeric_assortativity_coefficient', 'networkx.algorithms.assortativity.tests.test_mixing.TestDegreeMixingMatrix.test_degree_mixing_matrix_selfloop', 'networkx.algorithms.assortativity.tests.test_mixing.TestDegreeMixingMatrix.test_degree_mixing_matrix_directed', 'networkx.algorithms.tests.test_clique.TestCliques', 'networkx.readwrite.graphml.GraphMLWriterLxml.__init__', 'networkx.algorithms.assortativity.correlation.degree_assortativity_coefficient', 'networkx.algorithms.community.tests.test_modularity_max.test_greedy_modularity_communities_relabeled', 'networkx.drawing.tests.test_pylab.test_draw_networkx_arrows_default_undirected', 'networkx.algorithms.components.tests.test_weakly_connected.TestWeaklyConnected', 'networkx.linalg.graphmatrix.incidence_matrix', 'networkx.algorithms.community.tests.test_modularity_max.test_greed_modularity_communities_multidigraph_weighted', 'networkx.utils.decorators.preserve_random_state', 'networkx.algorithms.community.modularity_max.greedy_modularity_communities', 'networkx.utils.tests.test_mapped_queue.test_HeapElement_getitem', 'networkx.algorithms.flow.dinitz_alg.dinitz', 'networkx.utils.tests.test_mapped_queue.TestMappedQueue.test_siftup_left_child', 'networkx.algorithms.assortativity.neighbor_degree._average_nbr_deg', 'networkx.algorithms.components.tests.test_weakly_connected.TestWeaklyConnected.test_connected_raise', 'networkx.algorithms.bipartite.centrality.betweenness_centrality', 'networkx.algorithms.smallworld.random_reference', 'networkx.utils.mapped_queue.MappedQueue.__init__', 'networkx.readwrite.graphml.read_graphml', 'networkx.algorithms.community.tests.test_modularity_max.test_greedy_modularity_communities_multigraph_weighted', 'networkx.algorithms.centrality.closeness.closeness_centrality', 'networkx.generators.trees.prefix_tree', 'networkx.utils.tests.test_decorators.TestArgmap.test_trivial_function', 'networkx.algorithms.traversal.depth_first_search.dfs_edges', 'networkx.utils.tests.test_mapped_queue.TestMappedQueue.test_siftdown_leaf', 'networkx.algorithms.assortativity.mixing.degree_mixing_matrix', 'networkx.readwrite.graphml.GraphMLWriterLxml', 'networkx.readwrite.tests.test_graphml.TestReadGraphML', 'networkx.utils.mapped_queue._HeapElement.__init__', 'networkx.algorithms.assortativity.tests.test_correlation.TestNumericMixingCorrelation.test_numeric_assortativity_float', 'networkx.algorithms.link_analysis.hits_alg.hits_numpy', 'networkx.classes.multidigraph.MultiDiGraph.add_edge', 'networkx.classes.graph.Graph.add_node', 'networkx.algorithms.centrality.betweenness_subset.betweenness_centrality_subset', 'networkx.readwrite.graphml.generate_graphml', 'networkx.algorithms.assortativity.tests.base_test.BaseTestNumericMixing.setup_class', 'networkx.algorithms.community.quality.inter_community_edges', 'networkx.algorithms.centrality.percolation.percolation_centrality', 'networkx.utils.tests.test_mapped_queue.test_HeapElement_gtlt', 'networkx.readwrite.graphml.GraphMLWriter', 'networkx.algorithms.components.tests.test_biconnected.test_connected_raise', 'networkx.algorithms.traversal.edgedfs.edge_dfs', 'networkx.algorithms.community.tests.test_modularity_max.test_greedy_modularity_communities_directed', 'networkx.classes.graph.Graph.update', 'networkx.algorithms.assortativity.tests.test_neighbor_degree.TestAverageNeighbor.test_degree_p4_weighted', 'networkx.algorithms.connectivity.tests.test_connectivity.test_white_harary_1', 'networkx.algorithms.tests.test_lowest_common_ancestors.TestTreeLCA.test_tree_all_pairs_lowest_common_ancestor10', 'networkx.readwrite.graphml.write_graphml_xml', 'networkx.utils.tests.test_decorators.TestArgmap.nop', 'networkx.utils.decorators.argmap._name', 'networkx.utils.decorators.argmap._indent', 'networkx.utils.decorators.argmap._flatten', 