docs(skills): expand extxyz format documentation in dpdata-cli skill#1036
docs(skills): expand extxyz format documentation in dpdata-cli skill#1036SchrodingersCattt wants to merge 8 commits into
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🤖 Prompt for all review comments with AI agents
Verify each finding against current code. Fix only still-valid issues, skip the
rest with a brief reason, keep changes minimal, and validate.
Inline comments:
In `@skills/dpdata-cli/SKILL.md`:
- Line 227: Update the conversion documentation to state that virial uses the
configured stress_sign, with stress_sign = -1 representing the default ASE
convention, rather than presenting virial = −volume × stress as unconditional.
Clarify that non-default stress_sign values alter the conversion accordingly.
- Around line 234-243: Update every uvx dpdata command in the examples,
including the multi and explicit type-map variants, to use the same tested
pinned dpdata version. Preserve all existing arguments and output paths while
applying the pin consistently.
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- Create a new PR with the fixes
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skills/dpdata-cli/SKILL.md
| #### Stress and Virial Conventions | ||
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| - Stress can be **9-component** (3×3 flat) or **6-component** (Voigt order: xx yy zz yz xz xy) | ||
| - Conversion: `virial = −volume × stress` (ASE sign convention) |
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🗄️ Data Integrity & Integration | 🟡 Minor | ⚡ Quick win
Document the stress sign as the default convention
The parser accepts a configurable stress_sign; -1 is only the default ASE convention. Calling virial = −volume × stress unconditionally could cause users with a non-default sign configuration to generate incorrect virials.
Suggested wording
-Conversion: `virial = −volume × stress` (ASE sign convention)
+Conversion by default: `virial = −volume × stress` (ASE sign convention; the sign can be configured)📝 Committable suggestion
‼️ IMPORTANT
Carefully review the code before committing. Ensure that it accurately replaces the highlighted code, contains no missing lines, and has no issues with indentation. Thoroughly test & benchmark the code to ensure it meets the requirements.
| - Conversion: `virial = −volume × stress` (ASE sign convention) | |
| Conversion by default: `virial = −volume × stress` (ASE sign convention; the sign can be configured) |
🧰 Tools
🪛 SkillSpector (2.3.11)
[warning] 20: [RP1] null: uvx/uv tool run commands without ==version create a rug-pull risk.
Remediation: Pin the version: uvx package-name==1.2.3
(MCP Rug Pull (RP1))
[warning] 51: [RP1] null: uvx/uv tool run commands without ==version create a rug-pull risk.
Remediation: Pin the version: uvx package-name==1.2.3
(MCP Rug Pull (RP1))
[warning] 57: [RP1] null: uvx/uv tool run commands without ==version create a rug-pull risk.
Remediation: Pin the version: uvx package-name==1.2.3
(MCP Rug Pull (RP1))
[warning] 63: [RP1] null: uvx/uv tool run commands without ==version create a rug-pull risk.
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(MCP Rug Pull (RP1))
[warning] 69: [RP1] null: uvx/uv tool run commands without ==version create a rug-pull risk.
Remediation: Pin the version: uvx package-name==1.2.3
(MCP Rug Pull (RP1))
[warning] 75: [RP1] null: uvx/uv tool run commands without ==version create a rug-pull risk.
Remediation: Pin the version: uvx package-name==1.2.3
(MCP Rug Pull (RP1))
[warning] 81: [RP1] null: uvx/uv tool run commands without ==version create a rug-pull risk.
Remediation: Pin the version: uvx package-name==1.2.3
(MCP Rug Pull (RP1))
[warning] 234: [RP1] null: uvx/uv tool run commands without ==version create a rug-pull risk.
Remediation: Pin the version: uvx package-name==1.2.3
(MCP Rug Pull (RP1))
[warning] 237: [RP1] null: uvx/uv tool run commands without ==version create a rug-pull risk.
Remediation: Pin the version: uvx package-name==1.2.3
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[warning] 240: [RP1] null: uvx/uv tool run commands without ==version create a rug-pull risk.
Remediation: Pin the version: uvx package-name==1.2.3
(MCP Rug Pull (RP1))
[warning] 243: [RP1] null: uvx/uv tool run commands without ==version create a rug-pull risk.
Remediation: Pin the version: uvx package-name==1.2.3
(MCP Rug Pull (RP1))
[warning] 35: [MP2] Context Window Stuffing: Skill attempts to fill the context window with filler content, displacing legitimate instructions and safety constraints. This can degrade agent performance or bypass safety boundaries.
Remediation: Implement context-window management that detects and rejects padding or stuffing attempts. Prioritize system instructions over user-injected content.
(Memory Poisoning (MP2))
[warning] 101: [MP2] Context Window Stuffing: Skill attempts to fill the context window with filler content, displacing legitimate instructions and safety constraints. This can degrade agent performance or bypass safety boundaries.
Remediation: Implement context-window management that detects and rejects padding or stuffing attempts. Prioritize system instructions over user-injected content.
(Memory Poisoning (MP2))
[warning] 117: [MP2] Context Window Stuffing: Skill attempts to fill the context window with filler content, displacing legitimate instructions and safety constraints. This can degrade agent performance or bypass safety boundaries.
Remediation: Implement context-window management that detects and rejects padding or stuffing attempts. Prioritize system instructions over user-injected content.
(Memory Poisoning (MP2))
[warning] 149: [MP2] Context Window Stuffing: Skill attempts to fill the context window with filler content, displacing legitimate instructions and safety constraints. This can degrade agent performance or bypass safety boundaries.
Remediation: Implement context-window management that detects and rejects padding or stuffing attempts. Prioritize system instructions over user-injected content.
