chore: add mdformat for markdown#1866
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📝 WalkthroughWalkthroughAdds an mdformat markdown pre-commit hook and sets ci.autoupdate_branch to devel. Large-scale documentation edits across many docs: JSON examples reformatted into multi-line blocks, expanded examples and file-tree samples, reflowed guides, and minor wording/formatting fixes. No functional code changes. Changes
Estimated code review effort🎯 3 (Moderate) | ⏱️ ~25 minutes Possibly related PRs
🚥 Pre-merge checks | ✅ 3✅ Passed checks (3 passed)
✏️ Tip: You can configure your own custom pre-merge checks in the settings. ✨ Finishing Touches🧪 Generate unit tests (beta)
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the .md files in the tests/ and examples/init/abacus folder should not be treated as markdown files.
Sync pre-commit config from deepmd-kit@69eb0c3bb10be0ace823a5240c9fef6d0bb26c08 Changes: - Add mdformat for markdown formatting - Add mdformat plugins: myst, ruff, web, config, beautysh, gfm-alerts Authored by OpenClaw (model: glm-5)
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⚠️ Outside diff range comments (4)
doc/autotest/property/properties/EOS-post.md (1)
30-30:⚠️ Potential issue | 🟡 MinorCorrect sample output key typo.
Line 30 likely has a typo:
onf_dirshould beconf_dirto match the intended directory label.🤖 Prompt for AI Agents
Verify each finding against the current code and only fix it if needed. In `@doc/autotest/property/properties/EOS-post.md` at line 30, Fix the typo in the sample YAML key: replace the incorrect key name "onf_dir" with "conf_dir" in the EOS-post sample so the directory key matches the intended configuration label (look for the "onf_dir" entry in the EOS-post sample content and update it to "conf_dir").doc/init/init-reaction.md (1)
22-24:⚠️ Potential issue | 🟡 MinorFix typos in user-facing links/text.
Please correct
parametes→parametersandgenereated→generatedto avoid broken trust in docs quality.🤖 Prompt for AI Agents
Verify each finding against the current code and only fix it if needed. In `@doc/init/init-reaction.md` around lines 22 - 24, Replace the two typos in the user-facing text: change the string "parametes" to "parameters" in the link text referencing init-reaction-jdata.rst, and change "genereated" to "generated" in the sentence about the data to fix the copy and ensure the links/readability are correct; update the markdown content where those exact words appear.doc/autotest/refine/Refine-make.md (1)
24-24:⚠️ Potential issue | 🟡 MinorFix article typo in user-facing text.
Line 24 has a grammar error: “an new directory” → “a new directory”.
🤖 Prompt for AI Agents
Verify each finding against the current code and only fix it if needed. In `@doc/autotest/refine/Refine-make.md` at line 24, Fix the grammar typo in the user-facing sentence that reads "an new directory `vacancy_01` would be established and the starting configuration links to previous results." — replace "an new directory" with "a new directory" so the sentence reads "a new directory `vacancy_01` would be established..." in the Refine-make documentation.doc/autotest/relaxation/Relaxation-make.md (1)
19-30:⚠️ Potential issue | 🟡 MinorAdd a language specifier to fenced code blocks showing tree output
The plain
```blocks for file-tree output (and also Lines 43–56) are flagged by markdownlint (MD040). Usingtextas the language satisfies the linter without implying any syntax highlighting.✏️ Proposed fix
-``` +```text confs/std-fcc/relaxation/ |-- INCAR ...🤖 Prompt for AI Agents
Verify each finding against the current code and only fix it if needed. In `@doc/autotest/relaxation/Relaxation-make.md` around lines 19 - 30, The fenced code blocks in Relaxation-make.md that show file-tree output (the triple-backtick blocks around the tree snippet and the other block at lines 43–56) lack a language specifier and trigger markdownlint MD040; update those fences to use the "text" language (i.e., change ``` to ```text) so the linter treats them as plain text without implying syntax highlighting.
🟡 Minor comments (23)
doc/autotest/property/Property-run.md-7-7 (1)
7-7:⚠️ Potential issue | 🟡 MinorFix grammar and phrasing in the new sentence.
Line 7 should use plural noun agreement and clearer wording.
✏️ Proposed edit
-the result file `log.lammps`, `dump.relax`, and `outlog` would be sent back. +The result files `log.lammps`, `dump.relax`, and `outlog` will be sent back.🤖 Prompt for AI Agents
Verify each finding against the current code and only fix it if needed. In `@doc/autotest/property/Property-run.md` at line 7, Update the sentence in Property-run.md to use plural agreement and clearer wording: replace "the result file `log.lammps`, `dump.relax`, and `outlog` would be sent back." with a grammatically correct form such as "The result files `log.lammps`, `dump.relax`, and `outlog` will be sent back." to fix number agreement and improve clarity.doc/autotest/property/properties/EOS-post.md-16-16 (1)
16-16:⚠️ Potential issue | 🟡 MinorFix grammar typo in the
result.jsonintro.Line 16 says “is give as”; it should be “is given as”.
