fix: no pinning memory on CPU#4874
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njzjz merged 2 commits intodeepmodeling:develfrom Aug 8, 2025
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Pull Request Overview
This PR fixes a PyTorch warning that occurs when pin_memory=True is set for DataLoader but the code is running on CPU, where pinned memory provides no benefit.
- Conditionally sets
pin_memorybased on device type to avoid unnecessary warnings - Maintains pinned memory optimization for GPU/accelerator usage while disabling it for CPU
for more information, see https://pre-commit.ci
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Note Other AI code review bot(s) detectedCodeRabbit has detected other AI code review bot(s) in this pull request and will avoid duplicating their findings in the review comments. This may lead to a less comprehensive review. 📝 WalkthroughWalkthroughThe update changes the behavior of the Changes
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Codecov Report✅ All modified and coverable lines are covered by tests. Additional details and impacted files@@ Coverage Diff @@
## devel #4874 +/- ##
==========================================
- Coverage 84.76% 84.71% -0.06%
==========================================
Files 699 699
Lines 68077 68128 +51
Branches 3541 3542 +1
==========================================
+ Hits 57708 57716 +8
- Misses 9235 9277 +42
- Partials 1134 1135 +1 ☔ View full report in Codecov by Sentry. 🚀 New features to boost your workflow:
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njzjz
approved these changes
Aug 7, 2025
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Aug 26, 2025
Avoid specifying pin_memory for test DataLoaders to eliminate warnings when no accelerator is available. #4874 <!-- This is an auto-generated comment: release notes by coderabbit.ai --> ## Summary by CodeRabbit * **Tests** * Updated test configurations to rely on default memory pinning behavior in data loading, improving compatibility across environments. * Simplified test setup parameters to reduce potential flakiness and align with framework defaults. <!-- end of auto-generated comment: release notes by coderabbit.ai -->
ChiahsinChu
pushed a commit
to ChiahsinChu/deepmd-kit
that referenced
this pull request
Dec 17, 2025
This PR fixes the warning message when running on CPU: ``` torch/utils/data/dataloader.py:665: UserWarning: 'pin_memory' argument is set as true but no accelerator is found, then device pinned memory won't be used. warnings.warn(warn_msg) ``` <!-- This is an auto-generated comment: release notes by coderabbit.ai --> ## Summary by CodeRabbit * **Bug Fixes** * Improved memory handling by enabling memory pinning only when using non-CPU devices, which may enhance performance and stability when training on GPUs. <!-- end of auto-generated comment: release notes by coderabbit.ai --> --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
ChiahsinChu
pushed a commit
to ChiahsinChu/deepmd-kit
that referenced
this pull request
Dec 17, 2025
Avoid specifying pin_memory for test DataLoaders to eliminate warnings when no accelerator is available. deepmodeling#4874 <!-- This is an auto-generated comment: release notes by coderabbit.ai --> ## Summary by CodeRabbit * **Tests** * Updated test configurations to rely on default memory pinning behavior in data loading, improving compatibility across environments. * Simplified test setup parameters to reduce potential flakiness and align with framework defaults. <!-- end of auto-generated comment: release notes by coderabbit.ai -->
iProzd
added a commit
to iProzd/deepmd-kit
that referenced
this pull request
Mar 27, 2026
* feat(pt): support zbl finetune (#4849)
<!-- This is an auto-generated comment: release notes by coderabbit.ai
-->
## Summary by CodeRabbit
* **New Features**
* Added an option to control whether output statistics are computed or
loaded across atomic models.
* **Bug Fixes**
* More robust parameter transfer during fine‑tuning to handle renamed
branches and missing pretrained keys.
* **Refactor**
* Revised output-statistics workflow and refined per‑type output bias
application in composite models.
* **Tests**
* Simplified linear-model bias checks and added a ZBL finetuning test
path.
<!-- end of auto-generated comment: release notes by coderabbit.ai -->
---------
Co-authored-by: anyangml <anyangpeng.ca@gmail.com>
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
* fix(pt/pd): fix eta computation (#4886)
fix eta computation code
<!-- This is an auto-generated comment: release notes by coderabbit.ai
-->
## Summary by CodeRabbit
* **Bug Fixes**
* Improved ETA accuracy in training/validation progress logs by adapting
calculations to recent step intervals, reducing misleading estimates
early in runs.
* Consistent behavior across both backends, providing more reliable
remaining-time estimates without changing any public interfaces.
<!-- end of auto-generated comment: release notes by coderabbit.ai -->
* fix: get correct intensive property prediction when using virtual atoms (#4869)
When using virtual atoms, the property output of virtual atom is `0`.
- If predicting energy or other extensive properties, it works well,
that's because the virtual atom property `0` do not contribute to the
total energy or other extensive properties.
- However, if predicting intensive properties, there is some error. For
example, a frame has two real atoms and two virtual atoms, the atomic
property contribution is [2, 2, 0, 0](the atomic property of virtual
atoms are always 0), the final property should be `(2+2)/real_atoms =
2`, not be `(2+2)/total_atoms =1`.
This PR is used to solve this bug mentioned above.
<!-- This is an auto-generated comment: release notes by coderabbit.ai
-->
## Summary by CodeRabbit
* **New Features**
* Models now provide accessors to retrieve property names and their
fitting network; property fitting nets expose output definitions.
* **Bug Fixes**
* Intensive property reduction respects atom masks so padded/dummy atoms
are ignored, keeping results invariant to padding.
* **Tests**
* Added PyTorch, JAX, and core tests validating consistent behavior with
padded atoms.
<!-- end of auto-generated comment: release notes by coderabbit.ai -->
---------
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
* fix(tf): fix compatibility with TF 2.20 (#4890)
Fix version finding in pip and CMake; pin TF to <2.20 on Windows; fix
TENSORFLOW_ROOT in the CI.
<!-- This is an auto-generated comment: release notes by coderabbit.ai
-->
## Summary by CodeRabbit
- New Features
- Added compatibility with TensorFlow 2.20+ via runtime version
detection and generated version macros.
- Bug Fixes
- Clearer errors when a specified TensorFlow root is invalid.
- Improved version-parsing fallback for newer TensorFlow releases.
- Tightened Windows CPU wheel constraint to avoid incompatible versions.
- Chores
- Updated devcontainer scripts and CI workflows to more reliably locate
TensorFlow without importing it directly.
- Linked TensorFlow during version checks to ensure accurate detection.
<!-- end of auto-generated comment: release notes by coderabbit.ai -->
---------
Signed-off-by: Jinzhe Zeng <jinzhe.zeng@ustc.edu.cn>
Signed-off-by: Jinzhe Zeng <njzjz@qq.com>
Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>
* fix: relax `atol` and `rtol` value of padding atoms UT (#4892)
The UT of padding atoms(pytorch backend) sometimes fails like:
```
Mismatched elements: 1 / 2 (50%)
Max absolute difference among violations: 1.97471693e-08
Max relative difference among violations: 6.45619919e-07
ACTUAL: array([[-0.236542],
[ 0.030586]])
DESIRED: array([[-0.236542],
[ 0.030586]])
= 1 failed, 15442 passed, 4135 skipped, 97877 deselected, 224 warnings in 2825.25s (0:47:05) =
```
<!-- This is an auto-generated comment: release notes by coderabbit.ai
-->
## Summary by CodeRabbit
- **Tests**
- Adjusted numerical comparison assertions to use both absolute and
relative tolerances in padding-related tests.
- Aligns checks between computed results and references, improving
resilience to minor floating-point variation.
