Merge devel to master (deepmodeling#3165)

Prepare v2.2.8

.github/labeler.yml

@@ -1,15 +1,39 @@
 Python:
-- deepmd/**/*
-- deepmd_cli/**/*
-- source/tests/**/*
-Docs: doc/**/*
-Examples: examples/**/*
-Core: source/lib/**/*
-CUDA: source/lib/src/gpu/**/*
-ROCM: source/lib/src/gpu/**/*
-OP: source/op/**/*
-C++: source/api_cc/**/*
-C: source/api_c/**/*
-LAMMPS: source/lmp/**/*
-Gromacs: source/gmx/**/*
-i-Pi: source/ipi/**/*
+- changed-files:
+  - any-glob-to-any-file:
+    - deepmd/**/*
+    - deepmd_utils/**/*
+    - source/tests/**/*
+Docs:
+- changed-files:
+  - any-glob-to-any-file: doc/**/*
+Examples:
+- changed-files:
+  - any-glob-to-any-file: examples/**/*
+Core:
+- changed-files:
+  - any-glob-to-any-file: source/lib/**/*
+CUDA:
+- changed-files:
+  - any-glob-to-any-file: source/lib/src/gpu/**/*
+ROCM:
+- changed-files:
+  - any-glob-to-any-file: source/lib/src/gpu/**/*
+OP:
+- changed-files:
+  - any-glob-to-any-file: source/op/**/*
+C++:
+- changed-files:
+  - any-glob-to-any-file: source/api_cc/**/*
+C:
+- changed-files:
+  - any-glob-to-any-file: source/api_c/**/*
+LAMMPS:
+- changed-files:
+  - any-glob-to-any-file: source/lmp/**/*
+Gromacs:
+- changed-files:
+  - any-glob-to-any-file: source/gmx/**/*
+i-Pi:
+- changed-files:
+  - any-glob-to-any-file: source/ipi/**/*

.github/release.yml

@@ -0,0 +1,34 @@
+changelog:
+  exclude:
+    authors:
+      - app/pre-commit-ci
+      - app/dependabot
+  categories:
+    - title: Breaking Changes
+      labels:
+        - "breaking change"
+    - title: New Features
+      labels:
+        - "new feature"
+    - title: Enhancement
+      labels:
+        - enhancement
+    - title: Documentation
+      labels:
+        # automatically added
+        - Docs
+        # for docs outside the doc directory
+        - "other docs"
+      exclude:
+        labels:
+          - build
+          - bug
+    - title: Build and release
+      labels:
+        - build
+    - title: Bug fixings
+      labels:
+        - bug
+    - title: Other Changes
+      labels:
+        - "*"

.github/workflows/build_cc.yml

@@ -21,7 +21,7 @@ jobs:
           dp_variant: clang
     steps:
     - uses: actions/checkout@v4
-    - uses: actions/setup-python@v4
+    - uses: actions/setup-python@v5
       with:
         python-version: '3.11'
         cache: 'pip'
@@ -37,7 +37,7 @@ jobs:
          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-cudart-dev-12-0 cuda-nvcc-12-0
+         && sudo apt-get -y install cuda-cudart-dev-12-2 cuda-nvcc-12-2
       if: matrix.variant == 'cuda120'
       env:
         DEBIAN_FRONTEND: noninteractive

.github/workflows/build_wheel.yml

@@ -33,6 +33,13 @@ jobs:
             python: 311
             platform_id: manylinux_x86_64
             dp_variant: cuda
+            cuda_version: 12.2
+          - os: ubuntu-latest
+            python: 311
+            platform_id: manylinux_x86_64
+            dp_variant: cuda
+            cuda_version: 11.8
+            dp_pkg_name: deepmd-kit-cu11
           # macos-x86-64
           - os: macos-latest
             python: 311
@@ -68,8 +75,11 @@ jobs:
           CIBW_ARCHS: all
           CIBW_BUILD: cp${{ matrix.python }}-${{ matrix.platform_id }}
           DP_VARIANT: ${{ matrix.dp_variant }}
-      - uses: actions/upload-artifact@v3
+          CUDA_VERSION: ${{ matrix.cuda_version }}
+          DP_PKG_NAME: ${{ matrix.dp_pkg_name }}
+      - uses: actions/upload-artifact@v4
         with:
+          name: cibw-cp${{ matrix.python }}-${{ matrix.platform_id }}-cu${{ matrix.cuda_version }}-${{ strategy.job-index }}
           path: ./wheelhouse/*.whl
   build_sdist:
     name: Build source distribution
@@ -78,7 +88,7 @@ jobs:
       - uses: actions/checkout@v4
         with:
           fetch-depth: 0
-      - uses: actions/setup-python@v4
+      - uses: actions/setup-python@v5
         name: Install Python
         with:
           python-version: '3.11'
@@ -87,8 +97,9 @@ jobs:
       - name: Build sdist
         run: python -m build --sdist
 