🤖 Prompt for AI Agents
Verify each finding against the current code and only fix it if needed. In `@doc/autotest/property/properties/EOS-post.md` at line 16, Fix the grammatical typo in the sentence that reads "An example of `result.json` is give as:"—change "is give as" to "is given as" in the line containing the `result.json` intro so it reads "An example of `result.json` is given as:".doc/user-guide/common-errors.md-62-62 (1)
62-62:⚠️ Potential issue | 🟡 MinorFix pronoun typo:
you environment→your environment✏️ Proposed fix
-You can ignore this warning if you don't need Gromacs. It just show that Gromacs is not installed in you environment. +You can ignore this warning if you don't need Gromacs. It just show that Gromacs is not installed in your environment.🤖 Prompt for AI Agents
Verify each finding against the current code and only fix it if needed. In `@doc/user-guide/common-errors.md` at line 62, Replace the typo in the sentence "You can ignore this warning if you don't need Gromacs. It just show that Gromacs is not installed in you environment." by changing "you environment" to "your environment" and also fix the grammar "It just show" → "It just shows" so the full corrected sentence reads: "You can ignore this warning if you don't need Gromacs. It just shows that Gromacs is not installed in your environment."doc/user-guide/common-errors.md-15-15 (1)
15-15:⚠️ Potential issue | 🟡 MinorFix missing space:
youhave→you have✏️ Proposed fix
-Please check your parameters with [DPGEN's Document](https://docs.deepmodeling.com/projects/dpgen/en/latest/). Maybe youhave superfluous parentheses in your parameter file. +Please check your parameters with [DPGEN's Document](https://docs.deepmodeling.com/projects/dpgen/en/latest/). Maybe you have superfluous parentheses in your parameter file.🤖 Prompt for AI Agents
Verify each finding against the current code and only fix it if needed. In `@doc/user-guide/common-errors.md` at line 15, Fix the typo in the sentence "Please check your parameters with [DPGEN's Document](https://docs.deepmodeling.com/projects/dpgen/en/latest/). Maybe youhave superfluous parentheses in your parameter file." by changing "youhave" to "you have" so the sentence reads "...Maybe you have superfluous parentheses in your parameter file."; update the text where the exact token "youhave" appears.doc/autotest/reproduce/Reproduce-make.md-7-8 (1)
7-8:⚠️ Potential issue | 🟡 MinorLGTM — minor capitalisation nit on the prose line.
The blank line added at line 7 is correct mdformat normalisation; no concerns there.
Line 8 starts a sentence with a lowercase letter (
the output will be:). Consider capitalising it for consistency with typical documentation style.✏️ Suggested fix
-the output will be: +The output will be:🤖 Prompt for AI Agents
Verify each finding against the current code and only fix it if needed. In `@doc/autotest/reproduce/Reproduce-make.md` around lines 7 - 8, Update the prose in the markdown so the sentence starting "the output will be:" is capitalised to "The output will be:"; locate the line containing the exact phrase "the output will be:" in Reproduce-make.md and change only the leading lowercase "t" to an uppercase "T" to match documentation style and mdformat normalization.doc/init/init_surf.md-21-21 (1)
21-21:⚠️ Potential issue | 🟡 MinorCorrect stage name typo.
Pertubshould bePerturbin the stage description.🤖 Prompt for AI Agents
Verify each finding against the current code and only fix it if needed. In `@doc/init/init_surf.md` at line 21, Fix the typo in the stage description line "1. Pertub and scale in folder `01.scale_pert`" by changing "Pertub" to "Perturb" so the stage reads "1. Perturb and scale in folder `01.scale_pert`"; update that exact text in doc/init/init_surf.md.examples/init/abacus/fcc-Al-lcao/INPUT.md-2-2 (1)
2-2:⚠️ Potential issue | 🟡 MinorFix MD018: add space after
#in section-header comment lines.Since this PR introduces the mdformat pre-commit hook, all
.mdfiles — including these ABACUS INPUT files — will be continuously linted. Lines 2, 8, 12, 15, and 19 use#Parameterswithout the required space, which will trigger MD018 violations on every future pre-commit run. Adding a space is safe for ABACUS (it treats everything after#as a comment regardless of spacing).🛠️ Proposed fix
-#Parameters (1.General) +# Parameters (1.General) ... -#Parameters (2.Iteration) +# Parameters (2.Iteration) ... -#Parameters (3.Basis) +# Parameters (3.Basis) ... -#Parameters (4.Smearing) +# Parameters (4.Smearing) ... -#Parameters (5.Mixing) +# Parameters (5.Mixing)Also applies to: 8-8, 12-12, 15-15, 19-19
🤖 Prompt for AI Agents
Verify each finding against the current code and only fix it if needed. In `@examples/init/abacus/fcc-Al-lcao/INPUT.md` at line 2, The section headers like "#Parameters (1.General)" violate MD018; update each header to include a space after the hash (e.g., change "#Parameters (1.General)" to "# Parameters (1.General)") for the occurrences at the top and the other headers (the lines containing "#Parameters" at the same pattern); ensure all instances (the lines with "#Parameters") are updated so the markdown linter no longer flags MD018 while preserving the rest of the text.examples/init/abacus/fcc-Al-pw/INPUT.md-2-2 (1)
2-2:⚠️ Potential issue | 🟡 MinorSame MD018 issue: add space after
#in all section-header comment lines.Identical problem as in
fcc-Al-lcao/INPUT.md— the#Parameterslines will be flagged by markdownlint on every pre-commit run after this PR lands. Lines 2, 10, 15, 18, and 22 are all affected.🛠️ Proposed fix
-#Parameters (1.General) +# Parameters (1.General) ... -#Parameters (2.Iteration) +# Parameters (2.Iteration) ... -#Parameters (3.Basis) +# Parameters (3.Basis) ... -#Parameters (4.Smearing) +# Parameters (4.Smearing) ... -#Parameters (5.Mixing) +# Parameters (5.Mixing)Also applies to: 10-10, 15-15, 18-18, 22-22
🤖 Prompt for AI Agents
Verify each finding against the current code and only fix it if needed. In `@examples/init/abacus/fcc-Al-pw/INPUT.md` at line 2, The markdown headings like "#Parameters (1.General)" violate MD018; update each section-header comment so there is a space after the hash (e.g., change "#Parameters (1.General)" to "# Parameters (1.General)") — apply the same fix to the other header occurrences with the same pattern (e.g., the headers at the other affected spots such as "10-10", "15-15", "18-18", "22-22") so all section-header lines include a space after the leading '#'.doc/autotest/refine/Refine-post.md-7-7 (1)
7-7:⚠️ Potential issue | 🟡 MinorPolish sentence casing and wording for readability.
