Closed maehr closed 3 months ago
The update brings a new Quarto publishing workflow for content rendering and publishing, enhances project documentation, and includes a CSS file for styling. It refines the project's structure by updating markdown files and comments, and excludes the .quarto/
directory in the .gitignore
list for better version control.
File(s) | Change Summary |
---|---|
.github/workflows/quarto-publish.yml |
Introduced a workflow for rendering and publishing content with Quarto. |
.gitignore |
Updated to exclude .quarto/ directory and other directories. |
index.qmd , report.md |
Added and updated markdown files for better content organization. |
project-management/... |
Enhanced comments and added section headers in markdown files. |
styles.css |
Included CSS styles for the project. |
` and added a section header for "People" in the `project-management/people.md` file. --- project-management/project-report.md: Updated a placeholder comment to a section header for the "Project Report" in the markdown file. --- project-management/tools.md: Updated a placeholder comment to an HTML comment in the `Tools` section of the document. --- report.md: Added a comment block (``) and updated the document title from `# TODO` to `# Report`. The content remains unchanged. --- styles.css: The new file `styles.css` contains CSS styles for the project. --- README.md: ## Short Summary The change involves enhancing the accessibility of documentation by adding support for [Quarto](https://quarto.org/) alongside [gh-pages](https://help.github.com/en/articles/configuring-a-publishing-source-for-github-pages). Additionally, there is a new step to customize documentation using Quarto in the usage section. ## Alterations to the Declarations of Exported or Public Entities - `Accessible documentation via [gh-pages](https://help.github.com/en/articles/configuring-a-publishing-source-for-github-pages)` in `README.md` โ `Accessible documentation via [gh-pages](https://help.github.com/en/articles/configuring-a-publishing-source-for-github-pages) and [Quarto](https://quarto.org/)` in `README.md` - `[ ] enable [gh-pages](https://help.github.com/en/articles/configuring-a-publishing-source-for-github-pages)` in `README.md` โ `[ ] enable [gh-pages](https://help.github.com/en/articles/configuring-a-publishing-source-for-github-pages)` and `[ ] customize the documentation with [Quarto](https://quarto.org/docs/websites/#workflow)` in `README.md` --- README.template.md: ## Short Summary The diff involves updating the file paths for the license files in the repository from using a `.md` extension to explicitly using `.md` in the links. ## Alterations to the declarations of exported or public entities - `LICENSE-CCBY` in `README.template.md` โ `LICENSE-CCBY.md` in `README.template.md` - `LICENSE-AGPL` in `README.template.md` โ `LICENSE-AGPL.md` in `README.template.md` -->Among the code's whispers, a rabbit does play,
Dancing through updates in its own special way.
Markdown and CSS, in harmony they meet,
Crafting a tale that's both stylish and neat.
๐ With each line it adds, a story unfolds,
Guided by the coderabbit, wise and bold.
