Use conda-incubator/setup-miniconda to setup GH actions

.github/workflows/pythonpackage.yml

@@ -13,32 +13,31 @@ jobs:
         python-version: [3.6, 3.7, 3.8]
 
     steps:
-    - uses: actions/checkout@v1
-    - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v1
+    - uses: actions/checkout@v2
+
+    - uses: conda-incubator/setup-miniconda@v2
       with:
+        auto-update-conda: true
         python-version: ${{ matrix.python-version }}
-    - name: Include $CONDA in $PATH
-      run: echo ::add-path::$CONDA/bin
+
     - name: Install dependencies
+      shell: bash -l {0}
       run: |
+        conda env update --file environment.yml
         python -m pip install --upgrade pip
+        pip install flake8 pytest
         pip install -e .
-        conda install pytorch==1.6.0 torchvision cpuonly -c pytorch
-        conda install dgl==0.5.0 -c dglteam
-        conda install pymatgen==2020.8.13 -c conda-forge
-        conda install rdkit==2020.03.5 -c conda-forge
-        conda install openbabel==3.1.1 -c conda-forge
+
     - name: Lint with flake8
+      shell: bash -l {0}
       run: |
-        pip install flake8
         # stop the build if there are Python syntax errors or undefined names
         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
+      shell: bash -l {0}
       run: |
-        pip install pytest
         # ignore tests in "tests/prediction/". They need the pre-trained
         # models, but these are stored as LFS on GitHub and Action cannot get
         # access to it.

binder/environment.yml

@@ -1,14 +1,12 @@
-name: bondnet
 channels:
-  - conda-forge
   - pytorch
   - dglteam
+  - conda-forge
   - defaults
 dependencies:
   - pip
   - pymatgen==2020.8.13
   - rdkit==2020.03.5
   - openbabel==3.1.1
   - pytorch==1.6.0
-  - torchvision
-  - dgl==0.5.0
+  - dgl==0.5.2