edsger 0.1.1__cp311-cp311-macosx_11_0_arm64.whl

edsger/star.pyx

@@ -0,0 +1,356 @@
+"""
+Forward and reverse star representations of networks.
+
+
+cpdef functions:
+
+- convert_graph_to_csr_uint32
+    Convert an edge dataframe in COO format into CSR format, with uint32
+    data.
+- convert_graph_to_csc_uint32
+    Convert an edge dataframe in COO format into CSC format, with uint32
+    data.
+- convert_graph_to_csr_float64
+    Convert an edge dataframe in COO format into CSR format, with float64
+    data.
+- convert_graph_to_csc_float64
+    Convert an edge dataframe in COO format into CSC format, with float64
+    data.
+
+
+cdef functions:
+
+- _coo_to_csr_uint32
+- _coo_to_csc_uint32
+- _coo_to_csr_float64
+- _coo_to_csc_float64
+"""
+
+import numpy as np
+cimport numpy as cnp
+
+
+cpdef convert_graph_to_csr_uint32(edges, tail, head, data, vertex_count):
+    """
+    Convert an edge dataframe in COO format into CSR format, with uint32
+    data.
+
+    Parameters
+    ----------
+    edges : pandas.core.frame.DataFrame
+        The edges dataframe.
+    tail : str
+        The column name in the edges dataframe for the tail vertex index.
+    head : str
+        The column name in the edges dataframe for the head vertex index.
+    data : str
+        The column name in the edges dataframe for the int edge attribute.
+    vertex_count : int
+        The vertex count in the given network edges.
+
+    Returns
+    -------
+    tuple[numpy.ndarray, numpy.ndarray, numpy.ndarray]
+    """
+
+    fs_indptr = np.zeros(
+        vertex_count + 1, dtype=np.uint32
+    )  # make sure it is filled with zeros
+    edge_count = len(edges)
+    fs_indices = np.empty(edge_count, dtype=np.uint32)
+    fs_data = np.empty(edge_count, dtype=np.uint32)
+
+    _coo_to_csr_uint32(
+        edges[tail].values.astype(np.uint32),
+        edges[head].values.astype(np.uint32),
+        edges[data].values.astype(np.uint32),
+        fs_indptr,
+        fs_indices,
+        fs_data,
+    )
+
+    return fs_indptr, fs_indices, fs_data
+
+
+cpdef convert_graph_to_csc_uint32(edges, tail, head, data, vertex_count):
+    """
+    Convert an edge dataframe in COO format into CSC format, with uint32
+    data.
+
+    Parameters
+    ----------
+    edges : pandas.core.frame.DataFrame
+        The edges dataframe.
+    tail : str
+        The column name in the edges dataframe for the tail vertex index.
+    head : str
+        The column name in the edges dataframe for the head vertex index.
+    data : str
+        The column name in the edges dataframe for the int edge attribute.
+    vertex_count : int
+        The vertex count in the given network edges.
+
+    Returns
+    -------
+    tuple[numpy.ndarray, numpy.ndarray, numpy.ndarray]
+    """
+
+    rs_indptr = np.zeros(
+        vertex_count + 1, dtype=np.uint32
+    )  # make sure it is filled with zeros
+    edge_count = len(edges)
+    rs_indices = np.empty(edge_count, dtype=np.uint32)
+    rs_data = np.empty(edge_count, dtype=np.uint32)
+
+    _coo_to_csc_uint32(
+        edges[tail].values.astype(np.uint32),
+        edges[head].values.astype(np.uint32),
+        edges[data].values.astype(np.uint32),
+        rs_indptr,
