Merge pull request #14 from twitter-research/BC/repo_badge

Bc/repo badge

.github/workflows/python-package.yml

@@ -0,0 +1,67 @@
+name: Build and Test
+
+on:
+  pull_request:
+    branches:
+      - main
+  push:
+    branches:
+      - main
+  schedule:
+    # Run the tests at 00:00 each day
+    - cron: "0 0 * * *"
+
+jobs:
+  build:
+
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: [3.8]
+    defaults:
+      run:
+        shell: bash -l {0}
+
+    steps:
+      - uses: actions/checkout@v2
+      - name: cache conda
+        uses: actions/cache@v2
+        env:
+          # Increase this value to reset cache if etc/example-environment.yml has not changed
+          CACHE_NUMBER: 0
+        with:
+          path: ~/conda_pkgs_dir
+          key:
+            ${{ runner.os }}-conda-${{ env.CACHE_NUMBER }}-${{
+            hashFiles('requirements.txt') }}
+      - uses: conda-incubator/setup-miniconda@v2
+        with:
+          activate-environment: test
+          python-version: 3.8
+          use-only-tar-bz2: true # IMPORTANT: This needs to be set for caching to work properly!
+      - name: Set up env
+        run: |
+          conda activate test
+          conda install pip
+      - name: Cache pip
+        uses: actions/cache@v2
+        with:
+          # This path is specific to Ubuntu
+          path: ~/.cache/pip
+          # Look to see if there is a cache hit for the corresponding requirements file
+          key: ${{ runner.os }}-pip-${{ hashFiles('requirements.txt') }}
+          restore-keys: |
+            ${{ runner.os }}-pip-
+            ${{ runner.os }}-
+      - name: pytorch
+        run: |
+          conda install -y pytorch=1.7.1 torchvision cudatoolkit=10.2 -c pytorch --update-deps
+      - name: Install pyG
+        run: |
+          ./pyG_install.sh cu102
+      - name: Install dependencies
+        run: |
+          pip install -r requirements.txt
+      - name: Test with pytest
+        run: |
+          pytest -v

README.md

@@ -1,3 +1,5 @@
+![example workflow](https://github.com/twitter-research/graph-neural-pde/actions/workflows/python-package.yml/badge.svg)
+
 ![Cora_animation_16](https://user-images.githubusercontent.com/5874124/143270624-265c2d01-39ca-488c-b118-b68f876dfbfa.gif)
 
 ## Introduction

pyG_install.sh

@@ -0,0 +1,8 @@
+#!/usr/bin/env bash
+TORCH=1.7.1
+CUDA=$1  # Supply as command line cpu or cu102
+pip install torch-scatter==2.0.5 -f https://pytorch-geometric.com/whl/torch-${TORCH}+${CUDA}.html
+pip install torch-sparse==0.6.8 -f https://pytorch-geometric.com/whl/torch-${TORCH}+${CUDA}.html
+pip install torch-cluster==1.5.8 -f https://pytorch-geometric.com/whl/torch-${TORCH}+${CUDA}.html
+pip install torch-spline-conv==1.2.0 -f https://pytorch-geometric.com/whl/torch-${TORCH}+${CUDA}.html
+pip install torch-geometric==1.6.3