(Memory Poisoning (MP2))
[warning] 151: [MP2] Context Window Stuffing: Skill attempts to fill the context window with filler content, displacing legitimate instructions and safety constraints. This can degrade agent performance or bypass safety boundaries.
Remediation: Implement context-window management that detects and rejects padding or stuffing attempts. Prioritize system instructions over user-injected content.
(Memory Poisoning (MP2))
[warning] 153: [MP2] Context Window Stuffing: Skill attempts to fill the context window with filler content, displacing legitimate instructions and safety constraints. This can degrade agent performance or bypass safety boundaries.
Remediation: Implement context-window management that detects and rejects padding or stuffing attempts. Prioritize system instructions over user-injected content.
(Memory Poisoning (MP2))
[warning] 154: [MP2] Context Window Stuffing: Skill attempts to fill the context window with filler content, displacing legitimate instructions and safety constraints. This can degrade agent performance or bypass safety boundaries.
Remediation: Implement context-window management that detects and rejects padding or stuffing attempts. Prioritize system instructions over user-injected content.
(Memory Poisoning (MP2))
[warning] 155: [MP2] Context Window Stuffing: Skill attempts to fill the context window with filler content, displacing legitimate instructions and safety constraints. This can degrade agent performance or bypass safety boundaries.
Remediation: Implement context-window management that detects and rejects padding or stuffing attempts. Prioritize system instructions over user-injected content.
(Memory Poisoning (MP2))
[warning] 156: [MP2] Context Window Stuffing: Skill attempts to fill the context window with filler content, displacing legitimate instructions and safety constraints. This can degrade agent performance or bypass safety boundaries.
Remediation: Implement context-window management that detects and rejects padding or stuffing attempts. Prioritize system instructions over user-injected content.
(Memory Poisoning (MP2))
[warning] 157: [MP2] Context Window Stuffing: Skill attempts to fill the context window with filler content, displacing legitimate instructions and safety constraints. This can degrade agent performance or bypass safety boundaries.
Remediation: Implement context-window management that detects and rejects padding or stuffing attempts. Prioritize system instructions over user-injected content.
(Memory Poisoning (MP2))
[warning] 158: [MP2] Context Window Stuffing: Skill attempts to fill the context window with filler content, displacing legitimate instructions and safety constraints. This can degrade agent performance or bypass safety boundaries.
Remediation: Implement context-window management that detects and rejects padding or stuffing attempts. Prioritize system instructions over user-injected content.
(Memory Poisoning (MP2))
[warning] 159: [MP2] Context Window Stuffing: Skill attempts to fill the context window with filler content, displacing legitimate instructions and safety constraints. This can degrade agent performance or bypass safety boundaries.
Remediation: Implement context-window management that detects and rejects padding or stuffing attempts. Prioritize system instructions over user-injected content.
(Memory Poisoning (MP2))
[warning] 162: [MP2] Context Window Stuffing: Skill attempts to fill the context window with filler content, displacing legitimate instructions and safety constraints. This can degrade agent performance or bypass safety boundaries.
Remediation: Implement context-window management that detects and rejects padding or stuffing attempts. Prioritize system instructions over user-injected content.
(Memory Poisoning (MP2))
[warning] 163: [MP2] Context Window Stuffing: Skill attempts to fill the context window with filler content, displacing legitimate instructions and safety constraints. This can degrade agent performance or bypass safety boundaries.
Remediation: Implement context-window management that detects and rejects padding or stuffing attempts. Prioritize system instructions over user-injected content.
(Memory Poisoning (MP2))
[warning] 164: [MP2] Context Window Stuffing: Skill attempts to fill the context window with filler content, displacing legitimate instructions and safety constraints. This can degrade agent performance or bypass safety boundaries.
Remediation: Implement context-window management that detects and rejects padding or stuffing attempts. Prioritize system instructions over user-injected content.
(Memory Poisoning (MP2))
[warning] 166: [MP2] Context Window Stuffing: Skill attempts to fill the context window with filler content, displacing legitimate instructions and safety constraints. This can degrade agent performance or bypass safety boundaries.
Remediation: Implement context-window management that detects and rejects padding or stuffing attempts. Prioritize system instructions over user-injected content.
(Memory Poisoning (MP2))
[warning] 167: [MP2] Context Window Stuffing: Skill attempts to fill the context window with filler content, displacing legitimate instructions and safety constraints. This can degrade agent performance or bypass safety boundaries.
Remediation: Implement context-window management that detects and rejects padding or stuffing attempts. Prioritize system instructions over user-injected content.
(Memory Poisoning (MP2))
[warning] 168: [MP2] Context Window Stuffing: Skill attempts to fill the context window with filler content, displacing legitimate instructions and safety constraints. This can degrade agent performance or bypass safety boundaries.
Remediation: Implement context-window management that detects and rejects padding or stuffing attempts. Prioritize system instructions over user-injected content.
(Memory Poisoning (MP2))
[warning] 169: [MP2] Context Window Stuffing: Skill attempts to fill the context window with filler content, displacing legitimate instructions and safety constraints. This can degrade agent performance or bypass safety boundaries.
Remediation: Implement context-window management that detects and rejects padding or stuffing attempts. Prioritize system instructions over user-injected content.
(Memory Poisoning (MP2))
[warning] 170: [MP2] Context Window Stuffing: Skill attempts to fill the context window with filler content, displacing legitimate instructions and safety constraints. This can degrade agent performance or bypass safety boundaries.
Remediation: Implement context-window management that detects and rejects padding or stuffing attempts. Prioritize system instructions over user-injected content.
(Memory Poisoning (MP2))
[warning] 171: [MP2] Context Window Stuffing: Skill attempts to fill the context window with filler content, displacing legitimate instructions and safety constraints. This can degrade agent performance or bypass safety boundaries.