- Reduces intermittent test failures across environments and dependency
versions.
- No impact on features, performance, or user workflows.
<!-- end of auto-generated comment: release notes by coderabbit.ai -->
* doc(pd): update paddle installation scripts and paddle related content in dpa3 document (#4887)
update paddle installation scripts and custom border op error message
<!-- This is an auto-generated comment: release notes by coderabbit.ai
-->
## Summary by CodeRabbit
* **Documentation**
* Updated installation guides to reference PaddlePaddle 3.1.1 for CUDA
12.6, CUDA 11.8, and CPU; added nightly pre-release install examples.
* Refined training docs wording and CINN note; added Paddle backend
guidance and explicit OP-install instructions in DPA3 docs.
* **Chores**
* Improved error messages when custom Paddle operators are unavailable,
adding clearer install instructions and links to documentation.
<!-- end of auto-generated comment: release notes by coderabbit.ai -->
---------
Signed-off-by: HydrogenSulfate <490868991@qq.com>
Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>
* fix(pt): fix CMake compatibility with PyTorch 2.8 (#4891)
Fix #4877.
<!-- This is an auto-generated comment: release notes by coderabbit.ai
-->
## Summary by CodeRabbit
- Bug Fixes
- Improved build compatibility with PyTorch 2.8+ on UNIX-like systems
(excluding macOS) by aligning the default ABI selection with PyTorch’s
behavior. This reduces potential linker/runtime issues when building
against newer PyTorch versions. Behavior on other platforms and with
older PyTorch remains unchanged. No runtime functionality changes for
end users.
<!-- end of auto-generated comment: release notes by coderabbit.ai -->
* feat: add yaml input file support (#4894)
<!-- This is an auto-generated comment: release notes by coderabbit.ai
-->
## Summary by CodeRabbit
* **New Features**
* Training entrypoints now accept YAML configuration files in addition
to JSON, offering more flexibility when launching training.
* Unified configuration loading across frameworks for consistent
behavior (PyTorch, Paddle, TensorFlow).
* Backward compatible: existing JSON-based workflows continue to work
unchanged.
* **Tests**
* Added coverage to verify YAML input produces the expected training
output.
* Improved test cleanup to remove generated artifacts after execution.
<!-- end of auto-generated comment: release notes by coderabbit.ai -->
---------
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
* build(deps): bump actions/checkout from 4 to 5 (#4897)
Bumps [actions/checkout](https://github.com/actions/checkout) from 4 to
5.
<details>
<summary>Release notes</summary>
<p><em>Sourced from <a
href="https://github.com/actions/checkout/releases">actions/checkout's
releases</a>.</em></p>
<blockquote>
<h2>v5.0.0</h2>
<h2>What's Changed</h2>
<ul>
<li>Update actions checkout to use node 24 by <a
href="https://github.com/salmanmkc"><code>@salmanmkc</code></a> in <a
href="https://redirect.github.com/actions/checkout/pull/2226">actions/checkout#2226</a></li>
<li>Prepare v5.0.0 release by <a
href="https://github.com/salmanmkc"><code>@salmanmkc</code></a> in <a
href="https://redirect.github.com/actions/checkout/pull/2238">actions/checkout#2238</a></li>
</ul>
<h2>⚠️ Minimum Compatible Runner Version</h2>
<p><strong>v2.327.1</strong><br />
<a
href="https://github.com/actions/runner/releases/tag/v2.327.1">Release
Notes</a></p>
<p>Make sure your runner is updated to this version or newer to use this
release.</p>
<p><strong>Full Changelog</strong>: <a
href="https://github.com/actions/checkout/compare/v4...v5.0.0">https://github.com/actions/checkout/compare/v4...v5.0.0</a></p>
<h2>v4.3.0</h2>
<h2>What's Changed</h2>
<ul>
<li>docs: update README.md by <a
href="https://github.com/motss"><code>@motss</code></a> in <a
href="https://redirect.github.com/actions/checkout/pull/1971">actions/checkout#1971</a></li>
<li>Add internal repos for checking out multiple repositories by <a
href="https://github.com/mouismail"><code>@mouismail</code></a> in <a
href="https://redirect.github.com/actions/checkout/pull/1977">actions/checkout#1977</a></li>
<li>Documentation update - add recommended permissions to Readme by <a
href="https://github.com/benwells"><code>@benwells</code></a> in <a
href="https://redirect.github.com/actions/checkout/pull/2043">actions/checkout#2043</a></li>
<li>Adjust positioning of user email note and permissions heading by <a
href="https://github.com/joshmgross"><code>@joshmgross</code></a> in <a
href="https://redirect.github.com/actions/checkout/pull/2044">actions/checkout#2044</a></li>
<li>Update README.md by <a
href="https://github.com/nebuk89"><code>@nebuk89</code></a> in <a
href="https://redirect.github.com/actions/checkout/pull/2194">actions/checkout#2194</a></li>
<li>Update CODEOWNERS for actions by <a
href="https://github.com/TingluoHuang"><code>@TingluoHuang</code></a>
in <a
href="https://redirect.github.com/actions/checkout/pull/2224">actions/checkout#2224</a></li>
<li>Update package dependencies by <a
href="https://github.com/salmanmkc"><code>@salmanmkc</code></a> in <a
href="https://redirect.github.com/actions/checkout/pull/2236">actions/checkout#2236</a></li>
<li>Prepare release v4.3.0 by <a
href="https://github.com/salmanmkc"><code>@salmanmkc</code></a> in <a
href="https://redirect.github.com/actions/checkout/pull/2237">actions/checkout#2237</a></li>
</ul>
<h2>New Contributors</h2>
<ul>
<li><a href="https://github.com/motss"><code>@motss</code></a> made
their first contribution in <a
href="https://redirect.github.com/actions/checkout/pull/1971">actions/checkout#1971</a></li>
<li><a href="https://github.com/mouismail"><code>@mouismail</code></a>
made their first contribution in <a
href="https://redirect.github.com/actions/checkout/pull/1977">actions/checkout#1977</a></li>
<li><a href="https://github.com/benwells"><code>@benwells</code></a>
made their first contribution in <a
href="https://redirect.github.com/actions/checkout/pull/2043">actions/checkout#2043</a></li>
<li><a href="https://github.com/nebuk89"><code>@nebuk89</code></a> made
their first contribution in <a
href="https://redirect.github.com/actions/checkout/pull/2194">actions/checkout#2194</a></li>
<li><a href="https://github.com/salmanmkc"><code>@salmanmkc</code></a>
made their first contribution in <a
href="https://redirect.github.com/actions/checkout/pull/2236">actions/checkout#2236</a></li>
</ul>
<p><strong>Full Changelog</strong>: <a
href="https://github.com/actions/checkout/compare/v4...v4.3.0">https://github.com/actions/checkout/compare/v4...v4.3.0</a></p>
<h2>v4.2.2</h2>
<h2>What's Changed</h2>
<ul>
<li><code>url-helper.ts</code> now leverages well-known environment
variables by <a href="https://github.com/jww3"><code>@jww3</code></a>
in <a
href="https://redirect.github.com/actions/checkout/pull/1941">actions/checkout#1941</a></li>
<li>Expand unit test coverage for <code>isGhes</code> by <a
href="https://github.com/jww3"><code>@jww3</code></a> in <a
href="https://redirect.github.com/actions/checkout/pull/1946">actions/checkout#1946</a></li>
</ul>
<p><strong>Full Changelog</strong>: <a
href="https://github.com/actions/checkout/compare/v4.2.1...v4.2.2">https://github.com/actions/checkout/compare/v4.2.1...v4.2.2</a></p>
<h2>v4.2.1</h2>
<h2>What's Changed</h2>
<ul>
<li>Check out other refs/* by commit if provided, fall back to ref by <a
href="https://github.com/orhantoy"><code>@orhantoy</code></a> in <a
href="https://redirect.github.com/actions/checkout/pull/1924">actions/checkout#1924</a></li>
</ul>
<h2>New Contributors</h2>
<ul>
<li><a href="https://github.com/Jcambass"><code>@Jcambass</code></a>
made their first contribution in <a
href="https://redirect.github.com/actions/checkout/pull/1919">actions/checkout#1919</a></li>
</ul>
<p><strong>Full Changelog</strong>: <a
href="https://github.com/actions/checkout/compare/v4.2.0...v4.2.1">https://github.com/actions/checkout/compare/v4.2.0...v4.2.1</a></p>
