merge devel to master (v1.0.0) #909
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…eling#858) The previous results are not reliable, due to CodSpeedHQ/pytest-codspeed#37. The new method is good. See https://docs.codspeed.io/instruments/walltime/#usage-with-github-actions <!-- This is an auto-generated comment: release notes by coderabbit.ai --> ## Summary by CodeRabbit * **Chores** * Updated the benchmark workflow to run only for the "deepmodeling" repository owner and switched the runner environment to a custom setup. <!-- end of auto-generated comment: release notes by coderabbit.ai -->
<!--pre-commit.ci start--> updates: - [github.com/astral-sh/ruff-pre-commit: v0.12.5 → v0.12.7](astral-sh/ruff-pre-commit@v0.12.5...v0.12.7) <!--pre-commit.ci end--> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
…gered (deepmodeling#861) <!-- This is an auto-generated comment: release notes by coderabbit.ai --> ## Summary by CodeRabbit * **Bug Fixes** * Improved error handling to detect and alert users when there is a mismatch between atom counts and types in VASP OUTCAR files, preventing silent data inconsistencies. * **Refactor** * Enhanced file handling for frame extraction to ensure files are properly closed and code is more maintainable. * **Tests** * Added a new test to verify correct error reporting for OUTCAR files with more than 10 atom types. <!-- end of auto-generated comment: release notes by coderabbit.ai --> Co-authored-by: Han Wang <[email protected]>
<!-- This is an auto-generated comment: release notes by coderabbit.ai --> ## Summary by CodeRabbit * **New Features** * Added an option to filter VASP XML calculation steps based on SCF convergence status. * Introduced a new parameter to enable or disable convergence checking when loading VASP XML files. * **Tests** * Added new tests to verify behavior with and without SCF convergence filtering using sample VASP XML files. * Included a new sample VASP XML output file for testing purposes. <!-- end of auto-generated comment: release notes by coderabbit.ai --> --------- Signed-off-by: Han Wang <[email protected]> Co-authored-by: Han Wang <[email protected]> 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 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> <li>See full diff in <a href="https://github.com/actions/checkout/compare/v4...v5">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] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
<!--pre-commit.ci start--> updates: - [github.com/pre-commit/pre-commit-hooks: v5.0.0 → v6.0.0](pre-commit/pre-commit-hooks@v5.0.0...v6.0.0) - [github.com/astral-sh/ruff-pre-commit: v0.12.7 → v0.12.8](astral-sh/ruff-pre-commit@v0.12.7...v0.12.8) <!--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: v0.12.8 → v0.12.9](astral-sh/ruff-pre-commit@v0.12.8...v0.12.9) <!--pre-commit.ci end--> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
…ction (deepmodeling#867) This PR adds comprehensive support for different LAMMPS atom styles beyond the previously supported "atomic" style. The implementation now supports 8 common LAMMPS atom styles with **automatic detection** and charge extraction while maintaining full backward compatibility. ## Supported Atom Styles - **atomic**: atom-ID atom-type x y z (default fallback) - **full**: atom-ID molecule-ID atom-type q x y z (includes charges and molecule IDs) - **charge**: atom-ID atom-type q x y z (includes charges) - **bond**: atom-ID molecule-ID atom-type x y z (includes molecule IDs) - **angle**: atom-ID molecule-ID atom-type x y z - **molecular**: atom-ID molecule-ID atom-type x y z - **dipole**: atom-ID atom-type q x y z mux muy muz (includes charges) - **sphere**: atom-ID atom-type diameter density x y z ## Key Features - **Automatic atom style detection**: Parses LAMMPS data file headers and comments (e.g., `Atoms # full`) with intelligent fallback based on column analysis - **Automatic charge extraction and registration**: For atom styles that include charges (full, charge, dipole), charges are automatically extracted, stored, and properly registered as a DataType - **Smart defaults**: `atom_style="auto"` is now the default, eliminating the need for manual specification in most cases - **Backward compatibility**: Existing code continues to work without any changes - **Robust error handling**: Clear error messages for unsupported atom styles with graceful fallbacks ## Usage ```python # Automatic detection (new default behavior) system = dpdata.System("data.lmp", type_map=["O", "H"]) # Detects style automatically # Full style with charges and molecule IDs system = dpdata.System("data.lmp", type_map=["O", "H"]) # Auto-detects "full" style print(system["charges"]) # Access extracted charges # Explicit styles still supported for edge cases system = dpdata.System("data.lmp", type_map=["O", "H"], atom_style="charge") ``` ## Implementation Details The solution adds intelligent atom style detection that: 1. Parses header comments after "Atoms" sections for explicit style declarations 2. Uses heuristic analysis of column count and content patterns as fallback 3. Maintains the existing configurable atom style parameter for explicit control 4. Automatically registers charge DataType when charge data is present All parsing functions (`get_atype`, `get_posi`, `get_charges`) were updated to handle different column arrangements with full type hints. Comprehensive tests cover both comment-based and heuristic detection scenarios. Fixes deepmodeling#853. <!-- 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. --------- Co-authored-by: copilot-swe-agent[bot] <[email protected]> Co-authored-by: njzjz <[email protected]> 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: v0.12.9 → v0.12.10](astral-sh/ruff-pre-commit@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>