'networkx.algorithms.community.tests.test_modularity_max.test_greed_modularity_communities_multidigraph', 'networkx.classes.digraph.DiGraph.add_edge', 'networkx.algorithms.approximation.clustering_coefficient.average_clustering', 'networkx.algorithms.community.tests.test_modularity_max.test_greedy_modularity_communities_multigraph', 'networkx.utils.decorators.argmap', 'networkx.utils.tests.test_mapped_queue.TestMappedQueue.test_siftup_multiple', 'networkx.algorithms.connectivity.tests.test_connectivity.test_white_harary_2', 'networkx.algorithms.assortativity.correlation.numeric_ac', 'networkx.utils.tests.test_mapped_queue.TestMappedQueue.test_siftdown_multiple', 'networkx.utils.tests.test_mapped_queue.TestMappedDict.test_update_leaf', 'networkx.algorithms.approximation.tests.test_traveling_salesman.TestSimulatedAnnealingTSP.test_error_on_input_order_mistake', 'networkx.classes.tests.test_graph.BaseAttrGraphTester.test_to_directed_as_view', 'networkx.utils.mapped_queue._HeapElement.__hash__', 'networkx.algorithms.assortativity.tests.test_mixing.TestDegreeMixingMatrix.test_degree_mixing_matrix_mapping', 'networkx.readwrite.graphml.GraphMLReader', 'networkx.classes.digraph.DiGraph.to_undirected', 'networkx.utils.tests.test_mapped_queue.TestMappedDict._make_mapped_queue', 'networkx.algorithms.assortativity.tests.test_correlation.TestNumericMixingCorrelation.test_numeric_assortativity_mixed', 'networkx.classes.tests.test_graph.BaseAttrGraphTester']

diff: 2.6.3(original) 2.6
['networkx.utils.tests.test_mapped_queue.TestMappedQueue.test_siftup_left_child', 'networkx.utils.mapped_queue._HeapElement.__getitem__', 'networkx.utils.tests.test_mapped_queue.test_HeapElement_getitem', 'networkx.utils.tests.test_mapped_queue.test_HeapElement_eq', 'networkx.utils.tests.test_mapped_queue.TestMappedQueue.test_siftdown_single', 'networkx.utils.tests.test_mapped_queue.TestMappedDict', 'networkx.algorithms.community.tests.test_modularity_max.test_modularity_communities_directed_weighted', 'networkx.utils.tests.test_mapped_queue.TestMappedQueue.test_push', 'networkx.utils.mapped_queue.MappedQueue.__init__', 'networkx.utils.tests.test_mapped_queue.TestMappedQueue.test_siftup_leaf', 'networkx.algorithms.community.tests.test_modularity_max.test_greedy_modularity_communities_multigraph_weighted', 'networkx.utils.tests.test_mapped_queue.TestMappedQueue.test_siftup_right_child', 'networkx.algorithms.community.modularity_max.naive_greedy_modularity_communities', 'networkx.utils.tests.test_mapped_queue.TestMappedQueue.test_remove_root', 'networkx.utils.tests.test_mapped_queue.test_HeapElement_iter', 'networkx.utils.tests.test_mapped_queue.TestMappedQueue.test_siftdown_leaf', 'networkx.algorithms.community.tests.test_modularity_max.test_modularity_communities_floating_point', 'networkx.utils.mapped_queue._HeapElement.__repr__', 'networkx.utils.mapped_queue._HeapElement.__init__', 'networkx.utils.tests.test_mapped_queue.TestMappedQueue.test_update_leaf', 'networkx.utils.mapped_queue.MappedQueue.update', 'networkx.utils.mapped_queue._HeapElement.__iter__', 'networkx.utils.mapped_queue.MappedQueue', 'networkx.utils.mapped_queue.MappedQueue._siftup', 'networkx.utils.mapped_queue._HeapElement.__eq__', 'networkx.algorithms.community.tests.test_modularity_max.test_modularity_communities_weighted', 'networkx.utils.tests.test_mapped_queue.TestMappedQueue._check_map', 'networkx.utils.mapped_queue._HeapElement', 'networkx.algorithms.community.tests.test_modularity_max.test_n_communities_parameter', 'networkx.utils.mapped_queue.MappedQueue.remove', 'networkx.utils.tests.test_mapped_queue.test_HeapElement_gtlt', 'networkx.utils.mapped_queue.MappedQueue.__len__', 'networkx.utils.tests.test_mapped_queue.TestMappedQueue.test_update_root', 'networkx.utils.tests.test_mapped_queue.TestMappedQueue.test_siftup_one_child', 'networkx.utils.tests.test_mapped_queue.TestMappedDict.test_push', 'networkx.utils.mapped_queue.MappedQueue.push', 'networkx.utils.mapped_queue._HeapElement.