Feat/doc #192
Feat/doc #192
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Caution Review failedThe pull request is closed. WalkthroughThis change updates the README.md file by modifying the image file reference for the research flow diagram, adds a trailing newline after the image, and appends a Git repository SSH URL at the end of the Contribution section. No code or logic is affected. Changes
Estimated code review effort1 (<10 minutes) Possibly related PRs
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Actionable comments posted: 2
🧹 Nitpick comments (3)
README.md (1)
60-62: Improve HTML-based image markup for accessibility and HTML validity
style="align: center"is not a valid CSS declaration – usestyle="display:block;margin:0 auto"or rely on the surrounding<p align="center">.- The alt text
"joint management of code,data,model,..."is cryptic; make it a concise description of the graphic for screen-reader users (e.g. “Diagram showing joint management of code, data and models”).- Consider replacing the raw HTML with Markdown syntax to keep the README more maintainable unless specific HTML attributes are strictly required.
-<img style="align: center" alt="joint management of code,data,model,..." src="./docs/jzfs-joint-management.png" width="400" /> +<img src="./docs/jzfs-joint-management.png" + alt="Diagram showing joint management of code, data and models" + width="400" + style="display:block;margin:0 auto" />docs/jzfs.md (2)
14-15: Trim wordinessThe phrase “In order to maximize its utility and target audience” can be simplified to “To maximize its utility and reach”.
- In order to maximize its utility and target audience, + To maximize its utility and reach,
26-27: Replace “Last but not least” with concise alternativeConsider simply “Finally,” or remove the transitional phrase entirely to improve readability.
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docs/jzfs-logo-words-light.pngis excluded by!**/*.pngdocs/jzfs-logo-words.pngis excluded by!**/*.pngdocs/jzfs-research-flow.pngis excluded by!**/*.png
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README.md(2 hunks)docs/jzfs.md(1 hunks)
🧰 Additional context used
🪛 LanguageTool
docs/jzfs.md
[style] ~14-~14: Consider a more concise word here.
Context: ...urality of existing tools and services. In order to maximize its utility and target audienc...
(IN_ORDER_TO_PREMIUM)
[style] ~26-~26: ‘Last but not least’ might be wordy. Consider a shorter alternative.
Context: ...lete and rarely automatically captured. Last but not least, in the absence of standardized data pa...
(EN_WORDINESS_PREMIUM_LAST_BUT_NOT_LEAST)
[grammar] ~38-~38: Ensure spelling is correct
Context: ...lar version control system for software development1 . It is a distributed content management ...
(QB_NEW_EN_ORTHOGRAPHY_ERROR_IDS_1)
[grammar] ~44-~44: Ensure spelling is correct
Context: ...th tailored access to individual files. Gitannex takes advantage of Git’s ability to eff...
(QB_NEW_EN_ORTHOGRAPHY_ERROR_IDS_1)
[style] ~60-~60: To reduce wordiness, try specifying a number or using “many” or “numerous” instead.
Context: ...datasets contain millions of files, but a large number of files precludes managing such a dataset...
(LARGE_NUMBER_OF)
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| Statement of Need | ||
| Code, data and computing environments are core components of scientific projects. While | ||
| the collaborative development and use of research software and code is streamlined with established procedures and infrastructures, such as software distributions, distributed version | ||
| control systems, and social coding portals like GitHub, other components of scientific projects | ||
| are not as transparently managed or accessible. Data consumption is complicated by disconnected data portals that require a large variety of different data access and authentication | ||
| methods. Compared with code in software development, data tend not to be as precisely | ||
| identified because data versioning is rarely or only coarsely practiced. Scientific computation | ||
| is not reproducible enough, because data provenance, the information of how a digital file | ||
| came to be, is often incomplete and rarely automatically captured. Last but not least, in | ||
| the absence of standardized data packages, there is no uniform way to declare actionable | ||
| data dependencies and derivative relationships between inputs and outputs of a computation. DataLad aims to solve these issues by providing streamlined, transparent management | ||
| of code, data, computing environments, and their relationship. It provides targeted interfaces | ||
| and interoperability adapters to established scientific and commercial tools and services to | ||
| set up unobstructed, unified access to all elements of scientific projects. This unique set of | ||
| features enables workflows that are particularly suited for reproducible science, such as actionable process provenance capture for arbitrary command execution that affords automatic | ||
| re-execution. To this end, it builds on and extends two established tools for version control | ||
| and transport logistics, Git and git-annex. | ||
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| Why Git and git-annex? |
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🛠️ Refactor suggestion
Headings rendered as plain text – prefix with Markdown ##
Statement of Need, Why Git and git-annex?, and subsequent section titles are missing the #/## prefix, so they render as body text rather than headings. This hurts document structure and TOC generation.
