merge master

.github/workflows/build_cc.yml

@@ -0,0 +1,25 @@
+on:
+  push:
+  pull_request:
+name: Build C++
+jobs:
+  testpython:
+    name: Build C++
+    runs-on: ubuntu-20.04
+    strategy:  
+      matrix:
+        include:
+        - variant: cpu
+        - variant: cuda
+    steps:
+    - uses: actions/checkout@master
+      with:
+        submodules: true
+    - run: sudo apt update && sudo apt install g++-7
+    - run: sudo apt install nvidia-cuda-toolkit
+      if: matrix.variant == 'cuda'
+    - run: source/install/build_cc.sh
+      env:
+        DP_VARIANT: ${{ matrix.variant }}
+        CC: gcc-7
+        CXX: g++-7

.github/workflows/build_wheel.yml

@@ -0,0 +1,68 @@
+name: Build and upload to PyPI
+
+on:
+  push:
+  pull_request:
+
+jobs:
+  build_wheels:
+    name: Build wheels on ${{ matrix.os }}
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        os: [ubuntu-18.04]  #, windows-latest, macos-latest]
+
+    steps:
+      - uses: actions/checkout@v2
+      - uses: actions/setup-python@v2
+        name: Install Python
+        with:
+          python-version: '3.8'
+
+      - name: Install cibuildwheel
+        run: |
+          python -m pip install cibuildwheel
+
+      - name: Build wheels
+        env:
+          CIBW_BUILD: "cp36-* cp37-* cp38-* cp39-*"
+          CIBW_MANYLINUX_X86_64_IMAGE: ghcr.io/deepmodeling/manylinux2010_x86_64_tensorflow
+          CIBW_BEFORE_BUILD: pip install tensorflow
+          CIBW_SKIP: "*-win32 *-manylinux_i686"
+        run: |
+          python -m cibuildwheel --output-dir wheelhouse
+      - uses: actions/upload-artifact@v2
+        with:
+          path: ./wheelhouse/*.whl
+
+  build_sdist:
+    name: Build source distribution
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v2
+      - uses: actions/setup-python@v2
+        name: Install Python
+        with:
+          python-version: '3.8'
+      - run: pip install -U scikit-build tensorflow setuptools_scm
+      - name: Build sdist
+        run: python setup.py sdist
+
+      - uses: actions/upload-artifact@v2
+        with:
+          path: dist/*.tar.gz
+
+  upload_pypi:
+    needs: [build_wheels, build_sdist]
+    runs-on: ubuntu-latest
+    if: startsWith(github.event.ref, 'refs/tags/v')
+    steps:
+      - uses: actions/download-artifact@v2
+        with:
+          name: artifact
+          path: dist
+
+      - uses: pypa/gh-action-pypi-publish@master
+        with:
+          user: __token__
+          password: ${{ secrets.pypi_password }}

.github/workflows/lint_python.yml

@@ -0,0 +1,33 @@
+on:
+  push:
+  pull_request:
+name: Lint Python
+jobs:
+  lintpython:
+    name: Lint Python
+    runs-on: ubuntu-20.04
+    strategy:
+      matrix:
+        python-version: [3.8]
+
+    steps:
+    - uses: actions/checkout@v1
+    - uses: actions/setup-python@v2
+      with:
+        python-version: ${{ matrix.python }}
+    - name: Install requirements
+      run: pip install -r requirements.txt
+    - uses: marian-code/python-lint-annotate@v2.5.0
+      with:
+        python-root-list: "./deepmd/*.py ./deepmd/*/*.py ./source/train/*.py ./source/tests/*.py ./source/op/*.py"
+        use-black: true
+        use-isort: true
+        use-mypy: true
+        use-pycodestyle: true
+        use-pydocstyle: true
+        extra-pycodestyle-options: "--max-line-length=88"
+        use-pylint: false
+        use-flake8: false
+        use-vulture: true
+        conda-python-version: "3.8"
+

.github/workflows/mirror_gitee.yml

@@ -0,0 +1,18 @@
+name: Mirror to Gitee Repo
+
+on: [ push, delete, create ]
+
+# Ensures that only one mirror task will run at a time.
+concurrency:
+  group: git-mirror
+
+jobs:
+  git-mirror:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: wearerequired/git-mirror-action@v1
+        env:
+          SSH_PRIVATE_KEY: ${{ secrets.SYNC_GITEE_PRIVATE_KEY }}
+        with:
+          source-repo: "git@github.com:deepmodeling/deepmd-kit.git"
+          destination-repo: "git@gitee.com:deepmodeling/deepmd-kit.git"

