Merge devel into master (#2559)

.github/workflows/build_cc.yml

@@ -6,7 +6,6 @@ jobs:
   buildcc:
     name: Build C++
     runs-on: ubuntu-latest
-    container: ghcr.io/deepmodeling/deepmd-kit-test-cc:latest
     strategy:
       matrix:
         include:
@@ -21,32 +20,31 @@ jobs:
         - variant: clang
           dp_variant: clang
     steps:
-    - name: work around permission issue
-      run: git config --global --add safe.directory /__w/deepmd-kit/deepmd-kit
     - uses: actions/checkout@v3
       with:
         submodules: true
-    - run: apt-get update && apt-get install -y nvidia-cuda-toolkit
+    - uses: actions/setup-python@v4
+      with:
+        python-version: '3.11'
+    - run: python -m pip install tensorflow
+    - run: sudo apt-get update && sudo apt-get install -y nvidia-cuda-toolkit
       if: matrix.variant == 'cuda'
     - run: |
-         apt-get update \
-         && apt-get -y install wget \
-         && wget https://developer.download.nvidia.com/compute/cuda/repos/ubuntu2204/x86_64/cuda-keyring_1.0-1_all.deb \
-         && dpkg -i cuda-keyring_1.0-1_all.deb \
-         && apt-get update \
-         && apt-get -y install cuda-12-0
+         wget https://developer.download.nvidia.com/compute/cuda/repos/ubuntu2204/x86_64/cuda-keyring_1.0-1_all.deb \
+         && sudo dpkg -i cuda-keyring_1.0-1_all.deb \
+         && sudo apt-get update \
+         && sudo apt-get -y install cuda-12-0
       if: matrix.variant == 'cuda120'
       env:
         DEBIAN_FRONTEND: noninteractive
     - run: |
-         apt-get update && apt-get install -y gnupg2 \
-         && echo 'deb [arch=amd64] https://repo.radeon.com/rocm/apt/5.3/ jammy main' | tee /etc/apt/sources.list.d/rocm.list \
-         && printf 'Package: *\nPin: release o=repo.radeon.com\nPin-Priority: 600' | tee /etc/apt/preferences.d/rocm-pin-600 \
-         && curl -s https://repo.radeon.com/rocm/rocm.gpg.key | apt-key add - \
-         && apt-get update \
-         && apt-get install -y rocm-dev hipcub-dev
+         echo 'deb [arch=amd64] https://repo.radeon.com/rocm/apt/5.3/ jammy main' | sudo tee /etc/apt/sources.list.d/rocm.list \
+         && printf 'Package: *\nPin: release o=repo.radeon.com\nPin-Priority: 600' | sudo tee /etc/apt/preferences.d/rocm-pin-600 \
+         && curl -s https://repo.radeon.com/rocm/rocm.gpg.key | sudo apt-key add - \
+         && sudo apt-get update \
+         && sudo apt-get install -y rocm-dev hipcub-dev
       if: matrix.variant == 'rocm'
-    - run: apt-get update && apt-get install -y clang
+    - run: sudo apt-get update && sudo apt-get install -y clang
       if: matrix.variant == 'clang'
     - run: source/install/build_cc.sh
       env:

.github/workflows/build_wheel.yml

@@ -14,17 +14,17 @@ jobs:
         include:
           # linux-64
           - os: ubuntu-latest
-            python: 310
+            python: 311
             platform_id: manylinux_x86_64
             dp_variant: cuda
           # macos-x86-64
           - os: macos-latest
-            python: 310
+            python: 311
             platform_id: macosx_x86_64
             dp_variant: cpu
           # win-64
           - os: windows-2019
-            python: 310
+            python: 311
             platform_id: win_amd64
             dp_variant: cpu
           # linux-aarch64
@@ -42,7 +42,7 @@ jobs:
         name: Setup QEMU
         if: matrix.platform_id == 'manylinux_aarch64'
       - name: Build wheels
-        uses: pypa/cibuildwheel@v2.12.1
+        uses: pypa/cibuildwheel@v2.12.3
         env:
           CIBW_BUILD_VERBOSITY: 1
           CIBW_ARCHS: all
@@ -61,7 +61,7 @@ jobs:
       - uses: actions/setup-python@v4
         name: Install Python
         with:
-          python-version: '3.10'
+          python-version: '3.11'
       - run: python -m pip install build
       - name: Build sdist
         run: python -m build --sdist
@@ -73,16 +73,16 @@ jobs:
   upload_pypi:
     needs: [build_wheels, build_sdist]
     runs-on: ubuntu-latest
+    permissions:
+      # IMPORTANT: this permission is mandatory for trusted publishing
+      id-token: write
     if: github.event_name == 'push' && startsWith(github.event.ref, 'refs/tags/v')
     steps:
       - uses: actions/download-artifact@v3
         with:
           name: artifact
           path: dist
       - uses: pypa/gh-action-pypi-publish@release/v1
-        with:
-          user: __token__
-          password: ${{ secrets.pypi_password }}
 
   build_docker:
     # use the already built wheels to build docker
@@ -95,15 +95,15 @@ jobs:
           name: artifact
           path: source/install/docker/dist
       - name: Log in to the Container registry
-        uses: docker/login-action@f054a8b539a109f9f41c372932f1ae047eff08c9
+        uses: docker/login-action@f4ef78c080cd8ba55a85445d5b36e214a81df20a
         with:
           registry: ghcr.io
           username: ${{ github.actor }}
           password: ${{ secrets.GITHUB_TOKEN }}
 