-Statement of Need
+## Statement of Need
...
-Why Git and git-annex?
+## Why Git and git-annex?Repeat for other section titles.
📝 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.
| Statement of Need | |
| Code, data and computing environments are core components of scientific projects. While | |
| the collaborative development and use of research software and code is streamlined with established procedures and infrastructures, such as software distributions, distributed version | |
| control systems, and social coding portals like GitHub, other components of scientific projects | |
| are not as transparently managed or accessible. Data consumption is complicated by disconnected data portals that require a large variety of different data access and authentication | |
| methods. Compared with code in software development, data tend not to be as precisely | |
| identified because data versioning is rarely or only coarsely practiced. Scientific computation | |
| is not reproducible enough, because data provenance, the information of how a digital file | |
| came to be, is often incomplete and rarely automatically captured. Last but not least, in | |
| the absence of standardized data packages, there is no uniform way to declare actionable | |
| data dependencies and derivative relationships between inputs and outputs of a computation. DataLad aims to solve these issues by providing streamlined, transparent management | |
| of code, data, computing environments, and their relationship. It provides targeted interfaces | |
| and interoperability adapters to established scientific and commercial tools and services to | |
| set up unobstructed, unified access to all elements of scientific projects. This unique set of | |
| features enables workflows that are particularly suited for reproducible science, such as actionable process provenance capture for arbitrary command execution that affords automatic | |
| re-execution. To this end, it builds on and extends two established tools for version control | |
| and transport logistics, Git and git-annex. | |
| Why Git and git-annex? | |
| ## Statement of Need | |
| Code, data and computing environments are core components of scientific projects. While | |
| the collaborative development and use of research software and code is streamlined with established procedures and infrastructures, such as software distributions, distributed version | |
| control systems, and social coding portals like GitHub, other components of scientific projects | |
| are not as transparently managed or accessible. Data consumption is complicated by disconnected data portals that require a large variety of different data access and authentication | |
| methods. Compared with code in software development, data tend not to be as precisely | |
| identified because data versioning is rarely or only coarsely practiced. Scientific computation | |
| is not reproducible enough, because data provenance, the information of how a digital file | |
| came to be, is often incomplete and rarely automatically captured. Last but not least, in | |
| the absence of standardized data packages, there is no uniform way to declare actionable | |
| data dependencies and derivative relationships between inputs and outputs of a computation. DataLad aims to solve these issues by providing streamlined, transparent management | |
| of code, data, computing environments, and their relationship. It provides targeted interfaces | |
| and interoperability adapters to established scientific and commercial tools and services to | |
| set up unobstructed, unified access to all elements of scientific projects. This unique set of | |
| features enables workflows that are particularly suited for reproducible science, such as actionable process provenance capture for arbitrary command execution that affords automatic | |
| re-execution. To this end, it builds on and extends two established tools for version control | |
| and transport logistics, Git and git-annex. | |
| ## Why Git and git-annex? |
🧰 Tools
🪛 LanguageTool
[style] ~26-~26: ‘Last but not least’ might be wordy. Consider a shorter alternative.
Context: ...lete and rarely automatically captured. Last but not least, in the absence of standardized data pa...
(EN_WORDINESS_PREMIUM_LAST_BUT_NOT_LEAST)
🤖 Prompt for AI Agents
In docs/jzfs.md between lines 17 and 37, the section titles like "Statement of
Need" and "Why Git and git-annex?" are missing Markdown heading prefixes (# or
##), causing them to render as plain text instead of headings. To fix this, add
appropriate Markdown heading prefixes (e.g., ##) before each section title to
ensure they render correctly as headings and improve document structure and TOC
generation. Repeat this fix for all other section titles throughout the
document.
