Merge branch 'Thinklab-SJTU:main' into main

heatingma · Dec 1, 2023 · ed731b3 · ed731b3
2 parents 086e182 + 14894f9
commit ed731b3
Show file tree

Hide file tree

Showing 398 changed files with 1,266 additions and 1,593 deletions.
diff --git a/.github/workflows/python-package.yml b/.github/workflows/python-package.yml
@@ -39,7 +39,7 @@ jobs:
         flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
         # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
         flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
-    - name: Test with pytest. They are divided into two runs because MindSpore will interfer with Paddle.
+    - name: Test with pytest. They are divided into two runs because MindSpore will interfere with Paddle.
       run: |
         if [ "${{ matrix.python-version }}" != "3.10" ]; then 
           pytest --cov=pygmtools --cov-report=xml --backend=mindspore tests/test_classic_solvers.py; fi
@@ -50,7 +50,7 @@ jobs:
 
   macos:
 
-    runs-on: macos-latest
+    runs-on: macos-12
     strategy:
       fail-fast: false
       matrix:
@@ -76,13 +76,13 @@ jobs:
           flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
           # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
           flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
-      - name: Test with pytest. They are divided into two runs because MindSpore will interfer with Paddle.
+      - name: Test with pytest. They are divided into two runs because MindSpore will interfere with Paddle.
         run: |
           pytest --cov=pygmtools --cov-report=xml --backend=mindspore tests/test_classic_solvers.py
           pytest --cov=pygmtools --cov-report=xml --cov-append
   windows:
 
-    runs-on: windows-latest
+    runs-on: windows-2022
     strategy:
       fail-fast: false
       matrix:
@@ -108,7 +108,7 @@ jobs:
           flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
           # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
           flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
-      - name: Test with pytest. They are divided into two runs because MindSpore will interfer with Paddle.
+      - name: Test with pytest. They are divided into two runs because MindSpore will interfere with Paddle.
         run: |
           pytest --cov=pygmtools --cov-report=xml --backend=mindspore tests/test_classic_solvers.py
-          pytest --cov=pygmtools --cov-report=xml --cov-append
+          pytest --cov=pygmtools --cov-report=xml --cov-append
diff --git a/.github/workflows/python-publish.yml b/.github/workflows/python-publish.yml
@@ -14,7 +14,7 @@ on:
 
 jobs:
   deploy:
-    runs-on: ubuntu-latest
+    runs-on: ubuntu-20.04
 
     steps:
     - uses: actions/checkout@v2
@@ -27,6 +27,7 @@ jobs:
         python -m pip install --upgrade pip
         pip install wheel
         pip install cython
+        pip install setuptools
     - name: Build package
       run: python setup.py sdist
     - name: Upload new version to PyPI
@@ -40,7 +41,7 @@ jobs:
 
   linux:
     needs: deploy
-    runs-on: ubuntu-latest
+    runs-on: ubuntu-20.04
     strategy:
       fail-fast: false
       matrix:
@@ -55,7 +56,7 @@ jobs:
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip
-        pip install -r docs/publish_req.txt
+        pip install -r pygmtools/publish_requirements.txt
     - name: Build Wheel
       run: |
         python setup.py bdist_wheel
@@ -85,7 +86,7 @@ jobs:
       - name: Install dependencies
         run: |
           python -m pip install --upgrade pip
-          pip install -r docs/publish_req.txt
+          pip install -r pygmtools/publish_requirements.txt
       - name: Build Wheel
         run: |
           python setup.py bdist_wheel
@@ -114,7 +115,7 @@ jobs:
       - name: Install dependencies
         run: |
           python -m pip install --upgrade pip
-          pip install -r docs/publish_req.txt
+          pip install -r pygmtools/publish_requirements.txt
       - name: Build Wheel
         run: |
           python setup.py bdist_wheel

diff --git a/README.md b/README.md
@@ -122,7 +122,7 @@ The following backends are available:
 
 <img src="https://pygmtools.readthedocs.io/en/latest/_images/tensorflow_logo.png" alt="tensorflow logo" width="200"/>
 