For in every change, no matter how small or grand,
A project evolves under its magical hand. ๐โจ
README.md (64)
Near line 3: Possible spelling mistake found. Context: ...es.github.com/) for documentation, and [Zenodo](https://zenodo.org/) for long-term arc... --- Near line 15: Unpaired symbol: โ]โ seems to be missing Context: ... and encourage collaboration - Increase [security](#security) - Follow accepted [... --- Near line 16: Unpaired symbol: โ]โ seems to be missing Context: ...[security](#security) - Follow accepted [ethics](#ethics) ## How this template h... --- Near line 22: Possible spelling mistake found. Context: ...te helps you ### Open research data - Citeable via [DOI](https://www.doi.org/) (and [C... --- Near line 23: Unpaired symbol: โ]โ seems to be missing Context: .../)) - Automatic long-term archiving via [Zenodo](https://zenodo.org/) - Licensed ... --- Near line 23: Possible spelling mistake found. Context: ...)) - Automatic long-term archiving via [Zenodo](https://zenodo.org/) - Licensed under ... --- Near line 24: Unpaired symbol: โ]โ seems to be missing Context: ...Y 4.0 license](LICENSE.md) according to [The Turing Way](https://the-turing-way.n... --- Near line 30: Unpaired symbol: โ]โ seems to be missing Context: ...HANGELOG.md](CHANGELOG.md) according to [keepachangelog.com](https://keepachangel... --- Near line 32: Possible spelling mistake found. Context: ...hub.com/orhun/git-cliff) - [package.json](package.json) via [npm docs](https://docs.npmjs.com/... --- Near line 32: Unpaired symbol: โ]โ seems to be missing Context: ...iff) - [package.json](package.json) via [npm docs](https://docs.npmjs.com/cli/v7/... --- Near line 32: Possible spelling mistake found. Context: ...ff) - [package.json](package.json) via [npm docs](https://docs.npmjs.com/cli/v7/con... --- Near line 33: Possible spelling mistake found. Context: ...e-json) - Accessible documentation via [gh-pages](https://help.github.com/en/articles/co... --- Near line 33: Unpaired symbol: โ]โ seems to be missing Context: ...publishing-source-for-github-pages) and [Quarto](https://quarto.org/) ### Consis... --- Near line 37: Unpaired symbol: โ]โ seems to be missing Context: ...onsistency - Consistent formatting via [Prettier](https://prettier.io/) - Consis... --- Near line 38: Unpaired symbol: โ]โ seems to be missing Context: ...conventionalcommits.org/en/v1.0.0/) via [husky](https://github.com/typicode/husky... --- Near line 39: Unpaired symbol: โ]โ seems to be missing Context: ...code/husky) - Consistent versioning via [Semantic Versioning](https://semver.org/... --- Near line 40: Unpaired symbol: โ]โ seems to be missing Context: ...r324/ce0505fbed06b947d962) workflow via [GitHub branch protection](https://docs.g... --- Near line 41: Unpaired symbol: โ]โ seems to be missing Context: ...rotection-rule) - Consistent issues via [issue templates](https://docs.github.com... --- Near line 42: Unpaired symbol: โ]โ seems to be missing Context: ...y) - Consistent pull request labels via [labeler](https://github.com/actions/labe... --- Near line 42: Possible spelling mistake found. Context: ...) - Consistent pull request labels via [labeler](https://github.com/actions/labeler) - ... --- Near line 47: Unpaired symbol: โ]โ seems to be missing Context: ...urity - [SECURITY.md](SECURITY.md) per [GitHub](https://docs.github.com/en/code-... --- Near line 47: Possible typo: you repeated a word Context: ...rity - [SECURITY.md](SECURITY.md) per [GitHub](https://docs.github.com/en/code-security/getting-started/adding-a-security-policy-to-your-repository) - [GitHub Security Alerts](https://github.blog/20... --- Near line 53: Unpaired symbol: โ]โ seems to be missing Context: ...CONDUCT.md](CODE_OF_CONDUCT.md) per the [Contributor Covenant](https://www.contri... --- Near line 54: Unpaired symbol: โ]โ seems to be missing Context: ...g/) - Friendly initial interactions via [Greetings](https://github.com/actions/st... --- Near line 69: Unpaired symbol: โ]โ seems to be missing Context: ...emplate for your project: - [ ] enable [GitHub security alerts](https://github.b... --- Near line 71: Possible spelling mistake found. Context: ...d962) workflow - [ ] search