chore: sync devel into master (2026-02-26)#944
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njzjz-bot wants to merge 40 commits intodeepmodeling:masterfrom
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chore: sync devel into master (2026-02-26)#944njzjz-bot wants to merge 40 commits intodeepmodeling:masterfrom
njzjz-bot wants to merge 40 commits intodeepmodeling:masterfrom
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<!--pre-commit.ci start--> updates: - [github.com/astral-sh/ruff-pre-commit: v0.14.1 → v0.14.2](astral-sh/ruff-pre-commit@v0.14.1...v0.14.2) <!--pre-commit.ci end--> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
<!--pre-commit.ci start--> updates: - [github.com/astral-sh/ruff-pre-commit: v0.14.2 → v0.14.3](astral-sh/ruff-pre-commit@v0.14.2...v0.14.3) <!--pre-commit.ci end--> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
<!--pre-commit.ci start--> updates: - [github.com/astral-sh/ruff-pre-commit: v0.14.3 → v0.14.5](astral-sh/ruff-pre-commit@v0.14.3...v0.14.5) <!--pre-commit.ci end--> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
<!--pre-commit.ci start--> updates: - [github.com/astral-sh/ruff-pre-commit: v0.14.5 → v0.14.6](astral-sh/ruff-pre-commit@v0.14.5...v0.14.6) <!--pre-commit.ci end--> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Bumps [actions/checkout](https://github.com/actions/checkout) from 5 to 6. <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>v6.0.0</h2> <h2>What's Changed</h2> <ul> <li>Update README to include Node.js 24 support details and requirements by <a href="https://github.com/salmanmkc"><code>@salmanmkc</code></a> in <a href="https://redirect.github.com/actions/checkout/pull/2248">actions/checkout#2248</a></li> <li>Persist creds to a separate file by <a href="https://github.com/ericsciple"><code>@ericsciple</code></a> in <a href="https://redirect.github.com/actions/checkout/pull/2286">actions/checkout#2286</a></li> <li>v6-beta by <a href="https://github.com/ericsciple"><code>@ericsciple</code></a> in <a href="https://redirect.github.com/actions/checkout/pull/2298">actions/checkout#2298</a></li> <li>update readme/changelog for v6 by <a href="https://github.com/ericsciple"><code>@ericsciple</code></a> in <a href="https://redirect.github.com/actions/checkout/pull/2311">actions/checkout#2311</a></li> </ul> <p><strong>Full Changelog</strong>: <a href="https://github.com/actions/checkout/compare/v5.0.0...v6.0.0">https://github.com/actions/checkout/compare/v5.0.0...v6.0.0</a></p> <h2>v6-beta</h2> <h2>What's Changed</h2> <p>Updated persist-credentials to store the credentials under <code>$RUNNER_TEMP</code> instead of directly in the local git config.</p> <p>This requires a minimum Actions Runner version of <a href="https://github.com/actions/runner/releases/tag/v2.329.0">v2.329.0</a> to access the persisted credentials for <a href="https://docs.github.com/en/actions/tutorials/use-containerized-services/create-a-docker-container-action">Docker container action</a> scenarios.</p> <h2>v5.0.1</h2> <h2>What's Changed</h2> <ul> <li>Port v6 cleanup to v5 by <a href="https://github.com/ericsciple"><code>@ericsciple</code></a> in <a href="https://redirect.github.com/actions/checkout/pull/2301">actions/checkout#2301</a></li> </ul> <p><strong>Full Changelog</strong>: <a href="https://github.com/actions/checkout/compare/v5...v5.0.1">https://github.com/actions/checkout/compare/v5...v5.0.1</a></p> </blockquote> </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>V6.0.0</h2> <ul> <li>Persist creds to a separate file by <a href="https://github.com/ericsciple"><code>@ericsciple</code></a> in <a href="https://redirect.github.com/actions/checkout/pull/2286">actions/checkout#2286</a></li> <li>Update README to include Node.js 24 support details and requirements by <a href="https://github.com/salmanmkc"><code>@salmanmkc</code></a> in <a