+        rs_indices,
+        rs_data,
+    )
+
+    return rs_indptr, rs_indices, rs_data
+
+
+cpdef convert_graph_to_csr_float64(edges, tail, head, data, vertex_count):
+    """
+    Convert an edge dataframe in COO format into CSR format, with float64
+    data.
+
+    Parameters
+    ----------
+    edges : pandas.core.frame.DataFrame
+        The edges dataframe.
+    tail : str
+        The column name in the edges dataframe for the tail vertex index.
+    head : str
+        The column name in the edges dataframe for the head vertex index.
+    data : str
+        The column name in the edges dataframe for the real edge attribute.
+    vertex_count : int
+        The vertex count in the given network edges.
+
+    Returns
+    -------
+    tuple[numpy.ndarray, numpy.ndarray, numpy.ndarray]
+    """
+
+    fs_indptr = np.zeros(
+        vertex_count + 1, dtype=np.uint32
+    )  # make sure it is filled with zeros
+    edge_count = len(edges)
+    fs_indices = np.empty(edge_count, dtype=np.uint32)
+    fs_data = np.empty(edge_count, dtype=np.float64)
+
+    _coo_to_csr_float64(
+        edges[tail].values.astype(np.uint32),
+        edges[head].values.astype(np.uint32),
+        edges[data].values.astype(np.float64),
+        fs_indptr,
+        fs_indices,
+        fs_data,
+    )
+
+    return fs_indptr, fs_indices, fs_data
+
+
+cpdef convert_graph_to_csc_float64(edges, tail, head, data, vertex_count):
+    """
+    Convert an edge dataframe in COO format into CSC format, with float64
+    data.
+
+    Parameters
+    ----------
+    edges : pandas.core.frame.DataFrame
+        The edges dataframe.
+    tail : str
+        The column name in the edges dataframe for the tail vertex index.
+    head : str
+        The column name in the edges dataframe for the head vertex index.
+    data : str
+        The column name in the edges dataframe for the real edge attribute.
+    vertex_count : int
+        The vertex count in the given network edges.
+
+    Returns
+    -------
+    tuple[numpy.ndarray, numpy.ndarray, numpy.ndarray]
+    """
+
+    rs_indptr = np.zeros(
+        vertex_count + 1, dtype=np.uint32
+    )  # make sure it is filled with zeros
+    edge_count = len(edges)
+    rs_indices = np.empty(edge_count, dtype=np.uint32)
+    rs_data = np.empty(edge_count, dtype=np.float64)
+
+    _coo_to_csc_float64(
+        edges[tail].values.astype(np.uint32),
+        edges[head].values.astype(np.uint32),
+        edges[data].values.astype(np.float64),
+        rs_indptr,
+        rs_indices,
+        rs_data,
+    )
+
+    return rs_indptr, rs_indices, rs_data
+
+
+cdef void _coo_to_csr_uint32(
+        cnp.uint32_t [::1] Ai,
+        cnp.uint32_t [::1] Aj,
+        cnp.uint32_t [::1] Ax,
+        cnp.uint32_t [::1] Bp,
+        cnp.uint32_t [::1] Bj,
+        cnp.uint32_t [::1] Bx) nogil noexcept:
+
+    cdef:
+        size_t i, row, dest
+        size_t n_vert = <size_t>(Bp.shape[0] - 1)
+        size_t n_edge = <size_t>Bj.shape[0]
+        cnp.uint32_t temp, cumsum, last
+
+    for i in range(n_edge):
+        Bp[<size_t>Ai[i]] += 1
+
+    cumsum = 0
+    for i in range(n_vert):
+        temp = Bp[i]
+        Bp[i] = cumsum
+        cumsum += temp
+    Bp[n_vert] = <cnp.uint32_t>n_edge