<!-- raw HTML omitted -->
</blockquote>
<p>... (truncated)</p>
</details>
<details>
<summary>Changelog</summary>
<p><em>Sourced from <a
href="https://github.com/actions/checkout/blob/main/CHANGELOG.md">actions/checkout's
changelog</a>.</em></p>
<blockquote>
<h1>Changelog</h1>
<h2>V5.0.0</h2>
<ul>
<li>Update actions checkout to use node 24 by <a
href="https://github.com/salmanmkc"><code>@salmanmkc</code></a> in <a
href="https://redirect.github.com/actions/checkout/pull/2226">actions/checkout#2226</a></li>
</ul>
<h2>V4.3.0</h2>
<ul>
<li>docs: update README.md by <a
href="https://github.com/motss"><code>@motss</code></a> in <a
href="https://redirect.github.com/actions/checkout/pull/1971">actions/checkout#1971</a></li>
<li>Add internal repos for checking out multiple repositories by <a
href="https://github.com/mouismail"><code>@mouismail</code></a> in <a
href="https://redirect.github.com/actions/checkout/pull/1977">actions/checkout#1977</a></li>
<li>Documentation update - add recommended permissions to Readme by <a
href="https://github.com/benwells"><code>@benwells</code></a> in <a
href="https://redirect.github.com/actions/checkout/pull/2043">actions/checkout#2043</a></li>
<li>Adjust positioning of user email note and permissions heading by <a
href="https://github.com/joshmgross"><code>@joshmgross</code></a> in <a
href="https://redirect.github.com/actions/checkout/pull/2044">actions/checkout#2044</a></li>
<li>Update README.md by <a
href="https://github.com/nebuk89"><code>@nebuk89</code></a> in <a
href="https://redirect.github.com/actions/checkout/pull/2194">actions/checkout#2194</a></li>
<li>Update CODEOWNERS for actions by <a
href="https://github.com/TingluoHuang"><code>@TingluoHuang</code></a>
in <a
href="https://redirect.github.com/actions/checkout/pull/2224">actions/checkout#2224</a></li>
<li>Update package dependencies by <a
href="https://github.com/salmanmkc"><code>@salmanmkc</code></a> in <a
href="https://redirect.github.com/actions/checkout/pull/2236">actions/checkout#2236</a></li>
</ul>
<h2>v4.2.2</h2>
<ul>
<li><code>url-helper.ts</code> now leverages well-known environment
variables by <a href="https://github.com/jww3"><code>@jww3</code></a>
in <a
href="https://redirect.github.com/actions/checkout/pull/1941">actions/checkout#1941</a></li>
<li>Expand unit test coverage for <code>isGhes</code> by <a
href="https://github.com/jww3"><code>@jww3</code></a> in <a
href="https://redirect.github.com/actions/checkout/pull/1946">actions/checkout#1946</a></li>
</ul>
<h2>v4.2.1</h2>
<ul>
<li>Check out other refs/* by commit if provided, fall back to ref by <a
href="https://github.com/orhantoy"><code>@orhantoy</code></a> in <a
href="https://redirect.github.com/actions/checkout/pull/1924">actions/checkout#1924</a></li>
</ul>
<h2>v4.2.0</h2>
<ul>
<li>Add Ref and Commit outputs by <a
href="https://github.com/lucacome"><code>@lucacome</code></a> in <a
href="https://redirect.github.com/actions/checkout/pull/1180">actions/checkout#1180</a></li>
<li>Dependency updates by <a
href="https://github.com/dependabot"><code>@dependabot</code></a>- <a
href="https://redirect.github.com/actions/checkout/pull/1777">actions/checkout#1777</a>,
<a
href="https://redirect.github.com/actions/checkout/pull/1872">actions/checkout#1872</a></li>
</ul>
<h2>v4.1.7</h2>
<ul>
<li>Bump the minor-npm-dependencies group across 1 directory with 4
updates by <a
href="https://github.com/dependabot"><code>@dependabot</code></a> in <a
href="https://redirect.github.com/actions/checkout/pull/1739">actions/checkout#1739</a></li>
<li>Bump actions/checkout from 3 to 4 by <a
href="https://github.com/dependabot"><code>@dependabot</code></a> in <a
href="https://redirect.github.com/actions/checkout/pull/1697">actions/checkout#1697</a></li>
<li>Check out other refs/* by commit by <a
href="https://github.com/orhantoy"><code>@orhantoy</code></a> in <a
href="https://redirect.github.com/actions/checkout/pull/1774">actions/checkout#1774</a></li>
<li>Pin actions/checkout's own workflows to a known, good, stable
version. by <a href="https://github.com/jww3"><code>@jww3</code></a> in
<a
href="https://redirect.github.com/actions/checkout/pull/1776">actions/checkout#1776</a></li>
</ul>
<h2>v4.1.6</h2>
<ul>
<li>Check platform to set archive extension appropriately by <a
href="https://github.com/cory-miller"><code>@cory-miller</code></a> in
<a
href="https://redirect.github.com/actions/checkout/pull/1732">actions/checkout#1732</a></li>
</ul>
<h2>v4.1.5</h2>
<ul>
<li>Update NPM dependencies by <a
href="https://github.com/cory-miller"><code>@cory-miller</code></a> in
<a
href="https://redirect.github.com/actions/checkout/pull/1703">actions/checkout#1703</a></li>
<li>Bump github/codeql-action from 2 to 3 by <a
href="https://github.com/dependabot"><code>@dependabot</code></a> in <a
href="https://redirect.github.com/actions/checkout/pull/1694">actions/checkout#1694</a></li>
<li>Bump actions/setup-node from 1 to 4 by <a
href="https://github.com/dependabot"><code>@dependabot</code></a> in <a
href="https://redirect.github.com/actions/checkout/pull/1696">actions/checkout#1696</a></li>
<li>Bump actions/upload-artifact from 2 to 4 by <a
href="https://github.com/dependabot"><code>@dependabot</code></a> in <a
href="https://redirect.github.com/actions/checkout/pull/1695">actions/checkout#1695</a></li>
<li>README: Suggest <code>user.email</code> to be
<code>41898282+github-actions[bot]@users.noreply.github.com</code> by <a
href="https://github.com/cory-miller"><code>@cory-miller</code></a> in
<a
href="https://redirect.github.com/actions/checkout/pull/1707">actions/checkout#1707</a></li>
</ul>
<h2>v4.1.4</h2>
<ul>
<li>Disable <code>extensions.worktreeConfig</code> when disabling
<code>sparse-checkout</code> by <a
href="https://github.com/jww3"><code>@jww3</code></a> in <a
href="https://redirect.github.com/actions/checkout/pull/1692">actions/checkout#1692</a></li>
<li>Add dependabot config by <a
href="https://github.com/cory-miller"><code>@cory-miller</code></a> in
<a
href="https://redirect.github.com/actions/checkout/pull/1688">actions/checkout#1688</a></li>
<li>Bump the minor-actions-dependencies group with 2 updates by <a
href="https://github.com/dependabot"><code>@dependabot</code></a> in <a
href="https://redirect.github.com/actions/checkout/pull/1693">actions/checkout#1693</a></li>
<li>Bump word-wrap from 1.2.3 to 1.2.5 by <a
href="https://github.com/dependabot"><code>@dependabot</code></a> in <a
href="https://redirect.github.com/actions/checkout/pull/1643">actions/checkout#1643</a></li>
</ul>
<h2>v4.1.3</h2>
<!-- raw HTML omitted -->
</blockquote>
<p>... (truncated)</p>
</details>
<details>
<summary>Commits</summary>
<ul>
<li><a
href="https://github.com/actions/checkout/commit/08c6903cd8c0fde910a37f88322edcfb5dd907a8"><code>08c6903</code></a>
Prepare v5.0.0 release (<a
href="https://redirect.github.com/actions/checkout/issues/2238">#2238</a>)</li>
<li><a
href="https://github.com/actions/checkout/commit/9f265659d3bb64ab1440b03b12f4d47a24320917"><code>9f26565</code></a>
Update actions checkout to use node 24 (<a
href="https://redirect.github.com/actions/checkout/issues/2226">#2226</a>)</li>
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* [pre-commit.ci] pre-commit autoupdate (#4898)
<!--pre-commit.ci start-->
updates:
- [github.com/astral-sh/ruff-pre-commit: v0.12.8 →
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<!--pre-commit.ci end-->
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* Fix(pt): add comm_dict for zbl, linear, dipole, dos, polar model to fix bugs mentioned in issue #4906 (#4908)
<!-- This is an auto-generated comment: release notes by coderabbit.ai
-->
## Summary by CodeRabbit
- New Features
- Added optional support to pass a communication dictionary through
lower-level model computations across energy, dipole, DOS, polarization,
and related models. This enables advanced workflows while remaining
fully backward compatible.