Line 7 should start with uppercase and read more naturally (e.g., “The post-processing of
refineis similar to the corresponding property workflow.”).🤖 Prompt for AI Agents
Verify each finding against the current code and only fix it if needed. In `@doc/autotest/refine/Refine-post.md` at line 7, Replace the lowercase, awkward sentence "the post process of `refine` is similar to the corresponding property." with a clearer, capitalized phrasing such as "The post-processing of `refine` is similar to the corresponding property workflow." — update the line containing "post process of `refine`" to use "The post-processing of `refine`" and append "workflow" for readability.examples/machine/DeePMD-kit-2.x/lebesgue_v2_machine_README.md-3-3 (1)
3-3:⚠️ Potential issue | 🟡 MinorFix malformed/awkward markdown around “manual”.
Line 3 uses escaped brackets (
\[manual\]) in prose, which reads like broken markdown. Prefer plain textmanualor a proper markdown link target.🤖 Prompt for AI Agents
Verify each finding against the current code and only fix it if needed. In `@examples/machine/DeePMD-kit-2.x/lebesgue_v2_machine_README.md` at line 3, The README line contains awkward escaped brackets around "manual" (currently `\[manual\]`); update the phrasing to use plain inline code or a proper markdown link target—for example replace `\[manual\]` with `manual` (or `manual` in backticks) or convert it to a real link text—so the sentence reads naturally (locate and edit the text containing "DPGEN" and `\[manual\]` in lebesgue_v2_machine_README.md).doc/autotest/refine/Refine-run.md-7-7 (1)
7-7:⚠️ Potential issue | 🟡 MinorImprove clarity of the added explanatory sentence.
Line 7 is understandable, but “similar to before” is vague. Consider explicitly naming the referenced workflow and capitalize sentence start.
🤖 Prompt for AI Agents
Verify each finding against the current code and only fix it if needed. In `@doc/autotest/refine/Refine-run.md` at line 7, Replace the vague sentence "the run process of `refine` is similar to before." with a clearer, capitalized sentence that explicitly names the referenced workflow (e.g., "The run process of `refine` follows the same workflow as the previous `refine-init`/`refine-build` steps.") — locate the sentence containing the exact text the run process of `refine` and update it to explicitly reference the prior workflow name(s) and start with a capital letter.doc/overview/code-structure.md-53-54 (1)
53-54:⚠️ Potential issue | 🟡 MinorCorrect typo and keep list structure consistent.
Line 53 has a typo (“hase” → “has”), and Line 54 should likely remain a bullet item like adjacent entries for consistent section structure.
🤖 Prompt for AI Agents
Verify each finding against the current code and only fix it if needed. In `@doc/overview/code-structure.md` around lines 53 - 54, Fix the typo "hase" → "has" in the sentence containing the dpdispatcher link and make the following line about `generator` a bullet item (consistent with adjacent entries) so the list structure remains uniform; update the sentence that currently reads "**Notice this part hase been integrated into [dpdispatcher](https://github.com/deepmodeling/dpdispatcher)**" to "**Notice this part has been integrated into [dpdispatcher](https://github.com/deepmodeling/dpdispatcher)**" and ensure the `generator` description remains prefixed as a list item like the surrounding entries.doc/autotest/Auto-test.md-135-135 (1)
135-135:⚠️ Potential issue | 🟡 MinorMinor grammar nit: hyphenate "post-process".
"post process" used as a compound noun/verb should be hyphenated.
✏️ Proposed fix
-The post process of calculation results would be performed. +The post-process of calculation results would be performed.🤖 Prompt for AI Agents
Verify each finding against the current code and only fix it if needed. In `@doc/autotest/Auto-test.md` at line 135, Replace the unhyphenated phrase "post process" with the correct compound form "post-process" in the sentence that describes performing the post process of calculation results (the line starting with "The post process of calculation results would be performed..."); ensure both occurrences in that sentence are changed so it reads "post-process" consistently.doc/overview/overview.md-20-20 (1)
20-20:⚠️ Potential issue | 🟡 MinorTypo:
"succusefully"→"successfully".Proposed fix
-- **User-friendly and automatic**: Users may install and run DP-GEN easily. Once succusefully running, DP-GEN can dispatch and handle all jobs on HPCs, and thus there's no need for any personal effort. +- **User-friendly and automatic**: Users may install and run DP-GEN easily. Once successfully running, DP-GEN can dispatch and handle all jobs on HPCs, and thus there's no need for any personal effort.🤖 Prompt for AI Agents
Verify each finding against the current code and only fix it if needed. In `@doc/overview/overview.md` at line 20, Fix the typo "succusefully" to "successfully" in the overview sentence that begins "User-friendly and automatic: Users may install and run DP-GEN easily." Update the markdown content so the sentence reads "Once successfully running, DP-GEN can dispatch and handle all jobs on HPCs..." to correct spelling while preserving punctuation and surrounding text.doc/overview/overview.md-28-28 (1)
28-28:⚠️ Potential issue | 🟡 MinorBroken inline code formatting for conda install command.