+
+    for i in range(n_edge):
+        row = <size_t>Ai[i]
+        dest = <size_t>Bp[row]
+        Bj[dest] = Aj[i]
+        Bx[dest] = Ax[i]
+        Bp[row] += 1
+
+    last = 0
+    for i in range(n_vert + 1):
+        temp = Bp[i]
+        Bp[i] = last
+        last = temp
+
+
+cdef void _coo_to_csc_uint32(
+        cnp.uint32_t [::1] Ai,
+        cnp.uint32_t [::1] Aj,
+        cnp.uint32_t [::1] Ax,
+        cnp.uint32_t [::1] Bp,
+        cnp.uint32_t [::1] Bi,
+        cnp.uint32_t [::1] Bx) nogil:
+
+    cdef:
+        size_t i, col, dest
+        size_t n_vert = <size_t>(Bp.shape[0] - 1)
+        size_t n_edge = <size_t>Bi.shape[0]
+        cnp.uint32_t temp, cumsum, last
+
+    for i in range(n_edge):
+        Bp[<size_t>Aj[i]] += 1
+
+    cumsum = 0
+    for i in range(n_vert):
+        temp = Bp[i]
+        Bp[i] = cumsum
+        cumsum += temp
+    Bp[<size_t>n_vert] = <cnp.uint32_t>n_edge
+
+    for i in range(n_edge):
+        col = <size_t>Aj[i]
+        dest = <size_t>Bp[col]
+        Bi[dest] = Ai[i]
+        Bx[dest] = Ax[i]
+        Bp[col] += 1
+
+    last = 0
+    for i in range(n_vert + 1):
+        temp = Bp[i]
+        Bp[i] = last
+        last = temp
+
+
+cpdef void _coo_to_csr_float64(
+        cnp.uint32_t  [::1] Ai,
+        cnp.uint32_t  [::1] Aj,
+        cnp.float64_t [::1] Ax,
+        cnp.uint32_t  [::1] Bp,
+        cnp.uint32_t  [::1] Bj,
+        cnp.float64_t [::1] Bx) nogil noexcept:
+
+    cdef:
+        size_t i, row, dest
+        size_t n_vert = <size_t>(Bp.shape[0] - 1)
+        size_t n_edge = <size_t>Bj.shape[0]
+        cnp.uint32_t temp, cumsum, last
+
+    for i in range(n_edge):
+        Bp[<size_t>Ai[i]] += 1
+
+    cumsum = 0
+    for i in range(n_vert):
+        temp = Bp[i]
+        Bp[i] = cumsum
+        cumsum += temp
+    Bp[n_vert] = <cnp.uint32_t>n_edge
+
+    for i in range(n_edge):
+        row = <size_t>Ai[i]
+        dest = <size_t>Bp[row]
+        Bj[dest] = Aj[i]
+        Bx[dest] = Ax[i]
+        Bp[row] += 1
+
+    last = 0
+    for i in range(n_vert + 1):
+        temp = Bp[i]
+        Bp[i] = last
+        last = temp
+
+
+cpdef void _coo_to_csc_float64(
+        cnp.uint32_t  [::1] Ai,
+        cnp.uint32_t  [::1] Aj,
+        cnp.float64_t [::1] Ax,
+        cnp.uint32_t  [::1] Bp,
+        cnp.uint32_t  [::1] Bi,
+        cnp.float64_t [::1] Bx) nogil noexcept:
+
+    cdef:
+        size_t i, col, dest
+        size_t n_vert = <size_t>(Bp.shape[0] - 1)
+        size_t n_edge = <size_t>Bi.shape[0]
+        cnp.uint32_t temp, cumsum, last
+
+    for i in range(n_edge):
+        Bp[<size_t>Aj[i]] += 1
+
+    cumsum = 0
+    for i in range(n_vert):
+        temp = Bp[i]
+        Bp[i] = cumsum
+        cumsum += temp
+    Bp[<size_t>n_vert] = <cnp.uint32_t>n_edge
+
+    for i in range(n_edge):
+        col = <size_t>Aj[i]
+        dest = <size_t>Bp[col]
+        Bi[dest] = Ai[i]
+        Bx[dest] = Ax[i]
+        Bp[col] += 1
+
+    last = 0
+    for i in range(n_vert + 1):
+        temp = Bp[i]
+        Bp[i] = last
+        last = temp
+
+
+# author : Francois Pacull
+# copyright : Architecture & Performance
+# email: francois.pacull@architecture-performance.fr
+# license : MIT