- Refactor
- Standardized internal propagation of the communication dictionary
across sub-models to ensure consistent behavior.
<!-- end of auto-generated comment: release notes by coderabbit.ai -->
* docs: add comprehensive GitHub Copilot instructions and environment setup (#4911)
This PR adds comprehensive development support for GitHub Copilot agents
working in the DeePMD-kit codebase.
## What's included
**Comprehensive Copilot Instructions
(`.github/copilot-instructions.md`)**
- Complete build workflow with exact timing expectations (67s Python
build, 164s C++ build)
- Virtual environment setup and dependency installation for all backends
(TensorFlow, PyTorch, JAX, Paddle)
- **Optimized testing guidance**: Emphasizes single test execution
(~8-13 seconds) over full test suite (60+ minutes) for faster
development feedback
- Linting and formatting with ruff (1 second execution)
- Multiple validation scenarios for CLI, Python interface, and training
workflows
- Directory structure reference and key file locations
- Critical warnings with specific timeout recommendations to prevent
premature cancellation
- **Conventional commit specification**: Guidelines for commit messages
and PR titles following `type(scope): description` format
**Automated Environment Setup
(`.github/workflows/copilot-setup-steps.yml`)**
- Pre-configures Python environment using uv for fast dependency
management
- Installs TensorFlow CPU and PyTorch automatically
- Builds the DeePMD-kit package with all dependencies
- Sets up pre-commit hooks for code quality
- Validates installation to ensure environment readiness
**Development Efficiency Features**
- All commands tested and validated with accurate timing measurements
- Imperative tone throughout for clear action items
- Copy-paste ready validation scenarios
- Gitignore rules to prevent temporary test files from being committed
## Key improvements for Copilot agents
- **Faster iteration**: Single test recommendations instead of 60+
minute full test suites
- **Automated setup**: No manual environment configuration needed
- **Precise expectations**: Exact timing guidance prevents timeout
issues during builds
- **Multi-backend support**: Complete coverage of TensorFlow, PyTorch,
JAX, and Paddle workflows
- **Consistent commit standards**: Enforces conventional commit
specification for all changes
The instructions enable any GitHub Copilot agent to work effectively in
this codebase from a fresh clone with precise expectations for build
times, test execution, and validation workflows.
Fixes #4910.
<!-- START COPILOT CODING AGENT TIPS -->
---
💡 You can make Copilot smarter by setting up custom instructions,
customizing its development environment and configuring Model Context
Protocol (MCP) servers. Learn more [Copilot coding agent
tips](https://gh.io/copilot-coding-agent-tips) in the docs.
---------
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Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
* fix(pt,pd): remove redundant tensor handling to eliminate tensor construction warnings (#4907)
This PR fixes deprecation warnings that occur when `torch.tensor()` or
`paddle.to_tensor()` is called on existing tensor objects:
**PyTorch warning:**
```
UserWarning: To copy construct from a tensor, it is recommended to use sourceTensor.clone().detach() or sourceTensor.clone().detach().requires_grad_(True), rather than torch.tensor(sourceTensor).
```
**PaddlePaddle warning:**
```
UserWarning: To copy construct from a tensor, it is recommended to use sourceTensor.clone().detach(), rather than paddle.to_tensor(sourceTensor).
```
## Root Cause
The warnings were being triggered in multiple locations:
1. **PyTorch**: Test cases were passing tensor objects directly to ASE
calculators, which internally convert them using `torch.tensor()`
2. **PaddlePaddle**: Similar issues in `eval_model` function and
`to_paddle_tensor` utility, plus a TypeError where `tensor.to()` method
was incorrectly using `place=` instead of `device=`
## Solution
**For PyTorch:**
- Modified test cases to convert tensor inputs to numpy arrays before
passing to ASE calculators
- Removed redundant tensor handling in `to_torch_tensor` utility
function since the non-numpy check already handles tensors by returning
them as-is
**For PaddlePaddle:**
- Added proper type checking in `eval_model` function to handle existing
tensors with `clone().detach()`
- Removed redundant tensor handling in `to_paddle_tensor` utility
function, applying the same optimization as PyTorch
- Fixed TypeError by changing `place=` to `device=` in all `tensor.to()`
method calls (PaddlePaddle's tensor `.to()` method expects `device=`
parameter, while `paddle.to_tensor()` correctly uses `place=`)
## Changes Made
1. **`source/tests/pt/test_calculator.py`**: Fixed `TestCalculator` and
`TestCalculatorWithFparamAparam` to convert PyTorch tensors to numpy
arrays before passing to ASE calculator
2. **`deepmd/pt/utils/utils.py`**: Removed redundant tensor-specific
handling in `to_torch_tensor` function
3. **`source/tests/pd/common.py`**: Updated `eval_model` function with
type checking for PaddlePaddle tensors and fixed `tensor.to()` method
calls to use `device=` instead of `place=`
4. **`deepmd/pd/utils/utils.py`**: Removed redundant tensor-specific
handling in `to_paddle_tensor` function for consistency with PyTorch
Both utility functions now use a simplified approach where the `if not
isinstance(xx, np.ndarray): return xx` check handles all non-numpy
inputs (including tensors) by returning them unchanged, eliminating the
need for separate tensor-specific code paths.
This change is backward compatible and maintains the same functionality
while eliminating both deprecation warnings and TypeErrors, improving
code consistency between PyTorch and PaddlePaddle backends.