Remediation: Implement context-window management that detects and rejects padding or stuffing attempts. Prioritize system instructions over user-injected content.
(Memory Poisoning (MP2))
[warning] 172: [MP2] Context Window Stuffing: Skill attempts to fill the context window with filler content, displacing legitimate instructions and safety constraints. This can degrade agent performance or bypass safety boundaries.
Remediation: Implement context-window management that detects and rejects padding or stuffing attempts. Prioritize system instructions over user-injected content.
(Memory Poisoning (MP2))
[warning] 173: [MP2] Context Window Stuffing: Skill attempts to fill the context window with filler content, displacing legitimate instructions and safety constraints. This can degrade agent performance or bypass safety boundaries.
Remediation: Implement context-window management that detects and rejects padding or stuffing attempts. Prioritize system instructions over user-injected content.
(Memory Poisoning (MP2))
[warning] 174: [MP2] Context Window Stuffing: Skill attempts to fill the context window with filler content, displacing legitimate instructions and safety constraints. This can degrade agent performance or bypass safety boundaries.
Remediation: Implement context-window management that detects and rejects padding or stuffing attempts. Prioritize system instructions over user-injected content.
(Memory Poisoning (MP2))
[warning] 38: [RA2] Session Persistence: Skill establishes unauthorized persistence across sessions via cron jobs, startup scripts, or state files. Session persistence allows an attacker to maintain access beyond the current interaction.
Remediation: Remove any persistence mechanisms (cron jobs, startup scripts, state files). Skills should not maintain state across sessions without explicit user consent.
(Rogue Agent (RA2))
🤖 Prompt for AI Agents
Verify each finding against current code. Fix only still-valid issues, skip the
rest with a brief reason, keep changes minimal, and validate.
In `@skills/dpdata-cli/SKILL.md` at line 227, Update the conversion documentation
to state that virial uses the configured stress_sign, with stress_sign = -1
representing the default ASE convention, rather than presenting virial = −volume
× stress as unconditional. Clarify that non-default stress_sign values alter the
conversion accordingly.
| uvx dpdata data.xyz -i extxyz -O deepmd_data -o deepmd/npy | ||
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| # Heterogeneous extxyz (mixed compositions) → deepmd/npy/mixed | ||
| uvx dpdata data.xyz -i extxyz -O deepmd_data -o deepmd/npy/mixed --multi | ||
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| # Convert extxyz to VASP POSCAR (first frame) | ||
| uvx dpdata data.xyz -i extxyz -O POSCAR -o vasp/poscar | ||
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| # Convert with explicit type map | ||
| uvx dpdata data.xyz -i extxyz -O deepmd_data -o deepmd/npy -t H C N O |
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🔒 Security & Privacy | 🟡 Minor | ⚡ Quick win
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rg -n --hidden --no-ignore-vcs -F 'uvx dpdata' skills . || true
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echo '--- search dpdata== ---'
rg -n --hidden --no-ignore-vcs -F 'dpdata==' skills . || true
echo
echo '--- search uvx examples in skills/dpdata-cli ---'
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🌐 Web query:
uvx pin package version syntax documentation package==version reproducibility
💡 Result:
The uvx command, which is an alias for uv tool run, provides several methods for specifying package versions and managing tool environments. Version Syntax You can specify versions using the following syntax: 1. Exact version suffix: Append @ to the package name (e.g., uvx ruff@0.3.0). This supports only exact versions [1][2]. 2. The --from option: Allows more flexible specification, including version ranges or exact version pinning, using standard requirement syntax (e.g., uvx --from 'ruff==0.3.0' ruff or uvx --from 'ruff>0.2.0,<0.3.0' ruff) [1][3]. 3. Latest version: Use @latest to ensure the tool is run with the latest available version [1][4]. Reproducibility and Locking uvx is primarily designed for running ephemeral, isolated tools, and it does not natively support project-level lockfiles (like uv.lock) for these isolated environments [5][6][7]. This has significant implications for reproducibility: - Caching behavior: By default, uvx caches the environment created for a tool. Subsequent runs will reuse this cached environment [4][8]. However, the cache can be pruned or refreshed, which may lead to different versions being installed in the future [4][7]. - No inherent lockfile support: Because uvx does not read project-level configuration (like pyproject.toml or uv.lock), it does not automatically enforce locked dependency versions [5]. - Ensuring specific versions: To achieve higher reproducibility for a specific tool, it is recommended to use uv tool install @, which installs the tool into a dedicated tools directory. This creates a persistent environment that will not be automatically updated or cleared like the ephemeral environment used by uvx [7]. For complex dependencies that require strict locking, developers are encouraged to add the tool as a project dependency using uv add, which allows the use of uv.lock to guarantee reproducible environments [6][9]. As of July 2026, there are ongoing community discussions and proposals regarding mechanisms to better support embedded lockfiles or explicit lockfile usage with uvx [9][10].
Citations:
- 1: https://docs.astral.sh/uv/guides/tools/
- 2: https://github.com/astral-sh/uv/blob/main/docs/guides/tools.md
- 3: https://astral-sh-uv.mintlify.app/guides/tools
- 4: https://docs.astral.sh/uv/concepts/tools/
- 5:
uvx {tool}defaults to version that has been installed viauv tool install {tool}-- is this by design? Should it be? astral-sh/uv#17734 - 6: uvx --from git+https://....git@... ignores the lockfile astral-sh/uv#13414
- 7: https://stackoverflow.com/questions/79581046/lock-specific-dependency-versions-with-uvx-uv-tool-run
- 8: https://pydevtools.com/handbook/reference/uvx/
- 9: Add option to force use of
uv.lockfile when adding dependency or installing a tool astral-sh/uv#5815 - 10: Proposal: uvx reads embedded uv.lock from wheel dist-info as resolution preferences astral-sh/uv#18825
Pin the dpdata version in all uvx examples
These commands will otherwise track the latest release and can change behavior over time. Use a tested pin consistently, e.g. uvx dpdata@<tested-version> ... (or uvx --from 'dpdata==<tested-version>' dpdata ...).