…tic commit guidelines (deepmodeling#873) This PR adds a comprehensive `.github/copilot-instructions.md` file that provides GitHub Copilot coding agents with detailed guidance on how to work effectively in the dpdata repository. The instructions include: **Package Management with uv:** - Uses `uv pip install` for all package installations instead of pip - Provides faster and more reliable dependency management - Includes troubleshooting for network timeouts and installation issues **Semantic Commit Guidelines:** - Enforces semantic commit message format: `type(scope): description` - Defines commit types: feat, fix, docs, style, refactor, test, chore - Requires semantic format for both commits and PR titles - Provides clear examples for different scenarios **Core Development Workflow:** - Step-by-step installation process using uv - Test execution commands with timing expectations (~10 seconds for full suite) - Linting and formatting using ruff with "NEVER CANCEL" warnings - Documentation build process using Sphinx **Validated Commands:** All commands have been tested and validated: - CLI functionality (`dpdata --version`, `dpdata --help`) - Test suite execution (`python -m unittest discover`) - Individual test modules (`python -m unittest test_<module>.py`) - Code quality tools (`ruff check`, `ruff format`) - Coverage reporting **Key Features:** - Imperative tone throughout with clear directives - Timing expectations for all operations - Comprehensive troubleshooting section - Repository structure overview - Format-specific development workflows - Clear validation scenarios for testing changes **Additional Improvements:** - Updated `.gitignore` to exclude test artifacts (`tests/data_*`, `tests/tmp.*`, `tests/.coverage`) - Documented core vs optional dependency relationships - Included guidance for plugin development The instructions follow GitHub Copilot's expected format with firm directives to reference them first before falling back to search or bash commands. Fixes deepmodeling#872. <!-- 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. --------- Co-authored-by: copilot-swe-agent[bot] <[email protected]> Co-authored-by: njzjz <[email protected]> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Abacus updates its output format, so these keywords were not right. I have updated them to support both eariler ones and latest one by removing the unit part. <!-- This is an auto-generated comment: release notes by coderabbit.ai --> ## Summary by CodeRabbit * **Bug Fixes** * Improved robustness when reading ABACUS simulation outputs by accepting more variations of energy, force, and stress headers. * More permissive header matching reduces failures from minor log-format differences. * Preserves existing convergence and extraction behavior while improving tolerance for alternate log phrasing. * Reduces missed or incomplete parses, increasing reliability across ABACUS log variants. <!-- 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>
…deling#882) This PR implements the missing `to_system` method for the `LAMMPSDumpFormat` class, enabling conversion from LAMMPS .lmp files to .dump format. ## Problem Previously, users could not convert LAMMPS data files (.lmp) to dump format (.dump) because the `LAMMPSDumpFormat` class only supported reading dump files (`from_system`) but not writing them (`to_system`). This resulted in a `NotImplementedError` when attempting the conversion: ```python import dpdata system = dpdata.System('minimized_structure.output', fmt='lammps/lmp') system.to('lammps/dump', 'output.dump') # Raised NotImplementedError ``` ## Solution Added the missing functionality by: 1. **Implementing `from_system_data()` function** in `dpdata/lammps/dump.py` that converts system data to LAMMPS dump format string with proper: - Timestep headers - Atom count information - Box bounds and tilt parameters - Coordinate data with correct LAMMPS indexing 2. **Adding `to_system()` method** to `LAMMPSDumpFormat` class that uses the new conversion function 3. **Adding comprehensive tests** to verify the conversion works correctly and maintains data integrity ## Verification - All existing tests continue to pass (101 LAMMPS-related tests) - Round-trip conversions (LMP → DUMP → LMP) preserve coordinates with perfect precision - Generated dump files follow LAMMPS standard format and can be loaded back successfully - The exact use case from the issue now works as expected ## Example Usage ```python import dpdata # Load LAMMPS data file system = dpdata.System('data.lmp', fmt='lammps/lmp', type_map=['O', 'H']) # Convert to dump format (now works!) system.to('lammps/dump', 'output.dump') # Generated dump file can be loaded back system2 = dpdata.System('output.dump', fmt='lammps/dump', type_map=['O', 'H']) ``` Fixes deepmodeling#664. <!-- 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. --------- Co-authored-by: copilot-swe-agent[bot] <[email protected]> Co-authored-by: njzjz <[email protected]>
…methods with file handler support (deepmodeling#888) Implements export functionality for QUIP/GAP XYZ format with support for both file paths and file handlers. ## Key Features - **Single System Export**: `to_labeled_system` writes individual systems to QUIP/GAP XYZ format - **Multi-System Export**: `to_multi_systems` yields file handlers for writing multiple systems to a single file - **File Handler Support**: Both methods accept file paths or file handlers as input - **Smart Write Logic**: Always overwrites for file paths, appends only when using file handlers ## Implementation Details The `to_multi_systems` method uses a generator pattern that yields file handlers instead of filenames, enabling more flexible file management. The `to_labeled_system` method handles both file paths and file handlers appropriately, with different write modes for each. When writing multiple systems to the same file handler, configurations are written directly adjacent to each other without separator lines, matching the standard QUIP/GAP XYZ format specification. ## Testing Comprehensive test suite covers: - Single system export functionality - Multi-system export to shared file - Roundtrip consistency verification - All existing QUIP/GAP XYZ tests continue to pass (121 tests) This maintains full backward compatibility while adding the requested export capabilities. <!-- START COPILOT CODING AGENT TIPS --> --- ✨ Let Copilot coding agent [set things up for you](https://github.com/deepmodeling/dpdata/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) — coding agent works faster and does higher quality work when set up for your repo. --------- Signed-off-by: Jinzhe Zeng <[email protected]> Co-authored-by: copilot-swe-agent[bot] <[email protected]> Co-authored-by: njzjz <[email protected]> Co-authored-by: Jinzhe Zeng <[email protected]> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
This PR adds extended XYZ format support and comprehensive
cross-compatibility testing with ASE (Atomic Simulation Environment),
including rigorous verification of energy and force preservation.