requirements.txt

@@ -1,211 +1,31 @@
 # This file may be used to create an environment using:
 # $ conda create --name <env> --file <this file>
 # platform: osx-64
-absl-py=0.9.0=pypi_0
-aiohttp=3.7.2=pypi_0
-aiohttp-cors=0.7.0=pypi_0
-aioredis=1.3.1=pypi_0
-appnope=0.1.0=py38_1001
-argon2-cffi=20.1.0=py38haf1e3a3_1
-ase=3.20.1=pypi_0
-async-timeout=3.0.1=pypi_0
-async_generator=1.10=py_0
-attrs=20.2.0=py_0
-ax-platform=0.1.18=pypi_0
-backcall=0.2.0=py_0
-beautifulsoup4=4.9.3=pypi_0
-blas=1.0=mkl
-bleach=3.2.1=py_0
-blessings=1.7=pypi_0
-boltons=20.2.1=pypi_0
-botorch=0.3.2=pypi_0
-ca-certificates=2020.10.14=0
-cachetools=4.1.0=pypi_0
-certifi=2020.6.20=pyhd3eb1b0_3
-cffi=1.14.3=py38hed5b41f_0
-chardet=3.0.4=pypi_0
-click=7.1.2=pypi_0
-colorama=0.4.4=pypi_0
-colorful=0.5.4=pypi_0
-cycler=0.10.0=py38_0
-dbus=1.13.18=h18a8e69_0
-decorator=4.4.2=pypi_0
-defusedxml=0.6.0=py_0
-dgl=0.4.3.post2=pypi_0
-entrypoints=0.3=py38_0
-et-xmlfile=1.0.1=pypi_0
-expat=2.2.10=hb1e8313_2
-filelock=3.0.12=pypi_0
-freetype=2.10.2=ha233b18_0
-future=0.18.2=pypi_0
-gettext=0.19.8.1=hb0f4f8b_2
-glib=2.66.1=h9bbe63b_0
-google=3.0.0=pypi_0
-google-api-core=1.23.0=pypi_0
-google-auth=1.23.0=pypi_0
-google-auth-oauthlib=0.4.1=pypi_0
-googleapis-common-protos=1.52.0=pypi_0
-googledrivedownloader=0.4=pypi_0
-gpustat=0.6.0=pypi_0
-gputil=1.4.0=pypi_0
-gpytorch=1.2.1=pypi_0
-grpcio=1.30.0=pypi_0
-h5py=2.10.0=pypi_0
-hiredis=1.1.0=pypi_0
-icu=58.2=h0a44026_3
-idna=2.10=pypi_0
-importlib-metadata=2.0.0=py_1
-importlib_metadata=2.0.0=1
-iniconfig=1.1.1=py_0
-intel-openmp=2019.4=233
-ipykernel=5.3.4=py38h5ca1d4c_0
-ipython=7.18.1=py38h5ca1d4c_0
-ipython_genutils=0.2.0=py38_0
-ipywidgets=7.5.1=py_1
-isodate=0.6.0=pypi_0
-jdcal=1.4.1=pypi_0
-jedi=0.17.2=py38_0
-jinja2=2.11.2=py_0
-joblib=0.15.1=py_0
-jpeg=9b=he5867d9_2
-jsonschema=3.2.0=py_2
-jupyter=1.0.0=py38_7
-jupyter_client=6.1.7=py_0
-jupyter_console=6.2.0=py_0
-jupyter_core=4.6.3=py38_0
-jupyterlab_pygments=0.1.2=py_0
-kiwisolver=1.2.0=py38h04f5b5a_0
-libcxx=10.0.0=1
-libedit=3.1.20191231=haf1e3a3_0
-libffi=3.3=h0a44026_1
-libgfortran=3.0.1=h93005f0_2
-libiconv=1.16=h1de35cc_0
-libpng=1.6.37=ha441bb4_0
-libprotobuf=3.13.0.1=hab81aa3_0
-libsodium=1.0.18=h1de35cc_0
-libtiff=4.1.0=hcb84e12_1
-littleutils=0.2.2=pypi_0
-llvm-openmp=10.0.0=h28b9765_0
-llvmlite=0.34.0=pypi_0
-lz4-c=1.9.2=h0a44026_0
-markdown=3.2.2=pypi_0
-markupsafe=1.1.1=py38h1de35cc_1
-matplotlib=3.2.2=0
-matplotlib-base=3.2.2=py38h5670ca0_0
-mistune=0.8.4=py38h1de35cc_1001
-mkl=2019.4=233
-mkl-service=2.3.0=py38hfbe908c_0
-mkl_fft=1.1.0=py38hc64f4ea_0
-mkl_random=1.1.1=py38h959d312_0
-more-itertools=8.5.0=py_0
-msgpack=1.0.0=pypi_0
-multidict=5.0.0=pypi_0
-nbclient=0.5.1=py_0
-nbconvert=6.0.7=py38_0
-nbformat=5.0.8=py_0
-ncurses=6.2=h0a44026_1
-nest-asyncio=1.4.1=py_0
-networkx=2.4=pypi_0
-ninja=1.9.0=py38h04f5b5a_0
-notebook=6.1.4=py38_0
-numba=0.51.2=pypi_0
-numpy=1.19.3=pypi_0
-numpy-base=1.18.5=py38h3304bdc_0