🧰 Tools
🪛 SkillSpector (2.3.11)
[warning] 20: [RP1] null: uvx/uv tool run commands without ==version create a rug-pull risk.
Remediation: Pin the version: uvx package-name==1.2.3
(MCP Rug Pull (RP1))
[warning] 51: [RP1] null: uvx/uv tool run commands without ==version create a rug-pull risk.
Remediation: Pin the version: uvx package-name==1.2.3
(MCP Rug Pull (RP1))
[warning] 57: [RP1] null: uvx/uv tool run commands without ==version create a rug-pull risk.
Remediation: Pin the version: uvx package-name==1.2.3
(MCP Rug Pull (RP1))
[warning] 63: [RP1] null: uvx/uv tool run commands without ==version create a rug-pull risk.
Remediation: Pin the version: uvx package-name==1.2.3
(MCP Rug Pull (RP1))
[warning] 69: [RP1] null: uvx/uv tool run commands without ==version create a rug-pull risk.
Remediation: Pin the version: uvx package-name==1.2.3
(MCP Rug Pull (RP1))
[warning] 75: [RP1] null: uvx/uv tool run commands without ==version create a rug-pull risk.
Remediation: Pin the version: uvx package-name==1.2.3
(MCP Rug Pull (RP1))
[warning] 81: [RP1] null: uvx/uv tool run commands without ==version create a rug-pull risk.
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(MCP Rug Pull (RP1))
[warning] 234: [RP1] null: uvx/uv tool run commands without ==version create a rug-pull risk.
Remediation: Pin the version: uvx package-name==1.2.3
(MCP Rug Pull (RP1))
[warning] 237: [RP1] null: uvx/uv tool run commands without ==version create a rug-pull risk.
Remediation: Pin the version: uvx package-name==1.2.3
(MCP Rug Pull (RP1))
[warning] 240: [RP1] null: uvx/uv tool run commands without ==version create a rug-pull risk.
Remediation: Pin the version: uvx package-name==1.2.3
(MCP Rug Pull (RP1))
[warning] 243: [RP1] null: uvx/uv tool run commands without ==version create a rug-pull risk.
Remediation: Pin the version: uvx package-name==1.2.3
(MCP Rug Pull (RP1))
[warning] 35: [MP2] Context Window Stuffing: Skill attempts to fill the context window with filler content, displacing legitimate instructions and safety constraints. This can degrade agent performance or bypass safety boundaries.
Remediation: Implement context-window management that detects and rejects padding or stuffing attempts. Prioritize system instructions over user-injected content.
(Memory Poisoning (MP2))
[warning] 101: [MP2] Context Window Stuffing: Skill attempts to fill the context window with filler content, displacing legitimate instructions and safety constraints. This can degrade agent performance or bypass safety boundaries.
Remediation: Implement context-window management that detects and rejects padding or stuffing attempts. Prioritize system instructions over user-injected content.
(Memory Poisoning (MP2))
[warning] 117: [MP2] Context Window Stuffing: Skill attempts to fill the context window with filler content, displacing legitimate instructions and safety constraints. This can degrade agent performance or bypass safety boundaries.
Remediation: Implement context-window management that detects and rejects padding or stuffing attempts. Prioritize system instructions over user-injected content.
(Memory Poisoning (MP2))
[warning] 149: [MP2] Context Window Stuffing: Skill attempts to fill the context window with filler content, displacing legitimate instructions and safety constraints. This can degrade agent performance or bypass safety boundaries.
Remediation: Implement context-window management that detects and rejects padding or stuffing attempts. Prioritize system instructions over user-injected content.
(Memory Poisoning (MP2))
[warning] 151: [MP2] Context Window Stuffing: Skill attempts to fill the context window with filler content, displacing legitimate instructions and safety constraints. This can degrade agent performance or bypass safety boundaries.
Remediation: Implement context-window management that detects and rejects padding or stuffing attempts. Prioritize system instructions over user-injected content.
(Memory Poisoning (MP2))
[warning] 153: [MP2] Context Window Stuffing: Skill attempts to fill the context window with filler content, displacing legitimate instructions and safety constraints. This can degrade agent performance or bypass safety boundaries.
Remediation: Implement context-window management that detects and rejects padding or stuffing attempts. Prioritize system instructions over user-injected content.
(Memory Poisoning (MP2))
[warning] 154: [MP2] Context Window Stuffing: Skill attempts to fill the context window with filler content, displacing legitimate instructions and safety constraints. This can degrade agent performance or bypass safety boundaries.
Remediation: Implement context-window management that detects and rejects padding or stuffing attempts. Prioritize system instructions over user-injected content.
(Memory Poisoning (MP2))
[warning] 155: [MP2] Context Window Stuffing: Skill attempts to fill the context window with filler content, displacing legitimate instructions and safety constraints. This can degrade agent performance or bypass safety boundaries.
Remediation: Implement context-window management that detects and rejects padding or stuffing attempts. Prioritize system instructions over user-injected content.
(Memory Poisoning (MP2))
[warning] 156: [MP2] Context Window Stuffing: Skill attempts to fill the context window with filler content, displacing legitimate instructions and safety constraints. This can degrade agent performance or bypass safety boundaries.
