Merge with private

.clang-format

@@ -0,0 +1,88 @@
+---
+AccessModifierOffset: -1
+AlignAfterOpenBracket: AlwaysBreak
+AlignConsecutiveAssignments: false
+AlignConsecutiveDeclarations: false
+AlignEscapedNewlinesLeft: true
+AlignOperands:   false
+AlignTrailingComments: false
+AllowAllParametersOfDeclarationOnNextLine: false
+AllowShortBlocksOnASingleLine: false
+AllowShortCaseLabelsOnASingleLine: false
+AllowShortFunctionsOnASingleLine: Empty
+AllowShortIfStatementsOnASingleLine: false
+AllowShortLoopsOnASingleLine: false
+AlwaysBreakAfterReturnType: None
+AlwaysBreakBeforeMultilineStrings: true
+AlwaysBreakTemplateDeclarations: true
+BinPackArguments: false
+BinPackParameters: false
+BraceWrapping:
+  AfterClass:      false
+  AfterControlStatement: false
+  AfterEnum:       false
+  AfterFunction:   false
+  AfterNamespace:  false
+  AfterObjCDeclaration: false
+  AfterStruct:     false
+  AfterUnion:      false
+  BeforeCatch:     false
+  BeforeElse:      false
+  IndentBraces:    false
+BreakBeforeBinaryOperators: None
+BreakBeforeBraces: Attach
+BreakBeforeTernaryOperators: true
+BreakConstructorInitializersBeforeComma: false
+BreakAfterJavaFieldAnnotations: false
+BreakStringLiterals: false
+ColumnLimit:     120
+CommentPragmas:  '^ IWYU pragma:'
+CompactNamespaces: false
+ConstructorInitializerAllOnOneLineOrOnePerLine: true
+ConstructorInitializerIndentWidth: 4
+ContinuationIndentWidth: 4
+Cpp11BracedListStyle: true
+DerivePointerAlignment: false
+DisableFormat:   false
+ForEachMacros:   [ FOR_EACH_RANGE, FOR_EACH, ]
+IncludeCategories:
+  - Regex:           '^<.*\.h(pp)?>'
+    Priority:        1
+  - Regex:           '^<.*'
+    Priority:        2
+  - Regex:           '.*'
+    Priority:        3
+IndentCaseLabels: true
+IndentWidth:     2
+IndentWrappedFunctionNames: false
+KeepEmptyLinesAtTheStartOfBlocks: false
+MacroBlockBegin: ''
+MacroBlockEnd:   ''
+MaxEmptyLinesToKeep: 1
+NamespaceIndentation: None
+ObjCBlockIndentWidth: 2
+ObjCSpaceAfterProperty: false
+ObjCSpaceBeforeProtocolList: false
+PenaltyBreakBeforeFirstCallParameter: 1
+PenaltyBreakComment: 300
+PenaltyBreakFirstLessLess: 120
+PenaltyBreakString: 1000
+PenaltyExcessCharacter: 1000000
+PenaltyReturnTypeOnItsOwnLine: 2000000
+PointerAlignment: Left
+ReflowComments:  true
+SortIncludes:    true
+SpaceAfterCStyleCast: false
+SpaceBeforeAssignmentOperators: true
+SpaceBeforeParens: ControlStatements
+SpaceInEmptyParentheses: false
+SpacesBeforeTrailingComments: 1
+SpacesInAngles:  false
+SpacesInContainerLiterals: true
+SpacesInCStyleCastParentheses: false
+SpacesInParentheses: false
+SpacesInSquareBrackets: false
+Standard:        Cpp11
+TabWidth:        8
+UseTab:          Never
+...