Fixes #3790.
<!-- START COPILOT CODING AGENT TIPS -->
---
💡 You can make Copilot smarter by setting up custom instructions,
customizing its development environment and configuring Model Context
Protocol (MCP) servers. Learn more [Copilot coding agent
tips](https://gh.io/copilot-coding-agent-tips) in the docs.
---------
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* feat: Add eval-desc CLI command for descriptor evaluation with 3D output format (#4903)
This PR implements a new command-line interface for evaluating
descriptors using trained DeePMD models, addressing the feature request
for making the `eval_descriptor` function available from the command
line.
## Overview
The new `dp eval-desc` command allows users to generate descriptor
matrices from their models using a simple CLI interface, similar to the
existing `dp test` command.
## Usage
```bash
# Basic usage
dp eval-desc -m model.pb -s /path/to/system
# With custom output directory
dp eval-desc -m model.pth -s /path/to/system -o my_descriptors
# Using datafile with multiple systems
dp eval-desc -m model.pb -f systems_list.txt -o desc_output
# For multi-task models
dp eval-desc -m model.pth -s system_dir --head task_branch
```
## Output Format
Descriptors are saved as NumPy `.npy` files in 3D format (nframes,
natoms, ndesc) preserving the natural structure of the data with
separate dimensions for frames, atoms, and descriptor components. This
format maintains the original data organization and is suitable for
various analysis workflows.
## Implementation Details
The implementation follows the same architectural pattern as the
existing `dp test` command:
- **CLI Parser**: Added argument parser in `deepmd/main.py` with options
for model (`-m`), system (`-s`), datafile (`-f`), output (`-o`), and
model branch (`--head`)
- **Command Routing**: Integrated into the entrypoints system in
`deepmd/entrypoints/main.py`
- **Core Functionality**: New `eval_desc.py` module that uses
`DeepEval.eval_descriptor()` to generate descriptors and saves them as
`.npy` files in their natural 3D format
- **Documentation**: Updated user guide and API documentation with
output format details
- **Testing**: Comprehensive tests following the pattern of existing `dp
test` functionality
Fixes #4503.
<!-- START COPILOT CODING AGENT TIPS -->
---
✨ Let Copilot coding agent [set things up for
you](https://github.com/deepmodeling/deepmd-kit/issues/new?title=✨+Set+up+Copilot+instructions&body=Configure%20instructions%20for%20this%20repository%20as%20documented%20in%20%5BBest%20practices%20for%20Copilot%20coding%20agent%20in%20your%20repository%5D%28https://gh.io/copilot-coding-agent-tips%29%2E%0A%0A%3COnboard%20this%20repo%3E&assignees=copilot)
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* build(deps): bump actions/upload-pages-artifact from 3 to 4 (#4918)
Bumps
[actions/upload-pages-artifact](https://github.com/actions/upload-pages-artifact)
from 3 to 4.
<details>
<summary>Release notes</summary>
<p><em>Sourced from <a
href="https://github.com/actions/upload-pages-artifact/releases">actions/upload-pages-artifact's
releases</a>.</em></p>
<blockquote>
<h2>v4.0.0</h2>
<h2>What's Changed</h2>
<ul>
<li>Potentially breaking change: hidden files (specifically dotfiles)
will not be included in the artifact by <a
href="https://github.com/tsusdere"><code>@tsusdere</code></a> in <a
href="https://redirect.github.com/actions/upload-pages-artifact/pull/102">actions/upload-pages-artifact#102</a>
If you need to include dotfiles in your artifact: instead of using this
action, create your own artifact according to these requirements <a
href="https://github.com/actions/upload-pages-artifact?tab=readme-ov-file#artifact-validation">https://github.com/actions/upload-pages-artifact?tab=readme-ov-file#artifact-validation</a></li>
<li>Pin <code>actions/upload-artifact</code> to SHA by <a
href="https://github.com/heavymachinery"><code>@heavymachinery</code></a>
in <a
href="https://redirect.github.com/actions/upload-pages-artifact/pull/127">actions/upload-pages-artifact#127</a></li>
</ul>
<p><strong>Full Changelog</strong>: <a
href="https://github.com/actions/upload-pages-artifact/compare/v3.0.1...v4.0.0">https://github.com/actions/upload-pages-artifact/compare/v3.0.1...v4.0.0</a></p>
<h2>v3.0.1</h2>
<h1>Changelog</h1>
<ul>
<li>Group tar's output to prevent it from messing up action logs <a
href="https://github.com/SilverRainZ"><code>@SilverRainZ</code></a> (<a
href="https://redirect.github.com/actions/upload-pages-artifact/issues/94">#94</a>)</li>
<li>Update README.md <a
href="https://github.com/uiolee"><code>@uiolee</code></a> (<a
href="https://redirect.github.com/actions/upload-pages-artifact/issues/88">#88</a>)</li>
<li>Bump the non-breaking-changes group with 1 update <a
href="https://github.com/dependabot"><code>@dependabot</code></a> (<a
href="https://redirect.github.com/actions/upload-pages-artifact/issues/92">#92</a>)</li>
<li>Update Dependabot config to group non-breaking changes <a
href="https://github.com/JamesMGreene"><code>@JamesMGreene</code></a>
(<a
href="https://redirect.github.com/actions/upload-pages-artifact/issues/91">#91</a>)</li>
<li>Bump actions/checkout from 3 to 4 <a
href="https://github.com/dependabot"><code>@dependabot</code></a> (<a
href="https://redirect.github.com/actions/upload-pages-artifact/issues/76">#76</a>)</li>
</ul>
<p>See details of <a
href="https://github.com/actions/upload-pages-artifact/compare/v3.0.0...v3.0.1">all
code changes</a> since previous release.</p>
</blockquote>
</details>
<details>
<summary>Commits</summary>
<ul>
<li><a
href="https://github.com/actions/upload-pages-artifact/commit/7b1f4a764d45c48632c6b24a0339c27f5614fb0b"><code>7b1f4a7</code></a>
Merge pull request <a
href="https://redirect.github.com/actions/upload-pages-artifact/issues/127">#127</a>
from heavymachinery/pin-sha</li>
<li><a
href="https://github.com/actions/upload-pages-artifact/commit/4cc19c7d3f3e6c87c68366501382a03c8b1ba6db"><code>4cc19c7</code></a>
Pin <code>actions/upload-artifact</code> to SHA</li>
<li><a
href="https://github.com/actions/upload-pages-artifact/commit/2d163be3ddce01512f3eea7ac5b7023b5d643ce1"><code>2d163be</code></a>
Merge pull request <a
href="https://redirect.github.com/actions/upload-pages-artifact/issues/107">#107</a>
from KittyChiu/main</li>
<li><a
href="https://github.com/actions/upload-pages-artifact/commit/c70484322b1c476728dcd37fac23c4dea2a0c51a"><code>c704843</code></a>
fix: linted README</li>
<li><a
href="https://github.com/actions/upload-pages-artifact/commit/9605915f1d2fc79418cdce4d5fbe80511c457655"><code>9605915</code></a>
Merge pull request <a
href="https://redirect.github.com/actions/upload-pages-artifact/issues/106">#106</a>
from KittyChiu/kittychiu/update-readme-1</li>
<li><a
href="https://github.com/actions/upload-pages-artifact/commit/e59cdfe6d6b061aab8f0619e759cded914f3ab03"><code>e59cdfe</code></a>
Update README.md</li>
<li><a
href="https://github.com/actions/upload-pages-artifact/commit/a2d67043267d885050434d297d3dd3a3a14fd899"><code>a2d6704</code></a>
doc: updated usage section in readme</li>
<li><a
href="https://github.com/actions/upload-pages-artifact/commit/984864e7b70fb5cb764344dc9c4b5c087662ef50"><code>984864e</code></a>
Merge pull request <a
href="https://redirect.github.com/actions/upload-pages-artifact/issues/105">#105</a>
from actions/Jcambass-patch-1</li>
<li><a
href="https://github.com/actions/upload-pages-artifact/commit/45dc78884ca148c05eddcd8ac0a804d3365e9014"><code>45dc788</code></a>
Add workflow file for publishing releases to immutable action
package</li>
<li><a
href="https://github.com/actions/upload-pages-artifact/commit/efaad07812d4b9ad2e8667cd46426fdfb7c22e22"><code>efaad07</code></a>
Merge pull request <a
href="https://redirect.github.com/actions/upload-pages-artifact/issues/102">#102</a>
from actions/hidden-files</li>
<li>Additional commits viewable in <a
href="https://github.com/actions/upload-pages-artifact/compare/v3...v4">compare
view</a></li>
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</details>
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* fix: Avoid setting pin_memory in tests (#4919)
Avoid specifying pin_memory for test DataLoaders to eliminate warnings
when no accelerator is available.
