Merge pull request #121 from yo123abxd/pybind11

Integrate gpu_easygraph into cpp_easygraph

.github/workflows/buildwheel.yml

@@ -5,32 +5,76 @@ on: workflow_dispatch
 jobs:
 
 
-  build-wheel:
-    runs-on: ${{ matrix.os }}
-    strategy:
-      matrix:
-        os: [ windows-latest, ubuntu-20.04, ubuntu-latest, macos-latest,  windows-2019,	macos-13,  macos-11]
-        python-version: [ "3.8", "3.9", "3.10","3.11"]
-
-    steps:
-      - uses: actions/checkout@v2
-      - name: Set up python
-        uses: actions/setup-python@v2
-        with:
-          python-version: ${{ matrix.python-version }}
-      - name: build wheel
-        run: |
-          mkdir -p path/to/artifact
-          pip install --upgrade pip
-          pip install --upgrade setuptools
-          pip install pybind11
-          pip install wheel
-          python setup.py bdist_wheel
-          ls
-      - uses: actions/upload-artifact@v3
-        with:
-           name: my-artifact
-           path: dist/ # or path/to/artifact
+#  build-wheel:
+#    runs-on: ${{ matrix.os }}
+#    strategy:
+#      matrix:
+#        os: [ windows-latest, ubuntu-20.04, ubuntu-latest, macos-latest,  windows-2019,	macos-13,  macos-11, macos-14]
+##        python-version: [ "3.8", "3.9", "3.10","3.11", "3.12"]
+#
+#    steps:
+#      - uses: actions/checkout@v4
+#      - name: Set up python
+#        uses: actions/setup-python@v4
+#        with:
+#          python-version: ${{ matrix.python-version }}
+    build_wheels:
+      name: Build wheels on ${{ matrix.os }}
+      runs-on: ${{ matrix.os }}
+      strategy:
+        matrix:
+          # macos-13 is an intel runner, macos-14 is apple silicon
+          os: [ ubuntu-latest, windows-latest, macos-13, macos-14, ubuntu-20.04]
+#          python-version: [ "3.8", "3.9", "3.10","3.11", "3.12"]
+
+      steps:
+        - uses: actions/checkout@v4
+
+        - name: Build wheels
+          uses: pypa/[email protected]
+
+        - uses: actions/upload-artifact@v4
+          with:
+
+            python-version: ${{ matrix.python-version }}
+            name: cibw-wheels-${{ matrix.os }}-${{ strategy.job-index }}
+            path: ./wheelhouse/*.whl
+
+    build_sdist:
+      name: Build source distribution
+      runs-on: ubuntu-latest
+      steps:
+        - uses: actions/checkout@v4
+
+        - name: Build sdist
+          run: pipx run build --sdist
+
+        - uses: actions/upload-artifact@v4
+          with:
+            name: cibw-sdist
+            path: dist/*.tar.gz
+
+    upload_pypi:
+      needs: [ build_wheels, build_sdist ]
+      runs-on: ubuntu-latest
+      environment: pypi
+      permissions:
+        id-token: write
+#      if: github.event_name == 'release' && github.event.action == 'published'
+      # or, alternatively, upload to PyPI on every tag starting with 'v' (remove on: release above to use this)
+      # if: github.event_name == 'push' && startsWith(github.ref, 'refs/tags/v')
+      steps:
+        - uses: actions/download-artifact@v4
+          with:
+            # unpacks all CIBW artifacts into dist/
+            pattern: cibw-*
+            path: dist
+            merge-multiple: true
+
+#      - uses: actions/upload-artifact@v3
+#        with:
+#           name: my-artifact
+#           path: dist/ # or path/to/artifact
 
 
 

.github/workflows/release-cibuildwheel.yaml

@@ -39,17 +39,17 @@ jobs:
       matrix:
 #         os: [ubuntu-20.04, windows-latest, macos-latest]
         os: [ubuntu-20.04]
-        python-version: [ "3.8", "3.9", "3.10", "3.11"]
+        python-version: [ "3.8", "3.9", "3.10", "3.11", "3.12"]
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         with:
           ref: ${{ github.ref }}
 
       - uses: actions/setup-python@v3
 
       - name: Install cibuildwheel
-        run: python -m pip install cibuildwheel==2.15.0
+        run: python -m pip install cibuildwheel==2.17.0
 
       - name: Build wheels
         run: python -m cibuildwheel --output-dir wheelhouse

.github/workflows/test.yaml

@@ -10,7 +10,7 @@ jobs:
       fail-fast: false
       matrix:
         # ubuntu 22.04 has deprecated python 3.6
-        python-version: [ "3.8", "3.9", "3.10","3.11"]
+        python-version: [ "3.8", "3.9", "3.10","3.11", "3.12"]
     steps:
       - name: Set up Python ${{ matrix.python-version }}
         uses: actions/setup-python@v4