Remediation: Implement context-window management that detects and rejects padding or stuffing attempts. Prioritize system instructions over user-injected content.
(Memory Poisoning (MP2))
[warning] 157: [MP2] Context Window Stuffing: Skill attempts to fill the context window with filler content, displacing legitimate instructions and safety constraints. This can degrade agent performance or bypass safety boundaries.
Remediation: Implement context-window management that detects and rejects padding or stuffing attempts. Prioritize system instructions over user-injected content.
(Memory Poisoning (MP2))
[warning] 158: [MP2] Context Window Stuffing: Skill attempts to fill the context window with filler content, displacing legitimate instructions and safety constraints. This can degrade agent performance or bypass safety boundaries.
Remediation: Implement context-window management that detects and rejects padding or stuffing attempts. Prioritize system instructions over user-injected content.
(Memory Poisoning (MP2))
[warning] 159: [MP2] Context Window Stuffing: Skill attempts to fill the context window with filler content, displacing legitimate instructions and safety constraints. This can degrade agent performance or bypass safety boundaries.
Remediation: Implement context-window management that detects and rejects padding or stuffing attempts. Prioritize system instructions over user-injected content.
(Memory Poisoning (MP2))
[warning] 162: [MP2] Context Window Stuffing: Skill attempts to fill the context window with filler content, displacing legitimate instructions and safety constraints. This can degrade agent performance or bypass safety boundaries.
Remediation: Implement context-window management that detects and rejects padding or stuffing attempts. Prioritize system instructions over user-injected content.
(Memory Poisoning (MP2))
[warning] 163: [MP2] Context Window Stuffing: Skill attempts to fill the context window with filler content, displacing legitimate instructions and safety constraints. This can degrade agent performance or bypass safety boundaries.
Remediation: Implement context-window management that detects and rejects padding or stuffing attempts. Prioritize system instructions over user-injected content.
(Memory Poisoning (MP2))
[warning] 164: [MP2] Context Window Stuffing: Skill attempts to fill the context window with filler content, displacing legitimate instructions and safety constraints. This can degrade agent performance or bypass safety boundaries.
Remediation: Implement context-window management that detects and rejects padding or stuffing attempts. Prioritize system instructions over user-injected content.
(Memory Poisoning (MP2))
[warning] 166: [MP2] Context Window Stuffing: Skill attempts to fill the context window with filler content, displacing legitimate instructions and safety constraints. This can degrade agent performance or bypass safety boundaries.
Remediation: Implement context-window management that detects and rejects padding or stuffing attempts. Prioritize system instructions over user-injected content.
(Memory Poisoning (MP2))
[warning] 167: [MP2] Context Window Stuffing: Skill attempts to fill the context window with filler content, displacing legitimate instructions and safety constraints. This can degrade agent performance or bypass safety boundaries.
Remediation: Implement context-window management that detects and rejects padding or stuffing attempts. Prioritize system instructions over user-injected content.
(Memory Poisoning (MP2))
[warning] 168: [MP2] Context Window Stuffing: Skill attempts to fill the context window with filler content, displacing legitimate instructions and safety constraints. This can degrade agent performance or bypass safety boundaries.
Remediation: Implement context-window management that detects and rejects padding or stuffing attempts. Prioritize system instructions over user-injected content.
(Memory Poisoning (MP2))
[warning] 169: [MP2] Context Window Stuffing: Skill attempts to fill the context window with filler content, displacing legitimate instructions and safety constraints. This can degrade agent performance or bypass safety boundaries.
Remediation: Implement context-window management that detects and rejects padding or stuffing attempts. Prioritize system instructions over user-injected content.
(Memory Poisoning (MP2))
[warning] 170: [MP2] Context Window Stuffing: Skill attempts to fill the context window with filler content, displacing legitimate instructions and safety constraints. This can degrade agent performance or bypass safety boundaries.
Remediation: Implement context-window management that detects and rejects padding or stuffing attempts. Prioritize system instructions over user-injected content.
(Memory Poisoning (MP2))
[warning] 171: [MP2] Context Window Stuffing: Skill attempts to fill the context window with filler content, displacing legitimate instructions and safety constraints. This can degrade agent performance or bypass safety boundaries.
Remediation: Implement context-window management that detects and rejects padding or stuffing attempts. Prioritize system instructions over user-injected content.
(Memory Poisoning (MP2))
[warning] 172: [MP2] Context Window Stuffing: Skill attempts to fill the context window with filler content, displacing legitimate instructions and safety constraints. This can degrade agent performance or bypass safety boundaries.
Remediation: Implement context-window management that detects and rejects padding or stuffing attempts. Prioritize system instructions over user-injected content.
(Memory Poisoning (MP2))
[warning] 173: [MP2] Context Window Stuffing: Skill attempts to fill the context window with filler content, displacing legitimate instructions and safety constraints. This can degrade agent performance or bypass safety boundaries.
Remediation: Implement context-window management that detects and rejects padding or stuffing attempts. Prioritize system instructions over user-injected content.
(Memory Poisoning (MP2))
[warning] 174: [MP2] Context Window Stuffing: Skill attempts to fill the context window with filler content, displacing legitimate instructions and safety constraints. This can degrade agent performance or bypass safety boundaries.
Remediation: Implement context-window management that detects and rejects padding or stuffing attempts. Prioritize system instructions over user-injected content.
(Memory Poisoning (MP2))
[warning] 38: [RA2] Session Persistence: Skill establishes unauthorized persistence across sessions via cron jobs, startup scripts, or state files. Session persistence allows an attacker to maintain access beyond the current interaction.
Remediation: Remove any persistence mechanisms (cron jobs, startup scripts, state files). Skills should not maintain state across sessions without explicit user consent.