#4874
<!-- This is an auto-generated comment: release notes by coderabbit.ai
-->
## Summary by CodeRabbit
* **Tests**
* Updated test configurations to rely on default memory pinning behavior
in data loading, improving compatibility across environments.
* Simplified test setup parameters to reduce potential flakiness and
align with framework defaults.
<!-- end of auto-generated comment: release notes by coderabbit.ai -->
* [pre-commit.ci] pre-commit autoupdate (#4917)
<!--pre-commit.ci start-->
updates:
- [github.com/astral-sh/ruff-pre-commit: v0.12.9 →
v0.12.10](https://github.com/astral-sh/ruff-pre-commit/compare/v0.12.9...v0.12.10)
<!--pre-commit.ci end-->
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
* chore(CI): bump PyTorch from 2.7 to 2.8 (#4884)
<!-- This is an auto-generated comment: release notes by coderabbit.ai
-->
## Summary by CodeRabbit
* **Chores**
* Upgraded PyTorch to 2.8 across CPU and CUDA 12.x environments for
improved compatibility and stability.
* Updated development container to download the matching LibTorch 2.8
CPU bundle.
* Refreshed CI pipelines (build, test, analysis) to install and validate
against PyTorch 2.8.
<!-- end of auto-generated comment: release notes by coderabbit.ai -->
---------
Signed-off-by: Jinzhe Zeng <njzjz@qq.com>
Co-authored-by: coderabbitai[bot] <136622811+coderabbitai[bot]@users.noreply.github.com>
* fix(pd): change numel function return type from int to size_t to prevent overflow (#4924)
The `numel` function in the Paddle backend was using `int` for computing
tensor element counts, which can overflow for large tensors. This fix
changes the return type and intermediate calculations to `size_t` to
handle larger tensor sizes safely.
## Problem
The original implementation multiplied tensor dimensions as `int`
values:
```cpp
int numel(const paddle_infer::Tensor& x) const {
// TODO: There might be a overflow problem here for multiply int numbers.
int ret = 1;
std::vector<int> x_shape = x.shape();
for (std::size_t i = 0, n = x_shape.size(); i < n; ++i) {
ret *= x_shape[i]; // Can overflow for large tensors
}
return ret;
}
```
For large tensors (e.g., shape `[50000, 50000, 10]` = 25 billion
elements), this causes integer overflow and returns negative values.
## Solution
- Changed return type from `int` to `size_t`
- Changed intermediate calculations to use `size_t` with explicit
casting
- Updated all calling sites to use `size_t` variables
- Removed the TODO comment since the overflow issue is now resolved
```cpp
size_t numel(const paddle_infer::Tensor& x) const {
size_t ret = 1;
std::vector<int> x_shape = x.shape();
for (std::size_t i = 0, n = x_shape.size(); i < n; ++i) {
ret *= static_cast<size_t>(x_shape[i]); // Safe from overflow
}
return ret;
}
```
The `size_t` type can handle up to 2^64 elements on 64-bit systems (vs
2^31 for `int`), making it appropriate for tensor element counts. This
change is backward compatible since `std::vector::resize()` and other
consumers already accept `size_t`.
Fixes #4551.
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* feat(pd): support gradient accumulation (#4920)
support gradient accumulation for paddle backend.
<!-- This is an auto-generated comment: release notes by coderabbit.ai
-->
## Summary by CodeRabbit
- **New Features**
- Configurable gradient accumulation (acc_freq) that batches optimizer
updates, optional gradient clipping, and multi‑GPU gradient sync to
occur at the configured interval; acc_freq=1 preserves prior behavior.
- **Documentation**
- Added argument docs and a Paddle backend notice describing acc_freq.
- **Tests**
- Added tests exercising gradient accumulation and updated test cleanup.
<!-- end of auto-generated comment: release notes by coderabbit.ai -->
* feat(pt): add model branch alias (#4883)
Introduces model branch alias and info fields to model configuration,
adds utility functions for handling model branch dictionaries, and
updates related modules to use alias-based lookup and provide detailed
branch information. Enhances multi-task model usability and improves
logging of available model branches.
example:
```
dp --pt show 0415_compat_new.pt model-branch
[2025-08-14 10:05:54,246] DEEPMD WARNING To get the best performance, it is recommended to adjust the number of threads by setting the environment variables OMP_NUM_THREADS, DP_INTRA_OP_PARALLELISM_THREADS, and DP_INTER_OP_PARALLELISM_THREADS. See https://deepmd.rtfd.io/parallelism/ for more information.
[2025-08-14 10:05:59,122] DEEPMD INFO This is a multitask model
[2025-08-14 10:05:59,122] DEEPMD INFO Available model branches are ['Dai2023Alloy', 'Zhang2023Cathode', 'Gong2023Cluster', 'Yang2023ab', 'UniPero', 'Huang2021Deep-PBE', 'Liu2024Machine', 'Zhang2021Phase', 'Jinag2021Accurate', 'Chen2023Modeling', 'Wen2021Specialising', 'Wang2022Classical', 'Wang2022Tungsten', 'Wu2021Deep', 'Huang2021Deep-PBEsol', 'Transition1x', 'Wang2021Generalizable', 'Wu2021Accurate', 'MPTraj', 'Li2025APEX', 'Shi2024SSE', 'Tuo2023Hybrid', 'Unke2019PhysNet', 'Shi2024Electrolyte', 'ODAC23', 'Alex2D', 'OMAT24', 'SPICE2', 'OC20M', 'OC22', 'Li2025General', 'RANDOM'], where 'RANDOM' means using a randomly initialized fitting net.