__gt__', 'networkx.utils.mapped_queue.MappedQueue._heapify', 'networkx.algorithms.community.tests.test_modularity_max.test_greedy_modularity_communities_directed', 'networkx.algorithms.community.tests.test_modularity_max.test_modularity_communities', 'networkx.algorithms.community.quality.modularity', 'networkx.utils.mapped_queue.MappedQueue.pop', 'networkx.utils.tests.test_mapped_queue.TestMappedDict.test_update_root', 'networkx.utils.tests.test_mapped_queue.TestMappedQueue.test_remove_leaf', 'networkx.utils.tests.test_mapped_queue.TestMappedQueue', 'networkx.utils.mapped_queue.MappedQueue._siftdown', 'networkx.utils.tests.test_mapped_queue.TestMappedQueue.test_push_duplicate', 'networkx.algorithms.community.tests.test_modularity_max.test_modularity_communities_categorical_labels', 'networkx.algorithms.community.tests.test_modularity_max.test_greed_modularity_communities_multidigraph', 'networkx.algorithms.community.tests.test_modularity_max.test_greedy_modularity_communities_multigraph', 'networkx.algorithms.community.tests.test_modularity_max.test_greedy_modularity_communities_relabeled', 'networkx.utils.tests.test_mapped_queue.TestMappedQueue.test_siftup_multiple', 'networkx.utils.tests.test_mapped_queue.TestMappedDict.test_update_leaf', 'networkx.utils.tests.test_mapped_queue.TestMappedQueue.test_siftdown_multiple', 'networkx.utils.tests.test_mapped_queue.TestMappedQueue._make_mapped_queue', 'networkx.utils.mapped_queue._HeapElement.__hash__', 'networkx.utils.tests.test_mapped_queue.TestMappedDict.test_push_duplicate', 'networkx.utils.tests.test_mapped_queue.TestMappedDict._make_mapped_queue', 'networkx.algorithms.community.tests.test_modularity_max.test_greed_modularity_communities_multidigraph_weighted', 'networkx.algorithms.community.modularity_max.greedy_modularity_communities', 'networkx.utils.mapped_queue._HeapElement.__lt__', 'networkx.utils.tests.test_mapped_queue.TestMappedQueue.test_pop']

diff: 2.6.3(original) 2.6.1
['networkx.utils.tests.test_mapped_queue.TestMappedQueue.test_siftup_left_child', 'networkx.utils.mapped_queue._HeapElement.__getitem__', 'networkx.utils.tests.test_mapped_queue.test_HeapElement_getitem', 'networkx.utils.tests.test_mapped_queue.test_HeapElement_eq', 'networkx.utils.tests.test_mapped_queue.TestMappedQueue.test_siftdown_single', 'networkx.utils.tests.test_mapped_queue.TestMappedDict', 'networkx.algorithms.community.tests.test_modularity_max.test_modularity_communities_directed_weighted', 'networkx.utils.tests.test_mapped_queue.TestMappedQueue.test_push', 'networkx.utils.mapped_queue.MappedQueue.__init__', 'networkx.utils.tests.test_mapped_queue.TestMappedQueue.test_siftup_leaf', 'networkx.algorithms.community.tests.test_modularity_max.test_greedy_modularity_communities_multigraph_weighted', 'networkx.utils.tests.test_mapped_queue.TestMappedQueue.test_siftup_right_child', 'networkx.algorithms.community.modularity_max.naive_greedy_modularity_communities', 'networkx.utils.tests.test_mapped_queue.TestMappedQueue.test_remove_root', 'networkx.utils.tests.test_mapped_queue.test_HeapElement_iter', 'networkx.utils.tests.test_mapped_queue.TestMappedQueue.test_siftdown_leaf', 'networkx.algorithms.community.tests.test_modularity_max.test_modularity_communities_floating_point', 'networkx.utils.mapped_queue._HeapElement.__repr__', 'networkx.utils.mapped_queue._HeapElement.__init__', 'networkx.utils.tests.test_mapped_queue.TestMappedQueue.test_update_leaf', 'networkx.utils.mapped_queue.MappedQueue.update', 'networkx.utils.mapped_queue._HeapElement.__iter__', 'networkx.utils.mapped_queue.MappedQueue', 'networkx.utils.mapped_queue.MappedQueue._siftup', 'networkx.utils.mapped_queue._HeapElement.