-### Development status (0.4.1)
+### Development status (0.4.2)
 
 |                     | Numpy | PyTorch | Jittor | PaddlePaddle | Tensorflow | MindSpore |
 | ------------------- | ----- | ------- | ------ | ------------ | ---------- | --------- |

diff --git a/...atching_isomorphic_graphs/images/sphx_glr_plot_isomorphic_graphs_jittor_001.png b/...atching_isomorphic_graphs/images/sphx_glr_plot_isomorphic_graphs_jittor_001.png
diff --git a/...atching_isomorphic_graphs/images/sphx_glr_plot_isomorphic_graphs_jittor_002.png b/...atching_isomorphic_graphs/images/sphx_glr_plot_isomorphic_graphs_jittor_002.png
diff --git a/...atching_isomorphic_graphs/images/sphx_glr_plot_isomorphic_graphs_jittor_003.png b/...atching_isomorphic_graphs/images/sphx_glr_plot_isomorphic_graphs_jittor_003.png
diff --git a/...atching_isomorphic_graphs/images/sphx_glr_plot_isomorphic_graphs_jittor_004.png b/...atching_isomorphic_graphs/images/sphx_glr_plot_isomorphic_graphs_jittor_004.png
diff --git a/...atching_isomorphic_graphs/images/sphx_glr_plot_isomorphic_graphs_jittor_005.png b/...atching_isomorphic_graphs/images/sphx_glr_plot_isomorphic_graphs_jittor_005.png
diff --git a/...atching_isomorphic_graphs/images/sphx_glr_plot_isomorphic_graphs_jittor_006.png b/...atching_isomorphic_graphs/images/sphx_glr_plot_isomorphic_graphs_jittor_006.png
diff --git a/...atching_isomorphic_graphs/images/sphx_glr_plot_isomorphic_graphs_jittor_007.png b/...atching_isomorphic_graphs/images/sphx_glr_plot_isomorphic_graphs_jittor_007.png
diff --git a/...atching_isomorphic_graphs/images/sphx_glr_plot_isomorphic_graphs_jittor_008.png b/...atching_isomorphic_graphs/images/sphx_glr_plot_isomorphic_graphs_jittor_008.png
diff --git a/...atching_isomorphic_graphs/images/sphx_glr_plot_isomorphic_graphs_jittor_009.png b/...atching_isomorphic_graphs/images/sphx_glr_plot_isomorphic_graphs_jittor_009.png
diff --git a/...matching_isomorphic_graphs/images/sphx_glr_plot_isomorphic_graphs_numpy_001.png b/...matching_isomorphic_graphs/images/sphx_glr_plot_isomorphic_graphs_numpy_001.png
diff --git a/...matching_isomorphic_graphs/images/sphx_glr_plot_isomorphic_graphs_numpy_002.png b/...matching_isomorphic_graphs/images/sphx_glr_plot_isomorphic_graphs_numpy_002.png
diff --git a/...matching_isomorphic_graphs/images/sphx_glr_plot_isomorphic_graphs_numpy_003.png b/...matching_isomorphic_graphs/images/sphx_glr_plot_isomorphic_graphs_numpy_003.png
diff --git a/...matching_isomorphic_graphs/images/sphx_glr_plot_isomorphic_graphs_numpy_004.png b/...matching_isomorphic_graphs/images/sphx_glr_plot_isomorphic_graphs_numpy_004.png
diff --git a/...matching_isomorphic_graphs/images/sphx_glr_plot_isomorphic_graphs_numpy_005.png b/...matching_isomorphic_graphs/images/sphx_glr_plot_isomorphic_graphs_numpy_005.png
diff --git a/...matching_isomorphic_graphs/images/sphx_glr_plot_isomorphic_graphs_numpy_006.png b/...matching_isomorphic_graphs/images/sphx_glr_plot_isomorphic_graphs_numpy_006.png
diff --git a/...matching_isomorphic_graphs/images/sphx_glr_plot_isomorphic_graphs_numpy_007.png b/...matching_isomorphic_graphs/images/sphx_glr_plot_isomorphic_graphs_numpy_007.png
diff --git a/...matching_isomorphic_graphs/images/sphx_glr_plot_isomorphic_graphs_numpy_008.png b/...matching_isomorphic_graphs/images/sphx_glr_plot_isomorphic_graphs_numpy_008.png