.gitmodules

@@ -1,3 +1,3 @@
-[submodule "gpu_easygraph/pybind11"]
-	path = gpu_easygraph/pybind11
-	url = git@github.com:pybind/pybind11.git
+[submodule "cpp_easygraph/pybind11"]
+	path = cpp_easygraph/pybind11
+	url = https://github.com/pybind/pybind11.git

CMakeLists.txt

@@ -0,0 +1,23 @@
+cmake_minimum_required(VERSION 3.23)
+
+project(easygraph)
+
+option(EASYGRAPH_ENABLE_GPU "EASYGRAPH_ENABLE_GPU" OFF)
+
+add_subdirectory(cpp_easygraph)
+
+if (EASYGRAPH_ENABLE_GPU)
+
+    message("easygraph gpu module is enabled")
+
+    add_subdirectory(gpu_easygraph)
+
+    target_include_directories(cpp_easygraph
+        PRIVATE gpu_easygraph
+    )
+
+else()
+
+    message("easygraph gpu module is disabled")
+
+endif()

README.md

@@ -0,0 +1,126 @@
+EasyGraph
+==================
+
+Copyright (C) <2020-2024> by DataNET Group, Fudan University
+
+___________________________________________________________________________
+
+[![PyPI Version][pypi-image]][pypi-url]
+[![Python][python-image]][python-url]
+[![License][license-image]][license-url]
+[![Downloads][downloads-image]][downloads-url]
+
+[pypi-image]: https://img.shields.io/pypi/v/Python-EasyGraph.svg?label=PyPI
+[pypi-url]: https://pypi.org/project/Python-EasyGraph/
+[python-image]: https://img.shields.io/pypi/pyversions/Python-EasyGraph.svg?label=Python
+[python-url]: https://pypi.org/project/Python-EasyGraph/
+[license-image]: https://img.shields.io/pypi/l/Python-EasyGraph?label=License
+[license-url]: https://github.com/easy-graph/Easy-Graph/blob/master/LICENSE
+[downloads-image]: https://static.pepy.tech/personalized-badge/python-easygraph?period=total&units=international_system&left_color=brightgreen&right_color=yellowgreen&left_text=Downloads
+[downloads-url]: https://pypi.org/project/Python-EasyGraph/
+
+- **Documentation:** https://easy-graph.github.io/
+- **Source Code:** https://github.com/easy-graph/Easy-Graph
+- **Issue Tracker:** https://github.com/easy-graph/Easy-Graph/issues
+- **PyPI Homepage:** https://pypi.org/project/Python-EasyGraph/
+- **Youtube channel:** https://www.youtube.com/@python-easygraph
+
+Introduction
+------------
+**EasyGraph** is an open-source network analysis library. It is mainly written in Python and supports analysis for undirected networks and directed networks. EasyGraph supports various formats of network data and covers a series of important network analysis algorithms for community detection, structural hole spanner detection, network embedding, and motif detection. Moreover, EasyGraph implements some key elements using C++ and introduces multiprocessing optimization to achieve better efficiency.
+
+New Features in Version 1.1
+--------------------------
+- **Support for more hypergraph metrics and algorithms.** Such as [hypercoreness](https://www.nature.com/articles/s41467-023-41887-2), [vector-centrality](https://www.sciencedirect.com/science/article/pii/S0960077922006075), [s-centrality](https://epjds.epj.org/articles/epjdata/abs/2020/01/13688_2020_Article_231/13688_2020_Article_231.html), and so on.
+- **Support for more hypergraph datasets.** Static hypergraph datasets and dynamic datasets can be both loaded by calling corresponding dataset name.
+- **Support for more flexible dynamic hypergraph visualization.** Users can define dynamic hypergraphs and visualize the structure of the hypergraph at each timestamp.
+- **Support for more efficient hypergraph computation and hypergraph learning.** Adoption of suitable storage structure and caching strategy for different metrics/hypergraph neural networks.
+
+If you need more details, please see our [documentation](https://easy-graph.github.io/) of the latest version.
+
+
+News
+----
+- [04-09-2024] We release EasyGraph 1.2! This version now fully supports Python 3.12.
+- [02-05-2024] We release EasyGraph 1.1! This version features hypergraph analysis and learning for higher-order network modeling and representation.
+- [08-17-2023] We release EasyGraph 1.0!