href="https://redirect.github.com/actions/checkout/pull/2248">actions/checkout#2248</a></li> </ul> <h2>V5.0.1</h2> <ul> <li>Port v6 cleanup to v5 by <a href="https://github.com/ericsciple"><code>@ericsciple</code></a> in <a href="https://redirect.github.com/actions/checkout/pull/2301">actions/checkout#2301</a></li> </ul> <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>V4.3.1</h2> <ul> <li>Port v6 cleanup to v4 by <a href="https://github.com/ericsciple"><code>@ericsciple</code></a> in <a href="https://redirect.github.com/actions/checkout/pull/2305">actions/checkout#2305</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> </ul> <!-- raw HTML omitted --> </blockquote> <p>... (truncated)</p> </details> <details> <summary>Commits</summary> <ul> <li><a href="https://github.com/actions/checkout/commit/1af3b93b6815bc44a9784bd300feb67ff0d1eeb3"><code>1af3b93</code></a> update readme/changelog for v6 (<a href="https://redirect.github.com/actions/checkout/issues/2311">#2311</a>)</li> <li><a href="https://github.com/actions/checkout/commit/71cf2267d89c5cb81562390fa70a37fa40b1305e"><code>71cf226</code></a> v6-beta (<a href="https://redirect.github.com/actions/checkout/issues/2298">#2298</a>)</li> <li><a href="https://github.com/actions/checkout/commit/069c6959146423d11cd0184e6accf28f9d45f06e"><code>069c695</code></a> Persist creds to a separate file (<a href="https://redirect.github.com/actions/checkout/issues/2286">#2286</a>)</li> <li><a href="https://github.com/actions/checkout/commit/ff7abcd0c3c05ccf6adc123a8cd1fd4fb30fb493"><code>ff7abcd</code></a> Update README to include Node.js 24 support details and requirements (<a href="https://redirect.github.com/actions/checkout/issues/2248">#2248</a>)</li> <li>See full diff in <a href="https://github.com/actions/checkout/compare/v5...v6">compare view</a></li> </ul> </details> <br /> [](https://docs.github.com/en/github/managing-security-vulnerabilities/about-dependabot-security-updates#about-compatibility-scores) Dependabot will resolve any conflicts with this PR as long as you don't alter it yourself. You can also trigger a rebase manually by commenting `@dependabot rebase`. [//]: # (dependabot-automerge-start) [//]: # (dependabot-automerge-end) --- <details> <summary>Dependabot commands and options</summary> <br /> You can trigger Dependabot actions by commenting on this PR: - `@dependabot rebase` will rebase this PR - `@dependabot recreate` will recreate this PR, overwriting any edits that have been made to it - `@dependabot merge` will merge this PR after your CI passes on it - `@dependabot squash and merge` will squash and merge this PR after your CI passes on it - `@dependabot cancel merge` will cancel a previously requested merge and block automerging - `@dependabot reopen` will reopen this PR if it is closed - `@dependabot close` will close this PR and stop Dependabot recreating it. You can achieve the same result by closing it manually - `@dependabot show <dependency name> ignore conditions` will show all of the ignore conditions of the specified dependency - `@dependabot ignore this major version` will close this PR and stop Dependabot creating any more for this major version (unless you reopen the PR or upgrade to it yourself) - `@dependabot ignore this minor version` will close this PR and stop Dependabot creating any more for this minor version (unless you reopen the PR or upgrade to it yourself) - `@dependabot ignore this dependency` will close this PR and stop Dependabot creating any more for this dependency (unless you reopen the PR or upgrade to it yourself) </details> Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
<!--pre-commit.ci start--> updates: - [github.com/astral-sh/ruff-pre-commit: v0.14.6 → v0.14.7](astral-sh/ruff-pre-commit@v0.14.6...v0.14.7) <!--pre-commit.ci end--> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