## Changes Made
- **Added extended XYZ format alias**: `extxyz` now aliases to the
existing QuipGapXYZFormat implementation
- **Added additional format aliases**: `gpumd`, `nequip`, and `mace` all
point to the same QuipGapXYZFormat for compatibility
- **Added comprehensive ASE cross-compatibility tests**: Tests verify
that:
- dpdata can read extxyz files that ASE can also read
- Basic xyz files can be exchanged between dpdata and ASE
- Manual extxyz files work with both systems
- **Added energy and force verification**: Uses the `CompLabeledSys`
utility to rigorously verify that energies and forces are correctly
preserved through dpdata ↔ ASE round-trip conversion:
- Reads extxyz files with dpdata (including energies and forces)
- Processes through ASE (reads with ASE, writes back with ASE)
- Reads ASE output back with dpdata
- Verifies energies, forces, coordinates, and all system properties
match within specified tolerance
## Example Usage
```python
import dpdata
# All these aliases now work for extended XYZ format
ms1 = dpdata.MultiSystems.from_file("data.xyz", fmt="extxyz")
ms2 = dpdata.MultiSystems.from_file("data.xyz", fmt="gpumd")
ms3 = dpdata.MultiSystems.from_file("data.xyz", fmt="nequip")
ms4 = dpdata.MultiSystems.from_file("data.xyz", fmt="mace")
```
The implementation leverages existing code without duplicating
functionality, providing multiple entry points for the same robust
extended XYZ format handling while ensuring full compatibility with
ASE's extxyz implementation.
<!-- START COPILOT CODING AGENT TIPS -->
---
✨ Let Copilot coding agent [set things up for
you](https://github.com/deepmodeling/dpdata/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)
— coding agent works faster and does higher quality work when set up for
your repo.
---------
Signed-off-by: Jinzhe Zeng <[email protected]>
Co-authored-by: copilot-swe-agent[bot] <[email protected]>
Co-authored-by: njzjz <[email protected]>
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Co-authored-by: Jinzhe Zeng <[email protected]>
<!--pre-commit.ci start--> updates: - [github.com/astral-sh/ruff-pre-commit: v0.12.10 → v0.12.11](astral-sh/ruff-pre-commit@v0.12.10...v0.12.11) <!--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: v0.12.11 → v0.12.12](astral-sh/ruff-pre-commit@v0.12.11...v0.12.12) - [github.com/asottile/blacken-docs: 1.19.1 → 1.20.0](adamchainz/blacken-docs@1.19.1...1.20.0) <!--pre-commit.ci end--> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Bumps [actions/setup-python](https://github.com/actions/setup-python) from 5 to 6. <details> <summary>Release notes</summary> <p><em>Sourced from <a href="https://github.com/actions/setup-python/releases">actions/setup-python's releases</a>.</em></p> <blockquote> <h2>v6.0.0</h2> <h2>What's Changed</h2> <h3>Breaking Changes</h3> <ul> <li>Upgrade to node 24 by <a href="https://github.com/salmanmkc"><code>@salmanmkc</code></a> in <a href="https://redirect.github.com/actions/setup-python/pull/1164">actions/setup-python#1164</a></li> </ul> <p>Make sure your runner is on version v2.327.1 or later to ensure compatibility with this release. <a href="https://github.com/actions/runner/releases/tag/v2.327.1">See Release Notes</a></p> <h3>Enhancements:</h3> <ul> <li>Add support for <code>pip-version</code> by <a href="https://github.com/priyagupta108"><code>@priyagupta108</code></a> in <a href="https://redirect.github.com/actions/setup-python/pull/1129">actions/setup-python#1129</a></li> <li>Enhance reading from .python-version by <a href="https://github.com/krystof-k"><code>@krystof-k</code></a> in <a href="https://redirect.github.com/actions/setup-python/pull/787">actions/setup-python#787</a></li> <li>Add version parsing from Pipfile by <a href="https://github.com/aradkdj"><code>@aradkdj</code></a> in <a href="https://redirect.github.com/actions/setup-python/pull/1067">actions/setup-python#1067</a></li> </ul> <h3>Bug fixes:</h3> <ul> <li>Clarify pythonLocation behaviour for PyPy and GraalPy in environment variables by <a href="https://github.com/aparnajyothi-y"><code>@aparnajyothi-y</code></a> in <a href="https://redirect.github.com/actions/setup-python/pull/1183">actions/setup-python#1183</a></li> <li>Change missing cache directory error to warning by <a href="https://github.com/aparnajyothi-y"><code>@aparnajyothi-y</code></a> in <a href="https://redirect.github.com/actions/setup-python/pull/1182">actions/setup-python#1182</a></li> <li>Add Architecture-Specific PATH Management for Python with --user Flag on Windows by <a href="https://github.com/aparnajyothi-y"><code>@aparnajyothi-y</code></a> in <a href="https://redirect.github.com/actions/setup-python/pull/1122">actions/setup-python#1122</a></li> <li>Include python version in PyPy python-version output by <a href="https://github.com/cdce8p"><code>@cdce8p</code></a> in <a href="https://redirect.github.com/actions/setup-python/pull/1110">actions/setup-python#1110</a></li> <li>Update docs: clarification on pip authentication with setup-python by <a