diff --git a/...matching_isomorphic_graphs/images/sphx_glr_plot_isomorphic_graphs_numpy_009.png b/...matching_isomorphic_graphs/images/sphx_glr_plot_isomorphic_graphs_numpy_009.png
diff --git a/...atching_isomorphic_graphs/images/sphx_glr_plot_isomorphic_graphs_paddle_001.png b/...atching_isomorphic_graphs/images/sphx_glr_plot_isomorphic_graphs_paddle_001.png
diff --git a/...atching_isomorphic_graphs/images/sphx_glr_plot_isomorphic_graphs_paddle_002.png b/...atching_isomorphic_graphs/images/sphx_glr_plot_isomorphic_graphs_paddle_002.png
diff --git a/...atching_isomorphic_graphs/images/sphx_glr_plot_isomorphic_graphs_paddle_003.png b/...atching_isomorphic_graphs/images/sphx_glr_plot_isomorphic_graphs_paddle_003.png
diff --git a/...atching_isomorphic_graphs/images/sphx_glr_plot_isomorphic_graphs_paddle_004.png b/...atching_isomorphic_graphs/images/sphx_glr_plot_isomorphic_graphs_paddle_004.png
diff --git a/...atching_isomorphic_graphs/images/sphx_glr_plot_isomorphic_graphs_paddle_005.png b/...atching_isomorphic_graphs/images/sphx_glr_plot_isomorphic_graphs_paddle_005.png
diff --git a/...atching_isomorphic_graphs/images/sphx_glr_plot_isomorphic_graphs_paddle_006.png b/...atching_isomorphic_graphs/images/sphx_glr_plot_isomorphic_graphs_paddle_006.png
diff --git a/...atching_isomorphic_graphs/images/sphx_glr_plot_isomorphic_graphs_paddle_007.png b/...atching_isomorphic_graphs/images/sphx_glr_plot_isomorphic_graphs_paddle_007.png
diff --git a/...atching_isomorphic_graphs/images/sphx_glr_plot_isomorphic_graphs_paddle_008.png b/...atching_isomorphic_graphs/images/sphx_glr_plot_isomorphic_graphs_paddle_008.png
diff --git a/...atching_isomorphic_graphs/images/sphx_glr_plot_isomorphic_graphs_paddle_009.png b/...atching_isomorphic_graphs/images/sphx_glr_plot_isomorphic_graphs_paddle_009.png
diff --git a/...tching_isomorphic_graphs/images/sphx_glr_plot_isomorphic_graphs_pytorch_001.png b/...tching_isomorphic_graphs/images/sphx_glr_plot_isomorphic_graphs_pytorch_001.png
diff --git a/...tching_isomorphic_graphs/images/sphx_glr_plot_isomorphic_graphs_pytorch_002.png b/...tching_isomorphic_graphs/images/sphx_glr_plot_isomorphic_graphs_pytorch_002.png
diff --git a/...tching_isomorphic_graphs/images/sphx_glr_plot_isomorphic_graphs_pytorch_003.png b/...tching_isomorphic_graphs/images/sphx_glr_plot_isomorphic_graphs_pytorch_003.png
diff --git a/...tching_isomorphic_graphs/images/sphx_glr_plot_isomorphic_graphs_pytorch_004.png b/...tching_isomorphic_graphs/images/sphx_glr_plot_isomorphic_graphs_pytorch_004.png
diff --git a/...tching_isomorphic_graphs/images/sphx_glr_plot_isomorphic_graphs_pytorch_005.png b/...tching_isomorphic_graphs/images/sphx_glr_plot_isomorphic_graphs_pytorch_005.png
diff --git a/...tching_isomorphic_graphs/images/sphx_glr_plot_isomorphic_graphs_pytorch_006.png b/...tching_isomorphic_graphs/images/sphx_glr_plot_isomorphic_graphs_pytorch_006.png
diff --git a/...tching_isomorphic_graphs/images/sphx_glr_plot_isomorphic_graphs_pytorch_007.png b/...tching_isomorphic_graphs/images/sphx_glr_plot_isomorphic_graphs_pytorch_007.png
diff --git a/...tching_isomorphic_graphs/images/sphx_glr_plot_isomorphic_graphs_pytorch_008.png b/...tching_isomorphic_graphs/images/sphx_glr_plot_isomorphic_graphs_pytorch_008.png