<!--pre-commit.ci start--> updates: - [github.com/astral-sh/ruff-pre-commit: v0.14.7 → v0.14.8](astral-sh/ruff-pre-commit@v0.14.7...v0.14.8) <!--pre-commit.ci end--> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
<!--pre-commit.ci start--> updates: - [github.com/astral-sh/ruff-pre-commit: v0.14.8 → v0.14.9](astral-sh/ruff-pre-commit@v0.14.8...v0.14.9) <!--pre-commit.ci end--> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
<!--pre-commit.ci start--> updates: - [github.com/astral-sh/ruff-pre-commit: v0.14.9 → v0.14.10](astral-sh/ruff-pre-commit@v0.14.9...v0.14.10) <!--pre-commit.ci end--> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
<!--pre-commit.ci start--> updates: - [github.com/astral-sh/ruff-pre-commit: v0.14.10 → v0.14.11](astral-sh/ruff-pre-commit@v0.14.10...v0.14.11) <!--pre-commit.ci end--> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
…son (deepmodeling#924) `math.isclose()` requires scalar arguments but was receiving 1D numpy arrays, causing `TypeError: only 0-dimensional arrays can be converted to Python scalars` in CP2K AIMD output parsing. ## Changes - Extract scalar values from `energies` arrays using `[0]` indexing before comparison in `Cp2kSystems.__next__()` ```python # Before assert math.isclose( log_info_dict["energies"], xyz_info_dict["energies"], abs_tol=1.0e-6 ) # After assert math.isclose( log_info_dict["energies"][0], xyz_info_dict["energies"][0], abs_tol=1.0e-6 ) ``` Both `log_info_dict["energies"]` and `xyz_info_dict["energies"]` are shape `(1,)` arrays created by `np.asarray([energy])`, so `[0]` extracts the scalar energy value for comparison while preserving the original arrays in the assertion message for debugging. <!-- START COPILOT ORIGINAL PROMPT --> <details> <summary>Original prompt</summary> > > ---- > > *This section details on the original issue you should resolve* > > <issue_title>[BUG] cp2k: `TypeError: only 0-dimensional arrays can be converted to Python scalars`</issue_title> > <issue_description>### Bug summary > > The recent CI runs reported an error on CP2K tests: `TypeError: only 0-dimensional arrays can be converted to Python scalars`. See the log below. > > ### dpdata Version > > devel > > ### Input Files, Running Commands, Error Log, etc. > > ``` > ====================================================================== > ERROR: test_nframs (test_cp2k_aimd_output.TestCp2kAimdStressOutput.test_nframs) > ---------------------------------------------------------------------- > Traceback (most recent call last): > File "/home/runner/work/dpdata/dpdata/tests/test_cp2k_aimd_output.py", line 23, in setUp > self.system_1 = dpdata.LabeledSystem("cp2k/aimd_stress", fmt="cp2k/aimd_output") > ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ > File "/home/runner/work/dpdata/dpdata/dpdata/system.py", line 197, in __init__ > self.from_fmt( > File "/home/runner/work/dpdata/dpdata/dpdata/system.py", line 234, in from_fmt > return self.from_fmt_obj(load_format(fmt), file_name, **kwargs) > ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ > File "/home/runner/work/dpdata/dpdata/dpdata/system.py", line 1224, in from_fmt_obj > data = fmtobj.from_labeled_system(file_name, **kwargs) > ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ > File "/home/runner/work/dpdata/dpdata/dpdata/plugins/cp2k.py", line 25, in from_labeled_system > return tuple(Cp2kSystems(log_file, xyz_file, restart)) > ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ > File "/home/runner/work/dpdata/dpdata/dpdata/cp2k/output.py", line 67, in __next__ > assert math.isclose( > ^^^^^^^^^^^^^ > TypeError: only 0-dimensional arrays can be converted to Python scalars > ``` > > ### Steps to Reproduce > > Run the UT. > > ### Further Information, Files, and Links > > _No response_</issue_description> > > ## Comments on the Issue (you are @copilot in this section) > > <comments> > </comments> > </details> <!-- START COPILOT CODING AGENT SUFFIX --> - Fixes deepmodeling#922 <!-- 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.