(Rogue Agent (RA2))
🤖 Prompt for AI Agents
Verify each finding against current code. Fix only still-valid issues, skip the
rest with a brief reason, keep changes minimal, and validate.
In `@skills/dpdata-cli/SKILL.md` around lines 234 - 243, Update every uvx dpdata
command in the examples, including the multi and explicit type-map variants, to
use the same tested pinned dpdata version. Preserve all existing arguments and
output paths while applying the pin consistently.
Source: Linters/SAST tools
- Add extxyz format aliases table (extxyz, quip/gap/xyz, mace/xyz, nequip/xyz, gpumd/xyz) - Document file structure, recognized header keys, and Properties descriptor syntax - Add CLI examples specific to extxyz (including --multi for heterogeneous data) - Clarify xyz vs extxyz distinction to prevent common agent confusion - Document stress/virial conversion conventions
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for more information, see https://pre-commit.ci
Signed-off-by: Ming-Yu Guo <guomy26@mail2.sysu.edu.cn>
There was a problem hiding this comment.
Actionable comments posted: 1
🤖 Prompt for all review comments with AI agents
Verify each finding against current code. Fix only still-valid issues, skip the
rest with a brief reason, keep changes minimal, and validate.
Inline comments:
In `@skills/dpdata-cli/SKILL.md`:
- Line 186: Revise the Important note in the XYZ format documentation to clarify
that plain xyz includes atom species/type tokens, while omitting extended
per-frame data such as energies, forces, cell information, and periodic boundary
conditions. Keep the distinction from extxyz and remove the implication that xyz
has no labels.
🪄 Autofix (Beta)
Fix all unresolved CodeRabbit comments on this PR:
- Push a commit to this branch (recommended)
- Create a new PR with the fixes
ℹ️ Review info
⚙️ Run configuration
Configuration used: Organization UI
Review profile: CHILL
Plan: Pro
Run ID: 88ad2925-296b-4b1a-a529-9d43b07fe71d
📒 Files selected for processing (1)
skills/dpdata-cli/SKILL.md
| - `nequip/xyz` — NequIP model training data | ||
| - `gpumd/xyz` — GPUMD simulation data | ||
|
|
||
| > **Important:** Plain `xyz` is a **different**, simpler format that only stores coordinates without labels (energies/forces), cell information, or periodic boundary conditions. Do not confuse `xyz` with `extxyz`. |
There was a problem hiding this comment.
🎯 Functional Correctness | 🟡 Minor | ⚡ Quick win
Clarify that plain xyz still contains atom species.
The plain XYZ reader extracts element/type tokens into atom_names and atom_types; what it does not provide is extended per-frame data such as energies, forces, cell information, or periodicity. Reword this to avoid implying that plain XYZ has no labels at all.
Suggested wording
-Plain `xyz` is a **different**, simpler format that only stores coordinates without labels (energies/forces), cell information, or periodic boundary conditions.
+Plain `xyz` is a **different**, simpler format that stores coordinates and atom species, but not extended labels such as energies/forces, cell information, or periodic boundary conditions.📝 Committable suggestion
‼️ IMPORTANT
Carefully review the code before committing. Ensure that it accurately replaces the highlighted code, contains no missing lines, and has no issues with indentation. Thoroughly test & benchmark the code to ensure it meets the requirements.
| > **Important:** Plain `xyz` is a **different**, simpler format that only stores coordinates without labels (energies/forces), cell information, or periodic boundary conditions. Do not confuse `xyz` with `extxyz`. | |
| > **Important:** Plain `xyz` is a **different**, simpler format that stores coordinates and atom species, but not extended labels such as energies/forces, cell information, or periodic boundary conditions. Do not confuse `xyz` with `extxyz`. |
🧰 Tools
🪛 SkillSpector (2.3.11)
[warning] 20: [RP1] null: uvx/uv tool run commands without ==version create a rug-pull risk.
Remediation: Pin the version: uvx package-name==1.2.3
(MCP Rug Pull (RP1))
[warning] 51: [RP1] null: uvx/uv tool run commands without ==version create a rug-pull risk.
Remediation: Pin the version: uvx package-name==1.2.3
(MCP Rug Pull (RP1))
[warning] 57: [RP1] null: uvx/uv tool run commands without ==version create a rug-pull risk.
Remediation: Pin the version: uvx package-name==1.2.3
(MCP Rug Pull (RP1))
[warning] 63: [RP1] null: uvx/uv tool run commands without ==version create a rug-pull risk.
Remediation: Pin the version: uvx package-name==1.2.3
(MCP Rug Pull (RP1))
[warning] 69: [RP1] null: uvx/uv tool run commands without ==version create a rug-pull risk.
Remediation: Pin the version: uvx package-name==1.2.3
(MCP Rug Pull (RP1))
[warning] 75: [RP1] null: uvx/uv tool run commands without ==version create a rug-pull risk.
Remediation: Pin the version: uvx package-name==1.2.3
(MCP Rug Pull (RP1))
[warning] 81: [RP1] null: uvx/uv tool run commands without ==version create a rug-pull risk.
Remediation: Pin the version: uvx package-name==1.2.3
(MCP Rug Pull (RP1))
[warning] 192: [RP1] null: uvx/uv tool run commands without ==version create a rug-pull risk.
Remediation: Pin the version: uvx package-name==1.2.3
(MCP Rug Pull (RP1))
[warning] 195: [RP1] null: uvx/uv tool run commands without ==version create a rug-pull risk.
Remediation: Pin the version: uvx package-name==1.2.3
(MCP Rug Pull (RP1))
[warning] 198: [RP1] null: uvx/uv tool run commands without ==version create a rug-pull risk.