href="https://github.com/priya-kinthali"><code>@priya-kinthali</code></a> in <a href="https://redirect.github.com/actions/setup-python/pull/1156">actions/setup-python#1156</a></li> </ul> <h3>Dependency updates:</h3> <ul> <li>Upgrade idna from 2.9 to 3.7 in /<strong>tests</strong>/data by <a href="https://github.com/dependabot"><code>@dependabot</code></a>[bot] in <a href="https://redirect.github.com/actions/setup-python/pull/843">actions/setup-python#843</a></li> <li>Upgrade form-data to fix critical vulnerabilities <a href="https://redirect.github.com/actions/setup-python/issues/182">#182</a> & <a href="https://redirect.github.com/actions/setup-python/issues/183">#183</a> by <a href="https://github.com/aparnajyothi-y"><code>@aparnajyothi-y</code></a> in <a href="https://redirect.github.com/actions/setup-python/pull/1163">actions/setup-python#1163</a></li> <li>Upgrade setuptools to 78.1.1 to fix path traversal vulnerability in PackageIndex.download by <a href="https://github.com/aparnajyothi-y"><code>@aparnajyothi-y</code></a> in <a href="https://redirect.github.com/actions/setup-python/pull/1165">actions/setup-python#1165</a></li> <li>Upgrade actions/checkout from 4 to 5 by <a href="https://github.com/dependabot"><code>@dependabot</code></a>[bot] in <a href="https://redirect.github.com/actions/setup-python/pull/1181">actions/setup-python#1181</a></li> <li>Upgrade <code>@actions/tool-cache</code> from 2.0.1 to 2.0.2 by <a href="https://github.com/dependabot"><code>@dependabot</code></a>[bot] in <a href="https://redirect.github.com/actions/setup-python/pull/1095">actions/setup-python#1095</a></li> </ul> <h2>New Contributors</h2> <ul> <li><a href="https://github.com/krystof-k"><code>@krystof-k</code></a> made their first contribution in <a href="https://redirect.github.com/actions/setup-python/pull/787">actions/setup-python#787</a></li> <li><a href="https://github.com/cdce8p"><code>@cdce8p</code></a> made their first contribution in <a href="https://redirect.github.com/actions/setup-python/pull/1110">actions/setup-python#1110</a></li> <li><a href="https://github.com/aradkdj"><code>@aradkdj</code></a> made their first contribution in <a href="https://redirect.github.com/actions/setup-python/pull/1067">actions/setup-python#1067</a></li> </ul> <p><strong>Full Changelog</strong>: <a href="https://github.com/actions/setup-python/compare/v5...v6.0.0">https://github.com/actions/setup-python/compare/v5...v6.0.0</a></p> <h2>v5.6.0</h2> <h2>What's Changed</h2> <ul> <li>Workflow updates related to Ubuntu 20.04 by <a href="https://github.com/aparnajyothi-y"><code>@aparnajyothi-y</code></a> in <a href="https://redirect.github.com/actions/setup-python/pull/1065">actions/setup-python#1065</a></li> <li>Fix for Candidate Not Iterable Error by <a href="https://github.com/aparnajyothi-y"><code>@aparnajyothi-y</code></a> in <a href="https://redirect.github.com/actions/setup-python/pull/1082">actions/setup-python#1082</a></li> <li>Upgrade semver and <code>@types/semver</code> by <a href="https://github.com/dependabot"><code>@dependabot</code></a> in <a href="https://redirect.github.com/actions/setup-python/pull/1091">actions/setup-python#1091</a></li> <li>Upgrade prettier from 2.8.8 to 3.5.3 by <a href="https://github.com/dependabot"><code>@dependabot</code></a> in <a href="https://redirect.github.com/actions/setup-python/pull/1046">actions/setup-python#1046</a></li> <li>Upgrade ts-jest from 29.1.2 to 29.3.2 by <a href="https://github.com/dependabot"><code>@dependabot</code></a> in <a href="https://redirect.github.com/actions/setup-python/pull/1081">actions/setup-python#1081</a></li> </ul> <p><strong>Full Changelog</strong>: <a href="https://github.com/actions/setup-python/compare/v5...v5.6.0">https://github.com/actions/setup-python/compare/v5...v5.6.0</a></p> <h2>v5.5.0</h2> <h2>What's Changed</h2> <h3>Enhancements:</h3> <ul> <li>Support free threaded Python versions like '3.13t' by <a href="https://github.com/colesbury"><code>@colesbury</code></a> in <a href="https://redirect.github.com/actions/setup-python/pull/973">actions/setup-python#973</a></li> <li>Enhance Workflows: Include ubuntu-arm runners, Add e2e Testing for free threaded and Upgrade <code>@action/cache</code> from 4.0.0 to 4.0.3 by <a href="https://github.com/priya-kinthali"><code>@priya-kinthali</code></a> in <a href="https://redirect.github.com/actions/setup-python/pull/1056">actions/setup-python#1056</a></li> <li>Add support for .tool-versions file in setup-python by <a href="https://github.com/mahabaleshwars"><code>@mahabaleshwars</code></a> in <a href="https://redirect.github.com/actions/setup-python/pull/1043">actions/setup-python#1043</a></li> </ul> <h3>Bug fixes:</h3> <ul> <li>Fix architecture for pypy on Linux ARM64 by <a href="https://github.com/mayeut"><code>@mayeut</code></a> in <a href="https://redirect.github.com/actions/setup-python/pull/1011">actions/setup-python#1011</a> This update maps arm64 to aarch64 for Linux ARM64 PyPy installations.</li> </ul> <!