The escaped backticks produce broken rendering:
\conda install -c conda-forge dpgen```. This is likely a mdformat artifact.Proposed fix
-- Install via conda: \`conda install -c conda-forge dpgen\`\` +- Install via conda: `conda install -c conda-forge dpgen`🤖 Prompt for AI Agents
Verify each finding against the current code and only fix it if needed. In `@doc/overview/overview.md` at line 28, Replace the escaped backticks sequence "\`conda install -c conda-forge dpgen\`" in the overview text with proper inline code formatting by removing the backslash escapes so it reads `conda install -c conda-forge dpgen`; update the line in overview.md where the install command appears (the current diff string "- Install via conda: \`conda install -c conda-forge dpgen\`\`") to use a single pair of backticks around the command.doc/run/overview-of-the-run-process.md-51-51 (1)
51-51:⚠️ Potential issue | 🟡 MinorTypo: missing space in table header —
"eachiteration"→"each iteration".Proposed fix
-| Index of iterations | Stage in eachiteration | Process | +| Index of iterations | Stage in each iteration | Process |🤖 Prompt for AI Agents
Verify each finding against the current code and only fix it if needed. In `@doc/run/overview-of-the-run-process.md` at line 51, Fix the typo in the table header by replacing "Stage in eachiteration" with "Stage in each iteration" in the markdown table row that currently reads "| Index of iterations | Stage in eachiteration | Process |" so the header shows the correct spacing.doc/overview/overview.md-11-11 (1)
11-11:⚠️ Potential issue | 🟡 MinorIncorrect expansion: "Deep Generator" should be "Deep Potential GENerator".
The README.md (Line 13) correctly states "DP-GEN (Deep Potential GENerator)". This file has a truncated/incorrect form.
Proposed fix
-DP-GEN (Deep Generator) is a software written in Python, delicately designed to generate a deep learning based model of interatomic potential energy and force field. DP-GEN is dependent on [DeepMD-kit](https://github.com/deepmodeling/deepmd-kit/blob/master/README.md). With highly scalable interface with common softwares for molecular simulation, DP-GEN is capable to automatically prepare scripts and maintain job queues on HPC machines (High Performance Cluster) and analyze results. +DP-GEN (Deep Potential GENerator) is a software written in Python, delicately designed to generate a deep learning based model of interatomic potential energy and force field. DP-GEN is dependent on [DeePMD-kit](https://github.com/deepmodeling/deepmd-kit/blob/master/README.md). With highly scalable interface with common softwares for molecular simulation, DP-GEN is capable to automatically prepare scripts and maintain job queues on HPC machines (High Performance Cluster) and analyze results.Note: also "DeepMD-kit" → "DeePMD-kit" to match the canonical spelling used in README.md and elsewhere.
🤖 Prompt for AI Agents
Verify each finding against the current code and only fix it if needed. In `@doc/overview/overview.md` at line 11, The text uses the incorrect expansion "DP-GEN (Deep Generator)" and the nonstandard spelling "DeepMD-kit"; update the phrase to "DP-GEN (Deep Potential GENerator)" and change "DeepMD-kit" to the canonical "DeePMD-kit" in the sentence that currently reads 'DP-GEN (Deep Generator) is a software ... dependent on [DeepMD-kit]'; ensure both replacements preserve the existing link and surrounding punctuation.doc/run/example-of-param.md-45-45 (1)
45-45:⚠️ Potential issue | 🟡 MinorUnintended space in path:
"...... /init/"should be"....../init/".The mdformat tool appears to have introduced a space between the dots and
/init/. This changes the documented path and could confuse users trying to replicate the example.Proposed fix
-Here, the init data is provided at "...... /init/CH4.POSCAR.01x01x01/02.md/sys-0004-0001/deepmd". These structures are divided into two groups and provided at "....../init/CH4.POSCAR.01x01x01/01.scale_pert/sys-0004-0001/scale\*/00000\*/POSCAR" and "....../init/CH4.POSCAR.01x01x01/01.scale_pert/sys-0004-0001/scale\*/00001\*/POSCAR". +Here, the init data is provided at "....../init/CH4.POSCAR.01x01x01/02.md/sys-0004-0001/deepmd". These structures are divided into two groups and provided at "....../init/CH4.POSCAR.01x01x01/01.scale_pert/sys-0004-0001/scale\*/00000\*/POSCAR" and "....../init/CH4.POSCAR.01x01x01/01.scale_pert/sys-0004-0001/scale\*/00001\*/POSCAR".🤖 Prompt for AI Agents
Verify each finding against the current code and only fix it if needed. In `@doc/run/example-of-param.md` at line 45, Fix the unintended space in the documented path by replacing the incorrect substring "...... /init/" with "....../init/" in the example text (the line that starts "Here, the init data is provided at ..."). Ensure there are no extra spaces between the leading dots and "/init/" so both shown paths ("....../init/CH4.POSCAR.01x01x01/02.md/sys-0004-0001/deepmd" and the two "....../init/CH4.POSCAR.01x01x01/01.scale_pert/..." entries) consistently use "....../init/" with no space.doc/autotest/relaxation/Relaxation-get-started-and-input-examples.md-74-79 (1)
74-79:⚠️ Potential issue | 🟡 MinorChange JSON key
"maximal"to"maxeval"on line 78.The JSON example uses
"maximal"but the autotest code explicitly checks for"maxeval"(dpgen/auto_test/Lammps.pyline 170:if "maxeval" in cal_setting:). Using the wrong key name will cause the setting to be silently ignored. This matches the table documentation on line 94, which correctly listsmaxeval.🤖 Prompt for AI Agents
Verify each finding against the current code and only fix it if needed. In `@doc/autotest/relaxation/Relaxation-get-started-and-input-examples.md` around lines 74 - 79, Replace the incorrect JSON key "maximal" with "maxeval" inside the cal_setting example so the autotest picks up the value; ensure the example uses "cal_setting": { "etol": 0, "ftol": 1e-10, "maxiter": 5000, "maxeval": 500000 } to match the code path that checks for "maxeval" in cal_setting and the table documentation.doc/contributing-guide/contributing-guide.md-27-36 (1)
27-36:⚠️ Potential issue | 🟡 MinorMinor brand-name capitalization: "Github" → "GitHub"
The official spelling uses a capital "H". These instances appear at Lines 27, 32, and 34 (and the section heading at Line 36). Since the entire file is being touched by mdformat, this is a good opportunity to correct them.