+- [08-08-2023] Our paper "EasyGraph: A Multifunctional, Cross-Platform, and Effective Library for Interdisciplinary Network Analysis" has been accepted by Patterns!
+
+Stargazers
+----------
+
+[![Stars][star-image]][star-url]
+
+[star-image]:https://reporoster.com/stars/easy-graph/Easy-Graph
+[star-url]: https://github.com/easy-graph/Easy-Graph/stargazers
+
+Install
+-------
+
+- **Prerequisites**
+
+``3.8 <= Python <= 3.12`` is required.
+
+- **Installation with** ``pip``
+```
+    $ pip install --upgrade Python-EasyGraph
+```
+The conda package is no longer updated or maintained.
+
+If you've installed EasyGraph this way before, please uninstall it with ``conda`` and install it with ``pip``.
+
+If prebuilt EasyGraph wheels are not supported for your platform (OS / CPU arch, check [here](https://pypi.org/simple/python-easygraph/)), you can build it locally this way:
+```
+    git clone https://github.com/easy-graph/Easy-Graph && cd Easy-Graph && git checkout pybind11
+    pip install pybind11
+    python3 setup.py build_ext
+    python3 setup.py install
+```
+- **Hint**
+
+    EasyGraph uses  1.12.1 <= [PyTorch](https://pytorch.org/get-started/locally/) < 2.0 for machine learning functions.
+    Note that this does not prevent your from running non-machine learning functions normally, if there is no PyTorch in your environment.
+    But you will receive some warnings which remind you some unavailable modules when they depend on it.
+
+Simple Example
+--------------
+
+This example shows the general usage of methods in EasyGraph.
+```python
+  >>> import easygraph as eg
+  >>> G = eg.Graph()
+  >>> G.add_edges([(1,2), (2,3), (1,3), (3,4), (4,5), (3,5), (5,6)])
+  >>> eg.pagerank(G)
+  {1: 0.14272233049003707, 2: 0.14272233049003694, 3: 0.2685427766200994, 4: 0.14336430577918527, 5: 0.21634929087322705, 6: 0.0862989657474143}
+```
+This is a simple example for the detection of [structural hole spanners](https://en.wikipedia.org/wiki/Structural_holes)
+using the [HIS](https://keg.cs.tsinghua.edu.cn/jietang/publications/WWW13-Lou&Tang-Structural-Hole-Information-Diffusion.pdf) algorithm.
+
+```python
+  >>> import easygraph as eg
+  >>> G = eg.Graph()
+  >>> G.add_edges([(1,2), (2,3), (1,3), (3,4), (4,5), (3,5), (5,6)])
+  >>> _, _, H = eg.get_structural_holes_HIS(G, C=[frozenset([1,2,3]), frozenset([4,5,6])])
+  >>> H # The structural hole score of each node. Note that node `4` is regarded as the most possible structural hole spanner.
+  {1: {0: 0.703948974609375},
+   2: {0: 0.703948974609375},
+   3: {0: 1.2799804687499998},
+   4: {0: 1.519976806640625},
+   5: {0: 1.519976806640625},
+   6: {0: 0.83595703125}
+  }
+```
+Citation
+--------
+
+If you use EasyGraph in a scientific publication, we would appreciate citations to the following paper:
+```
+  @article{gao2023easygraph,
+      title={{EasyGraph: A Multifunctional, Cross-Platform, and Effective Library for Interdisciplinary Network Analysis}},
+      author={Min Gao and Zheng Li and Ruichen Li and Chenhao Cui and Xinyuan Chen and Bodian Ye and Yupeng Li and Weiwei Gu and Qingyuan Gong and Xin Wang and Yang Chen},
+      year={2023},
+      journal={Patterns},
+      volume={4},
+      number={10}
+  }
+```

cpp_easygraph/CMakeLists.txt

@@ -0,0 +1,37 @@
+cmake_minimum_required(VERSION 3.23)
+project(cpp_easygraph)
+set(CMAKE_CXX_STANDARD 11)
+
+file(GLOB SOURCES
+    classes/*.cpp
+    common/*.cpp
+    functions/*/*.cpp
+    cpp_easygraph.cpp
+)
+
+add_subdirectory(pybind11)
+
+option(EASYGRAPH_ENABLE_GPU "EASYGRAPH_ENABLE_GPU" OFF)
+
+if (EASYGRAPH_ENABLE_GPU)
+
+    pybind11_add_module(cpp_easygraph
+        ${SOURCES}
+        $<TARGET_OBJECTS:gpu_easygraph>
+    )
+
+    target_compile_definitions(cpp_easygraph 
+        PRIVATE EASYGRAPH_ENABLE_GPU
+    )
+
+    target_link_libraries(cpp_easygraph
+        PRIVATE cudart_static
+    )
+
+else()
+
+    pybind11_add_module(cpp_easygraph
+        ${SOURCES}
+    )
+
+endif()