hiveplotlib 0.27.0__tar.gz → 0.28.1__tar.gz
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- {hiveplotlib-0.27.0 → hiveplotlib-0.28.1}/LICENSE +2 -2
- {hiveplotlib-0.27.0/src/hiveplotlib.egg-info → hiveplotlib-0.28.1}/PKG-INFO +26 -50
- {hiveplotlib-0.27.0 → hiveplotlib-0.28.1}/README.md +14 -9
- {hiveplotlib-0.27.0 → hiveplotlib-0.28.1}/pyproject.toml +19 -14
- {hiveplotlib-0.27.0 → hiveplotlib-0.28.1}/src/hiveplotlib/__init__.py +0 -1
- hiveplotlib-0.28.1/src/hiveplotlib/converters.py +166 -0
- {hiveplotlib-0.27.0 → hiveplotlib-0.28.1}/src/hiveplotlib/datasets/international_trade.py +1 -1
- {hiveplotlib-0.27.0 → hiveplotlib-0.28.1}/src/hiveplotlib/datasets/toy_hive_plots.py +96 -25
- {hiveplotlib-0.27.0 → hiveplotlib-0.28.1}/src/hiveplotlib/datasets/trade_data_harvard_growth_lab/international_exports_metadata_2019_8112.json +1 -1
- {hiveplotlib-0.27.0 → hiveplotlib-0.28.1}/src/hiveplotlib/edges.py +8 -2
- {hiveplotlib-0.27.0 → hiveplotlib-0.28.1}/src/hiveplotlib/exceptions/hive_plot.py +11 -0
- hiveplotlib-0.28.1/src/hiveplotlib/graph_features/__init__.py +858 -0
- hiveplotlib-0.28.1/src/hiveplotlib/graph_features/networkx/__init__.py +103 -0
- hiveplotlib-0.28.1/src/hiveplotlib/graph_features/networkx/_helpers.py +177 -0
- hiveplotlib-0.28.1/src/hiveplotlib/graph_features/networkx/edge_metrics.py +259 -0
- hiveplotlib-0.28.1/src/hiveplotlib/graph_features/networkx/node_metrics.py +913 -0
- {hiveplotlib-0.27.0 → hiveplotlib-0.28.1}/src/hiveplotlib/hiveplot.py +817 -432
- hiveplotlib-0.28.1/src/hiveplotlib/hiveplot_matrix.py +2274 -0
- {hiveplotlib-0.27.0 → hiveplotlib-0.28.1}/src/hiveplotlib/utils.py +2 -2
- {hiveplotlib-0.27.0 → hiveplotlib-0.28.1}/src/hiveplotlib/viz/bokeh.py +28 -7
- {hiveplotlib-0.27.0 → hiveplotlib-0.28.1}/src/hiveplotlib/viz/hiveplot_matrix.py +2 -2
- {hiveplotlib-0.27.0 → hiveplotlib-0.28.1}/src/hiveplotlib/viz/holoviews.py +3 -1
- {hiveplotlib-0.27.0 → hiveplotlib-0.28.1/src/hiveplotlib.egg-info}/PKG-INFO +26 -50
- {hiveplotlib-0.27.0 → hiveplotlib-0.28.1}/src/hiveplotlib.egg-info/SOURCES.txt +5 -1
- {hiveplotlib-0.27.0 → hiveplotlib-0.28.1}/src/hiveplotlib.egg-info/requires.txt +8 -9
- hiveplotlib-0.27.0/setup.py +0 -8
- hiveplotlib-0.27.0/src/hiveplotlib/converters.py +0 -44
- hiveplotlib-0.27.0/src/hiveplotlib/hiveplot_matrix.py +0 -1274
- {hiveplotlib-0.27.0 → hiveplotlib-0.28.1}/MANIFEST.in +0 -0
- {hiveplotlib-0.27.0 → hiveplotlib-0.28.1}/setup.cfg +0 -0
- {hiveplotlib-0.27.0 → hiveplotlib-0.28.1}/src/hiveplotlib/axis.py +0 -0
- {hiveplotlib-0.27.0 → hiveplotlib-0.28.1}/src/hiveplotlib/datasets/__init__.py +0 -0
- {hiveplotlib-0.27.0 → hiveplotlib-0.28.1}/src/hiveplotlib/datasets/toy_p2cps.py +0 -0
- {hiveplotlib-0.27.0 → hiveplotlib-0.28.1}/src/hiveplotlib/datasets/trade_data_harvard_growth_lab/international_exports_2019_8112.csv +0 -0
- {hiveplotlib-0.27.0 → hiveplotlib-0.28.1}/src/hiveplotlib/exceptions/__init__.py +0 -0
- {hiveplotlib-0.27.0 → hiveplotlib-0.28.1}/src/hiveplotlib/exceptions/node.py +0 -0
- {hiveplotlib-0.27.0 → hiveplotlib-0.28.1}/src/hiveplotlib/node.py +0 -0
- {hiveplotlib-0.27.0 → hiveplotlib-0.28.1}/src/hiveplotlib/p2cp.py +0 -0
- {hiveplotlib-0.27.0 → hiveplotlib-0.28.1}/src/hiveplotlib/viz/__init__.py +0 -0
- {hiveplotlib-0.27.0 → hiveplotlib-0.28.1}/src/hiveplotlib/viz/base.py +0 -0
- {hiveplotlib-0.27.0 → hiveplotlib-0.28.1}/src/hiveplotlib/viz/datashader.py +0 -0
- {hiveplotlib-0.27.0 → hiveplotlib-0.28.1}/src/hiveplotlib/viz/input_checks.py +0 -0
- {hiveplotlib-0.27.0 → hiveplotlib-0.28.1}/src/hiveplotlib/viz/matplotlib.py +0 -0
- {hiveplotlib-0.27.0 → hiveplotlib-0.28.1}/src/hiveplotlib/viz/plotly.py +0 -0
- {hiveplotlib-0.27.0 → hiveplotlib-0.28.1}/src/hiveplotlib.egg-info/dependency_links.txt +0 -0