__eq__', 'networkx.algorithms.community.tests.test_modularity_max.test_modularity_communities_weighted', 'networkx.utils.tests.test_mapped_queue.TestMappedQueue._check_map', 'networkx.utils.mapped_queue._HeapElement', 'networkx.algorithms.community.tests.test_modularity_max.test_n_communities_parameter', 'networkx.utils.mapped_queue.MappedQueue.remove', 'networkx.utils.tests.test_mapped_queue.test_HeapElement_gtlt', 'networkx.utils.mapped_queue.MappedQueue.__len__', 'networkx.utils.tests.test_mapped_queue.TestMappedQueue.test_update_root', 'networkx.utils.tests.test_mapped_queue.TestMappedQueue.test_siftup_one_child', 'networkx.utils.tests.test_mapped_queue.TestMappedDict.test_push', 'networkx.utils.mapped_queue.MappedQueue.push', 'networkx.utils.mapped_queue._HeapElement.__gt__', 'networkx.utils.mapped_queue.MappedQueue._heapify', 'networkx.algorithms.community.tests.test_modularity_max.test_greedy_modularity_communities_directed', 'networkx.algorithms.community.tests.test_modularity_max.test_modularity_communities', 'networkx.algorithms.community.quality.modularity', 'networkx.utils.mapped_queue.MappedQueue.pop', 'networkx.utils.tests.test_mapped_queue.TestMappedDict.test_update_root', 'networkx.utils.tests.test_mapped_queue.TestMappedQueue.test_remove_leaf', 'networkx.utils.tests.test_mapped_queue.TestMappedQueue', 'networkx.utils.mapped_queue.MappedQueue._siftdown', 'networkx.utils.tests.test_mapped_queue.TestMappedQueue.test_push_duplicate', 'networkx.algorithms.community.tests.test_modularity_max.test_modularity_communities_categorical_labels', 'networkx.algorithms.community.tests.test_modularity_max.test_greed_modularity_communities_multidigraph', 'networkx.algorithms.community.tests.test_modularity_max.test_greedy_modularity_communities_multigraph', 'networkx.algorithms.community.tests.test_modularity_max.test_greedy_modularity_communities_relabeled', 'networkx.utils.tests.test_mapped_queue.TestMappedQueue.test_siftup_multiple', 'networkx.utils.tests.test_mapped_queue.TestMappedDict.test_update_leaf', 'networkx.utils.tests.test_mapped_queue.TestMappedQueue.test_siftdown_multiple', 'networkx.utils.tests.test_mapped_queue.TestMappedQueue._make_mapped_queue', 'networkx.utils.mapped_queue._HeapElement.__hash__', 'networkx.utils.tests.test_mapped_queue.TestMappedDict.test_push_duplicate', 'networkx.utils.tests.test_mapped_queue.TestMappedDict._make_mapped_queue', 'networkx.algorithms.community.tests.test_modularity_max.test_greed_modularity_communities_multidigraph_weighted', 'networkx.algorithms.community.modularity_max.greedy_modularity_communities', 'networkx.utils.mapped_queue._HeapElement.__lt__', 'networkx.utils.tests.test_mapped_queue.TestMappedQueue.test_pop']

diff: 2.6.3(original) 2.6.2
['networkx.utils.tests.test_mapped_queue.TestMappedQueue.test_siftup_left_child', 'networkx.utils.mapped_queue._HeapElement.__getitem__', 'networkx.utils.tests.test_mapped_queue.test_HeapElement_getitem', 'networkx.utils.tests.test_mapped_queue.test_HeapElement_eq', 'networkx.utils.tests.test_mapped_queue.TestMappedQueue.test_siftdown_single', 'networkx.utils.tests.test_mapped_queue.TestMappedDict', 'networkx.algorithms.community.tests.test_modularity_max.test_modularity_communities_directed_weighted', 'networkx.utils.tests.test_mapped_queue.TestMappedQueue.test_push', 'networkx.utils.mapped_queue.MappedQueue.__init__', 'networkx.utils.tests.test_mapped_queue.TestMappedQueue.test_siftup_leaf', 'networkx.algorithms.community.tests.test_modularity_max.test_greedy_modularity_communities_multigraph_weighted', 'networkx.utils.tests.test_mapped_queue.TestMappedQueue.test_siftup_right_child', 'networkx.algorithms.community.modularity_max.naive_greedy_modularity_communities', 'networkx.utils.tests.test_mapped_queue.TestMappedQueue.test_remove_root', 'networkx.utils.tests.test_mapped_queue.test_HeapElement_iter', 'networkx.utils.tests.test_mapped_queue.TestMappedQueue.test_siftdown_leaf', 'networkx.algorithms.community.tests.test_modularity_max.test_modularity_communities_floating_point', 'networkx.utils.mapped_queue._HeapElement.