merge devel to master (v3.1.1) (#4999)

Author: njzjz

.devcontainer/build_cxx.sh

@@ -5,15 +5,15 @@ NPROC=$(nproc --all)
 SCRIPT_PATH=$(dirname $(realpath -s $0))
 
 export CMAKE_PREFIX_PATH=${SCRIPT_PATH}/../libtorch
-TENSORFLOW_ROOT=$(python -c 'import importlib,pathlib;print(pathlib.Path(importlib.util.find_spec("tensorflow").origin).parent)')
+TENSORFLOW_ROOT=$(python -c 'import importlib.util,pathlib;print(pathlib.Path(importlib.util.find_spec("tensorflow").origin).parent)')
 
 mkdir -p ${SCRIPT_PATH}/../buildcxx/
 cd ${SCRIPT_PATH}/../buildcxx/
 cmake -D ENABLE_TENSORFLOW=ON \
 	-D ENABLE_PYTORCH=ON \
 	-D ENABLE_PADDLE=ON \
 	-D CMAKE_INSTALL_PREFIX=${SCRIPT_PATH}/../dp/ \
-	-D LAMMPS_VERSION=stable_29Aug2024_update1 \
+	-D LAMMPS_VERSION=stable_22Jul2025_update1 \
 	-D CMAKE_BUILD_TYPE=Debug \
 	-D BUILD_TESTING:BOOL=TRUE \
 	-D TENSORFLOW_ROOT=${TENSORFLOW_ROOT} \

.devcontainer/devcontainer.json

@@ -11,7 +11,6 @@
     "PATH": "${containerEnv:PATH}:${containerWorkspaceFolder}/.venv/bin",
     "DP_ENABLE_PYTORCH": "1",
     "DP_VARIANT": "cpu",
-    "LMP_CXX11_ABI_0": "1",
     "UV_EXTRA_INDEX_URL": "https://download.pytorch.org/whl/cpu"
   }
 }

.devcontainer/download_libtorch.sh

@@ -4,5 +4,5 @@ set -ev
 SCRIPT_PATH=$(dirname $(realpath -s $0))
 cd ${SCRIPT_PATH}/..
 
-wget https://download.pytorch.org/libtorch/cpu/libtorch-cxx11-abi-shared-with-deps-2.7.0%2Bcpu.zip -O ~/libtorch.zip
+wget https://download.pytorch.org/libtorch/cpu/libtorch-cxx11-abi-shared-with-deps-2.8.0%2Bcpu.zip -O ~/libtorch.zip
 unzip ~/libtorch.zip

.devcontainer/gdb_lmp

@@ -2,7 +2,7 @@
 SCRIPT_PATH=$(dirname $(realpath -s $0))
 
 export CMAKE_PREFIX_PATH=${SCRIPT_PATH}/../libtorch
-TENSORFLOW_ROOT=$(python -c 'import importlib,pathlib;print(pathlib.Path(importlib.util.find_spec("tensorflow").origin).parent)')
+TENSORFLOW_ROOT=$(python -c 'import importlib.util,pathlib;print(pathlib.Path(importlib.util.find_spec("tensorflow").origin).parent)')
 
 env LAMMPS_PLUGIN_PATH=${SCRIPT_PATH}/../dp/lib/deepmd_lmp \
 	LD_LIBRARY_PATH=${SCRIPT_PATH}/../dp/lib:${CMAKE_PREFIX_PATH}/lib:${TENSORFLOW_ROOT} \

.devcontainer/gdb_pytest_lmp

@@ -2,7 +2,7 @@
 SCRIPT_PATH=$(dirname $(realpath -s $0))/../..
 
 export CMAKE_PREFIX_PATH=${SCRIPT_PATH}/../libtorch
-TENSORFLOW_ROOT=$(python -c 'import importlib,pathlib;print(pathlib.Path(importlib.util.find_spec("tensorflow").origin).parent)')
+TENSORFLOW_ROOT=$(python -c 'import importlib.util,pathlib;print(pathlib.Path(importlib.util.find_spec("tensorflow").origin).parent)')
 
 env LAMMPS_PLUGIN_PATH=${SCRIPT_PATH}/../dp/lib/deepmd_lmp \
 	LD_LIBRARY_PATH=${SCRIPT_PATH}/../dp/lib:${CMAKE_PREFIX_PATH}/lib:${TENSORFLOW_ROOT} \

.devcontainer/lmp

@@ -2,7 +2,7 @@
 SCRIPT_PATH=$(dirname $(realpath -s $0))
 
 export CMAKE_PREFIX_PATH=${SCRIPT_PATH}/../libtorch
-TENSORFLOW_ROOT=$(python -c 'import importlib,pathlib;print(pathlib.Path(importlib.util.find_spec("tensorflow").origin).parent)')
+TENSORFLOW_ROOT=$(python -c 'import importlib.util,pathlib;print(pathlib.Path(importlib.util.find_spec("tensorflow").origin).parent)')
 
 env LAMMPS_PLUGIN_PATH=${SCRIPT_PATH}/../dp/lib/deepmd_lmp \
 	LD_LIBRARY_PATH=${SCRIPT_PATH}/../dp/lib:${CMAKE_PREFIX_PATH}/lib:${TENSORFLOW_ROOT} \

.devcontainer/pytest_lmp

@@ -2,7 +2,7 @@
 SCRIPT_PATH=$(dirname $(realpath -s $0))/../..
 