-nvidia-ml-py3=7.352.0=pypi_0
-oauthlib=3.1.0=pypi_0
-ogb=1.2.4=pypi_0
-olefile=0.46=py_0
-opencensus=0.7.11=pypi_0
-opencensus-context=0.1.2=pypi_0
-openpyxl=3.0.5=pypi_0
-openssl=1.1.1h=haf1e3a3_0
-outdated=0.2.0=pypi_0
-packaging=20.4=py_0
-pandas=1.0.5=py38h959d312_0
-pandoc=2.11=h0dc7051_0
-pandocfilters=1.4.2=py38_1
-parso=0.7.0=py_0
-pcre=8.44=hb1e8313_0
-pexpect=4.8.0=py38_1
-pickleshare=0.7.5=py38_1001
-pillow=7.1.2=py38h4655f20_0
-pip=20.1.1=py38_1
-plotly=4.12.0=pypi_0
-pluggy=0.13.1=py38_0
-prometheus_client=0.8.0=py_0
-prompt-toolkit=3.0.8=py_0
-prompt_toolkit=3.0.8=0
-protobuf=3.12.2=pypi_0
-psutil=5.7.3=pypi_0
-ptyprocess=0.6.0=py38_0
-py=1.9.0=py_0
-py-spy=0.3.3=pypi_0
-pyasn1=0.4.8=pypi_0
-pyasn1-modules=0.2.8=pypi_0
-pycparser=2.20=py_2
-pygments=2.7.2=pyhd3eb1b0_0
-pykeops=1.4.1=pypi_0
-pyparsing=2.4.7=py_0
-pyqt=5.9.2=py38h655552a_2
-pyrsistent=0.17.3=py38haf1e3a3_0
-pytest=6.1.1=py38_0
-python=3.8.3=h26836e1_1
-python-dateutil=2.8.1=py_0
-pytorch-lightning=0.8.1=pypi_0
-pytz=2020.1=py_0
-pyzmq=19.0.2=py38hb1e8313_1
-qt=5.9.7=h468cd18_1
-qtconsole=4.7.7=py_0
-qtpy=1.9.0=py_0
-ray=1.0.0=pypi_0
-rdflib=5.0.0=pypi_0
-readline=8.0=h1de35cc_0
-redis=3.4.1=pypi_0
-requests=2.24.0=pypi_0
-requests-oauthlib=1.3.0=pypi_0
-retrying=1.3.3=pypi_0
-rsa=4.6=pypi_0
-scikit-learn=0.23.1=py38h603561c_0
-scipy=1.5.3=pypi_0
-send2trash=1.5.0=py38_0
-setuptools=47.3.1=py38_0
-sip=4.19.8=py38h0a44026_0
-six=1.15.0=py_0
-soupsieve=2.0.1=pypi_0
-sqlalchemy=1.3.20=pypi_0
-sqlite=3.32.3=hffcf06c_0
-tabulate=0.8.7=pypi_0
-tensorboard=2.2.2=pypi_0
-tensorboard-plugin-wit=1.7.0=pypi_0
-tensorboardx=2.1=pypi_0
-terminado=0.9.1=py38_0
-testpath=0.4.4=py_0
-threadpoolctl=2.1.0=pyh5ca1d4c_0
-tk=8.6.10=hb0a8c7a_0
-toml=0.10.1=py_0
-torch=1.6.0=pypi_0
-torch-geometric=1.6.1=pypi_0
-torch-scatter=2.0.5=pypi_0
-torch-sparse=0.6.7=pypi_0
-torchdiffeq=0.1.1=pypi_0
-torchsde=0.2.1=pypi_0
-torchsummary=1.5.1=pypi_0
-torchvision=0.7.0=pypi_0
-tornado=6.0.4=py38h1de35cc_1
-tqdm=4.46.1=pypi_0
-traitlets=5.0.5=py_0
-trampoline=0.1.2=pypi_0
-typeguard=2.10.0=pypi_0
-typing-extensions=3.7.4.3=pypi_0
-urllib3=1.25.9=pypi_0
-wcwidth=0.2.5=py_0
-webencodings=0.5.1=py38_1
-werkzeug=1.0.1=pypi_0
-wheel=0.34.2=py38_0
-widgetsnbextension=3.5.1=py38_0
-xz=5.2.5=h1de35cc_0
-yarl=1.6.2=pypi_0
-zeromq=4.3.3=hb1e8313_3
-zipp=3.4.0=pyhd3eb1b0_0
-zlib=1.2.11=h1de35cc_3
-zstd=1.4.4=h1990bb4_3
+h5py==2.10.0
+jupyter==1.0.0
+matplotlib==3.2.2
+networkx==2.4
+numba==0.51.2
+numpy==1.19.3
+ogb==1.2.4
+pandas==1.0.5
+pip==20.1.1
+pykeops==1.4.1
+pytest==6.1.1
+ray==1.0.0
+scikit-learn==0.23.1
+scipy==1.5.3
+six==1.15.0
+tqdm==4.46.1
+torchdiffeq==0.1.1
+tabulate==0.8.7
+
+# reliant on cuda version
+# torch==1.6.0=pypi_0
+# torch-geometric=1.6.1=pypi_0
+# torch-scatter=2.0.5=pypi_0
+# torch-sparse=0.6.7=pypi_0
+# torchdiffeq=0.1.1=pypi_0
+# torchsde=0.2.1=pypi_0
+# torchsummary=1.5.1=pypi_0
+# torchvision=0.7.0=pypi_0