__repr__', 'networkx.utils.mapped_queue._HeapElement.__init__', 'networkx.utils.tests.test_mapped_queue.TestMappedQueue.test_update_leaf', 'networkx.utils.mapped_queue.MappedQueue.update', 'networkx.utils.mapped_queue._HeapElement.__iter__', 'networkx.utils.mapped_queue.MappedQueue', 'networkx.utils.mapped_queue.MappedQueue._siftup', 'networkx.utils.mapped_queue._HeapElement.__eq__', 'networkx.algorithms.community.tests.test_modularity_max.test_modularity_communities_weighted', 'networkx.utils.tests.test_mapped_queue.TestMappedQueue._check_map', 'networkx.utils.mapped_queue._HeapElement', 'networkx.algorithms.community.tests.test_modularity_max.test_n_communities_parameter', 'networkx.utils.mapped_queue.MappedQueue.remove', 'networkx.utils.tests.test_mapped_queue.test_HeapElement_gtlt', 'networkx.utils.mapped_queue.MappedQueue.__len__', 'networkx.utils.tests.test_mapped_queue.TestMappedQueue.test_update_root', 'networkx.utils.tests.test_mapped_queue.TestMappedQueue.test_siftup_one_child', 'networkx.utils.tests.test_mapped_queue.TestMappedDict.test_push', 'networkx.utils.mapped_queue.MappedQueue.push', 'networkx.utils.mapped_queue._HeapElement.__gt__', 'networkx.utils.mapped_queue.MappedQueue._heapify', 'networkx.algorithms.community.tests.test_modularity_max.test_greedy_modularity_communities_directed', 'networkx.algorithms.community.tests.test_modularity_max.test_modularity_communities', 'networkx.algorithms.community.quality.modularity', 'networkx.utils.mapped_queue.MappedQueue.pop', 'networkx.utils.tests.test_mapped_queue.TestMappedDict.test_update_root', 'networkx.utils.tests.test_mapped_queue.TestMappedQueue.test_remove_leaf', 'networkx.utils.tests.test_mapped_queue.TestMappedQueue', 'networkx.utils.mapped_queue.MappedQueue._siftdown', 'networkx.utils.tests.test_mapped_queue.TestMappedQueue.test_push_duplicate', 'networkx.algorithms.community.tests.test_modularity_max.test_modularity_communities_categorical_labels', 'networkx.algorithms.community.tests.test_modularity_max.test_greed_modularity_communities_multidigraph', 'networkx.algorithms.community.tests.test_modularity_max.test_greedy_modularity_communities_multigraph', 'networkx.algorithms.community.tests.test_modularity_max.test_greedy_modularity_communities_relabeled', 'networkx.utils.tests.test_mapped_queue.TestMappedQueue.test_siftup_multiple', 'networkx.utils.tests.test_mapped_queue.TestMappedDict.test_update_leaf', 'networkx.utils.tests.test_mapped_queue.TestMappedQueue.test_siftdown_multiple', 'networkx.utils.tests.test_mapped_queue.TestMappedQueue._make_mapped_queue', 'networkx.utils.mapped_queue._HeapElement.__hash__', 'networkx.utils.tests.test_mapped_queue.TestMappedDict.test_push_duplicate', 'networkx.utils.tests.test_mapped_queue.TestMappedDict._make_mapped_queue', 'networkx.algorithms.community.tests.test_modularity_max.test_greed_modularity_communities_multidigraph_weighted', 'networkx.algorithms.community.modularity_max.greedy_modularity_communities', 'networkx.utils.mapped_queue._HeapElement.__lt__', 'networkx.utils.tests.test_mapped_queue.TestMappedQueue.test_pop']

As for other packages, the APIs of @outside_package_name are called by networkx in the call graph and the dependencies on these packages also stay the same in our suggested versions, thus avoiding any outside conflict.

Therefore, we believe that it is quite safe to loose your dependency on networkx from "networkx==2.6.3" to "networkx>=2.6rc1,<=2.6.3". This will improve the applicability of PBGENA and reduce the possibility of any further dependency conflict with other projects/packages.