Remediation: Pin the version: uvx package-name==1.2.3
(MCP Rug Pull (RP1))
[warning] 201: [RP1] null: uvx/uv tool run commands without ==version create a rug-pull risk.
Remediation: Pin the version: uvx package-name==1.2.3
(MCP Rug Pull (RP1))
[warning] 35: [MP2] Context Window Stuffing: Skill attempts to fill the context window with filler content, displacing legitimate instructions and safety constraints. This can degrade agent performance or bypass safety boundaries.
Remediation: Implement context-window management that detects and rejects padding or stuffing attempts. Prioritize system instructions over user-injected content.
(Memory Poisoning (MP2))
[warning] 101: [MP2] Context Window Stuffing: Skill attempts to fill the context window with filler content, displacing legitimate instructions and safety constraints. This can degrade agent performance or bypass safety boundaries.
Remediation: Implement context-window management that detects and rejects padding or stuffing attempts. Prioritize system instructions over user-injected content.
(Memory Poisoning (MP2))
[warning] 117: [MP2] Context Window Stuffing: Skill attempts to fill the context window with filler content, displacing legitimate instructions and safety constraints. This can degrade agent performance or bypass safety boundaries.
Remediation: Implement context-window management that detects and rejects padding or stuffing attempts. Prioritize system instructions over user-injected content.
(Memory Poisoning (MP2))
[warning] 149: [MP2] Context Window Stuffing: Skill attempts to fill the context window with filler content, displacing legitimate instructions and safety constraints. This can degrade agent performance or bypass safety boundaries.
Remediation: Implement context-window management that detects and rejects padding or stuffing attempts. Prioritize system instructions over user-injected content.
(Memory Poisoning (MP2))
[warning] 151: [MP2] Context Window Stuffing: Skill attempts to fill the context window with filler content, displacing legitimate instructions and safety constraints. This can degrade agent performance or bypass safety boundaries.
Remediation: Implement context-window management that detects and rejects padding or stuffing attempts. Prioritize system instructions over user-injected content.
(Memory Poisoning (MP2))
[warning] 153: [MP2] Context Window Stuffing: Skill attempts to fill the context window with filler content, displacing legitimate instructions and safety constraints. This can degrade agent performance or bypass safety boundaries.
Remediation: Implement context-window management that detects and rejects padding or stuffing attempts. Prioritize system instructions over user-injected content.
(Memory Poisoning (MP2))
[warning] 154: [MP2] Context Window Stuffing: Skill attempts to fill the context window with filler content, displacing legitimate instructions and safety constraints. This can degrade agent performance or bypass safety boundaries.
Remediation: Implement context-window management that detects and rejects padding or stuffing attempts. Prioritize system instructions over user-injected content.
(Memory Poisoning (MP2))
[warning] 155: [MP2] Context Window Stuffing: Skill attempts to fill the context window with filler content, displacing legitimate instructions and safety constraints. This can degrade agent performance or bypass safety boundaries.
Remediation: Implement context-window management that detects and rejects padding or stuffing attempts. Prioritize system instructions over user-injected content.
(Memory Poisoning (MP2))
[warning] 156: [MP2] Context Window Stuffing: Skill attempts to fill the context window with filler content, displacing legitimate instructions and safety constraints. This can degrade agent performance or bypass safety boundaries.
Remediation: Implement context-window management that detects and rejects padding or stuffing attempts. Prioritize system instructions over user-injected content.
(Memory Poisoning (MP2))
[warning] 157: [MP2] Context Window Stuffing: Skill attempts to fill the context window with filler content, displacing legitimate instructions and safety constraints. This can degrade agent performance or bypass safety boundaries.
Remediation: Implement context-window management that detects and rejects padding or stuffing attempts. Prioritize system instructions over user-injected content.
(Memory Poisoning (MP2))
[warning] 158: [MP2] Context Window Stuffing: Skill attempts to fill the context window with filler content, displacing legitimate instructions and safety constraints. This can degrade agent performance or bypass safety boundaries.
Remediation: Implement context-window management that detects and rejects padding or stuffing attempts. Prioritize system instructions over user-injected content.
(Memory Poisoning (MP2))
[warning] 159: [MP2] Context Window Stuffing: Skill attempts to fill the context window with filler content, displacing legitimate instructions and safety constraints. This can degrade agent performance or bypass safety boundaries.
Remediation: Implement context-window management that detects and rejects padding or stuffing attempts. Prioritize system instructions over user-injected content.
(Memory Poisoning (MP2))
[warning] 162: [MP2] Context Window Stuffing: Skill attempts to fill the context window with filler content, displacing legitimate instructions and safety constraints. This can degrade agent performance or bypass safety boundaries.
Remediation: Implement context-window management that detects and rejects padding or stuffing attempts. Prioritize system instructions over user-injected content.
(Memory Poisoning (MP2))
[warning] 163: [MP2] Context Window Stuffing: Skill attempts to fill the context window with filler content, displacing legitimate instructions and safety constraints. This can degrade agent performance or bypass safety boundaries.
Remediation: Implement context-window management that detects and rejects padding or stuffing attempts. Prioritize system instructions over user-injected content.
(Memory Poisoning (MP2))
[warning] 164: [MP2] Context Window Stuffing: Skill attempts to fill the context window with filler content, displacing legitimate instructions and safety constraints. This can degrade agent performance or bypass safety boundaries.
Remediation: Implement context-window management that detects and rejects padding or stuffing attempts. Prioritize system instructions over user-injected content.
(Memory Poisoning (MP2))
[warning] 166: [MP2] Context Window Stuffing: Skill attempts to fill the context window with filler content, displacing legitimate instructions and safety constraints. This can degrade agent performance or bypass safety boundaries.