.github/workflows/test_cc.yml

@@ -0,0 +1,11 @@
+on:
+  push:
+  pull_request:
+name: Test C++
+jobs:
+  testpython:
+    name: Test C++
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@master
+    - run: source/install/test_cc.sh

.github/workflows/test_python.yml

@@ -0,0 +1,79 @@
+on:
+  push:
+  pull_request:
+name: Test Python
+jobs:
+  testpython:
+    name: Test Python
+    runs-on: ubuntu-18.04
+    strategy:  
+      matrix:
+        include:
+          - python: 3.6
+            gcc: 4.8
+            tf: 1.8
+          - python: 3.6
+            gcc: 4.8
+            tf: 1.12
+          - python: 3.6
+            gcc: 4.8
+            tf: 1.14
+          - python: 3.6
+            gcc: 5
+            tf: 1.14
+          - python: 3.6
+            gcc: 8
+            tf: 1.14
+          - python: 3.7
+            gcc: 5
+            tf: 1.14
+          - python: 3.7
+            gcc: 6
+            tf: 1.14
+          - python: 3.7
+            gcc: 7
+            tf: 1.14
+          - python: 3.7
+            gcc: 8
+            tf: 1.14
+          - python: 3.7
+            gcc: 5
+            tf:
+          - python: 3.7
+            gcc: 8
+            tf:
+          - python: 3.8
+            gcc: 5
+            tf:
+          - python: 3.8
+            gcc: 8
+            tf:
+
+    steps:
+    - uses: actions/checkout@master
+    - uses: actions/setup-python@v2
+      with:
+        python-version: ${{ matrix.python }}
+    - name: pip cache
+      uses: actions/cache@v2
+      with:
+        path: ~/.cache/pip
+        key:
+          ${{ runner.os }}-pip-${{ hashFiles('**/setup.py') }}-${{ hashFiles('**/requirements.txt') }}
+        restore-keys: |
+          ${{ runner.os }}-pip-
+    - run: |
+        sudo apt update
+        sudo apt install gcc-${{ matrix.gcc }} g++-${{ matrix.gcc }}
+    - run: pip install -e .[cpu,test] codecov
+      env:
+        CC: gcc-${{ matrix.gcc }}
+        CXX: g++-${{ matrix.gcc }}
+        TENSORFLOW_VERSION: ${{ matrix.tf }}
+    - run: dp --version
+    - name: Prepare parallel runtime
+      if: ${{ matrix.tf == '' }}
+      run: |
+        sudo apt install libopenmpi-dev openmpi-bin
+        HOROVOD_WITHOUT_GLOO=1 HOROVOD_WITH_TENSORFLOW=1 pip install horovod mpi4py
+    - run: pytest --cov=deepmd source/tests && codecov

.gitignore

@@ -26,3 +26,9 @@ venv*
 .vscode/**
 _build
 _templates
+API_CC
+doc/api_py/
+dp/
+build_lammps/
+build_tests/
+build_cc_tests

.gitmodules

@@ -1,3 +1,3 @@
-[submodule "source/op/cuda/cub"]
-	path = source/op/cuda/cub
-	url = git://github.com/NVlabs/cub.git
+[submodule "source/lib/src/cuda/cub"]
+	path = source/lib/src/cuda/cub
+	url = git://github.com/NVIDIA/cub.git

CITATION.cff

@@ -0,0 +1,19 @@
+preferred-citation:
+  type: article
+  authors:
+  - family-names: "Wang"
+    given-names: "Han"
+  - family-names: "Zhang"
+    given-names: "Linfeng"
+  - family-names: "Han"
+    given-names: "Jiequn"
+  - family-names: "E"
+    given-names: "Weinan"
+  doi: "10.1016/j.cpc.2018.03.016"
+  journal: "Computer Physics Communications"
+  month: 7
+  start: 178 # First page number
+  end: 184 # Last page number
+  title: "DeePMD-kit: A deep learning package for many-body potential energy representation and molecular dynamics"
+  volume: 228
+  year: 2018