| Git is the most popular version control system for software development1 | ||
| . It is a distributed | ||
| content management system, specifically tuned towards managing and collaborating on text | ||
| files, and excels at making all committed content reliably and efficiently available to all clones | ||
| of a repository. At the same time, Git is not designed to efficiently handle large (e.g., over | ||
| a gigabyte) or binary files (see, e.g., Kenlon, 2016). This makes it hard or impossible to | ||
| use Git directly for distributed data storage with tailored access to individual files. Gitannex takes advantage of Git’s ability to efficiently manage textual information to overcome | ||
| this limitation. File content handled by git-annex is placed into a managed repository annex, | ||
| which avoids committing the file content directly to Git. Instead, git-annex commits a compact |
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Fix footnote artefact and git-annex spelling
- The “1” after “software development” looks like a dangling footnote marker – either add the reference or remove it.
- “Gitannex” is misspelled; the project name is “git-annex”.
- system for software development1 .
+ system for software development.
...
- Gitannex takes advantage of Git’s ability
+ git-annex takes advantage of Git’s ability📝 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.
| Git is the most popular version control system for software development1 | |
| . It is a distributed | |
| content management system, specifically tuned towards managing and collaborating on text | |
| files, and excels at making all committed content reliably and efficiently available to all clones | |
| of a repository. At the same time, Git is not designed to efficiently handle large (e.g., over | |
| a gigabyte) or binary files (see, e.g., Kenlon, 2016). This makes it hard or impossible to | |
| use Git directly for distributed data storage with tailored access to individual files. Gitannex takes advantage of Git’s ability to efficiently manage textual information to overcome | |
| this limitation. File content handled by git-annex is placed into a managed repository annex, | |
| which avoids committing the file content directly to Git. Instead, git-annex commits a compact | |
| Git is the most popular version control system for software development. | |
| It is a distributed | |
| content management system, specifically tuned towards managing and collaborating on text | |
| files, and excels at making all committed content reliably and efficiently available to all clones | |
| of a repository. At the same time, Git is not designed to efficiently handle large (e.g., over | |
| a gigabyte) or binary files (see, e.g., Kenlon, 2016). This makes it hard or impossible to | |
| use Git directly for distributed data storage with tailored access to individual files. git-annex takes advantage of Git’s ability to efficiently manage textual information to overcome | |
| this limitation. File content handled by git-annex is placed into a managed repository annex, | |
| which avoids committing the file content directly to Git. Instead, git-annex commits a compact |
🧰 Tools
🪛 LanguageTool
[grammar] ~38-~38: Ensure spelling is correct
Context: ...lar version control system for software development1 . It is a distributed content management ...
(QB_NEW_EN_ORTHOGRAPHY_ERROR_IDS_1)
[grammar] ~44-~44: Ensure spelling is correct
Context: ...th tailored access to individual files. Gitannex takes advantage of Git’s ability to eff...
(QB_NEW_EN_ORTHOGRAPHY_ERROR_IDS_1)
🤖 Prompt for AI Agents
In docs/jzfs.md around lines 38 to 46, remove the dangling footnote marker "1"
after "software development" by either deleting it or adding the appropriate
reference, and correct the spelling of "Gitannex" to "git-annex" wherever it
appears to match the official project name.
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Actionable comments posted: 0
🧹 Nitpick comments (2)
README.md (2)
60-62: Use Markdown-native image syntax and clean up invalid HTML attributes.Nitpicks that improve portability and accessibility:
<p align="center" width="100%">– thewidthattribute is invalid for a<p>element and will be ignored by most renderers.style="align: center"inside<img>is non-standard; alignment via CSS is preferable or can be dropped.- The ellipsis in the
alttext makes the description vague; keep alt text concise but meaningful.Consider the simpler, all-Markdown form:
-<p align="center" width="100%"> - <img style="align: center" alt="joint management of code,data,model,..." src="./docs/jzfs-joint-management.png" width="400" /> -</p> +<p align="center"> + <img src="./docs/jzfs-joint-management.png" + alt="Joint management of code, data and models" + width="400"> +</p>
96-96: Add descriptive alt text to meet accessibility lint (MD045).The image currently has no alternate text, triggering the markdown-lint warning.
- +
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README.md(2 hunks)
🧰 Additional context used
🪛 markdownlint-cli2 (0.17.2)
README.md
96-96: Images should have alternate text (alt text)
(MD045, no-alt-text)
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