✏️ Proposed fix
-You can use git with the command line, or open the repository on Github Desktop. +You can use git with the command line, or open the repository on GitHub Desktop.-> If you have never used Github before, remember to generate your ssh key and configure the public key in Github Settings. +> If you have never used GitHub before, remember to generate your ssh key and configure the public key in GitHub Settings.-> The explanation from Github see [Github Blog: token authentication requirements... +> The explanation from GitHub see [GitHub Blog: token authentication requirements...-### Use Github Desktop +### Use GitHub Desktop🤖 Prompt for AI Agents
Verify each finding against the current code and only fix it if needed. In `@doc/contributing-guide/contributing-guide.md` around lines 27 - 36, Replace all occurrences of the brand-name "Github" with the correct casing "GitHub" in the contributing-guide.md content (including the paragraph mentioning SSH keys/token, the linked blog text, the StackOverflow reference, and the "Use Github Desktop" section heading). Update the three inline instances shown in the diff and the section heading so the document consistently uses "GitHub".doc/autotest/property/Property-get-started-and-input-examples.md-117-118 (1)
117-118:⚠️ Potential issue | 🟡 MinorSame
1e-2/0.01notation inconsistency as in the Elastic file.The JSON block above (lines 26–27) now shows
0.01, but the example column in the table still displays1e-2. Aligning them avoids confusion.📝 Suggested table update
-| norm_deform | Float | 1e-2 | deformation in xx, yy, zz, default = 1e-2 | -| shear_deform | Float | 1e-2 | deformation in other directions, default = 1e-2 | +| norm_deform | Float | 0.01 | deformation in xx, yy, zz, default = 0.01 | +| shear_deform | Float | 0.01 | deformation in other directions, default = 0.01 |🤖 Prompt for AI Agents
Verify each finding against the current code and only fix it if needed. In `@doc/autotest/property/Property-get-started-and-input-examples.md` around lines 117 - 118, The table rows for norm_deform and shear_deform show the example value as "1e-2" but the JSON block uses "0.01"; update the Example column for the entries named norm_deform and shear_deform to "0.01" so both representations match exactly (leave the Type and Default columns unchanged).doc/autotest/property/Property-get-started-and-input-examples.md-153-153 (1)
153-153:⚠️ Potential issue | 🟡 Minor
add_fixtable example uses single quotes — not valid JSON notation.The example column shows
['true','true','false']with single quotes, while the JSON block above correctly uses double quotes ("true","true","false"). Readers copy-pasting this into a JSON config file would get a parse error.📝 Suggested fix
-| add_fix | List of String | ['true','true','false'] | whether to fix atoms in the direction, default = ['true','true','false'] (standard method) | +| add_fix | List of String | ["true","true","false"] | whether to fix atoms in the direction, default = ["true","true","false"] (standard method) |🤖 Prompt for AI Agents
Verify each finding against the current code and only fix it if needed. In `@doc/autotest/property/Property-get-started-and-input-examples.md` at line 153, The table row for the property named "add_fix" currently shows an example with single quotes (['true','true','false']) which is invalid JSON; update the example to use double quotes and valid JSON array notation (["true","true","false"]) in the table entry for add_fix and ensure it matches the JSON examples elsewhere (e.g., the JSON block above) so copy-paste will not produce a parse error.doc/autotest/property/properties/Elastic-get-started-and-input-examples.md-25-26 (1)
25-26:⚠️ Potential issue | 🟡 MinorMinor notation inconsistency between JSON example and description text.
mdformatnormalized1e-2→0.01in the JSON block, but line 32 still reads:the default values of
norm_deformandshear_deformare 1e-2 and 1e-2, respectively.The values are numerically identical, but readers scanning the file may be momentarily confused by the mixed notation. Consider aligning line 32 to use
0.01as well.📝 Suggested prose update (line 32)
-Here the default values of `norm_deform` and `shear_deform` are **1e-2** and **1e-2**, respectively. +Here the default values of `norm_deform` and `shear_deform` are **0.01** and **0.01**, respectively.🤖 Prompt for AI Agents
Verify each finding against the current code and only fix it if needed. In `@doc/autotest/property/properties/Elastic-get-started-and-input-examples.md` around lines 25 - 26, Update the prose that describes the default values for norm_deform and shear_deform (the sentence that currently states they are "1e-2 and 1e-2") to use the same decimal notation as the JSON example ("0.01 and 0.01") so the description matches the JSON block showing "norm_deform": 0.01 and "shear_deform": 0.01; ensure the variables norm_deform and shear_deform are referenced exactly as written in the file.