<!--pre-commit.ci start--> updates: - [github.com/astral-sh/ruff-pre-commit: v0.14.11 → v0.14.13](astral-sh/ruff-pre-commit@v0.14.11...v0.14.13) <!--pre-commit.ci end--> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Replace token-based authentication with OIDC (OpenID Connect) for codecov-action. This is more secure and eliminates the need to manage upload tokens. Changes: - Add use_oidc: true to codecov-action configuration - Add id-token: write permission at workflow level - Remove token parameter from codecov-action (ignored when using OIDC) This improves security and follows codecov-action best practices. Generated by the task: njzjz-bot/njzjz-bot#25. <!-- This is an auto-generated comment: release notes by coderabbit.ai --> ## Summary by CodeRabbit * **Chores** * Updated CI/CD workflow configuration to improve the build and testing process. <sub>✏️ Tip: You can customize this high-level summary in your review settings.</sub> <!-- end of auto-generated comment: release notes by coderabbit.ai -->
<!--pre-commit.ci start--> updates: - [github.com/astral-sh/ruff-pre-commit: v0.14.13 → v0.14.14](astral-sh/ruff-pre-commit@v0.14.13...v0.14.14) <!--pre-commit.ci end--> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
deepmodeling#554 dumps file names in short name. However, `dpgen simplify` replies on the filename to find a system in MultiSystems. This commit makes it possible to find a system by its short name. <!-- This is an auto-generated comment: release notes by coderabbit.ai --> ## Summary by CodeRabbit * **New Features** * Systems in collections can now be accessed by their short name as well as by formula-based keys. * **Tests** * Added test coverage verifying index-based access using a system's short name. <!-- end of auto-generated comment: release notes by coderabbit.ai --> --------- Signed-off-by: Jinzhe Zeng <njzjz@qq.com> Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>
<!-- This is an auto-generated comment: release notes by coderabbit.ai --> ## Summary by CodeRabbit * **New Features** * Add LMDB-backed storage to save/load single or multiple atomic systems with per-frame data, metadata, and configurable frame indexing. * **Tests** * Add extensive LMDB tests covering labeled/unlabeled systems, multi-system round-trips, error handling, custom data-type preservation, and auto-registration. * **Chores** * Add runtime dependencies for LMDB support (lmdb, msgpack-numpy). <!-- end of auto-generated comment: release notes by coderabbit.ai -->
<!--pre-commit.ci start--> updates: - [github.com/astral-sh/ruff-pre-commit: v0.14.14 → v0.15.0](astral-sh/ruff-pre-commit@v0.14.14...v0.15.0) <!--pre-commit.ci end--> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
) <!-- This is an auto-generated comment: release notes by coderabbit.ai --> ## Summary by CodeRabbit * **New Features** * Optional atom-count padding for DeepMD mixed-format: systems can be padded to a specified multiple using virtual atoms (type -1); virtual atoms are stripped on load. Systems are now grouped by padded atom counts, which can reduce subdirectories and reorganize storage. * Exposed option to enable padding when creating mixed-format datasets. * **Tests** * Added tests covering padding, type-mapping, and per-atom data (fparam/aparam) preservation. <!-- end of auto-generated comment: release notes by coderabbit.ai --> --------- Co-authored-by: Han Wang <wang_han@iapcm.ac.cn>
Reverts deepmodeling#837 Both issues have been fixed <!-- This is an auto-generated comment: release notes by coderabbit.ai --> ## Summary by CodeRabbit * **Chores** * Removed version constraints on chemistry and numeric dependencies in CI workflows (e.g., rdkit and numpy), switching to more permissive installs so the latest compatible package releases are used during automated tests. <!-- end of auto-generated comment: release notes by coderabbit.ai -->