-- raw HTML omitted --> </blockquote> <p>... (truncated)</p> </details> <details> <summary>Commits</summary> <ul> <li><a href="https://github.com/actions/setup-python/commit/e797f83bcb11b83ae66e0230d6156d7c80228e7c"><code>e797f83</code></a> Upgrade to node 24 (<a href="https://redirect.github.com/actions/setup-python/issues/1164">#1164</a>)</li> <li><a href="https://github.com/actions/setup-python/commit/3d1e2d2ca0a067f27da6fec484fce7f5256def85"><code>3d1e2d2</code></a> Revert "Enhance cache-dependency-path handling to support files outside the w...</li> <li><a href="https://github.com/actions/setup-python/commit/65b071217a8539818fdb8b54561bcbae40380a54"><code>65b0712</code></a> Clarify pythonLocation behavior for PyPy and GraalPy in environment variables...</li> <li><a href="https://github.com/actions/setup-python/commit/5b668cf7652160527499ee14ceaff4be9306cb88"><code>5b668cf</code></a> Bump actions/checkout from 4 to 5 (<a href="https://redirect.github.com/actions/setup-python/issues/1181">#1181</a>)</li> <li><a href="https://github.com/actions/setup-python/commit/f62a0e252fe7114e86949abfa6e1e89f85bb38c2"><code>f62a0e2</code></a> Change missing cache directory error to warning (<a href="https://redirect.github.com/actions/setup-python/issues/1182">#1182</a>)</li> <li><a href="https://github.com/actions/setup-python/commit/9322b3ca74000aeb2c01eb777b646334015ddd72"><code>9322b3c</code></a> Upgrade setuptools to 78.1.1 to fix path traversal vulnerability in PackageIn...</li> <li><a href="https://github.com/actions/setup-python/commit/fbeb884f69f0ac1c0257302f62aa524c2824b649"><code>fbeb884</code></a> Bump form-data to fix critical vulnerabilities <a href="https://redirect.github.com/actions/setup-python/issues/182">#182</a> & <a href="https://redirect.github.com/actions/setup-python/issues/183">#183</a> (<a href="https://redirect.github.com/actions/setup-python/issues/1163">#1163</a>)</li> <li><a href="https://github.com/actions/setup-python/commit/03bb6152f4f691b9d64579a1bd791904a083c452"><code>03bb615</code></a> Bump idna from 2.9 to 3.7 in /<strong>tests</strong>/data (<a href="https://redirect.github.com/actions/setup-python/issues/843">#843</a>)</li> <li><a href="https://github.com/actions/setup-python/commit/36da51d563b70a972897150555bb025096d65565"><code>36da51d</code></a> Add version parsing from Pipfile (<a href="https://redirect.github.com/actions/setup-python/issues/1067">#1067</a>)</li> <li><a href="https://github.com/actions/setup-python/commit/3c6f142cc0036d53007e92fa1e327564a4cfb7aa"><code>3c6f142</code></a> update documentation (<a href="https://redirect.github.com/actions/setup-python/issues/1156">#1156</a>)</li> <li>Additional commits viewable in <a href="https://github.com/actions/setup-python/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] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
<!--pre-commit.ci start--> updates: - [github.com/astral-sh/ruff-pre-commit: v0.12.12 → v0.13.0](astral-sh/ruff-pre-commit@v0.12.12...v0.13.0) <!--pre-commit.ci end--> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Added reading of fchk format files and support for saving hessian.npy <!-- This is an auto-generated comment: release notes by coderabbit.ai --> ## Summary by CodeRabbit * **New Features** * Added import support for Gaussian formatted checkpoint (.fchk) with automatic unit conversions for coordinates, energies, forces, and Hessians; Hessian data type is now supported and available; new Gaussian FCHK format handler added; non-periodic systems handled by default. * **Tests** * Added FCHK/LOG fixtures and unit tests validating presence, shapes, and cross-file consistency of energies, forces, coordinates, atom info, and Hessians. <!-- 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>
…#898) This PR moves the AI agent instructions from `.github/copilot-instructions.md` to `AGENTS.md` in the repository root, following the new GitHub standard for agent custom instructions. ## Background According to the [GitHub changelog](https://github.blog/changelog/2025-08-28-copilot-coding-agent-now-supports-agents-md-custom-instructions/), `AGENTS.md` is now the commonly used location for custom instructions that different AI agents can reference. This change improves compatibility across various AI coding assistants. ## Changes - **Moved** `.github/copilot-instructions.md` → `AGENTS.md` - **No content changes** - the comprehensive dpdata development instructions remain identical - **No functional impact** on the dpdata codebase or CLI functionality The file contains detailed instructions for AI agents working on dpdata, including: - Repository bootstrap and installation procedures - Testing and linting workflows - Build and documentation processes - Troubleshooting guides - Commit and PR guidelines ## Verification - ✅ dpdata CLI functionality remains intact (`dpdata --version`, `dpdata --help`) - ✅ All CLI tests continue to pass (7/7 tests successful) - ✅ File content preserved exactly (149 lines, 7,357 bytes) Fixes deepmodeling#897. <!