       - name: Extract metadata (tags, labels) for Docker
         id: meta
-        uses: docker/metadata-action@507c2f2dc502c992ad446e3d7a5dfbe311567a96
+        uses: docker/metadata-action@c4ee3adeed93b1fa6a762f209fb01608c1a22f1e
         with:
           images: ghcr.io/deepmodeling/deepmd-kit
 

.github/workflows/package_c.yml

@@ -12,15 +12,41 @@ jobs:
       - uses: actions/checkout@v3
       - name: Package C library
         run: ./source/install/docker_package_c.sh
-      - name: Test C library
-        run: ./source/install/docker_test_package_c.sh
       # for download and debug
       - name: Upload artifact
         uses: actions/upload-artifact@v3
         with:
+          name: libdeepmd_c
           path: ./libdeepmd_c.tar.gz
+      - name: Test C library
+        run: ./source/install/docker_test_package_c.sh
       - name: Release
         uses: softprops/action-gh-release@v1
         if: startsWith(github.ref, 'refs/tags/')
         with:
           files: libdeepmd_c.tar.gz
+  test_c:
+    name: Test building from C library
+    needs: [build_c]
+    runs-on: ubuntu-22.04
+    steps:
+      - uses: actions/checkout@v3
+      - name: Download artifact
+        uses: actions/download-artifact@v3
+        with:
+          name: libdeepmd_c
+      - run: tar -vxzf ./libdeepmd_c.tar.gz
+      - name: Test C library
+        run: ./source/install/build_from_c.sh
+        env:
+          DEEPMD_C_ROOT: ${{ github.workspace }}/libdeepmd_c
+  pass:
+    name: Pass building c library
+    needs: [build_c, test_c]
+    runs-on: ubuntu-latest
+    if: always()
+    steps:
+    - name: Decide whether the needed jobs succeeded or failed
+      uses: re-actors/alls-green@release/v1
+      with:
+        jobs: ${{ toJSON(needs) }}

.github/workflows/test_cc.yml

@@ -6,23 +6,26 @@ jobs:
   testcc:
     name: Test C++
     runs-on: ubuntu-latest
-    container: ghcr.io/deepmodeling/deepmd-kit-test-cc:latest
     steps:
-    - name: work around permission issue
-      run: git config --global --add safe.directory /__w/deepmd-kit/deepmd-kit
     - uses: actions/checkout@v3
+    - uses: actions/setup-python@v4
+      with:
+        python-version: '3.11'
+    - name: Setup MPI
+      uses: mpi4py/setup-mpi@v1
+      with:
+        mpi: mpich
+    - run: python -m pip install tensorflow
     - run: source/install/test_cc_local.sh
       env:
         OMP_NUM_THREADS: 1
         TF_INTRA_OP_PARALLELISM_THREADS: 1
         TF_INTER_OP_PARALLELISM_THREADS: 1
-        tensorflow_root: /usr/local
+        LMP_CXX11_ABI_0: 1
     # test lammps
-    - run: apt-get update && apt-get install -y python3-pip python3-venv
-    - run: source/install/build_lammps.sh
     - run: |
         python -m pip install -U pip
-        python -m pip install -e .[cpu,test]
+        python -m pip install -e .[cpu,test,lmp]
       env:
         DP_BUILD_TESTING: 1
     - run: pytest --cov=deepmd source/lmp/tests

.github/workflows/test_python.yml

@@ -21,16 +21,10 @@ jobs:
           - python: 3.7
             gcc: 8
             tf: 1.14
-          - python: 3.7
-            gcc: 5
-            tf:
-          - python: 3.7
+          - python: 3.8
             gcc: 8
             tf:
-          - python: "3.10"
-            gcc: 5
-            tf:
-          - python: "3.10"
+          - python: "3.11"
             gcc: 8
             tf:
 

.pre-commit-config.yaml

@@ -16,7 +16,7 @@ repos:
     -   id: check-toml
 # Python
 -   repo: https://github.com/psf/black
-    rev: 22.12.0
+    rev: 23.3.0
     hooks:
     -   id: black-jupyter
 -   repo: https://github.com/PyCQA/isort
@@ -26,7 +26,7 @@ repos:
       files: \.py$
 -   repo: https://github.com/charliermarsh/ruff-pre-commit
     # Ruff version.
-    rev: v0.0.243
+    rev: v0.0.269
     hooks:
     - id: ruff
       args: ["--fix"]
@@ -43,7 +43,7 @@ repos:
     -   id: blacken-docs
 # C++
 -   repo: https://github.com/pre-commit/mirrors-clang-format
-    rev: v15.0.7
+    rev: v16.0.4
     hooks:
     -   id: clang-format
         exclude: ^source/3rdparty|source/lib/src/cuda/cudart/.+\.inc
@@ -54,7 +54,7 @@ repos:
     -   id: csslint
 # Shell
 - repo: https://github.com/scop/pre-commit-shfmt
-  rev: v3.6.0-1
+  rev: v3.6.0-2
   hooks:
     - id: shfmt
 # CMake