<!--pre-commit.ci start--> updates: - [github.com/astral-sh/ruff-pre-commit: v0.15.0 → v0.15.1](astral-sh/ruff-pre-commit@v0.15.0...v0.15.1) <!--pre-commit.ci end--> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
…#936) Bumps [jakebailey/pyright-action](https://github.com/jakebailey/pyright-action) from 2 to 3. <details> <summary>Release notes</summary> <p><em>Sourced from <a href="https://github.com/jakebailey/pyright-action/releases">jakebailey/pyright-action's releases</a>.</em></p> <blockquote> <h2>v3.0.0</h2> <ul> <li>Update github actions (<a href="https://redirect.github.com/jakebailey/pyright-action/issues/208">#208</a>) (5ceb87e)</li> <li>Update actions/cache action to v5 (<a href="https://redirect.github.com/jakebailey/pyright-action/issues/210">#210</a>) (49e6fb4)</li> <li>Disable type lint of build script (d991920)</li> <li>Fix tests (1edc551)</li> <li>Update action related deps (ce79cd6)</li> <li>Update non-action deps (88a1ce8)</li> <li>More v24 updates (c45be15)</li> <li>Bump to v3, node24 (7dc11cf)</li> <li>Update deps (f8c6100)</li> <li>Update github actions (<a href="https://redirect.github.com/jakebailey/pyright-action/issues/191">#191</a>) (e20b42a)</li> <li>Update github actions to v6 (<a href="https://redirect.github.com/jakebailey/pyright-action/issues/195">#195</a>) (f5686a6)</li> <li>Update deps (e058033)</li> </ul> <h2>v2.3.3</h2> <ul> <li>Fix lint (4599f31)</li> <li>Replace jest-path-serializer (1349f1a)</li> <li>Fix deps (f701448)</li> <li>fmt (ec50111)</li> <li>Update engines (41972b7)</li> <li>Update github actions (<a href="https://redirect.github.com/jakebailey/pyright-action/issues/180">#180</a>) (86e183a)</li> <li>Update actions/checkout action to v5 (<a href="https://redirect.github.com/jakebailey/pyright-action/issues/190">#190</a>) (8b711b9)</li> <li>Update deps (9631dc2)</li> <li>Update deps (fa0d678)</li> <li>Update github actions (<a href="https://redirect.github.com/jakebailey/pyright-action/issues/163">#163</a>) (623784a)</li> <li>Fix eslint (73a65bd)</li> <li>Update deps (dee7200)</li> <li>Update deps (ea37d1c)</li> <li>Update nvmrc (fb32d81)</li> <li>Update eslint (b0c5af5)</li> <li>Update deps (f4851c1)</li> <li>Update actions/cache action to v4.2.0 (<a href="https://redirect.github.com/jakebailey/pyright-action/issues/159">#159</a>) (57f6678)</li> <li>Update codecov/codecov-action action to v5 (<a href="https://redirect.github.com/jakebailey/pyright-action/issues/154">#154</a>) (f572338)</li> <li>Update github actions (<a href="https://redirect.github.com/jakebailey/pyright-action/issues/146">#146</a>) (b7d7f8e)</li> <li>Update deps (b721321)</li> <li>Update deps (4156862)</li> <li>Update github actions (<a href="https://redirect.github.com/jakebailey/pyright-action/issues/121">#121</a>) (ec480a0)</li> <li>Update deps (bfe39b3)</li> </ul> <h2>v2.3.2</h2> <ul> <li>Support explicit "latest" version (f6f691c)</li> <li>Update deps (c1dc810)</li> <li>Update node to latest runner version (0b5777b)</li> <li>Update deps (66bf589)</li> <li>Fix lint fmt (222ed7c)</li> <li>Fix compile for now (fa845b7)</li> <li>Update deps (d7583ac)</li> <li>Update vitest (64b81cd)</li> <li>Update deps (a084e58)</li> <li>Update deps (cbcd89c)</li> </ul> <!