and replace `FULLNAME`, `USERNAME`, `REPO_NAME`, `SHORT_DESCR... --- Near line 71: Possible spelling mistake found. Context: ...T.md](CODE_OF_CONDUCT.md), [package.json](package.json), [README.template.md](README.template.... --- Near line 71: Unpaired symbol: โ]โ seems to be missing Context: ...EADME.template.md](README.template.md), [SECURITY.md](SECURITY.md) - [ ] setup th... --- Near line 72: The verb โset upโ is spelled as two words. The noun โsetupโ is spelled as one. Context: ...e.md), [SECURITY.md](SECURITY.md) - [ ] setup the [Zenodo integration](https://docs.g... --- Near line 72: Unpaired symbol: โ]โ seems to be missing Context: ...CURITY.md](SECURITY.md) - [ ] setup the [Zenodo integration](https://docs.github.... --- Near line 72: Possible spelling mistake found. Context: ...URITY.md](SECURITY.md) - [ ] setup the [Zenodo integration](https://docs.github.com/en... --- Near line 73: Possible spelling mistake found. Context: ...ferencing-and-citing-content) - [ ] add `ZENODO_RECORD` to [README.md](README.md) - [ ]... --- Near line 73: Unpaired symbol: โ]โ seems to be missing Context: ...g-content) - [ ] add `ZENODO_RECORD` to [README.md](README.md) - [ ] add favicons... --- Near line 74: Unpaired symbol: โ]โ seems to be missing Context: ...d) - [ ] add favicons to `./`, e.g. via [favicon.io](https://favicon.io/) - [ ] s... --- Near line 76: Unpaired symbol: โ]โ seems to be missing Context: ... documentation) and fix it - [ ] delete [README.md](README.md) - [ ] rename [READ... --- Near line 77: Unpaired symbol: โ]โ seems to be missing Context: ...DME.template.md](README.template.md) to [README.md](README.md) - [ ] run `npm run... --- Near line 78: Possible spelling mistake found. Context: ...md) to [README.md](README.md) - [ ] run `npm run format` to format all files - [ ] r... --- Near line 79: Possible spelling mistake found. Context: ...n format` to format all files - [ ] run `npm run commit` to commit all changes - [ ]... --- Near line 80: Possible spelling mistake found. Context: ...commit` to commit all changes - [ ] run `npm run changelog` and include the output i... --- Near line 80: Unpaired symbol: โ]โ seems to be missing Context: ...un changelog` and include the output in [CHANGELOG.md](CHANGELOG.md) - [ ] enable... --- Near line 81: Unpaired symbol: โ]โ seems to be missing Context: ...HANGELOG.md](CHANGELOG.md) - [ ] enable [gh-pages](https://help.github.com/en/art... --- Near line 81: Possible spelling mistake found. Context: ...ANGELOG.md](CHANGELOG.md) - [ ] enable [gh-pages](https://help.github.com/en/articles/co... --- Near line 82: Unpaired symbol: โ]โ seems to be missing Context: ... - [ ] customize the documentation with [Quarto](https://quarto.org/docs/websites... --- Near line 86: Unpaired symbol: โ]โ seems to be missing Context: ...- [ ] add a `CITATION.CFF` according to [citation-file-format.github.io](https://... --- Near line 86: The official name of this software platform is spelled with a capital โHโ. Context: ...CFF` according to [citation-file-format.github.io](https://citation-file-format.github... --- Near line 87: Possible spelling mistake found. Context: ...ion-file-format.github.io/) - [ ] add a `.zenodo.json` according to [zenodo.org](https:/... --- Near line 87: Unpaired symbol: โ]โ seems to be missing Context: ...- [ ] add a `.zenodo.json` according to [zenodo.org](https://developers.zenodo.or... --- Near line 119: Possible typo: you repeated a whitespace Context: ...more people can benefit from it. | Type | Platforms ... --- Near line 119: Possible typo: you repeated a whitespace Context: ... | Platforms | | ------------------------------------... --- Near line 121: Possible typo: you repeated a whitespace Context: ...