Remediation: Implement context-window management that detects and rejects padding or stuffing attempts. Prioritize system instructions over user-injected content.
(Memory Poisoning (MP2))
[warning] 167: [MP2] Context Window Stuffing: Skill attempts to fill the context window with filler content, displacing legitimate instructions and safety constraints. This can degrade agent performance or bypass safety boundaries.
Remediation: Implement context-window management that detects and rejects padding or stuffing attempts. Prioritize system instructions over user-injected content.
(Memory Poisoning (MP2))
[warning] 168: [MP2] Context Window Stuffing: Skill attempts to fill the context window with filler content, displacing legitimate instructions and safety constraints. This can degrade agent performance or bypass safety boundaries.
Remediation: Implement context-window management that detects and rejects padding or stuffing attempts. Prioritize system instructions over user-injected content.
(Memory Poisoning (MP2))
[warning] 169: [MP2] Context Window Stuffing: Skill attempts to fill the context window with filler content, displacing legitimate instructions and safety constraints. This can degrade agent performance or bypass safety boundaries.
Remediation: Implement context-window management that detects and rejects padding or stuffing attempts. Prioritize system instructions over user-injected content.
(Memory Poisoning (MP2))
[warning] 170: [MP2] Context Window Stuffing: Skill attempts to fill the context window with filler content, displacing legitimate instructions and safety constraints. This can degrade agent performance or bypass safety boundaries.
Remediation: Implement context-window management that detects and rejects padding or stuffing attempts. Prioritize system instructions over user-injected content.
(Memory Poisoning (MP2))
[warning] 171: [MP2] Context Window Stuffing: Skill attempts to fill the context window with filler content, displacing legitimate instructions and safety constraints. This can degrade agent performance or bypass safety boundaries.
Remediation: Implement context-window management that detects and rejects padding or stuffing attempts. Prioritize system instructions over user-injected content.
(Memory Poisoning (MP2))
[warning] 172: [MP2] Context Window Stuffing: Skill attempts to fill the context window with filler content, displacing legitimate instructions and safety constraints. This can degrade agent performance or bypass safety boundaries.
Remediation: Implement context-window management that detects and rejects padding or stuffing attempts. Prioritize system instructions over user-injected content.
(Memory Poisoning (MP2))
[warning] 173: [MP2] Context Window Stuffing: Skill attempts to fill the context window with filler content, displacing legitimate instructions and safety constraints. This can degrade agent performance or bypass safety boundaries.
Remediation: Implement context-window management that detects and rejects padding or stuffing attempts. Prioritize system instructions over user-injected content.
(Memory Poisoning (MP2))
[warning] 174: [MP2] Context Window Stuffing: Skill attempts to fill the context window with filler content, displacing legitimate instructions and safety constraints. This can degrade agent performance or bypass safety boundaries.
Remediation: Implement context-window management that detects and rejects padding or stuffing attempts. Prioritize system instructions over user-injected content.
(Memory Poisoning (MP2))
[warning] 38: [RA2] Session Persistence: Skill establishes unauthorized persistence across sessions via cron jobs, startup scripts, or state files. Session persistence allows an attacker to maintain access beyond the current interaction.
Remediation: Remove any persistence mechanisms (cron jobs, startup scripts, state files). Skills should not maintain state across sessions without explicit user consent.
(Rogue Agent (RA2))
🤖 Prompt for AI Agents
Verify each finding against current code. Fix only still-valid issues, skip the
rest with a brief reason, keep changes minimal, and validate.
In `@skills/dpdata-cli/SKILL.md` at line 186, Revise the Important note in the XYZ
format documentation to clarify that plain xyz includes atom species/type
tokens, while omitting extended per-frame data such as energies, forces, cell
information, and periodic boundary conditions. Keep the distinction from extxyz
and remove the implication that xyz has no labels.
Signed-off-by: Ming-Yu Guo <guomy26@mail2.sysu.edu.cn>
Merging this PR will improve performance by 10.47%
|
| Mode | Benchmark | BASE |
HEAD |
Efficiency | |
|---|---|---|---|---|---|
| ⚡ | WallTime | test_import |
12.4 ms | 11.2 ms | +10.47% |
Tip
Curious why this is faster? Comment @codspeedbot explain why this is faster on this PR, or directly use the CodSpeed MCP with your agent.
Comparing SchrodingersCattt:docs/extxyz-skill-expansion (797223d) with master (f856a09)
Codecov Report✅ All modified and coverable lines are covered by tests. Additional details and impacted files@@ Coverage Diff @@
## master #1036 +/- ##
=======================================
Coverage 86.95% 86.95%
=======================================
Files 90 90
Lines 8330 8330
=======================================
Hits 7243 7243
Misses 1087 1087 ☔ View full report in Codecov by Harness. 🚀 New features to boost your workflow:
|
1 participant
Summary
Expand the
dpdata-cliSKILL with detailed extended XYZ (extxyz) format documentation.Motivation
The extxyz format has 6 registered aliases (
extxyz,quip/gap/xyz,quip/gap/xyz_file,mace/xyz,nequip/xyz,gpumd/xyz) that all point to the sameQuipGapXYZFormatclass. AI agents and users frequently do not know these are equivalent, leading to confusion. Additionally, plainxyzvsextxyzis a common source of errors.Changes
xyzvsextxyzdisambiguationScope
skills/dpdata-cli/SKILL.md(+77 lines)Summary by CodeRabbit
dpdata-cliformat support documentation (still highlights “50+ formats”) with revised examples, including focus ondeepmd/npyand other application formats.extxyz) Format Details section covering equivalent aliases, an explicit note that plainxyzis different, and practical CLI examples (including heterogeneous frames with--multi) plus usage tips.