- {hiveplotlib-0.27.0 → hiveplotlib-0.28.1}/src/hiveplotlib.egg-info/top_level.txt +0 -0
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Copyright (c) 2020 - 2026, Gary Koplik
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Redistribution and use in source and binary forms, with or without modification,
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Neither the name of
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without specific prior written permission.
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Metadata-Version: 2.4
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Name: hiveplotlib
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Version: 0.
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Version: 0.28.1
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Summary: Visualize Network Data with Hive Plots
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Author-email: Gary Koplik <gary.koplik@
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License:
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without specific prior written permission.
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THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
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AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
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IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
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ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE
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LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
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INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
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CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
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THE POSSIBILITY OF SUCH DAMAGE.
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Author-email: Gary Koplik <gary.koplik@gmail.com>
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License-Expression: BSD-3-Clause
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Project-URL: Documentation, https://hiveplotlib.readthedocs.io/stable/
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Project-URL: Source, https://gitlab.com/
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Project-URL: Source, https://gitlab.com/hiveplotlib/hiveplotlib
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A plotting package for generating and visualizing static Hive Plots in Python.
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[](https://holoviews.org/index.html)
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[](https://plotly.com/python/)
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[](https://datashader.org/)
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# Installation
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`hiveplotlib` also supports large network visualization via the [datashader](https://datashader.org/) backend,
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which can be installed as `pip install hiveplotlib[datashader]`.
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Beyond the visualization backends, `hiveplotlib` integrates with [networkx](https://networkx.org/): build a hive plot
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# How to Use and Examples
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[Quick Start Hive Plots](https://hiveplotlib.readthedocs.io/stable/notebooks/quick_hive_plots.html) pages.
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[examples](https://gitlab.com/hiveplotlib/hiveplotlib/-/tree/master/examples) directory.