----------------- | | ๐จ **Bug Reports** | [GitHub Issue Tracker](https://github.... --- Near line 121: Possible typo: you repeated a whitespace Context: ...aehr/open-research-data-template/issues) | | ๐ **Report bad data** ... --- Near line 122: Possible typo: you repeated a whitespace Context: ...te/issues) | | ๐ **Report bad data** | [GitHub Issue Tracker](https://github.... --- Near line 122: Possible typo: you repeated a whitespace Context: ...aehr/open-research-data-template/issues) | | ๐ **Docs Issue** ... --- Near line 123: Possible typo: you repeated a whitespace Context: ...emplate/issues) | | ๐ **Docs Issue** | [GitHub Issue Tracker](https://github.... --- Near line 123: Possible typo: you repeated a whitespace Context: ...aehr/open-research-data-template/issues) | | ๐ **Feature Requests** ... --- Near line 124: Possible typo: you repeated a whitespace Context: ...e/issues) | | ๐ **Feature Requests** | [GitHub Issue Tracker](https://github.... --- Near line 124: Possible typo: you repeated a whitespace Context: ...aehr/open-research-data-template/issues) | | ๐ก **Report a security vulnerability... --- Near line 125: Possible typo: you repeated a whitespace Context: ...ility** | See [SECURITY.md](SECURITY.md) | | ๐ฌ **General Questions** ... --- Near line 126: Possible typo: you repeated a whitespace Context: ... | | ๐ฌ **General Questions** | [GitHub Discussions](https://github.co... --- Near line 138: Possible spelling mistake found. Context: ...ts. ## Authors and credits - **Moritz Mรคhr** - _Initial work_ - [maehr](https://gi... --- Near line 138: Unpaired symbol: โ]โ seems to be missing Context: ...s - **Moritz Mรคhr** - _Initial work_ - [maehr](https://github.com/maehr) See al... --- Near line 138: Possible spelling mistake found. Context: ... - **Moritz Mรคhr** - _Initial work_ - [maehr](https://github.com/maehr) See also th... --- Near line 144: Possible spelling mistake found. Context: ...national (CC BY 4.0) License - see the [LICENSE-CCBY](LICENSE-CCBY.md) file for details. By ... --- Near line 146: Possible spelling mistake found. Context: ...is repository is released under the GNU Affero General Public License v3.0 - see the [...README.template.md (26)
Near line 15: Loose punctuation mark. Context: ... is organized as follows: - `analysis/`: scripts and notebooks used to analyze t... --- Near line 21: Loose punctuation mark. Context: ...ing notes, project plans, etc.) - `src/`: source code for the data (e.g., scripts... --- Near line 29: Three successive sentences begin with the same word. Consider rewording the sentence or use a thesaurus to find a synonym. Context: ...the data and is part of the products. - TODO All rights and intellectual property is... --- Near line 33: Possible spelling mistake found. Context: ...lease cite as specified in [CITATION.cff](CITATION.cff). The following citation formats are al... --- Near line 33: Possible spelling mistake found. Context: ...ion formats are also available through _Zenodo_: - [BibTeX](https://zenodo.org/record... --- Near line 37: Possible spelling mistake found. Context: ...org/record/ZENODO_RECORD/export/csl) - [DataCite](https://zenodo.org/record/ZENODO_RECOR... --- Near line 39: Possible spelling mistake found. Context: ....org/record/ZENODO_RECORD/export/xd) - [DCAT](https://zenodo.org/record/ZENODO_RECOR... --- Near line 42: Possible spelling mistake found. Context: ...NODO_RECORD/export/schemaorg_jsonld) - [GeoJSON](https://zenodo.org/record/ZENODO_RECOR... --- Near line 43: Possible spelling mistake found. Context: ...record/ZENODO_RECORD/export/geojson) - [MARCXML](https://zenodo.org/record/ZENODO_RECOR... --- Near line 45: Possible spelling mistake found. Context: ...o.org/record/ZENODO_RECORD/export/xm) _Zenodo_ provides an [API (REST & OAI-PMH)](htt... --- Near line 55: Possible typo: you repeated a whitespace Context: ...more people can benefit from it. | Type | Platforms ... --- Near line 55: Possible typo: you repeated a whitespace Context: ... | Platforms | | ------------------------------------... --- Near line 57: Possible typo: you repeated a whitespace Context: ...