-      - uses: actions/upload-artifact@v3
+      - uses: actions/upload-artifact@v4
         with:
+          name: cibw-sdist
           path: dist/*.tar.gz
 
   upload_pypi:
@@ -99,22 +110,31 @@ jobs:
       id-token: write
     if: github.event_name == 'push' && startsWith(github.event.ref, 'refs/tags/v')
     steps:
-      - uses: actions/download-artifact@v3
+      - uses: actions/download-artifact@v4
         with:
-          name: artifact
+          pattern: cibw-*
           path: dist
+          merge-multiple: true
       - uses: pypa/gh-action-pypi-publish@release/v1
 
   build_docker:
     # use the already built wheels to build docker
     needs: [build_wheels]
     runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+      matrix:
+        include:
+          - variant: ""
+            cuda_version: "12"
+          - variant: "_cu11"
+            cuda_version: "11"
     steps:
       - uses: actions/checkout@v4
-      - uses: actions/download-artifact@v3
+      - uses: actions/download-artifact@v4
         with:
-          name: artifact
           path: source/install/docker/dist
+          merge-multiple: true
       - name: Log in to the Container registry
         uses: docker/login-action@343f7c4344506bcbf9b4de18042ae17996df046d
         with:
@@ -124,27 +144,30 @@ jobs:
 
       - name: Extract metadata (tags, labels) for Docker
         id: meta
-        uses: docker/metadata-action@96383f45573cb7f253c731d3b3ab81c87ef81934
+        uses: docker/metadata-action@dbef88086f6cef02e264edb7dbf63250c17cef6c
         with:
           images: ghcr.io/deepmodeling/deepmd-kit
 
       - name: Build and push Docker image
-        uses: docker/build-push-action@0565240e2d4ab88bba5387d719585280857ece09
+        uses: docker/build-push-action@4a13e500e55cf31b7a5d59a38ab2040ab0f42f56
         with:
           context: source/install/docker
-          push: ${{ github.repository_owner == 'deepmodeling' && github.event_name == 'push' }}
-          tags: ${{ steps.meta.outputs.tags }}
+          push: ${{ github.repository_owner == 'deepmodeling' && github.event_name == 'push' && github.actor != 'dependabot[bot]' }}
+          tags: ${{ steps.meta.outputs.tags }}${{ matrix.variant }}
           labels: ${{ steps.meta.outputs.labels }}
+          build-args: |
+            VARIANT=${{ matrix.variant }}
+            CUDA_VERSION=${{ matrix.cuda_version }}
 
   build_pypi_index:
     needs: [build_wheels, build_sdist]
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/download-artifact@v3
+      - uses: actions/download-artifact@v4
         with:
-          name: artifact
           path: dist/packages
-      - uses: actions/setup-python@v4
+          merge-multiple: true
+      - uses: actions/setup-python@v5
         name: Install Python
         with:
           python-version: '3.11'
@@ -153,7 +176,7 @@ jobs:
           ls dist/packages > package_list.txt
           dumb-pypi --output-dir dist --packages-url ../../packages --package-list package_list.txt --title "DeePMD-kit Developed Packages"
       - name: Upload Pages artifact
-        uses: actions/upload-pages-artifact@v2
+        uses: actions/upload-pages-artifact@v3
         with:
           path: dist
   deploy_pypi_index:
@@ -169,11 +192,11 @@ jobs:
     steps:
       - name: Deploy to GitHub Pages
         id: deployment
-        uses: actions/deploy-pages@v2
+        uses: actions/deploy-pages@v4
 
   pass:
     name: Pass testing build wheels
-    needs: [build_wheels, build_sdist]
+    needs: [build_wheels, build_sdist, build_docker, build_pypi_index]
     runs-on: ubuntu-latest
     if: always()
     steps:

.github/workflows/codeql.yml

@@ -0,0 +1,58 @@
+name: "CodeQL"
+
+on:
+  push:
+  pull_request:
+  schedule:
+    - cron: '45 2 * * 2'
+
+jobs:
+  analyze:
+    name: Analyze
+    runs-on: ${{ (matrix.language == 'swift' && 'macos-latest') || 'ubuntu-latest' }}
+    timeout-minutes: ${{ (matrix.language == 'swift' && 120) || 360 }}
+    permissions:
+      actions: read
+      contents: read
+      security-events: write
+
+    strategy:
+      fail-fast: false
+      matrix:
+        language: [ 'c-cpp', 'javascript-typescript', 'python' ]
+
+    steps:
+    - name: Checkout repository
+      uses: actions/checkout@v4
+    - uses: actions/setup-python@v5
+      with:
+        python-version: '3.11'
+        cache: 'pip'
+      if: matrix.language == 'c-cpp'
+    - name: "Setup dependencies"
+      if: matrix.language == 'c-cpp'
+      run: |
+        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-cudart-dev-12-2 cuda-nvcc-12-2
+        python -m pip install tensorflow
+      env:
+        DEBIAN_FRONTEND: noninteractive
+    # Initializes the CodeQL tools for scanning.
+    - name: Initialize CodeQL
+      uses: github/codeql-action/init@v3
+      with:
+        languages: ${{ matrix.language }}
+        queries: security-extended,security-and-quality
+    - name: "Run, Build Application using script"
+      run: source/install/build_cc.sh
+      env:
+        DP_VARIANT: cuda
+        DOWNLOAD_TENSORFLOW: "FALSE"
+      if: matrix.language == 'c-cpp'
+
+    - name: Perform CodeQL Analysis
+      uses: github/codeql-action/analyze@v3
+      with:
+        category: "/language:${{matrix.language}}"

.github/workflows/labeler.yml

@@ -9,6 +9,6 @@ jobs:
       pull-requests: write
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/labeler@v4
+    - uses: actions/labeler@v5
       with:
         repo-token: "${{ secrets.GITHUB_TOKEN }}"

.github/workflows/package_c.yml

@@ -8,33 +8,48 @@ jobs:
   build_c:
     name: Build C library
     runs-on: ubuntu-22.04
+    strategy:
+      matrix:
+        include:
+          - tensorflow_build_version: "2.15"
+            tensorflow_version: ""
+            filename: libdeepmd_c.tar.gz
+          - tensorflow_build_version: "2.14"
+            tensorflow_version: ">=2.5.0rc0,<2.15"
+            filename: libdeepmd_c_cu11.tar.gz
     steps:
       - uses: actions/checkout@v4
       - name: Package C library
         run: ./source/install/docker_package_c.sh
+        env:
+          TENSORFLOW_VERSION: ${{ matrix.tensorflow_version }}
+          TENSORFLOW_BUILD_VERSION: ${{ matrix.tensorflow_build_version }}
+      - run: cp libdeepmd_c.tar.gz ${{ matrix.filename }}
+        if: matrix.filename != 'libdeepmd_c.tar.gz'
       # for download and debug
       - name: Upload artifact
-        uses: actions/upload-artifact@v3
+        uses: actions/upload-artifact@v4
         with:
-          name: libdeepmd_c
-          path: ./libdeepmd_c.tar.gz
+          name: libdeepmd_c-${{ strategy.job-index }}-${{ matrix.filename }}
+          path: ${{ matrix.filename }}
       - 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
+          files: ${{ matrix.filename }}
   test_c:
     name: Test building from C library
     needs: [build_c]
     runs-on: ubuntu-22.04
     steps:
       - uses: actions/checkout@v4
       - name: Download artifact
-        uses: actions/download-artifact@v3
+        uses: actions/download-artifact@v4
         with:
-          name: libdeepmd_c
+          pattern: libdeepmd_c-*
+          merge-multiple: true
       - run: tar -vxzf ./libdeepmd_c.tar.gz
       - name: Test C library
         run: ./source/install/build_from_c.sh

.github/workflows/test_cc.yml

@@ -8,7 +8,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
     - uses: actions/checkout@v4
-    - uses: actions/setup-python@v4
+    - uses: actions/setup-python@v5
       with:
         python-version: '3.11'
         cache: 'pip'