v2.2.11

.git_archival.txt

@@ -0,0 +1,4 @@
+node: $Format:%H$
+node-date: $Format:%cI$
+describe-name: $Format:%(describe:tags=true,match=*[0-9]*)$
+ref-names: $Format:%D$

.gitattributes

@@ -1,2 +1,4 @@
 # do not show up detailed difference on GitHub
 source/3rdparty/* linguist-generated=true
+source/3rdparty/README.md linguist-generated=false
+.git_archival.txt  export-subst

.github/workflows/build_cc.yml

@@ -24,9 +24,9 @@ jobs:
     - uses: actions/setup-python@v5
       with:
         python-version: '3.11'
-        cache: 'pip'
     - uses: lukka/get-cmake@latest
-    - run: python -m pip install tensorflow
+    - run: python -m pip install uv
+    - run: source/install/uv_with_retry.sh pip install --system tensorflow
     - 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

@@ -65,30 +65,27 @@ jobs:
         with:
           # https://github.com/pypa/setuptools_scm/issues/480
           fetch-depth: 0
+      - name: Install uv
+        run: curl -LsSf https://astral.sh/uv/install.sh | sh
+        if: runner.os != 'Linux'
       - uses: docker/setup-qemu-action@v3
         name: Setup QEMU
         if: matrix.platform_id == 'manylinux_aarch64' && matrix.os == 'ubuntu-latest'
       # detect version in advance. See #3168
-      - uses: actions/setup-python@v5
-        name: Install Python
-        with:
-          python-version: '3.11'
-          cache: 'pip'
-        if: matrix.dp_pkg_name == 'deepmd-kit-cu11'
       - run: |
-          python -m pip install setuptools_scm
-          python -c "from setuptools_scm import get_version;print('SETUPTOOLS_SCM_PRETEND_VERSION='+get_version())" >> $GITHUB_ENV
+          echo "SETUPTOOLS_SCM_PRETEND_VERSION=$(pipx run uv tool run --from setuptools_scm python -m setuptools_scm)" >> $GITHUB_ENV
           rm -rf .git
         if: matrix.dp_pkg_name == 'deepmd-kit-cu11'
       - name: Build wheels
-        uses: pypa/cibuildwheel@v2.17
+        uses: pypa/cibuildwheel@v2.19
         env:
           CIBW_BUILD_VERBOSITY: 1
           CIBW_ARCHS: all
           CIBW_BUILD: cp${{ matrix.python }}-${{ matrix.platform_id }}
           DP_VARIANT: ${{ matrix.dp_variant }}
           CUDA_VERSION: ${{ matrix.cuda_version }}
           DP_PKG_NAME: ${{ matrix.dp_pkg_name }}
+          CIBW_BUILD_FRONTEND: 'build[uv]'
       - uses: actions/upload-artifact@v4
         with:
           name: cibw-cp${{ matrix.python }}-${{ matrix.platform_id }}-cu${{ matrix.cuda_version }}-${{ strategy.job-index }}
@@ -100,14 +97,8 @@ jobs:
       - uses: actions/checkout@v4
         with:
           fetch-depth: 0
-      - uses: actions/setup-python@v5
-        name: Install Python
-        with:
-          python-version: '3.11'
-          cache: 'pip'
-      - run: python -m pip install build
       - name: Build sdist
-        run: python -m build --sdist
+        run: pipx run uv tool run --with build[uv] --from build python -m build --installer uv --sdist
 
       - uses: actions/upload-artifact@v4
         with:
@@ -161,7 +152,7 @@ jobs:
           images: ghcr.io/deepmodeling/deepmd-kit
 
       - name: Build and push Docker image
-        uses: docker/build-push-action@v5
+        uses: docker/build-push-action@v6
         with:
           context: source/install/docker
           push: ${{ github.repository_owner == 'deepmodeling' && github.event_name == 'push' && github.actor != 'dependabot[bot]' }}

.github/workflows/package_c.yml

@@ -19,6 +19,8 @@ jobs:
             filename: libdeepmd_c_cu11.tar.gz
     steps:
       - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
       - name: Package C library
         run: ./source/install/docker_package_c.sh
         env:

.github/workflows/test_cc.yml

@@ -20,7 +20,8 @@ jobs:
       with:
         mpi: mpich
     - uses: lukka/get-cmake@latest
-    - run: python -m pip install tensorflow
+    - run: python -m pip install uv
+    - run: source/install/uv_with_retry.sh pip install --system tensorflow
     # https://github.com/actions/runner-images/issues/9491
     - name: Fix kernel mmap rnd bits
       run: sudo sysctl vm.mmap_rnd_bits=28
@@ -34,11 +35,9 @@ jobs:
         CMAKE_GENERATOR: Ninja
         CXXFLAGS: ${{ matrix.check_memleak && '-fsanitize=leak' || '' }}
     # test lammps
-    # ASE issue: https://gitlab.com/ase/ase/-/merge_requests/2843
-    # TODO: remove ase version when ase has new release
     - run: |
-        python -m pip install -U pip
-        python -m pip install -e .[cpu,test,lmp] mpi4py "ase @ https://gitlab.com/ase/ase/-/archive/8c5aa5fd6448c5cfb517a014dccf2b214a9dfa8f/ase-8c5aa5fd6448c5cfb517a014dccf2b214a9dfa8f.tar.gz"
+        export TENSORFLOW_ROOT=$(python -c 'import importlib,pathlib;print(pathlib.Path(importlib.util.find_spec("tensorflow").origin).parent)')
+        source/install/uv_with_retry.sh pip install --system -e .[cpu,test,lmp] mpi4py
       env:
         DP_BUILD_TESTING: 1
       if: ${{ !matrix.check_memleak }}