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- Krzywinski M, Birol I, Jones S, Marra M (2011). Hive Plots — Rational Approach to
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Visualizing Networks. Briefings in Bioinformatics (early access 9 December 2011,
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# Contributing
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## Acknowledgements
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urls = {Documentation="https://hiveplotlib.readthedocs.io/stable/", Source="https://gitlab.com/hiveplotlib/hiveplotlib" }
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dependencies = [
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# developer dependencies
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dev = [
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"bokeh>=3.0.0",
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"cartopy",
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"dask[dataframe]", # https://github.com/holoviz/datashader/issues/1319
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"datashader",
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"flexitext",
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"geopandas",
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"
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"hiveplotlib[bokeh]",
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"hiveplotlib[datashader]",
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"hiveplotlib[holoviews]",
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"hiveplotlib[networkx]",
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"hiveplotlib[plotly]",
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"jupyter",
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"
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"numba>0.54.0", # https://github.com/numba/numba/issues/9708
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"plotly",
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"nx-parallel", # CI-testable networkx dispatch backend for `graph_metric_backend` tests
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"pybadges",
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"seaborn",
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"tqdm",
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]
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@@ -72,7 +71,8 @@ holoviews = [
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]
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networkx = [
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"networkx"
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"networkx",
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"scipy", # for some graph feature computations
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]
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# performance profiling extras
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# ruff code hygeine checks
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ruff = [
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"ruff",
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"ruff==0.15.22", # pinned for the life of 0.28.x, ruff 0.16 expanded its default rules and formats markdown
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]
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testing = [
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"ty==0.0.20", # pinning for now, 0.0.21 would require non trivial type hint changes that affect the user
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]
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[tool.uv]
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# scope `uv lock` and `uv audit` to python 3.11+. Python 3.10's resolution is stuck on versions with unfixable advisories
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# (e.g. pillow 13 requires 3.11+), which would keep `uv_audit` red. Python 3.10 installs and CI tests are unaffected.
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environments = ["python_version >= '3.11'"]
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[tool.setuptools.packages.find]
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where = ["src"]
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include = ["hiveplotlib*"]
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@@ -0,0 +1,166 @@
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# converters.py
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"""
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Converters from various data structures to ``hiveplotlib``-ready structures.
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"""
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from typing import Optional
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import pandas as pd
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from hiveplotlib import Edges, NodeCollection
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try:
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import networkx as nx
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except ImportError as ie: # pragma: no cover
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msg = "`networkx` dependencies not installed, but can be installed by running `pip install hiveplotlib[networkx]`"
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raise ImportError(msg) from ie
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def networkx_to_nodes_edges(
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graph: nx.Graph,
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unique_id_name: str = "unique_id",
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check_uniqueness: bool = True,
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) -> tuple[NodeCollection, Edges]:
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"""
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Take a ``networkx`` graph and return ``hiveplotlib``-friendly data structures.
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Specifically, returns a ``NodeCollection`` instance of node data and an ``Edges`` instance of
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edge data. These outputs can be fed directly into :py:func:`~hiveplotlib.HivePlot`.
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:param graph: ``networkx`` graph (any of :py:class:`~networkx.Graph`, :py:class:`~networkx.DiGraph`,
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:py:class:`~networkx.MultiGraph`, or :py:class:`~networkx.MultiDiGraph`).
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:param unique_id_name: name to use for unique IDs.
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:param check_uniqueness: whether or not to check that provided ``Node`` instances have unique IDs.
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:return: a ``(NodeCollection, Edges)`` pair of ``hiveplotlib`` data structures.