.github/workflows/clang-format.yml

@@ -0,0 +1,26 @@
+name: clang-format
+
+on:
+  pull_request:
+  push:
+    branches:
+      - master
+  schedule:
+    - cron: '0 0 * * *'
+
+jobs:
+  clang-format:
+
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v1
+    - name: Lint with clang-format
+      run: |
+        find -name '*.cpp' -o -name '*.h' -o -name '*.cu' -o -name '*.cuh' | xargs clang-format -i
+        GIT_DIFF=$(git diff)
+        if [[ -z $GIT_DIFF ]]; then
+            exit 0
+        fi
+        echo $GIT_DIFF
+        exit 1

.github/workflows/cuda.yml

@@ -0,0 +1,41 @@
+name: cuda
+
+on:
+  pull_request:
+  push:
+    branches:
+      - master
+    paths:
+      - 'setup.py'
+      - 'torchani/cuaev/**'
+      - 'torchani/aev.py'
+      - 'ci/**'
+      - 'test/test_cuaev.py'
+  schedule:
+    - cron: '0 0 * * *'
+
+jobs:
+  cuda:
+
+    runs-on: ubuntu-latest
+    strategy:
+      max-parallel: 4
+      matrix:
+        python-version: [3.8]
+
+    steps:
+    - uses: actions/checkout@v1
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v1
+      with:
+        python-version: ${{ matrix.python-version }}
+    - name: Fetch submodules
+      run: git submodule update --init
+    - name: Install cuda
+      run: ci/install_cuda.sh
+    - name: Install dependencies
+      run: ci/install_dependencies.sh
+    - name: Install TorchANI
+      run: python setup.py install --cuaev
+    - name: Run cuaev test
+      run: pytest tests/test_cuaev.py -v

.github/workflows/deploy-docs.yml

@@ -5,7 +5,7 @@ on:
     types: [published]
 
 jobs:
-  build:
+  deploy-docs:
 
     runs-on: ubuntu-latest
     strategy:
@@ -20,10 +20,9 @@ jobs:
       with:
         python-version: ${{ matrix.python-version }}
     - name: Install dependencies
-      run: |
-        ci/install_dependencies.sh
-        pip install h5py tb-nightly sphinx sphinx_rtd_theme matplotlib pillow sphinx-gallery
-        pip install .
+      run: ci/install_dependencies.sh
+    - name: Install TorchANI
+      run: python setup.py install
     - name: Download data files
       run: ./download.sh
     # double check that this is indeed run under a release

.github/workflows/deploy-pypi.yml

@@ -5,7 +5,7 @@ on:
     types: [published]
 
 jobs:
-  build:
+  deploy-pypi:
 
     runs-on: ubuntu-latest
     strategy:
@@ -22,9 +22,7 @@ jobs:
     - name: Fail build on non-release commits
       run: git describe --exact-match --tags HEAD
     - name: Install dependencies
-      run: |
-        python -m pip install --upgrade pip
-        pip install twine wheel
+      run: ci/install_dependencies.sh
     - name: Deploy
       run: |
         rm -rf dist/*

.github/workflows/deploy-test-pypi.yml

@@ -9,7 +9,8 @@ on:
     - cron: '0 0 * * *'
 
 jobs:
-  deploy-test:
+  deploy-test-pypi:
+
 
     runs-on: ubuntu-latest
     strategy:
@@ -24,9 +25,7 @@ jobs:
       with:
         python-version: ${{ matrix.python-version }}
     - name: Install dependencies
-      run: |
-        python -m pip install --upgrade pip
-        pip install twine wheel
+      run: ci/install_dependencies.sh
     - name: Deploy
       run: |
         rm -rf dist/*