edsger/utils.py

@@ -0,0 +1,63 @@
+"""This module makes it easy to execute common tasks in Python scripts such as generate random
+graphs.
+"""
+
+import numpy as np
+import pandas as pd
+
+
+def generate_random_network(n_edges=100, n_verts=20, seed=124, sort=True):
+    """
+    Generate a random network with a specified number of edges and vertices.
+
+    Parameters
+    ----------
+    n_edges : int, optional
+        The number of edges in the network. Default is 100.
+    n_verts : int, optional
+        The number of vertices in the network. Default is 20.
+    seed : int, optional
+        The seed for the random number generator. Default is 124.
+    sort : bool, optional
+        Whether to sort the edges by tail and head vertices. Default is True.
+
+    Returns
+    -------
+    edges : pandas.DataFrame
+        A DataFrame containing the edges of the network with columns 'tail', 'head', and 'weight'.
+
+    Examples
+    --------
+    >>> generate_random_network(n_edges=5, n_verts=3, seed=42)
+       tail  head    weight
+    0     0     2  0.975622
+    1     1     0  0.128114
+    2     1     0  0.450386
+    3     1     2  0.786064
+    4     2     0  0.761140
+
+
+    Notes
+    -----
+    The 'tail' and 'head' columns represent the source and destination vertices of each edge,
+    respectively. The 'weight' column represents the weight of each edge, which is a random
+    float between 0 and 1.
+
+    If `sort` is True, the DataFrame is sorted by the 'tail' and 'head' columns and the index
+    is reset.
+    """
+    rng = np.random.default_rng(seed=seed)
+    tail = rng.integers(low=0, high=n_verts, size=n_edges)
+    head = rng.integers(low=0, high=n_verts, size=n_edges)
+    weight = rng.random(size=n_edges)
+    edges = pd.DataFrame(data={"tail": tail, "head": head, "weight": weight})
+    if sort:
+        edges.sort_values(by=["tail", "head"], inplace=True)
+        edges.reset_index(drop=True, inplace=True)
+    return edges
+
+
+# author : Francois Pacull
+# copyright : Architecture & Performance
+# email: francois.pacull@architecture-performance.fr
+# license : MIT