🧹 Nitpick comments (1)
doc/init/init-bulk.md (1)
67-70: Make thejsonexample valid standalone JSON.Since the block is fenced as
json, wrap it with{ ... }so users can copy/paste it directly without edits.Proposed doc snippet
```json -"from_poscar": true, -"from_poscar_path": "....../C_mp-47_conventional.POSCAR", +{ + "from_poscar": true, + "from_poscar_path": "....../C_mp-47_conventional.POSCAR" +}</details> <details> <summary>🤖 Prompt for AI Agents</summary>Verify each finding against the current code and only fix it if needed.
In
@doc/init/init-bulk.mdaround lines 67 - 70, The JSON snippet shown is not a
valid standalone JSON object; wrap the keys "from_poscar" and "from_poscar_path"
in an outer object and ensure proper JSON syntax (use braces { ... }, proper
boolean literal true, and no trailing comma) so users can copy/paste the fenced
jsonblock directly; update the fenced block in init-bulk.md to contain {
"from_poscar": true, "from_poscar_path": "....../C_mp-47_conventional.POSCAR" }.</details> </blockquote></details> </blockquote></details> <details> <summary>🤖 Prompt for all review comments with AI agents</summary>Verify each finding against the current code and only fix it if needed.
Inline comments:
In @.pre-commit-config.yaml:
- Around line 49-51: Replace the fragile git-fork dependency entry for
mdformat-myst in .pre-commit-config.yaml with the PyPI release; remove or
replace the line containing
"git+https://github.com/njzjz-bothub/mdformat-myst@d9c414e#egg=mdformat-myst"
and add "mdformat-myst==0.3.0" (or uncomment the commented reference to
mdformat-myst==0.3.0) so the pre-commit config uses the official PyPI package
for mdformat-myst.
Outside diff comments:
In@doc/autotest/property/properties/EOS-post.md:
- Line 30: Fix the typo in the sample YAML key: replace the incorrect key name
"onf_dir" with "conf_dir" in the EOS-post sample so the directory key matches
the intended configuration label (look for the "onf_dir" entry in the EOS-post
sample content and update it to "conf_dir").In
@doc/autotest/refine/Refine-make.md:
- Line 24: Fix the grammar typo in the user-facing sentence that reads "an new
directoryvacancy_01would be established and the starting configuration links
to previous results." — replace "an new directory" with "a new directory" so the
sentence reads "a new directoryvacancy_01would be established..." in the
Refine-make documentation.In
@doc/autotest/relaxation/Relaxation-make.md:
- Around line 19-30: The fenced code blocks in Relaxation-make.md that show
file-tree output (the triple-backtick blocks around the tree snippet and the
other block at lines 43–56) lack a language specifier and trigger markdownlint
MD040; update those fences to use the "text" language (i.e., change ``` tohighlighting. In `@doc/init/init-reaction.md`: - Around line 22-24: Replace the two typos in the user-facing text: change the string "parametes" to "parameters" in the link text referencing init-reaction-jdata.rst, and change "genereated" to "generated" in the sentence about the data to fix the copy and ensure the links/readability are correct; update the markdown content where those exact words appear. --- Minor comments: In `@doc/autotest/Auto-test.md`: - Line 135: Replace the unhyphenated phrase "post process" with the correct compound form "post-process" in the sentence that describes performing the post process of calculation results (the line starting with "The post process of calculation results would be performed..."); ensure both occurrences in that sentence are changed so it reads "post-process" consistently. In `@doc/autotest/property/properties/Elastic-get-started-and-input-examples.md`: - Around line 25-26: Update the prose that describes the default values for norm_deform and shear_deform (the sentence that currently states they are "1e-2 and 1e-2") to use the same decimal notation as the JSON example ("0.01 and 0.01") so the description matches the JSON block showing "norm_deform": 0.01 and "shear_deform": 0.01; ensure the variables norm_deform and shear_deform are referenced exactly as written in the file. In `@doc/autotest/property/properties/EOS-post.md`: - Line 16: Fix the grammatical typo in the sentence that reads "An example of `result.json` is give as:"—change "is give as" to "is given as" in the line containing the `result.json` intro so it reads "An example of `result.json` is given as:". In `@doc/autotest/property/Property-get-started-and-input-examples.md`: - Around line 117-118: The table rows for norm_deform and shear_deform show the example value as "1e-2" but the JSON block uses "0.01"; update the Example column for the entries named norm_deform and shear_deform to "0.01" so both representations match exactly (leave the Type and Default columns unchanged). - Line 153: The table row for the property named "add_fix" currently shows an example with single quotes (['true','true','false']) which is invalid JSON; update the example to use double quotes and valid JSON array notation (["true","true","false"]) in the table entry for add_fix and ensure it matches the JSON examples elsewhere (e.g., the JSON block above) so copy-paste will not produce a parse error. In `@doc/autotest/property/Property-run.md`: - Line 7: Update the sentence in Property-run.md to use plural agreement and clearer wording: replace "the result file `log.lammps`, `dump.relax`, and `outlog` would be sent back." with a grammatically correct form such as "The result files `log.lammps`, `dump.relax`, and `outlog` will be sent back." to fix number agreement and improve clarity. In `@doc/autotest/refine/Refine-post.md`: - Line 7: Replace the lowercase, awkward sentence "the post process of `refine` is similar to