-- START COPILOT CODING AGENT TIPS --> --- 💬 Share your feedback on Copilot coding agent for the chance to win a $200 gift card! Click [here](https://survey3.medallia.com/?EAHeSx-AP01bZqG0Ld9QLQ) to start the survey. --------- Co-authored-by: copilot-swe-agent[bot] <[email protected]> Co-authored-by: njzjz <[email protected]> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Bumps [CodSpeedHQ/action](https://github.com/codspeedhq/action) from 3 to 4. <details> <summary>Release notes</summary> <p><em>Sourced from <a href="https://github.com/codspeedhq/action/releases">CodSpeedHQ/action's releases</a>.</em></p> <blockquote> <h2>v4.0.0</h2> <h2>💥 BREAKING</h2> <p>It's now required to explicitly set the runner mode to <code>instrumentation</code> or <code>walltime</code> using either:</p> <ul> <li>the <code>mode</code> argument</li> <li>or the <code>CODSPEED_RUNNER_MODE</code> environment variable</li> </ul> <blockquote> <p>[!TIP] Before, this variable was automatically set to <code>instrumentation</code> on every runner except for <a href="https://codspeed.io/docs/instruments/walltime">CodSpeed macro runners</a> where it was set to <code>walltime</code> by default.</p> </blockquote> <p>Find more details in <a href="https://codspeed.io/docs/instruments">the instruments documentation</a>.</p> <h2>Details</h2> <h3><!-- raw HTML omitted -->🚀 Features</h3> <ul> <li>Make perf profiling enabled by default by <a href="https://github.com/GuillaumeLagrange"><code>@GuillaumeLagrange</code></a> in <a href="https://redirect.github.com/CodSpeedHQ/runner/pull/110">#110</a></li> <li>Make the runner mode argument required by <a href="https://github.com/GuillaumeLagrange"><code>@GuillaumeLagrange</code></a></li> <li>Use introspected node in walltime mode by <a href="https://github.com/GuillaumeLagrange"><code>@GuillaumeLagrange</code></a> in <a href="https://redirect.github.com/CodSpeedHQ/runner/pull/108">#108</a></li> <li>Add instrumented go shell script by <a href="https://github.com/not-matthias"><code>@not-matthias</code></a> in <a href="https://redirect.github.com/CodSpeedHQ/runner/pull/102">#102</a></li> </ul> <h3><!-- raw HTML omitted -->🐛 Bug Fixes</h3> <ul> <li>Compute proper load bias by <a href="https://github.com/not-matthias"><code>@not-matthias</code></a> in <a href="https://redirect.github.com/CodSpeedHQ/runner/pull/107">#107</a></li> <li>Increase timeout for first perf ping by <a href="https://github.com/GuillaumeLagrange"><code>@GuillaumeLagrange</code></a></li> <li>Prevent running with valgrind by <a href="https://github.com/not-matthias"><code>@not-matthias</code></a> in <a href="https://redirect.github.com/CodSpeedHQ/runner/pull/106">#106</a></li> </ul> <h3><!-- raw HTML omitted -->🏗️ Refactor</h3> <ul> <li>Change go-runner binary name by <a href="https://github.com/not-matthias"><code>@not-matthias</code></a> in <a href="https://redirect.github.com/CodSpeedHQ/runner/pull/111">#111</a></li> </ul> <p><strong>Full Runner Changelog</strong>: <a href="https://github.com/CodSpeedHQ/runner/blob/main/CHANGELOG.md">https://github.com/CodSpeedHQ/runner/blob/main/CHANGELOG.md</a></p> <h2>v3.8.1</h2> <h2>What's Changed</h2> <h3><!-- raw HTML omitted -->🐛 Bug Fixes</h3> <ul> <li>Don't show error when libpython is not found by <a href="https://github.com/not-matthias"><code>@not-matthias</code></a></li> </ul> <h3><!-- raw HTML omitted -->🏗️ Refactor</h3> <ul> <li>Improve conditional compilation in <code>get_pipe_open_options</code> by <a href="https://github.com/art049"><code>@art049</code></a> in <a href="https://redirect.github.com/CodSpeedHQ/runner/pull/100">#100</a></li> </ul> <h3><!-- raw HTML omitted -->⚙️ Internals</h3> <ul> <li>Change log level to warn for venv_compat error by <a href="https://github.com/not-matthias"><code>@not-matthias</code></a> in <a href="https://redirect.github.com/CodSpeedHQ/runner/pull/104">#104</a></li> </ul> <p><strong>Full Changelog</strong>: <a href="https://github.com/CodSpeedHQ/action/compare/v3.8.0...v3.8.1">https://github.com/CodSpeedHQ/action/compare/v3.8.0...v3.8.1</a> <strong>Full Runner Changelog</strong>: <a href="https://github.com/CodSpeedHQ/runner/blob/main/CHANGELOG.md">https://github.com/CodSpeedHQ/runner/blob/main/CHANGELOG.md</a></p> <h2>v3.8.0</h2> <h2>What's Changed</h2> <!-- raw HTML omitted --> </blockquote> <p>... (truncated)</p> </details> <details> <summary>Commits</summary> <ul> <li><a href="https://github.com/CodSpeedHQ/action/commit/6eeb021fd0f305388292348b775d96d95253adf4"><code>6eeb021</code></a> Release v4.0.0 🚀</li> <li><a href="https://github.com/CodSpeedHQ/action/commit/74312dabbeda98d198d62066e8d72dd30fa5e131"><code>74312da</code></a> chore: improve the release script</li> <li><a href="https://github.com/CodSpeedHQ/action/commit/8a17a350a8b455fac2f5c74d3d9a641bb07f4dc5"><code>8a17a35</code></a> ci: add modes to the matrix</li> <li><a href="https://github.com/CodSpeedHQ/action/commit/8e3f02a64957c1d93e9c06ba290d45850713cbca"><code>8e3f02a</code></a> feat: make the mode argument required</li> <li><a href="https://github.com/CodSpeedHQ/action/commit/97c7a6f5fcf3d5077dc63d5edd0d034311525a87"><code>97c7a6f</code></a> chore: bump runner version to 4.0.0</li> <li><a href="https://github.com/CodSpeedHQ/action/commit/8a4cadd026e555b22fbf5008ead29d5b92ed1283"><code>8a4cadd</code></a> chore: point the changelog to the runner</li> <li>See full diff in <a href="https://github.com/codspeedhq/action/compare/v3...v4">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] <[email protected]> Signed-off-by: Jinzhe Zeng <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Jinzhe Zeng <[email protected]>