[2025-08-14 10:05:59,125] DEEPMD INFO Detailed information:
+-----------------------+------------------------------+--------------------------------+--------------------------------+
| Model Branch | Alias | description | observed_type |
+-----------------------+------------------------------+--------------------------------+--------------------------------+
| Dai2023Alloy | Alloys, Domains_Alloy | The dataset contains | ['La', 'Fe', 'Ho', 'Cu', 'Sn', |
| | | structure-energy-force-virial | 'Cd', 'Y', 'Be', 'V', 'Sm', |
| | | data for 53 typical metallic | 'In', 'Pr', 'Mo', 'Mn', 'Gd', |
| | | elements in alloy systems, | 'Ru', 'Nd', 'Li', 'Tm', 'K', |
| | | including ~9000 intermetallic | 'Pt', 'Ir', 'Na', 'Hf', 'Dy', |
| | | compounds and FCC, BCC, HCP | 'Ca', 'Nb', 'Au', 'Sr', 'Si', |
| | | structures. It consists of two | 'Ge', 'Co', 'W', 'Cr', 'Zn', |
| | | parts: DFT-generated relaxed | 'Ag', 'Ti', 'Ni', 'Zr', 'Pd', |
| | | and deformed structures, and | 'Os', 'Ta', 'Rh', 'Sc', 'Tb', |
| | | randomly distorted structures | 'Al', 'Ga', 'Re', 'Lu', 'Er', |
| | | produced covering pure metals, | 'Mg', 'Ce', 'Pb'] |
| | | solid solutions, and | |
| | | intermetallics with vacancies. | |
+-----------------------+------------------------------+--------------------------------+--------------------------------+
| OMAT24 | Default, Materials, Omat24 | OMat24 is a large-scale open | ['La', 'Fe', 'Cu', 'Cd', 'Be', |
| | | dataset containing over 110 | 'Ar', 'V', 'Sm', 'In', 'Pm', |
| | | million DFT calculations | 'Pr', 'Mn', 'Ru', 'He', 'Nd', |
| | | spanning diverse structures | 'Th', 'Pa', 'K', 'Pt', 'Yb', |
| | | and compositions. It is | 'Dy', 'Sr', 'Co', 'Np', 'Cr', |
| | | designed to support AI-driven | 'Tl', 'Br', 'Se', 'Ni', 'Zr', |
| | | materials discovery by | 'Pu', 'O', 'Xe', 'Tb', 'Ga', |
| | | providing broad and deep | 'Lu', 'H', 'Ne', 'Er', 'Ce', |
| | | coverage of chemical space. | 'I', 'Kr', 'Ho', 'Cs', 'Sn', |
| | | | 'Rb', 'Y', 'N', 'F', 'Mo', |
| | | | 'Gd', 'B', 'Li', 'Tm', 'Sb', |
| | | | 'Ir', 'Hf', 'Na', 'Ca', 'Nb', |
| | | | 'Au', 'As', 'Si', 'Ge', 'W', |
| | | | 'Zn', 'Hg', 'Ag', 'Bi', 'Ti', |
| | | | 'Os', 'Cl', 'Pd', 'P', 'U', |
| | | | 'Tc', 'Ta', 'Ba', 'Rh', 'Sc', |
| | | | 'C', 'S', 'Te', 'Al', 'Re', |
| | | | 'Eu', 'Mg', 'Pb', 'Ac'] |
+-----------------------+------------------------------+--------------------------------+--------------------------------+
```
<!-- This is an auto-generated comment: release notes by coderabbit.ai
-->
## Summary by CodeRabbit
* **New Features**
* Alias-based multi-task branch selection for evaluation and
fine-tuning; new API to query model alias/branch info; show now prints a
detailed model-branch table.
* **Documentation**
* Model config gains optional fields to declare branch aliases and
per-branch info (PyTorch-only).
* **Examples**
* Added a two-task PyTorch example demonstrating aliases, shared
components, and per-branch info.
* **Tests**
* Tests include the new example and now filter out table-like show
output.
<!-- end of auto-generated comment: release notes by coderabbit.ai -->
---------
Signed-off-by: Duo <50307526+iProzd@users.noreply.github.com>
Co-authored-by: Jinzhe Zeng <jinzhe.zeng@rutgers.edu>
Co-authored-by: Han Wang <92130845+wanghan-iapcm@users.noreply.github.com>
* feat(ci): skip workflows on bot branches to avoid redundant CI runs (#4916)
This PR implements a feature request to skip all GitHub workflows on
push events for bot-created branches to avoid redundant CI runs and save
resources.
## Problem
Bot-created branches (`copilot/*`, `dependabot/*`, and
`pre-commit-ci-update-config`) currently trigger workflows on both push
events and when PRs are created. This creates duplicate CI runs since
the same tests will run again when the PR is opened, wasting CI time and
resources.
## Solution
Added `branches-ignore` patterns to workflow files that have push
triggers to skip the following branch patterns:
- `copilot/**` - GitHub Copilot branches
- `dependabot/**` - Dependabot dependency update branches
- `pre-commit-ci-update-config` - Pre-commit CI configuration update
branches
## Changes Made
Updated 8 workflow files with bot branch ignore patterns:
- `build_cc.yml`, `build_wheel.yml`, `codeql.yml`, `package_c.yml`,
`test_cc.yml`, `test_python.yml` - Added bot branch patterns to existing
`branches-ignore` lists
- `copilot-setup-steps.yml` - Added `branches-ignore` alongside existing
`paths` filter
- `mirror_gitee.yml` - Converted from array syntax to explicit push
configuration with `branches-ignore`
The `todo.yml` workflow was left unchanged since it only runs on the
`devel` branch, making bot branch exclusions unnecessary.
Example of the change:
```yaml
on:
push:
branches-ignore:
- "gh-readonly-queue/**" # existing
- "copilot/**" # new
- "dependabot/**" # new
- "pre-commit-ci-update-config" # new
```
## Impact
- ✅ Bot branches will skip workflows on push events but still trigger
them when PRs are created
- ✅ Normal development branches continue to trigger workflows as
expected
- ✅ Reduces unnecessary CI runs and resource usage
- ✅ Maintains full test coverage through PR-triggered workflows
- ✅ All workflow files maintain valid YAML syntax
Fixes #4915.
<!-- START COPILOT CODING AGENT TIPS -->
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---------
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Co-authored-by: njzjz <9496702+njzjz@users.noreply.github.com>
* feat: handle masked forces in test (#4893)
<!-- This is an auto-generated comment: release notes by coderabbit.ai
-->
## Summary by CodeRabbit
- New Features
- Added per-atom weighting for force evaluation: computes and reports
weighted MAE/RMSE alongside unweighted metrics, includes weighted
metrics in system-average summaries, logs weighted force metrics, and
safely handles zero-weight cases. Also propagates the per-atom weight
field into reporting.
- Tests
- Added end-to-end tests validating weighted vs unweighted force
MAE/RMSE and verifying evaluator outputs when using per-atom weight
masks.
<!-- end of auto-generated comment: release notes by coderabbit.ai -->
---------
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
* feat: add comprehensive type hints to core modules excluding backends and tests (#4936)
- [x] Add comprehensive type hints to core modules excluding backends
and tests
- [x] **Fixed type annotation issues from code review:**
- Fixed `head` parameter type from `Any` to `str` in calculator.py
- Fixed `neighbor_list` parameter type to use proper ASE NeighborList
type annotation
- Fixed `**kwargs` type from `object` to `Any` in deep_polar.py
- Fixed `write_model_devi_out` return type from `None` to `np.ndarray`
to match actual return value
- Fixed `get_natoms_vec` return type from `list[int]` to `np.ndarray` to
match actual return type
- Fixed `_get_natoms_2` return type from `list[int]` to `tuple[int,
np.ndarray]` to match actual return values
- Fixed `make_index` return type from `dict[str, int]` to `str` to match
actual return value
- Added missing imports for type annotations (ASE NeighborList, Any)
**Current status:** All type annotation suggestions from code review
have been addressed. All ruff checks pass with zero violations.
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* feat: support using train/valid data from input.json for dp test (#4859)
This pull request extends the testing functionality in DeepMD by
allowing users to specify training and validation data directly via
input JSON files, in addition to existing system and datafile options.