 export CMAKE_PREFIX_PATH=${SCRIPT_PATH}/../libtorch
-TENSORFLOW_ROOT=$(python -c 'import importlib,pathlib;print(pathlib.Path(importlib.util.find_spec("tensorflow").origin).parent)')
+TENSORFLOW_ROOT=$(python -c 'import importlib.util,pathlib;print(pathlib.Path(importlib.util.find_spec("tensorflow").origin).parent)')
 
 env LAMMPS_PLUGIN_PATH=${SCRIPT_PATH}/../dp/lib/deepmd_lmp \
 	LD_LIBRARY_PATH=${SCRIPT_PATH}/../dp/lib:${CMAKE_PREFIX_PATH}/lib:${TENSORFLOW_ROOT} \

.github/workflows/build_cc.yml

@@ -2,6 +2,9 @@ on:
   push:
     branches-ignore:
       - "gh-readonly-queue/**"
+      - "copilot/**"
+      - "dependabot/**"
+      - "pre-commit-ci-update-config"
   pull_request:
   merge_group:
 concurrency:
@@ -26,14 +29,14 @@ jobs:
         - variant: clang
           dp_variant: clang
     steps:
-    - uses: actions/checkout@v4
-    - uses: actions/setup-python@v5
+    - uses: actions/checkout@v5
+    - uses: actions/setup-python@v6
       with:
         python-version: '3.11'
     - uses: lukka/get-cmake@latest
     - run: python -m pip install uv
     - run: source/install/uv_with_retry.sh pip install --system tensorflow
-    - run: source/install/uv_with_retry.sh pip install --system 'torch==2.7' --index-url https://download.pytorch.org/whl/cpu
+    - run: source/install/uv_with_retry.sh pip install --system 'torch==2.8.*' --index-url https://download.pytorch.org/whl/cpu
     - 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 \

.github/workflows/build_wheel.yml

@@ -4,6 +4,9 @@ on:
   push:
     branches-ignore:
       - "gh-readonly-queue/**"
+      - "copilot/**"
+      - "dependabot/**"
+      - "pre-commit-ci-update-config"
     tags:
       - "v*"
   pull_request:
@@ -54,7 +57,7 @@ jobs:
             platform_id: manylinux_aarch64
             dp_variant: cpu
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v5
         with:
           # https://github.com/pypa/setuptools_scm/issues/480
           fetch-depth: 0
@@ -70,7 +73,7 @@ jobs:
           rm -rf .git
         if: matrix.dp_pkg_name == 'deepmd-kit-cu11'
       - name: Build wheels
-        uses: pypa/cibuildwheel@v2.23
+        uses: pypa/cibuildwheel@v3.1
         env:
           CIBW_BUILD_VERBOSITY: 1
           CIBW_ARCHS: all
@@ -87,7 +90,7 @@ jobs:
     name: Build source distribution
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v5
         with:
           fetch-depth: 0
       - name: Build sdist
@@ -106,7 +109,7 @@ jobs:
       id-token: write
     if: github.event_name == 'push' && startsWith(github.event.ref, 'refs/tags/v')
     steps:
-      - uses: actions/download-artifact@v4
+      - uses: actions/download-artifact@v5
         with:
           pattern: cibw-*
           path: dist
@@ -128,8 +131,8 @@ jobs:
     steps:
       - name: Delete huge unnecessary tools folder
         run: rm -rf /opt/hostedtoolcache
-      - uses: actions/checkout@v4
-      - uses: actions/download-artifact@v4
+      - uses: actions/checkout@v5
+      - uses: actions/download-artifact@v5
         with:
           path: source/install/docker/dist
           pattern: cibw-*-manylinux_x86_64-cu${{ matrix.cuda_version }}*
@@ -162,12 +165,12 @@ jobs:
     needs: [build_wheels, build_sdist]
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/download-artifact@v4
+      - uses: actions/download-artifact@v5
         with:
           path: dist/packages
           pattern: cibw-*
           merge-multiple: true
-      - uses: actions/setup-python@v5
+      - uses: actions/setup-python@v6
         name: Install Python
         with:
           python-version: '3.11'
@@ -176,7 +179,7 @@ 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@v3
+        uses: actions/upload-pages-artifact@v4
         with:
           path: dist
   deploy_pypi_index:

.github/workflows/codeql.yml

@@ -4,6 +4,9 @@ on:
   push:
     branches-ignore:
       - "gh-readonly-queue/**"
+      - "copilot/**"
+      - "dependabot/**"
+      - "pre-commit-ci-update-config"
   pull_request:
   schedule:
     - cron: '45 2 * * 2'
@@ -27,8 +30,8 @@ jobs:
 
     steps:
     - name: Checkout repository
-      uses: actions/checkout@v4
-    - uses: actions/setup-python@v5
+      uses: actions/checkout@v5
+    - uses: actions/setup-python@v6
       with:
         python-version: '3.11'
         cache: 'pip'
@@ -41,7 +44,7 @@ jobs:
          && sudo apt-get update \
          && sudo apt-get -y install cuda-cudart-dev-12-2 cuda-nvcc-12-2
         python -m pip install tensorflow
-        python -m pip install 'torch==2.7' --index-url https://download.pytorch.org/whl/cpu
+        python -m pip install 'torch==2.8.*' --index-url https://download.pytorch.org/whl/cpu
       env:
         DEBIAN_FRONTEND: noninteractive
     # Initializes the CodeQL tools for scanning.