edsger-0.1.1.dist-info/METADATA

@@ -0,0 +1,111 @@
+Metadata-Version: 2.4
+Name: edsger
+Version: 0.1.1
+Summary: Graph algorithms in Cython.
+Author-email: François Pacull <francois.pacull@architecture-performance.fr>
+Maintainer-email: François Pacull <francois.pacull@architecture-performance.fr>
+License: MIT License
+Project-URL: Repository, https://github.com/aetperf/Edsger
+Project-URL: Documentation, https://edsger.readthedocs.io
+Keywords: python,graph,shortest path,Dijkstra
+Platform: any
+Classifier: Development Status :: 4 - Beta
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.9
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Operating System :: OS Independent
+Classifier: Topic :: Scientific/Engineering
+Requires-Python: >=3.9
+Description-Content-Type: text/markdown
+License-File: LICENSE
+License-File: AUTHORS.rst
+Requires-Dist: setuptools
+Requires-Dist: setuptools_scm
+Requires-Dist: numpy>=1.26
+Requires-Dist: Cython>=3
+Requires-Dist: pandas
+Provides-Extra: dev
+Requires-Dist: black; extra == "dev"
+Provides-Extra: test
+Requires-Dist: pytest; extra == "test"
+Requires-Dist: scipy<1.11; extra == "test"
+Provides-Extra: doc
+Requires-Dist: sphinx; extra == "doc"
+Requires-Dist: sphinx_design; extra == "doc"
+Requires-Dist: sphinx_rtd_theme; extra == "doc"
+Dynamic: license-file
+
+
+![Tests Status](https://github.com/aetperf/edsger/actions/workflows/tests.yml/badge.svg?branch=release)
+[![codecov](https://codecov.io/gh/aetperf/edsger/branch/release/graph/badge.svg)](https://codecov.io/gh/aetperf/edsger)
+[![PyPI version](https://img.shields.io/pypi/v/edsger.svg)](https://pypi.org/project/edsger/)
+[![Downloads](https://static.pepy.tech/badge/edsger)](https://pepy.tech/project/edsger)
+[![Python 3.9 | 3.10 | 3.11 | 3.12 | 3.13](https://img.shields.io/badge/python-3.9%20%7C%203.10%20%7C%203.11%20%7C%203.12%20%7C%203.13-blue)](https://pypi.org/project/edsger/)
+[![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/psf/black)
+[![Cython lint: cython-lint](https://img.shields.io/badge/cython--lint-enabled-brightgreen.svg)](https://github.com/MarcoGorelli/cython-lint)
+[![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/licenses/MIT)
+
+# Edsger
+
+*Graph algorithms in Cython*
+
+Welcome to our Python library for graph algorithms. So far, the library only includes Dijkstra's algorithm but we should add a range of common path algorithms later. It is also open-source and easy to integrate with other Python libraries. To get started, simply install the library using pip, and import it into your Python project.
+
+Documentation : [https://edsger.readthedocs.io/en/latest/](https://edsger.readthedocs.io/en/latest/)
+
+## Small example : Dijkstra's Algorithm
+
+To use Dijkstra's algorithm, you can import the `Dijkstra` class from the `path` module. The function takes a graph and a source node as input, and returns the shortest path from the source node to all other nodes in the graph.
+
+```python
+import pandas as pd
+
+from edsger.path import Dijkstra
+
+# Create a DataFrame with the edges of the graph
+edges = pd.DataFrame({
+    'tail': [0, 0, 1, 2, 2, 3],
+    'head': [1, 2, 2, 3, 4, 4],
+    'weight': [1, 4, 2, 1, 3, 1]
+})
+edges
+```
+
+|    |   tail |   head |   weight |
+|---:|-------:|-------:|---------:|
+|  0 |      0 |      1 |        1 |
+|  1 |      0 |      2 |        4 |
+|  2 |      1 |      2 |        2 |
+|  3 |      2 |      3 |        1 |
+|  4 |      2 |      4 |        3 |
+|  5 |      3 |      4 |        1 |
+
+
+```python
+# Initialize the Dijkstra object
+dijkstra = Dijkstra(edges)
+
+# Run the algorithm from a source vertex
+shortest_paths = dijkstra.run(vertex_idx=0)
+print("Shortest paths:", shortest_paths)
+```
+
+    Shortest paths: [0. 1. 3. 4. 5.]
+
+We get the shortest paths from the source node 0 to all other nodes in the graph. The output is an array with the shortest path length to each node. A path length is the sum of the weights of the edges in the path.
+
+## Contributing
+
+We welcome contributions to the Edsger library. If you have any suggestions, bug reports, or feature requests, please open an issue on our [GitHub repository](https://github.com/aetperf/Edsger).
+
+## License
+
+Edsger is licensed under the MIT License. See the LICENSE file for more details.
+
+## Contact
+
+For any questions or inquiries, please contact François Pacull at [francois.pacull@architecture-performance.fr](mailto:francois.pacull@architecture-performance.fr).

edsger-0.1.1.dist-info/RECORD

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+edsger-0.1.1.dist-info/top_level.txt,sha256=QvhzFORJIIot6GzSnDrtGa9KQt9iifCbOC5ULlzY5dg,7
+edsger-0.1.1.dist-info/METADATA,sha256=XFq5xeiFwVheYlfC8ApWaFwqoUI8uQZ0272_gQhZQbQ,4678
+edsger-0.1.1.dist-info/licenses/LICENSE,sha256=eNjfz5CInLrVdczJbhazCKtb8-0qB0UaXZ3bXN0zio0,1111
+edsger-0.1.1.dist-info/licenses/AUTHORS.rst,sha256=9lqpqjiC4XukK7jdxXwKJJrddqwCV2DjpYTqhpP6znA,105

edsger-0.1.1.dist-info/WHEEL

@@ -0,0 +1,5 @@
+Wheel-Version: 1.0
+Generator: setuptools (80.9.0)
+Root-Is-Purelib: false
+Tag: cp311-cp311-macosx_11_0_arm64
+

edsger-0.1.1.dist-info/licenses/AUTHORS.rst

@@ -0,0 +1,5 @@
+============
+Contributors
+============
+
+* François Pacull <francois.pacull@architecture-performance.fr>

edsger-0.1.1.dist-info/licenses/LICENSE

@@ -0,0 +1,21 @@
+The MIT License (MIT)
+
+Copyright (c) 2022 Francois Pacull - Architecture & Performance
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

edsger-0.1.1.dist-info/top_level.txt

@@ -0,0 +1 @@
+edsger