.github/workflows/docs.yml

@@ -9,13 +9,14 @@ on:
     - cron: '0 0 * * *'
 
 jobs:
-  build:
+  docs:
 
     runs-on: ubuntu-latest
     strategy:
       max-parallel: 4
       matrix:
-        python-version: [3.6, 3.8]
+        python-version: [3.8]
+        tag: ["build", "push"]
 
     steps:
     - uses: actions/checkout@v1
@@ -24,10 +25,9 @@ jobs:
       with:
         python-version: ${{ matrix.python-version }}
     - name: Install dependencies
-      run: |
-        ci/install_dependencies.sh
-        pip install h5py tb-nightly sphinx sphinx_rtd_theme matplotlib pillow sphinx-gallery
-        pip install .
+      run: ci/install_dependencies.sh
+    - name: Install TorchANI
+      run: python setup.py install
     - name: Download data files
       run: ./download.sh
     # build docs
@@ -45,13 +45,12 @@ jobs:
         git config --global user.name "zasdfgbnm-bot"
     - name: Deploy
       run: |
-        [ ! -z "$GITHUB_HEAD_REF" ] && exit
+        [ ${{ matrix.tag }} == "push" ] || exit 0  # exit when build
         git clone git@github.com:aiqm/torchani-test-docs.git deploy_dir -b gh-pages
         rm -rf deploy_dir/*
         touch deploy_dir/.nojekyll
         cp -r build/* deploy_dir
         cd deploy_dir
         git add .
         git commit -m "update"
-        sh -c 'git push --force || true'
-
+        git push --force

.github/workflows/flake8.yml

@@ -9,7 +9,7 @@ on:
     - cron: '0 0 * * *'
 
 jobs:
-  build:
+  flake8:
 
     runs-on: ubuntu-latest
     strategy:
@@ -25,9 +25,7 @@ jobs:
         python-version: ${{ matrix.python-version }}
     - name: Install dependencies
       run: |
-        python -m pip install --upgrade pip
-        pip install .
-    - name: Lint with flake8
-      run: |
+        pip install --upgrade pip
         pip install flake8
-        flake8 .
+    - name: Lint with flake8
+      run: flake8 .

.github/workflows/mypy.yml

@@ -9,7 +9,7 @@ on:
     - cron: '0 0 * * *'
 
 jobs:
-  build:
+  mypy:
 
     runs-on: ubuntu-latest
     strategy:
@@ -23,8 +23,9 @@ jobs:
       uses: actions/setup-python@v1
       with:
         python-version: ${{ matrix.python-version }}
-    - name: Type checking with mypy
+    - name: Install dependencies
       run: |
         pip install --upgrade pip
         pip install mypy
-        mypy --no-site-packages --ignore-missing-imports torchani/{aev,nn,utils,models,ase}.py
+    - name: Type checking with mypy
+      run: mypy --ignore-missing-imports .

.github/workflows/runnable_submodules.yml

@@ -1,4 +1,4 @@
-name: runnable submodules
+name: runnable-submodules
 
 on:
   pull_request:
@@ -9,7 +9,7 @@ on:
     - cron: '0 0 * * *'
 
 jobs:
-  build:
+  runnable-submodules:
 
     runs-on: ubuntu-latest
     strategy:
@@ -24,10 +24,9 @@ jobs:
       with:
         python-version: ${{ matrix.python-version }}
     - name: Install dependencies
-      run: |
-        ci/install_dependencies.sh
-        pip install h5py .
-        pip install .
+      run: ci/install_dependencies.sh
+    - name: Install TorchANI
+      run: python setup.py install
     - name: Download data files
       run: ./download.sh
     - name: Run submodules

.github/workflows/stable-torch.yml

@@ -1,14 +1,15 @@
 name: stable-torch
 
 on:
+  pull_request:
   push:
     branches:
       - master
   schedule:
     - cron: '0 0 * * *'
 
 jobs:
-  build:
+  stable-torch:
 
     runs-on: ubuntu-latest
     strategy:
@@ -25,11 +26,9 @@ jobs:
     - name: Fetch submodules
       run: git submodule update --init
     - name: Install dependencies
-      run: |
-        pip install --upgrade pip
-        pip install torch pytest
-        pip install -r test_requirements.txt
-        pip install .
+      run: ci/install_dependencies.sh
+    - name: Install TorchANI
+      run: python setup.py install
     - name: Download data files
       run: ./download.sh
     - name: Run tests