…eepmodeling#900) When Quantum Espresso cp.x trajectory files contain only a single timestep, the `.evp` energy file has just one data line. This caused `np.loadtxt()` to return a 1D array instead of the expected 2D array, leading to an IndexError when the code attempted 2D indexing operations. ```python # Before: This would fail with single-line .evp files data = np.loadtxt(fname) # Returns 1D array for single line steps = [] for ii in data[begin::step, 0]: # IndexError: too many indices for array steps.append("%d" % ii) # After: Works consistently for both single and multi-line files data = np.loadtxt(fname, ndmin=2) # Always returns at least 2D array steps = [] for ii in data[begin::step, 0]: # Works correctly steps.append("%d" % ii) ``` The fix uses numpy's `ndmin=2` parameter to ensure the loaded data is always at least 2-dimensional, maintaining consistency between single-line and multi-line energy files without requiring additional reshaping logic. **Changes:** - Added `ndmin=2` parameter to `np.loadtxt()` call in `load_energy()` function - Added comprehensive test case to prevent regression **Testing:** - All existing QE tests continue to pass (63 tests) - New test specifically validates single-line `.evp` file handling - CLI functionality verified to work end-to-end Fixes deepmodeling#899. <!-- 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. --------- Co-authored-by: copilot-swe-agent[bot] <[email protected]> Co-authored-by: njzjz <[email protected]> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
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Bumps [astral-sh/setup-uv](https://github.com/astral-sh/setup-uv) from 6 to 7. <details> <summary>Release notes</summary> <p><em>Sourced from <a href="https://github.com/astral-sh/setup-uv/releases">astral-sh/setup-uv's releases</a>.</em></p> <blockquote> <h2>v7.0.0 🌈 node24 and a lot of bugfixes</h2> <h2>Changes</h2> <p>This release comes with a load of bug fixes and a speed up. Because of switching from node20 to node24 it is also a breaking change. If you are running on GitHub hosted runners this will just work, if you are using self-hosted runners make sure, that your runners are up to date. If you followed the normal installation instructions your self-hosted runner will keep itself updated.</p> <p>This release also removes the deprecated input <code>server-url</code> which was used to download uv releases from a different server. The <a href="https://github.com/astral-sh/setup-uv?tab=readme-ov-file#manifest-file">manifest-file</a> input supersedes that functionality by adding a flexible way to define available versions and where they should be downloaded from.</p> <h3>Fixes</h3> <ul> <li>The action now respects when the environment variable <code>UV_CACHE_DIR</code> is already set and does not overwrite it. It now also finds <a href="https://docs.astral.sh/uv/reference/settings/#cache-dir">cache-dir</a> settings in config files if you set them.</li> <li>Some users encountered problems that <a href="https://github.com/astral-sh/setup-uv?tab=readme-ov-file#disable-cache-pruning">cache pruning</a> took forever because they had some <code>uv</code> processes running in the background. Starting with uv version <code>0.8.24</code> this action uses <code>uv cache prune --ci --force</code> to ignore the running processes</li> <li>If you just want to install uv but not have it available in path, this action now respects <code>UV_NO_MODIFY_PATH</code></li> <li>Some other actions also set the env var <code>UV_CACHE_DIR</code>. This action can now deal with that but as this could lead to unwanted behavior in some edgecases a warning is now displayed.</li> </ul> <h3>Improvements</h3> <p>If you are using minimum version specifiers for the version of uv to install for example</p> <pre lang="toml"><code>[tool.uv] required-version = ">=0.8.17" </code></pre> <p>This action now detects that and directly uses the latest version. Previously it would download all available releases from the uv repo to determine the highest matching candidate for the version specifier, which took much more time.</p> <p>If you are using other specifiers like <code>0.8.x</code> this action still needs to download all available releases because the specifier defines an upper bound (not 0.9.0 or later) and "latest" would possibly not satisfy that.