It updates the command-line interface, the main test logic, and adds
comprehensive tests to cover these new features, including support for
recursive glob patterns when selecting systems from JSON files.
### Feature enhancements to testing data sources
* The `test` function in `deepmd/entrypoints/test.py` now accepts
`train_json` and `valid_json` arguments, allowing users to specify
training or validation systems for testing via input JSON files. It
processes these files to extract system paths, including support for
recursive glob patterns. The function also raises an error if no valid
data source is specified.
[[1]](diffhunk://#diff-299c01ed4ee7d0b3f636fe4cb4f0d660a5012b7e95ca0740098b3ace617ab16eL61-R71)
[[2]](diffhunk://#diff-299c01ed4ee7d0b3f636fe4cb4f0d660a5012b7e95ca0740098b3ace617ab16eL104-R151)
* **The command-line interface in `deepmd/main.py` is updated to add
`--train-data` and `--valid-data` arguments for the test subparser,
enabling direct specification of input JSON files for training and
validation data.**
### Test coverage improvements
* New and updated tests in `source/tests/pt/test_dp_test.py` verify the
ability to run tests using input JSON files for both training and
validation data, including cases with recursive glob patterns. This
ensures robust handling of various data source configurations.
[[1]](diffhunk://#diff-ce70e95ffdb1996c7887ea3f63b54d1ae0fef98059572ad03875ca36cfef3c34L33-R35)
[[2]](diffhunk://#diff-ce70e95ffdb1996c7887ea3f63b54d1ae0fef98059572ad03875ca36cfef3c34R49-R59)
[[3]](diffhunk://#diff-ce70e95ffdb1996c7887ea3f63b54d1ae0fef98059572ad03875ca36cfef3c34R103-R116)
[[4]](diffhunk://#diff-ce70e95ffdb1996c7887ea3f63b54d1ae0fef98059572ad03875ca36cfef3c34R164-R273)
* Additional argument parser tests in
`source/tests/common/test_argument_parser.py` confirm correct parsing of
the new `--train-data` and `--valid-data` options.
### Internal code improvements
* Refactored imports and type annotations in
`deepmd/entrypoints/test.py` to support the new functionality and
improve code clarity.
[[1]](diffhunk://#diff-299c01ed4ee7d0b3f636fe4cb4f0d660a5012b7e95ca0740098b3ace617ab16eR17)
[[2]](diffhunk://#diff-299c01ed4ee7d0b3f636fe4cb4f0d660a5012b7e95ca0740098b3ace617ab16eR42-R50)
[[3]](diffhunk://#diff-299c01ed4ee7d0b3f636fe4cb4f0d660a5012b7e95ca0740098b3ace617ab16eL77-R95)
<!-- This is an auto-generated comment: release notes by coderabbit.ai
-->
## Summary by CodeRabbit
- New Features
- Added support for supplying test systems via JSON files, including
selecting training or validation data.
- Introduced CLI options --train-data and --valid-data for the test
command.
- Supports resolving relative paths from JSON and optional recursive
glob patterns.
- Changes
- Test command now requires at least one data source (JSON, data file,
or system); clearer errors when none or no systems found.
- Tests
- Expanded test coverage for JSON-driven inputs and recursive glob
patterns; refactored helpers for improved readability.
<!-- end of auto-generated comment: release notes by coderabbit.ai -->
---------
Signed-off-by: Chun Cai <amoycaic@gmail.com>
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
* feat(tf): implement change-bias command (#4927)
Implements TensorFlow support for the `dp change-bias` command with
proper checkpoint handling and variable restoration. This brings the
TensorFlow backend to feature parity with the PyTorch implementation.
## Key Features
- **Checkpoint file support**: Handles individual checkpoint files
(`.ckpt`, `.meta`, `.data`, `.index`) and frozen models (`.pb`)
- **Proper variable restoration**: Variables are correctly restored from
checkpoints using session initialization before bias modification
- **User-defined bias support**: Supports `-b/--bias-value` option with
proper validation against model type_map
- **Data-based bias calculation**: Leverages existing
`change_energy_bias_lower` functionality for automatic bias computation
- **Checkpoint preservation**: Saves modified variables to separate
checkpoint directory for continued training
- **Cross-backend consistency**: Identical CLI interface and
functionality as PyTorch backend
## Before vs After
**Variable restoration**:
- Before: `Change energy bias of ['O', 'H'] from [0. 0.] to [calculated
values]` (variables never restored)
- After: `Change energy bias of ['O', 'H'] from [-93.57 -187.15] to
[-93.60 -187.19]` (proper restoration)
**Output**: Creates both updated checkpoint files AND frozen model for
continued training
**Documentation**: Comprehensive documentation covering both TensorFlow
and PyTorch backends with examples and backend-specific details
The implementation includes comprehensive test coverage with real model
training to validate functionality without mocks.
Fixes #4018.
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Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
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* style: complete type annotation enforcement for deepmd.pt (#4943)
This PR implements comprehensive type annotation coverage for the
deepmd.pt PyTorch backend and resolves critical TorchScript compilation
errors that prevented model deployment.
## Type Annotation Enforcement
Added complete type annotations to all deepmd.pt module functions,
eliminating 7,030+ ANN violations across 107 Python files. This
provides:
- Better IDE support and code maintainability
- Consistent typing standards throughout the PyTorch backend
- Enhanced developer experience with clear function signatures
## TorchScript Compilation Fixes
Resolved multiple TorchScript compilation errors that prevented model
deployment:
```python
# Before: TorchScript compilation failed
sw.to(dtype=env.GLOBAL_PT_FLOAT_PRECISION) # Error on Optional[Tensor]
# After: Proper None handling
sw.to(dtype=env.GLOBAL_PT_FLOAT_PRECISION) if sw is not None else None
```
Key fixes include:
- Added proper None checks before `.to()` calls on
`Optional[torch.Tensor]` values
- Resolved issues across all descriptor types (SE-A, SE-T, SE-T-TEBD,
DPA1, DPA2, DPA3)
- Fixed abstract method patterns that conflicted with TorchScript
compilation
- Corrected return type annotations in SpinModel to accurately reflect
Optional types
## Pre-commit Compliance
- Fixed deprecated type annotation imports (Dict→dict, Tuple→tuple)
- Resolved import ordering and undefined name issues
- Removed unnecessary imports and improved code consistency
- All pre-commit checks now pass with zero violations
The PyTorch backend now has complete type coverage and full TorchScript
deployment compatibility, enabling production model serving scenarios.
<!-- START COPILOT CODING AGENT TIPS -->
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Co-authored-by: Jinzhe Zeng <jinzhe.zeng@ustc.edu.cn>
* fix(tf): fix serialization of dipole fitting with sel_type (#4934)
Fix #3672.
Fixes backend conversion issues for dipole models when using the
`sel_type` parameter. The `dp convert-backend` command was failing due
to missing serialization support for `None` networks and incomplete
dipole fitting serialization.
- [x] Fix NetworkCollection serialization to handle `None` networks
- [x] Add missing `@variables` dictionary for DipoleFittingSeA PyTorch
compatibility
- [x] Include `sel_type` in serialized data for proper backend
conversion
- [x] Fix TF fitting deserialization to skip `None` networks
- [x] Add comprehensive tests for `sel_type` parameter
- [x] Remove duplicate test classes and merge parameterized tests
- [x] Clean up accidentally committed test output files
- [x] Refactor addi…
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This PR fixes the warning message when running on CPU:
Summary by CodeRabbit