-- raw HTML omitted --> </blockquote> <p>... (truncated)</p> </details> <details> <summary>Commits</summary> <ul> <li><a href="https://github.com/jakebailey/pyright-action/commit/8ec14b5cfe41f26e5f41686a31eb6012758217ef"><code>8ec14b5</code></a> Release v3.0.2</li> <li><a href="https://github.com/jakebailey/pyright-action/commit/03fd2c0c594f76acd9e4472e00361d0ac371d3c8"><code>03fd2c0</code></a> Update mentioned checkout in readme</li> <li><a href="https://github.com/jakebailey/pyright-action/commit/9fb0169fdc561233dc09859a051595e53957b9ca"><code>9fb0169</code></a> Update mentioned setup-python in readme</li> <li><a href="https://github.com/jakebailey/pyright-action/commit/19c6c236fc5e080abdd5561f14f026ca883378c5"><code>19c6c23</code></a> Switch to tiny-jsonc</li> <li><a href="https://github.com/jakebailey/pyright-action/commit/12964857f8310c85319bcada3388572b1f5cf412"><code>1296485</code></a> fix lint</li> <li><a href="https://github.com/jakebailey/pyright-action/commit/20b106db9ef172e8c30782f0a3c4d9a99afa6eee"><code>20b106d</code></a> output metafile in build</li> <li><a href="https://github.com/jakebailey/pyright-action/commit/9b73e5f097fdaa21dcce526700dcf7415e09d3e6"><code>9b73e5f</code></a> Release v3.0.1</li> <li><a href="https://github.com/jakebailey/pyright-action/commit/c781035d4810ccba2ce648980dcc58eb7169468a"><code>c781035</code></a> Make docs reference v3</li> <li><a href="https://github.com/jakebailey/pyright-action/commit/61e7045315c3d22664d21e4fed96f366a9459e06"><code>61e7045</code></a> Release v3.0.0</li> <li><a href="https://github.com/jakebailey/pyright-action/commit/5ceb87eecfe07b8c6b4c1aa53086b343fde0db9c"><code>5ceb87e</code></a> Update github actions (<a href="https://redirect.github.com/jakebailey/pyright-action/issues/208">#208</a>)</li> <li>Additional commits viewable in <a href="https://github.com/jakebailey/pyright-action/compare/v2...v3">compare view</a></li> </ul> </details> <br /> [](https://docs.github.com/en/github/managing-security-vulnerabilities/about-dependabot-security-updates#about-compatibility-scores) Dependabot will resolve any conflicts with this PR as long as you don't alter it yourself. You can also trigger a rebase manually by commenting `@dependabot rebase`. [//]: # (dependabot-automerge-start) [//]: # (dependabot-automerge-end) --- <details> <summary>Dependabot commands and options</summary> <br /> You can trigger Dependabot actions by commenting on this PR: - `@dependabot rebase` will rebase this PR - `@dependabot recreate` will recreate this PR, overwriting any edits that have been made to it - `@dependabot show <dependency name> ignore conditions` will show all of the ignore conditions of the specified dependency - `@dependabot ignore this major version` will close this PR and stop Dependabot creating any more for this major version (unless you reopen the PR or upgrade to it yourself) - `@dependabot ignore this minor version` will close this PR and stop Dependabot creating any more for this minor version (unless you reopen the PR or upgrade to it yourself) - `@dependabot ignore this dependency` will close this PR and stop Dependabot creating any more for this dependency (unless you reopen the PR or upgrade to it yourself) </details> Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
This PR adds an Agent Skill for using dpdata CLI to convert and manipulate atomic simulation data formats. ## What's included - `skills/dpdata-cli/SKILL.md` - Main skill file with: - CLI usage documentation (uvx dpdata) - All CLI arguments explained - Common conversion examples - 50+ supported formats reference (VASP, LAMMPS, QE, CP2K, Gaussian, ABACUS, DeePMD-kit, etc.) - Links to stable documentation - `skills/dpdata-cli/README.md` - Installation and usage guide ## Why This skill enables AI agents (like OpenClaw, Claude Code, etc.) to: - Convert between DFT/MD output formats - Prepare training data for DeePMD-kit - Handle atomic simulation data via command line Follows the [Agent Skills specification](https://agentskills.io/specification). Authored by OpenClaw (model: glm-5) <!