.github/workflows/test_cuda.yml

@@ -33,11 +33,9 @@ jobs:
          && sudo apt-get update \
          && sudo apt-get -y install cuda-12-2 libcudnn8=8.9.5.*-1+cuda12.2
       if: false  # skip as we use nvidia image
-    - name: Set PyPI mirror for Aliyun cloud machine
-      run: python -m pip config --user set global.index-url https://mirrors.aliyun.com/pypi/simple/
-    - run: python -m pip install -U "pip>=21.3.1,!=23.0.0"
-    - run: python -m pip install "tensorflow>=2.15.0rc0"
-    - run: python -m pip install -v -e .[gpu,test,lmp,cu12] "ase @ https://gitlab.com/ase/ase/-/archive/8c5aa5fd6448c5cfb517a014dccf2b214a9dfa8f/ase-8c5aa5fd6448c5cfb517a014dccf2b214a9dfa8f.tar.gz"
+    - run: python -m pip install -U uv
+    - run: source/install/uv_with_retry.sh pip install --system "tensorflow>=2.15.0rc0"
+    - run: source/install/uv_with_retry.sh pip install --system -v -e .[gpu,test,lmp,cu12]
       env:
         DP_BUILD_TESTING: 1
         DP_VARIANT: cuda

.github/workflows/test_python.yml

@@ -21,18 +21,20 @@ jobs:
     - uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python }}
-        cache: 'pip'
     - uses: mpi4py/setup-mpi@v1
       if: ${{ matrix.tf == '' }}
       with:
         mpi: openmpi
-    # https://github.com/pypa/pip/issues/11770
-    - run: python -m pip install -U "pip>=21.3.1,!=23.0.0"
-    - run: pip install -e .[cpu,test]
+    - run: curl -LsSf https://astral.sh/uv/install.sh | sh
+    - run: source/install/uv_with_retry.sh pip install --system -e .[cpu,test]
       env:
+        # Please note that uv has some issues with finding
+        # existing TensorFlow package. Currently, it uses
+        # TensorFlow in the build dependency, but if it
+        # changes, setting `TENSORFLOW_ROOT`.
         TENSORFLOW_VERSION: ${{ matrix.tf }}
         DP_BUILD_TESTING: 1
-    - run: pip install horovod mpi4py
+    - run: source/install/uv_with_retry.sh pip install --system --no-build-isolation horovod mpi4py
       if: ${{ matrix.tf == '' }}
       env:
         HOROVOD_WITH_TENSORFLOW: 1

.gitignore

@@ -43,3 +43,4 @@ build_cc_tests
 build_c_tests
 build_c/
 libdeepmd_c/
+.uv/

.pre-commit-config.yaml

@@ -2,7 +2,7 @@
 # See https://pre-commit.com/hooks.html for more hooks
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.5.0
+    rev: v4.6.0
     hooks:
       - id: trailing-whitespace
         exclude: "^.+\\.pbtxt$"
@@ -29,7 +29,7 @@ repos:
         exclude: ^source/3rdparty
   - repo: https://github.com/astral-sh/ruff-pre-commit
     # Ruff version.
-    rev: v0.3.5
+    rev: v0.4.10
     hooks:
       - id: ruff
         args: ["--fix"]
@@ -52,7 +52,7 @@ repos:
       - id: blacken-docs
   # C++
   - repo: https://github.com/pre-commit/mirrors-clang-format
-    rev: v18.1.2
+    rev: v18.1.7
     hooks:
       - id: clang-format
         exclude: ^source/3rdparty|source/lib/src/gpu/cudart/.+\.inc
@@ -75,6 +75,25 @@ repos:
     hooks:
       - id: cmake-format
       #- id: cmake-lint
+  - repo: https://github.com/njzjz/mirrors-bibtex-tidy
+    rev: v1.13.0
+    hooks:
+      - id: bibtex-tidy
+        args:
+          - --curly
+          - --numeric
+          - --align=13
+          - --blank-lines
+          # disable sort: the order of keys and fields has explict meanings
+          #- --sort=key
+          - --duplicates=key,doi,citation,abstract
+          - --merge=combine
+          #- --sort-fields
+          #- --strip-comments
+          - --trailing-commas
+          - --encode-urls
+          - --remove-empty-fields
+          - --wrap=80
   # license header
   - repo: https://github.com/Lucas-C/pre-commit-hooks
     rev: v1.5.5

.readthedocs.yml

@@ -2,7 +2,10 @@ version: 2
 build:
   os: ubuntu-20.04
   tools:
-    python: mambaforge-4.10
-conda:
-  environment: doc/environment.yml
+    python: "3.11"
+  jobs:
+    post_create_environment:
+      - pip install uv
+    post_install:
+      - VIRTUAL_ENV=$READTHEDOCS_VIRTUALENV_PATH uv pip install -r doc/requirements.txt
 formats: all