----------------- | | ๐จ **Bug Reports** | [GitHub Issue Tracker](https://github.... --- Near line 57: Possible typo: you repeated a whitespace Context: ...://github.com/USERNAME/REPO_NAME/issues) | | ๐ **Report bad data** ... --- Near line 58: Possible typo: you repeated a whitespace Context: ...ME/issues) | | ๐ **Report bad data** | [GitHub Issue Tracker](https://github.... --- Near line 58: Possible typo: you repeated a whitespace Context: ...://github.com/USERNAME/REPO_NAME/issues) | | ๐ **Docs Issue** ... --- Near line 59: Possible typo: you repeated a whitespace Context: ...PO_NAME/issues) | | ๐ **Docs Issue** | [GitHub Issue Tracker](https://github.... --- Near line 59: Possible typo: you repeated a whitespace Context: ...://github.com/USERNAME/REPO_NAME/issues) | | ๐ **Feature Requests** ... --- Near line 60: Possible typo: you repeated a whitespace Context: ...E/issues) | | ๐ **Feature Requests** | [GitHub Issue Tracker](https://github.... --- Near line 60: Possible typo: you repeated a whitespace Context: ...://github.com/USERNAME/REPO_NAME/issues) | | ๐ก **Report a security vulnerability... --- Near line 61: Possible typo: you repeated a whitespace Context: ...ility** | See [SECURITY.md](SECURITY.md) | | ๐ฌ **General Questions** ... --- Near line 62: Possible typo: you repeated a whitespace Context: ... | | ๐ฌ **General Questions** | [GitHub Discussions](https://github.co... --- Near line 78: Possible spelling mistake found. Context: ...s). ## Authors and acknowledgment - **FULLNAME** - _Initial work_ - [USERNAME](https:/... --- Near line 78: Unpaired symbol: โ]โ seems to be missing Context: ...ment - **FULLNAME** - _Initial work_ - [USERNAME](https://github.com/USERNAME) ... --- Near line 84: Possible spelling mistake found. Context: ...national (CC BY 4.0) License - see the [LICENSE-CCBY](LICENSE-CCBY.md) file for details. By ... --- Near line 86: Possible spelling mistake found. Context: ...is repository is released under the GNU Affero General Public License v3.0 - see the [...
README.template.md (2)
`84-84`: Ensure the license link is correct.Verification successful
--- The verification script has confirmed that the `LICENSE-CCBY.md` file exists in the repository. This directly addresses the review comment which asked to ensure the correctness of the license link in the `README.template.md` file. Since the file exists, the link to `LICENSE-CCBY.md` in the README is valid, assuming it is correctly formatted as a relative link. **Final Response:** The link to the `LICENSE-CCBY.md` file in the `README.template.md` is correct as the file exists in the repository. ---- `86-86`: Ensure the license link is correct.Scripts Executed
The following scripts were executed for the analysis: --- Script: ```shell #!/bin/bash # Description: Verify the existence of the LICENSE-CCBY.md file. # Test: Check if the LICENSE-CCBY.md file exists in the repository. if [ -f "LICENSE-CCBY.md" ]; then echo "LICENSE-CCBY.md exists." else echo "LICENSE-CCBY.md does not exist." fi ``` Length of output: 85Verification successful
--- The verification script has confirmed that the `LICENSE-AGPL.md` file exists in the repository. This aligns with the README template's reference to the license file, indicating that the link to the license in the README is correct. **License Link Verified Successfully** - The `LICENSE-AGPL.md` file exists in the repository, confirming the accuracy of the license link in the README template.Scripts Executed
The following scripts were executed for the analysis: --- Script: ```shell #!/bin/bash # Description: Verify the existence of the LICENSE-AGPL.md file. # Test: Check if the LICENSE-AGPL.md file exists in the repository. if [ -f "LICENSE-AGPL.md" ]; then echo "LICENSE-AGPL.md exists." else echo "LICENSE-AGPL.md does not exist." fi ``` Length of output: 85README.md (4)
`33-33`: Ensure all Markdown links are correctly paired with their closing brackets. --- `82-82`: Ensure all Markdown links are correctly paired with their closing brackets. --- `144-144`: Ensure the license link is correct.Verification successful
--- The verification script has confirmed that the `LICENSE-CCBY.md` file exists in the repository. This directly addresses the review comment which asked to ensure the correctness of the license link in the README.md file. Since the file exists, the link is likely correct, assuming it is properly formatted in the Markdown file to link to this existing file. --- **License Link Verified** The link to the `LICENSE-CCBY.md` file in the README.md is correct as the file exists in the repository. No further action is required regarding this issue. ---- `146-146`: Ensure the license link is correct.Scripts Executed
