Merge branch 'master' into 0330-default-pf

Signed-off-by: Duo <50307526+iProzd@users.noreply.github.com>

Author: iProzd

.github/DISCUSSION_TEMPLATE/README.md

@@ -0,0 +1,13 @@
+# Discussion Templates
+
+This directory contains GitHub Discussion category forms for DeePMD-kit.
+
+## Active template
+
+- `q-a.yml` → **Q&A**
+
+## Notes
+
+- The filename must match the discussion category slug exactly.
+- GitHub Discussion forms only support a limited set of top-level keys, such as `title`, `labels`, and `body`.
+- This Q&A template is intentionally lightweight; most fields are optional and should be filled only when relevant.

.github/DISCUSSION_TEMPLATE/q-a.yml

@@ -0,0 +1,92 @@
+title: "[Q&A] "
+labels: ["question"]
+body:
+  - type: markdown
+    attributes:
+      value: |
+        Use this form for Q&A discussions.
+
+        This template is intentionally lightweight.
+        **Only fill the technical fields below if they are relevant to your question.**
+
+        If your question is about using DeePMD-kit or diagnosing a problem, version info and a minimal reproducible example can help others answer faster.
+  - type: textarea
+    id: question
+    attributes:
+      label: Question
+      description: Please describe your question clearly.
+      placeholder: What would you like to ask?
+      value:
+    validations:
+      required: true
+  - type: input
+    id: version
+    attributes:
+      label: DeePMD-kit Version
+      description: "If applicable: `dp --version`."
+      placeholder: "e.g., 2.2.7"
+    validations:
+      required: false
+  - type: input
+    id: backend-version
+    attributes:
+      label: Backend and its version
+      description: "If applicable: the backend and its version will be printed when running DeePMD-kit, e.g. TensorFlow v2.15.0."
+      placeholder: "e.g., TensorFlow v2.15.0"
+    validations:
+      required: false
+  - type: textarea
+    id: other-version
+    attributes:
+      label: Python Version, CUDA Version, GCC Version, LAMMPS Version, etc
+      description: "If applicable, specify your platform or environment details."
+      placeholder:
+      value:
+    validations:
+      required: false
+  - type: textarea
+    id: details
+    attributes:
+      label: Details
+      description: "If applicable, add more context such as what you are trying to do, what you have tried, and where you got stuck."
+      placeholder:
+      value:
+    validations:
+      required: false
+  - type: textarea
+    id: reproducible-example
+    attributes:
+      label: Reproducible Example, Input Files, and Commands
+      description: |
+        If applicable, provide a minimal reproducible example.
+        For software-usage questions, this is often the fastest way to get a useful answer.
+      placeholder: |
+        Commands:
+        ```bash
+        dp train input.json
+        ```
+
+        Input / config:
+        ```json
+        {
+          "model": {}
+        }
+        ```
+
+        Expected behavior:
+        ...
+
+        Actual behavior / error message:
+        ...
+      value:
+    validations:
+      required: false
+  - type: textarea
+    id: further
+    attributes:
+      label: Further Information, Files, and Links
+      description: Put any additional information here, including links to docs, papers, related issues, screenshots, or external resources.
+      placeholder:
+      value:
+    validations:
+      required: false

.github/labeler.yml

@@ -30,9 +30,6 @@ 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/workflows/build_wheel.yml

@@ -171,7 +171,7 @@ 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@v4
+        uses: actions/upload-pages-artifact@v5
         with:
           path: dist
   deploy_pypi_index:

.github/workflows/package_c.yml

@@ -54,7 +54,7 @@ jobs:
       - name: Test C library
         run: ./source/install/docker_test_package_c.sh
       - name: Release
-        uses: softprops/action-gh-release@v2
+        uses: softprops/action-gh-release@v3
         if: startsWith(github.ref, 'refs/tags/')
         with:
           files: ${{ matrix.filename }}

.github/workflows/test_cc.yml

@@ -44,7 +44,7 @@ jobs:
       - run: python -m pip install uv
       - name: Install Python dependencies
         run: |
-          source/install/uv_with_retry.sh pip install --system --group pin_tensorflow_cpu --group pin_pytorch_cpu --group pin_jax --torch-backend cpu
+          source/install/uv_with_retry.sh pip install --system --group pin_tensorflow_cpu --group pin_pytorch_cpu --group pin_jax_cpu --torch-backend cpu
           export TENSORFLOW_ROOT=$(python -c 'import importlib.util,pathlib;print(pathlib.Path(importlib.util.find_spec("tensorflow").origin).parent)')
           source/install/uv_with_retry.sh pip install --system -e .[cpu,test,lmp,jax] mpi4py mpich
       - name: Convert models
@@ -98,7 +98,9 @@ jobs:
           ENABLE_JAX: ${{ matrix.enable_tensorflow && '1' || '0' }}
           ENABLE_PADDLE: ${{ matrix.enable_paddle && '1' || '0' }}
         if: ${{ !matrix.check_memleak }}
-      - uses: codecov/codecov-action@v5
+      - name: Upload coverage to Codecov (non-blocking)
+        uses: codecov/codecov-action@v6
+        continue-on-error: true
         with:
           use_oidc: true
     permissions:

.github/workflows/test_cuda.yml

@@ -43,7 +43,7 @@ jobs:
           && sudo apt-get -y install cuda-12-3 libcudnn8=8.9.5.*-1+cuda12.3
         if: false # skip as we use nvidia image
       - run: python -m pip install -U uv
-      - run: source/install/uv_with_retry.sh pip install --system --group pin_tensorflow_gpu --group pin_pytorch_gpu --group pin_jax "jax[cuda12]"
+      - run: source/install/uv_with_retry.sh pip install --system --group pin_tensorflow_gpu --group pin_pytorch_gpu --group pin_jax_gpu
       - run: |
           export PYTORCH_ROOT=$(python -c 'import torch;print(torch.__path__[0])')
           export TENSORFLOW_ROOT=$(python -c 'import importlib.util,pathlib;print(pathlib.Path(importlib.util.find_spec("tensorflow").origin).parent)')

.github/workflows/test_python.yml

@@ -31,7 +31,7 @@ jobs:
           source/install/uv_with_retry.sh pip install --system openmpi --group pin_tensorflow_cpu --group pin_pytorch_cpu --torch-backend cpu
           export TENSORFLOW_ROOT=$(python -c 'import importlib.util,pathlib;print(pathlib.Path(importlib.util.find_spec("tensorflow").origin).parent)')
           export PYTORCH_ROOT=$(python -c 'import torch;print(torch.__path__[0])')
-          source/install/uv_with_retry.sh pip install --system -e .[test,jax] mpi4py --group pin_jax
+          source/install/uv_with_retry.sh pip install --system -e .[test,jax] mpi4py --group pin_jax_cpu
           source/install/uv_with_retry.sh pip install --system --find-links "https://www.paddlepaddle.org.cn/packages/nightly/cpu/paddlepaddle/" --index-url https://pypi.org/simple --trusted-host www.paddlepaddle.org.cn --trusted-host paddlepaddle.org.cn paddlepaddle==3.4.0.dev20260310
         env:
           # Please note that uv has some issues with finding
@@ -76,7 +76,9 @@ jobs:
           name: split-${{ matrix.python }}-${{ matrix.group }}
           path: .test_durations_${{ matrix.group }}
           include-hidden-files: true
-      - uses: codecov/codecov-action@v5
+      - name: Upload coverage to Codecov (non-blocking)
+        uses: codecov/codecov-action@v6
+        continue-on-error: true
         with:
           use_oidc: true
     permissions:

.gitignore

@@ -62,6 +62,8 @@ test_dp_test_*.out
 
 # Training and model output files
 *.pth
+*.pte
+*.pt2
 *.ckpt*
 checkpoint
 lcurve.out
@@ -71,3 +73,4 @@ frozen_model.*
 
 # Test system directories
 system/
+*.expected

.pre-commit-config.yaml

@@ -23,14 +23,14 @@ repos:
       - id: check-toml
   # Python
   - repo: https://github.com/PyCQA/isort
-    rev: 8.0.1
+    rev: 9.0.0a3
     hooks:
       - id: isort
         files: \.py$
         exclude: ^source/3rdparty
   - repo: https://github.com/astral-sh/ruff-pre-commit
     # Ruff version.
-    rev: v0.15.7
+    rev: v0.15.12
     hooks:
       - id: ruff
         args: ["--fix"]
@@ -62,7 +62,7 @@ repos:
           - mdformat-gfm-alerts==2.0.0
   # C++
   - repo: https://github.com/pre-commit/mirrors-clang-format
-    rev: v22.1.1
+    rev: v22.1.4
     hooks:
       - id: clang-format
         exclude: ^(source/3rdparty|source/lib/src/gpu/cudart/.+\.inc|.+\.ipynb$|source/tests/infer/.+\.json$)
@@ -76,7 +76,7 @@ repos:
         exclude: ^(source/3rdparty|\.clang-format)
   # Shell
   - repo: https://github.com/scop/pre-commit-shfmt
-    rev: v3.12.0-2
+    rev: v3.13.1-1
     hooks:
       - id: shfmt
   # CMake