</p> <h2>🚨 Breaking changes</h2> <ul> <li>Use node24 instead of node20 <a href="https://github.com/eifinger"><code>@eifinger</code></a> (<a href="https://redirect.github.com/astral-sh/setup-uv/issues/608">#608</a>)</li> <li>Remove deprecated input server-url <a href="https://github.com/eifinger"><code>@eifinger</code></a> (<a href="https://redirect.github.com/astral-sh/setup-uv/issues/607">#607</a>)</li> </ul> <h2>🐛 Bug fixes</h2> <ul> <li>Respect UV_CACHE_DIR and cache-dir <a href="https://github.com/eifinger"><code>@eifinger</code></a> (<a href="https://redirect.github.com/astral-sh/setup-uv/issues/612">#612</a>)</li> <li>Use --force when pruning cache <a href="https://github.com/eifinger"><code>@eifinger</code></a> (<a href="https://redirect.github.com/astral-sh/setup-uv/issues/611">#611</a>)</li> <li>Respect UV_NO_MODIFY_PATH <a href="https://github.com/eifinger"><code>@eifinger</code></a> (<a href="https://redirect.github.com/astral-sh/setup-uv/issues/603">#603</a>)</li> <li>Warn when <code>UV_CACHE_DIR</code> has changed <a href="https://github.com/jamesbraza"><code>@jamesbraza</code></a> (<a href="https://redirect.github.com/astral-sh/setup-uv/issues/601">#601</a>)</li> </ul> <h2>🚀 Enhancements</h2> <ul> <li>Shortcut to latest version for minimum version specifier <a href="https://github.com/eifinger"><code>@eifinger</code></a> (<a href="https://redirect.github.com/astral-sh/setup-uv/issues/598">#598</a>)</li> </ul> <h2>🧰 Maintenance</h2> <ul> <li>Bump dependencies <a href="https://github.com/eifinger"><code>@eifinger</code></a> (<a href="https://redirect.github.com/astral-sh/setup-uv/issues/613">#613</a>)</li> <li>Fix test-uv-no-modify-path <a href="https://github.com/eifinger"><code>@eifinger</code></a> (<a href="https://redirect.github.com/astral-sh/setup-uv/issues/604">#604</a>)</li> </ul> <!-- raw HTML omitted --> </blockquote> <p>... (truncated)</p> </details> <details> <summary>Commits</summary> <ul> <li><a href="https://github.com/astral-sh/setup-uv/commit/3259c6206f993105e3a61b142c2d97bf4b9ef83d"><code>3259c62</code></a> Bump deps (<a href="https://redirect.github.com/astral-sh/setup-uv/issues/633">#633</a>)</li> <li><a href="https://github.com/astral-sh/setup-uv/commit/bf8e8ed895b7f686f85839659243f31a7df4a977"><code>bf8e8ed</code></a> Split up documentation (<a href="https://redirect.github.com/astral-sh/setup-uv/issues/632">#632</a>)</li> <li><a href="https://github.com/astral-sh/setup-uv/commit/9c6b5e9fb575cac8e82bb437dd7fc25a094bd85d"><code>9c6b5e9</code></a> Add resolution-strategy input to support oldest compatible version selection ...</li> <li><a href="https://github.com/astral-sh/setup-uv/commit/a5129e99f44f5d2ba22cdc54770745bd6f0d9c33"><code>a5129e9</code></a> Add copilot-instructions.md (<a href="https://redirect.github.com/astral-sh/setup-uv/issues/630">#630</a>)</li> <li><a href="https://github.com/astral-sh/setup-uv/commit/d18bcc753ac29c1ed721aa4a812a90eb937852d6"><code>d18bcc7</code></a> Add value of UV_PYTHON_INSTALL_DIR to path (<a href="https://redirect.github.com/astral-sh/setup-uv/issues/628">#628</a>)</li> <li><a href="https://github.com/astral-sh/setup-uv/commit/bd1f875aba1ebb6d38211b773b094ad1dcca58df"><code>bd1f875</code></a> Set output venv when activate-environment is used (<a href="https://redirect.github.com/astral-sh/setup-uv/issues/627">#627</a>)</li> <li><a href="https://github.com/astral-sh/setup-uv/commit/1a91c3851df47749b241e3c5c696350957c93ff0"><code>1a91c38</code></a> chore: update known checksums for 0.9.2 (<a href="https://redirect.github.com/astral-sh/setup-uv/issues/626">#626</a>)</li> <li><a href="https://github.com/astral-sh/setup-uv/commit/c79f606987cb4a0f3d1a95a3e44bcebfb0a9b303"><code>c79f606</code></a> chore: update known checksums for 0.9.1 (<a href="https://redirect.github.com/astral-sh/setup-uv/issues/625">#625</a>)</li> <li><a href="https://github.com/astral-sh/setup-uv/commit/e0249f159931b41f44fc8208c9b4cff085288cc9"><code>e0249f1</code></a> Fall back to PR for updating known versions (<a href="https://redirect.github.com/astral-sh/setup-uv/issues/623">#623</a>)</li> <li><a href="https://github.com/astral-sh/setup-uv/commit/6d2eb15b4979924f7be71aa06908c6211f80ac88"><code>6d2eb15</code></a> Cache python installs (<a href="https://redirect.github.com/astral-sh/setup-uv/issues/621">#621</a>)</li> <li>Additional commits viewable in <a href="https://github.com/astral-sh/setup-uv/compare/v6...v7">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] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
<!-- This is an auto-generated comment: release notes by coderabbit.ai --> ## Summary by CodeRabbit ## Release Notes * **Documentation** * Added DOI badge and credits section with formal citation information to README * Added bibliographic citation notice to the documentation landing page with research publication reference <!-- end of auto-generated comment: release notes by coderabbit.ai -->
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CodSpeed Performance ReportMerging #909 will not alter performanceComparing
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