-- This is an auto-generated comment: release notes by coderabbit.ai --> ## Summary by CodeRabbit * **Documentation** * Added comprehensive documentation and a dedicated skill guide for the dpdata CLI Agent, including installation and quick-start instructions, command-line usage and examples (format conversion, multi-system handling), a full list of supported formats (DeePMD-kit, VASP, LAMMPS, ABACUS, QE, CP2K, Gaussian, etc.), auto-detection tips, compressed output options, and references. <!-- end of auto-generated comment: release notes by coderabbit.ai --> Co-authored-by: njzjz-bot <njzjz-bot@users.noreply.github.com>
## Summary This PR updates configuration files to reference `master` branch instead of `devel`, in preparation for deprecating the `devel` branch (as discussed in deepmodeling#933). ## Changes - `.pre-commit-config.yaml`: Update `ci.autoupdate_branch` from `devel` to `master` - `.github/dependabot.yml`: Update `target-branch` from `devel` to `master` ## Related Closes deepmodeling#933 --- OpenClaw glm-5 <!-- This is an auto-generated comment: release notes by coderabbit.ai --> ## Summary by CodeRabbit * **Chores** * Updated dependency management configuration to target the repository's default branch instead of a specific branch * Updated pre-commit configuration to use the repository's default branch for auto-updates <!-- end of auto-generated comment: release notes by coderabbit.ai --> Co-authored-by: OpenClaw <bot@njzjz.win>
<!--pre-commit.ci start--> updates: - [github.com/astral-sh/ruff-pre-commit: v0.15.1 → v0.15.2](astral-sh/ruff-pre-commit@v0.15.1...v0.15.2) <!--pre-commit.ci end--> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Follow up deepmodeling/deepmd-kit@69eb0c3, use mdformat to format Markdown. - Replace blacken-docs with mdformat <!-- This is an auto-generated comment: release notes by coderabbit.ai --> ## Summary by CodeRabbit * **Chores** * Updated pre-commit config to switch to an mdformat-based markdown formatter, add exclusions for tests, and include several mdformat plugins. * **Documentation** * Added detailed BondOrderSystem docs with usage examples and sanitization/charge guidance. * Expanded and clarified multiple system docs (mixed, multi, system) with examples and formatting improvements. * Minor formatting/readability edits to AGENTS.md and dpdata-cli README/SKILL.md. <!-- end of auto-generated comment: release notes by coderabbit.ai --> --------- Co-authored-by: njzjz-bot <njzjz-bot@users.noreply.github.com> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
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## master #944 +/- ##
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+ Coverage 85.41% 86.37% +0.95%
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+ Misses 1105 1102 -3 ☔ View full report in Codecov by Sentry. 🚀 New features to boost your workflow:
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Merging this PR will degrade performance by 27.72%
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Comparing njzjz-bot:sync-devel-to-master-20260226 (ae134fe) with master (8b6a0a7)
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I realize that I can directly rename the branch. |
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Sync latest upstream devel into master by opening a PR from a branch cut at origin/devel.\n\n- Source branch tip:
ae134fe\n- Base branch tip:8b6a0a7\n\nAuthored by OpenClaw (model: gpt-5.3-codex)