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"""
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node_data = []
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for node, attributes in graph.nodes(data=True):
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node_data.append({unique_id_name: node, **attributes})
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node_df = pd.DataFrame(node_data)
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edge_df = nx.to_pandas_edgelist(graph, source="from", target="to")
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return NodeCollection(
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data=node_df,
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unique_id_column=unique_id_name,
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check_uniqueness=check_uniqueness,
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), Edges(data=edge_df)
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def nodes_edges_to_networkx(
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nodes: NodeCollection,
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edges: Edges,
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*,
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directed: bool = True,
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multigraph: bool = True,
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tag_attribute_name: str = "tag",
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source_attribute_name: Optional[str] = None,
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) -> nx.Graph:
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"""
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Convert a (``NodeCollection``, ``Edges``) pair to a ``networkx`` graph.
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The concrete return type is determined by ``directed`` and ``multigraph``:
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- ``directed=True``, ``multigraph=True`` → :py:class:`networkx.MultiDiGraph` (default).
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- ``directed=True``, ``multigraph=False`` → :py:class:`networkx.DiGraph`.
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- ``directed=False``, ``multigraph=True`` → :py:class:`networkx.MultiGraph`.
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- ``directed=False``, ``multigraph=False`` → :py:class:`networkx.Graph`.
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The defaults preserve duplicate edges faithfully and assume directed edges.
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All non-(from / to) ``Edges`` DataFrame columns become edge attributes on the resulting graph. All
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non-``unique_id_column`` node DataFrame columns become node attributes. The visualization-only attributes
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``node_viz_kwargs`` / ``edge_viz_kwargs`` are *not* included.
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Multi-tag :py:class:`hiveplotlib.Edges`: when more than one tag is present, the original tag is written as an edge
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attribute under ``tag_attribute_name`` (default ``"tag"``). If that name collides with an existing column on any
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tag's edge DataFrame, a :class:`ValueError` is raised. Single-tag input does not write a tag attribute.
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Optional source-row annotation: pass a string for ``source_attribute_name`` to tag each edge with a
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``(tag, row_index)`` tuple pointing back to its source row in the input :py:class:`hiveplotlib.Edges`. This is
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useful for joining graph-level computations (e.g. edge metrics) back onto the original edge DataFrame (including
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when there are multiple parallel edges in a multigraph). Default ``None`` skips this annotation.
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.. note::
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When ``multigraph=False`` but duplicate ``(from, to)`` pairs exist, ``networkx``'s :py:class:`networkx.Graph` /
|
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:py:class:`networkx.DiGraph` will silently merge duplicates (last write wins). For an undirected
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:py:class:`networkx.Graph`, reciprocal ``(a, b)`` / ``(b, a)`` rows likewise merge into a single undirected edge
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(last write wins), so the merged edge carries only the surviving row's attributes (e.g. a ``weight``). Build
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with ``multigraph=True`` to retain both edges as parallel edges, or pre-aggregate the weights into a single edge
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beforehand.
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+
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:param nodes: :py:class:`hiveplotlib.NodeCollection` of node data.
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:param edges: :py:class:`hiveplotlib.Edges` of edge data (single-tag or multi-tag).
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:param directed: whether to return a :py:class:`networkx.DiGraph`-family graph. Default ``True``.
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:param multigraph: whether to return a ``Multi*``-family graph. Default ``True``.
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:param tag_attribute_name: edge-attribute name to use when storing the original tag on multi-tag inputs. Default
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``"tag"``.
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:param source_attribute_name: optional edge-attribute name under which to store a ``(tag, row_index)`` source-row
|
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identifier for every edge, useful for joining graph-level computations back onto the original edge DataFrame.
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Default ``None`` skips annotation.
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:return: ``networkx`` graph (one of :py:class:`networkx.Graph`, :py:class:`networkx.DiGraph`,
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:py:class:`networkx.MultiGraph`, or :py:class:`networkx.MultiDiGraph`).
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:raises ValueError: if ``tag_attribute_name`` collides with an existing edge column on a multi-tag
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:py:class:`hiveplotlib.Edges` instance.
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:raises ValueError: if ``source_attribute_name`` is a string and collides with an existing edge column on any tag.