test/test_ICML_gnn.py

@@ -3,17 +3,21 @@
 """
 Test attention
 """
+import os
+import sys
+sys.path.append(os.path.abspath(os.path.join(os.path.dirname(__file__), '..', 'src')))
+
 import unittest
 import torch
 from torch import tensor
 from torch import nn
-from CGNN import gcn_norm_fill_val, coo2tensor, train_ray
-from data import get_dataset
 from torch_geometric.nn.conv.gcn_conv import gcn_norm
 from torch_geometric.utils.convert import to_scipy_sparse_matrix
 from ray.tune.utils import diagnose_serialization
 from functools import partial
-import os
+
+from CGNN import gcn_norm_fill_val, coo2tensor, train_ray
+from data import get_dataset
 from test_params import OPT
 
 

test/test_attention.py

@@ -3,10 +3,16 @@
 """
 Test attention
 """
+# needed for CI/CD
+import os
+import sys
+sys.path.append(os.path.abspath(os.path.join(os.path.dirname(__file__), '..', 'src')))
+
 import unittest
 import torch
 from torch import tensor
 from torch import nn
+
 from function_GAT_attention import SpGraphAttentionLayer, ODEFuncAtt
 from torch_geometric.utils import softmax, to_dense_adj
 from data import get_dataset

test/test_attention_ode_block.py

@@ -1,10 +1,15 @@
 #!/usr/bin/env python
 # -*- coding: utf-8 -*-
+# needed for CI/CD
+import os
+import sys
+sys.path.append(os.path.abspath(os.path.join(os.path.dirname(__file__), '..', 'src')))
 
 import unittest
 import torch
 from torch import tensor
 from torch import nn
+
 from data import get_dataset
 from function_laplacian_diffusion import LaplacianODEFunc
 from GNN import GNN