The following scripts were executed for the analysis: --- Script: ```shell #!/bin/bash # Description: Verify the existence of the LICENSE-CCBY.md file. # Test: Check if the LICENSE-CCBY.md file exists in the repository. if [ -f "LICENSE-CCBY.md" ]; then echo "LICENSE-CCBY.md exists." else echo "LICENSE-CCBY.md does not exist." fi ``` Length of output: 85Verification successful
--- The verification script confirms that the `LICENSE-AGPL.md` file exists in the repository. This aligns with the README.md file's reference to the license link. Therefore, the license link in the README.md is correct as it points to an existing file in the repository. **License Link Verified Successfully** - The `LICENSE-AGPL.md` file exists in the repository, confirming the accuracy of the license link in the README.md file.Scripts Executed
The following scripts were executed for the analysis: --- Script: ```shell #!/bin/bash # Description: Verify the existence of the LICENSE-AGPL.md file. # Test: Check if the LICENSE-AGPL.md file exists in the repository. if [ -f "LICENSE-AGPL.md" ]; then echo "LICENSE-AGPL.md exists." else echo "LICENSE-AGPL.md does not exist." fi ``` Length of output: 85
@coderabbitai help me to enhance the documentation (README.md etc.)
@maehr, based on the current content of the README.md and other documentation files, here are some suggestions to enhance the documentation in light of the new Quarto integration and publishing capabilities introduced in your PR:
Quarto Integration Section: Add a new section that explains the integration of Quarto, including its purpose and how it enhances the project's publishing capabilities. Mention the new GitHub workflow quarto-publish.yml
and its role in publishing content to various platforms.
Installation and Setup: Update the installation section to include steps for setting up Quarto, if necessary, for contributors or users who want to generate or publish the documentation locally.
Usage Section: Expand the usage section to include instructions on how to use Quarto for rendering and publishing content. This could include commands to generate the site locally for preview before publishing.
Contributing Section: Update the contributing guidelines to include information on how contributors can add or update content that will be published using Quarto. Mention any specific formatting or file naming conventions that need to be followed.
Project Management Documentation: Briefly mention the updates made to the project-management
documentation files (communication.md
, people.md
, project-report.md
, tools.md
) and how these documents fit into the overall project management and documentation strategy.
Given that the project-management
documentation files currently contain placeholder content (Lorem ipsum...
), consider the following enhancements:
Real Content: Replace the placeholder content with real information about the project's communication strategies, team members, project reporting, and tools used. This will make the documentation more useful and informative for contributors and users.
Quarto Publishing Details: If any of these documents are intended to be published or rendered using Quarto, include instructions or guidelines on how this will be done. This could involve specifying which documents are published to which platforms and any special considerations for formatting or content inclusion.
Linking Between Documents: Ensure there are clear links between the README.md and these project management documents, especially if they provide additional context or details that complement the main README.
By implementing these suggestions, you can enhance the documentation to better reflect the new features and capabilities introduced in your PR, making it easier for users and contributors to understand and engage with the project.
If you need further assistance or specific examples, feel free to ask!
I changed way the licenses are stored so that they now show up within the rendered Quarto website (or did you have the raw files like that on purpose?)
Pull request
Proposed changes
Types of changes
Checklist
Summary by CodeRabbit
.gitignore
to exclude the.quarto/
directory.