the corresponding property." with a clearer, capitalized phrasing such as "The post-processing of `refine` is similar to the corresponding property workflow." — update the line containing "post process of `refine`" to use "The post-processing of `refine`" and append "workflow" for readability. In `@doc/autotest/refine/Refine-run.md`: - Line 7: Replace the vague sentence "the run process of `refine` is similar to before." with a clearer, capitalized sentence that explicitly names the referenced workflow (e.g., "The run process of `refine` follows the same workflow as the previous `refine-init`/`refine-build` steps.") — locate the sentence containing the exact text the run process of `refine` and update it to explicitly reference the prior workflow name(s) and start with a capital letter. In `@doc/autotest/relaxation/Relaxation-get-started-and-input-examples.md`: - Around line 74-79: Replace the incorrect JSON key "maximal" with "maxeval" inside the cal_setting example so the autotest picks up the value; ensure the example uses "cal_setting": { "etol": 0, "ftol": 1e-10, "maxiter": 5000, "maxeval": 500000 } to match the code path that checks for "maxeval" in cal_setting and the table documentation. In `@doc/autotest/reproduce/Reproduce-make.md`: - Around line 7-8: Update the prose in the markdown so the sentence starting "the output will be:" is capitalised to "The output will be:"; locate the line containing the exact phrase "the output will be:" in Reproduce-make.md and change only the leading lowercase "t" to an uppercase "T" to match documentation style and mdformat normalization. In `@doc/contributing-guide/contributing-guide.md`: - Around line 27-36: Replace all occurrences of the brand-name "Github" with the correct casing "GitHub" in the contributing-guide.md content (including the paragraph mentioning SSH keys/token, the linked blog text, the StackOverflow reference, and the "Use Github Desktop" section heading). Update the three inline instances shown in the diff and the section heading so the document consistently uses "GitHub". In `@doc/init/init_surf.md`: - Line 21: Fix the typo in the stage description line "1. Pertub and scale in folder `01.scale_pert`" by changing "Pertub" to "Perturb" so the stage reads "1. Perturb and scale in folder `01.scale_pert`"; update that exact text in doc/init/init_surf.md. In `@doc/overview/code-structure.md`: - Around line 53-54: Fix the typo "hase" → "has" in the sentence containing the dpdispatcher link and make the following line about `generator` a bullet item (consistent with adjacent entries) so the list structure remains uniform; update the sentence that currently reads "**Notice this part hase been integrated into [dpdispatcher](https://github.com/deepmodeling/dpdispatcher)**" to "**Notice this part has been integrated into [dpdispatcher](https://github.com/deepmodeling/dpdispatcher)**" and ensure the `generator` description remains prefixed as a list item like the surrounding entries. In `@doc/overview/overview.md`: - Line 20: Fix the typo "succusefully" to "successfully" in the overview sentence that begins "User-friendly and automatic: Users may install and run DP-GEN easily." Update the markdown content so the sentence reads "Once successfully running, DP-GEN can dispatch and handle all jobs on HPCs..." to correct spelling while preserving punctuation and surrounding text. - Line 28: Replace the escaped backticks sequence "\`conda install -c conda-forge dpgen\`" in the overview text with proper inline code formatting by removing the backslash escapes so it reads `conda install -c conda-forge dpgen`; update the line in overview.md where the install command appears (the current diff string "- Install via conda: \`conda install -c conda-forge dpgen\`\`") to use a single pair of backticks around the command. - Line 11: The text uses the incorrect expansion "DP-GEN (Deep Generator)" and the nonstandard spelling "DeepMD-kit"; update the phrase to "DP-GEN (Deep Potential GENerator)" and change "DeepMD-kit" to the canonical "DeePMD-kit" in the sentence that currently reads 'DP-GEN (Deep Generator) is a software ... dependent on [DeepMD-kit]'; ensure both replacements preserve the existing link and surrounding punctuation. In `@doc/run/example-of-param.md`: - Line 45: Fix the unintended space in the documented path by replacing the incorrect substring "...... /init/" with "....../init/" in the example text (the line that starts "Here, the init data is provided at ..."). Ensure there are no extra spaces between the leading dots and "/init/" so both shown paths ("....../init/CH4.POSCAR.01x01x01/02.md/sys-0004-0001/deepmd" and the two "....../init/CH4.POSCAR.01x01x01/01.scale_pert/..." entries) consistently use "....../init/" with no space. In `@doc/run/overview-of-the-run-process.md`: - Line 51: Fix the typo in the table header by replacing "Stage in eachiteration" with "Stage in each iteration" in the markdown table row that currently reads "| Index of iterations | Stage in eachiteration | Process |" so the header shows the correct spacing. In `@doc/user-guide/common-errors.md`: - Line 62: Replace the typo in the sentence "You can ignore this warning if you don't need Gromacs. It just show that Gromacs is not installed in you environment." by changing "you environment" to "your environment" and also fix the grammar "It just show" → "It just shows" so the full corrected sentence reads: "You can ignore this warning if you don't need Gromacs. It just shows that Gromacs is not installed in your environment." - Line 15: Fix the typo in the sentence "Please check your parameters with [DPGEN's Document](https://docs.deepmodeling.com/projects/dpgen/en/latest/). Maybe youhave