diff --git a/...tching_isomorphic_graphs/images/sphx_glr_plot_isomorphic_graphs_pytorch_009.png b/...tching_isomorphic_graphs/images/sphx_glr_plot_isomorphic_graphs_pytorch_009.png
diff --git a/...isomorphic_graphs/images/thumb/sphx_glr_plot_isomorphic_graphs_jittor_thumb.png b/...isomorphic_graphs/images/thumb/sphx_glr_plot_isomorphic_graphs_jittor_thumb.png
diff --git a/..._isomorphic_graphs/images/thumb/sphx_glr_plot_isomorphic_graphs_numpy_thumb.png b/..._isomorphic_graphs/images/thumb/sphx_glr_plot_isomorphic_graphs_numpy_thumb.png
diff --git a/...isomorphic_graphs/images/thumb/sphx_glr_plot_isomorphic_graphs_paddle_thumb.png b/...isomorphic_graphs/images/thumb/sphx_glr_plot_isomorphic_graphs_paddle_thumb.png
diff --git a/...somorphic_graphs/images/thumb/sphx_glr_plot_isomorphic_graphs_pytorch_thumb.png b/...somorphic_graphs/images/thumb/sphx_glr_plot_isomorphic_graphs_pytorch_thumb.png
diff --git a/docs/auto_examples/1.matching_isomorphic_graphs/plot_isomorphic_graphs_jittor.ipynb b/docs/auto_examples/1.matching_isomorphic_graphs/plot_isomorphic_graphs_jittor.ipynb
@@ -1,16 +1,5 @@
 {
   "cells": [
-    {
-      "cell_type": "code",
-      "execution_count": null,
-      "metadata": {
-        "collapsed": false
-      },
-      "outputs": [],
-      "source": [
-        "%matplotlib inline"
-      ]
-    },
     {
       "cell_type": "markdown",
       "metadata": {},
@@ -44,7 +33,7 @@
       },
       "outputs": [],
       "source": [
-        "import jittor as jt # jittor backend\nimport pygmtools as pygm\nimport matplotlib.pyplot as plt # for plotting\nfrom matplotlib.patches import ConnectionPatch # for plotting matching result\nimport networkx as nx # for plotting graphs\npygm.BACKEND = 'jittor' # set default backend for pygmtools\n_ = jt.set_seed(1) # fix random seed\n\njt.flags.use_cuda = jt.has_cuda"
+        "import jittor as jt # jittor backend\nimport pygmtools as pygm\nimport matplotlib.pyplot as plt # for plotting\nfrom matplotlib.patches import ConnectionPatch # for plotting matching result\nimport networkx as nx # for plotting graphs\npygm.set_backend('jittor') # set default backend for pygmtools\n_ = jt.set_seed(1) # fix random seed"
       ]
     },
     {
@@ -352,7 +341,7 @@
       "name": "python",
       "nbconvert_exporter": "python",
       "pygments_lexer": "ipython3",
-      "version": "3.8.3"
+      "version": "3.10.13"
     }
   },
   "nbformat": 4,

diff --git a/docs/auto_examples/1.matching_isomorphic_graphs/plot_isomorphic_graphs_jittor.py b/docs/auto_examples/1.matching_isomorphic_graphs/plot_isomorphic_graphs_jittor.py
@@ -31,11 +31,9 @@
 import matplotlib.pyplot as plt # for plotting
 from matplotlib.patches import ConnectionPatch # for plotting matching result
 import networkx as nx # for plotting graphs
-pygm.BACKEND = 'jittor' # set default backend for pygmtools
+pygm.set_backend('jittor') # set default backend for pygmtools
 _ = jt.set_seed(1) # fix random seed
 
-jt.flags.use_cuda = jt.has_cuda
-
 ##############################################################################
 # Generate two isomorphic graphs
 # ------------------------------------

diff --git a/docs/auto_examples/1.matching_isomorphic_graphs/plot_isomorphic_graphs_jittor.py.md5 b/docs/auto_examples/1.matching_isomorphic_graphs/plot_isomorphic_graphs_jittor.py.md5
@@ -1 +1 @@
-2f0f2c7c1ef1f5fe8b1c9e88301ef680
+15ad629c0cbb43ce3f92bbbb2c5ef270