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+
"""
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+
if directed and multigraph:
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+
graph_class = nx.MultiDiGraph
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+
elif directed:
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graph_class = nx.DiGraph
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+
elif multigraph:
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+
graph_class = nx.MultiGraph
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+
else:
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+
graph_class = nx.Graph
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|
+
g = graph_class()
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+
|
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117
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+
unique_id_column = nodes.unique_id_column
|
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|
+
node_attr_cols = [c for c in nodes.data.columns if c != unique_id_column]
|
|
119
|
+
if node_attr_cols:
|
|
120
|
+
attr_records = nodes.data[node_attr_cols].to_dict(orient="records")
|
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+
g.add_nodes_from(zip(nodes.data[unique_id_column], attr_records, strict=True))
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+
else:
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+
g.add_nodes_from(nodes.data[unique_id_column])
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+
|
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125
|
+
from_col = edges.from_column_name
|
|
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|
+
to_col = edges.to_column_name
|
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|
+
multi_tag = len(edges._data) > 1
|
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|
+
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129
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+
if multi_tag:
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|
+
for tag, df in edges._data.items():
|
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|
+
if tag_attribute_name in df.columns:
|
|
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|
+
msg = (
|
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133
|
+
f"Cannot write tag attribute under name '{tag_attribute_name}' "
|
|
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|
+
f"because tag '{tag}' already has a column with that name. "
|
|
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|
+
"Pass `tag_attribute_name='<new_name>'` to choose a different "
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+
"attribute name."
|
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+
)
|
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|
+
raise ValueError(msg)
|
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139
|
+
|
|
140
|
+
if source_attribute_name is not None:
|
|
141
|
+
for tag, df in edges._data.items():
|
|
142
|
+
if source_attribute_name in df.columns:
|
|
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|
+
msg = (
|
|
144
|
+
f"Cannot write source attribute under name '{source_attribute_name}' "
|
|
145
|
+
f"because tag '{tag}' already has a column with that name. "
|
|
146
|
+
"Pass `source_attribute_name='<new_name>'` to choose a different "
|
|
147
|
+
"attribute name."
|
|
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|
+
)
|
|
149
|
+
raise ValueError(msg)
|
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150
|
+
|
|
151
|
+
for tag, df in edges._data.items():
|
|
152
|
+
edge_attr_cols = [c for c in df.columns if c not in (from_col, to_col)]
|
|
153
|
+
attr_records = (
|
|
154
|
+
df[edge_attr_cols].to_dict(orient="records")
|
|
155
|
+
if edge_attr_cols
|
|
156
|
+
else [{} for _ in range(len(df))]
|
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+
)
|
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158
|
+
if multi_tag:
|
|
159
|
+
for attrs in attr_records:
|
|
160
|
+
attrs[tag_attribute_name] = tag
|
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161
|
+
if source_attribute_name is not None:
|
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162
|
+
for attrs, row_index in zip(attr_records, df.index, strict=True):
|
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163
|
+
attrs[source_attribute_name] = (tag, row_index)
|
|
164
|
+
g.add_edges_from(zip(df[from_col], df[to_col], attr_records, strict=True))
|
|
165
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+
|
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166
|
+
return g
|
|
@@ -21,7 +21,7 @@ def international_trade_data(
|
|
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21
21
|
roughly 300mb. However, the raw data are available at the
|
|
22
22
|
`Harvard Growth Lab's website <https://doi.org/10.7910/DVN/T4CHWJ>`_, and the runner to produce the necessary
|
|
23
23
|
files to use this reader function is available in the
|
|
24
|
-
`repository <https://gitlab.com/
|
|
24
|
+
`repository <https://gitlab.com/hiveplotlib/hiveplotlib/-/blob/master/runners/make_trade_network_dataset.py>`_
|
|
25
25
|
(``make_trade_network_dataset.py``).
|
|
26
26
|
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|
27
27
|
If you are using the runner to make your own trade datasets that you will read in locally with this
|