superfluous parentheses in your parameter file." by changing "youhave" to "you have" so the sentence reads "...Maybe you have superfluous parentheses in your parameter file."; update the text where the exact token "youhave" appears. In `@examples/init/abacus/fcc-Al-lcao/INPUT.md`: - Line 2: The section headers like "#Parameters (1.General)" violate MD018; update each header to include a space after the hash (e.g., change "#Parameters (1.General)" to "# Parameters (1.General)") for the occurrences at the top and the other headers (the lines containing "#Parameters" at the same pattern); ensure all instances (the lines with "#Parameters") are updated so the markdown linter no longer flags MD018 while preserving the rest of the text. In `@examples/init/abacus/fcc-Al-pw/INPUT.md`: - Line 2: The markdown headings like "#Parameters (1.General)" violate MD018; update each section-header comment so there is a space after the hash (e.g., change "#Parameters (1.General)" to "# Parameters (1.General)") — apply the same fix to the other header occurrences with the same pattern (e.g., the headers at the other affected spots such as "10-10", "15-15", "18-18", "22-22") so all section-header lines include a space after the leading '#'. In `@examples/machine/DeePMD-kit-2.x/lebesgue_v2_machine_README.md`: - Line 3: The README line contains awkward escaped brackets around "manual" (currently `\[manual\]`); update the phrasing to use plain inline code or a proper markdown link target—for example replace `\[manual\]` with `manual` (or `manual` in backticks) or convert it to a real link text—so the sentence reads naturally (locate and edit the text containing "DPGEN" and `\[manual\]` in lebesgue_v2_machine_README.md). --- Nitpick comments: In `@doc/init/init-bulk.md`: - Around line 67-70: The JSON snippet shown is not a valid standalone JSON object; wrap the keys "from_poscar" and "from_poscar_path" in an outer object and ensure proper JSON syntax (use braces { ... }, proper boolean literal true, and no trailing comma) so users can copy/paste the fenced `json` block directly; update the fenced block in init-bulk.md to contain { "from_poscar": true, "from_poscar_path": "....../C_mp-47_conventional.POSCAR" }.
ℹ️ Review info
Configuration used: Organization UI
Review profile: CHILL
Plan: Pro
📒 Files selected for processing (46)
.pre-commit-config.yamlAGENTS.mdREADME.mddoc/autotest/Auto-test.mddoc/autotest/property/Property-get-started-and-input-examples.mddoc/autotest/property/Property-make.mddoc/autotest/property/Property-post.mddoc/autotest/property/Property-run.mddoc/autotest/property/properties/EOS-get-started-and-input-examples.mddoc/autotest/property/properties/EOS-make.mddoc/autotest/property/properties/EOS-post.mddoc/autotest/property/properties/Elastic-get-started-and-input-examples.mddoc/autotest/property/properties/Elastic-post.mddoc/autotest/property/properties/Interstitial-get-started-and-input-examples.mddoc/autotest/property/properties/Interstitial-post.mddoc/autotest/property/properties/Surface-get-started-and-input-examples.mddoc/autotest/property/properties/Surface-post.mddoc/autotest/property/properties/Vacancy-get-started-and-input-examples.mddoc/autotest/property/properties/Vacancy-post.mddoc/autotest/refine/Refine-get-started-and-input-examples.mddoc/autotest/refine/Refine-make.mddoc/autotest/refine/Refine-post.mddoc/autotest/refine/Refine-run.mddoc/autotest/relaxation/Relaxation-get-started-and-input-examples.mddoc/autotest/relaxation/Relaxation-make.mddoc/autotest/relaxation/Relaxation-post.mddoc/autotest/relaxation/Relaxation-run.mddoc/autotest/reproduce/Reproduce-get-started-and-input-examples.mddoc/autotest/reproduce/Reproduce-make.mddoc/autotest/reproduce/Reproduce-post.mddoc/contributing-guide/contributing-guide.mddoc/init/init-bulk.mddoc/init/init-reaction.mddoc/init/init_surf.mddoc/overview/code-structure.mddoc/overview/overview.mddoc/run/example-of-machine.mddoc/run/example-of-param.mddoc/run/overview-of-the-run-process.mddoc/simplify/simplify.mddoc/user-guide/common-errors.mddoc/user-guide/troubleshooting.mdexamples/init/abacus/fcc-Al-lcao/INPUT.mdexamples/init/abacus/fcc-Al-pw/INPUT.mdexamples/machine/DeePMD-kit-2.x/lebesgue_v2_machine_README.mdexamples/simplify-MAPbI3-scan-lebesgue/README.md
njzjz
approved these changes
Feb 25, 2026
wanghan-iapcm
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examples/init/abacus files should not be treated as markdown files.
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Addressed the review comments in follow-up commit 983e3df.\n\nChanges made:\n- switched dependency from the pinned fork URL to (PyPI)\n- updated mdformat exclude to skip in addition to , so ABACUS INPUT example files are not treated as Markdown\n\nAuthored by OpenClaw (model: gpt-5.3-codex) |
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Update after verification:
Latest commit: c27f996 Authored by OpenClaw (model: gpt-5.3-codex) |
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the changes to abacus inputs should be reverted |
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|
Thanks for the reminder — done. I reverted the changes in ABACUS INPUT examples and restored their original formatting in:\n- examples/init/abacus/fcc-Al-lcao/INPUT.md\n- examples/init/abacus/fcc-Al-pw/INPUT.md\n\nCommit: 5b60d34\n\nAuthored by OpenClaw (model: gpt-5.3-codex) |
wanghan-iapcm
approved these changes
Mar 1, 2026
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Sync pre-commit config from deepmd-kit@69eb0c3bb10be0ace823a5240c9fef6d0bb26c08
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Authored by OpenClaw (model: glm-5)
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