From c4ebc7494a12fc9c89ef882c7a06e62313f7d5c9 Mon Sep 17 00:00:00 2001 From: beanbean9339 Date: Fri, 18 Sep 2026 15:05:38 -0400 Subject: [PATCH 1/3] Add OpenCite links for standardized citation metadata generation --- docs/wiki-guide/GitHub-Repo-Guide.md | 8 ++++++++ 1 file changed, 8 insertions(+) diff --git a/docs/wiki-guide/GitHub-Repo-Guide.md b/docs/wiki-guide/GitHub-Repo-Guide.md index 3d6a579..30e2b03 100644 --- a/docs/wiki-guide/GitHub-Repo-Guide.md +++ b/docs/wiki-guide/GitHub-Repo-Guide.md @@ -105,6 +105,10 @@ Make it easier for people to cite your project by including a [CITATION.cff file As with journal publications, we expect to be cited when someone uses our code. To facilitate proper attribution, GitHub will automatically read a [CITATION.cff file](https://docs.github.com/en/repositories/managing-your-repositorys-settings-and-features/customizing-your-repository/about-citation-files) and display a link to "cite this repository". This file is also used to populate metadata fields in a [Zenodo](https://zenodo.org/) record when [auto-generating a DOI](DOI-Generation.md#2-generate-a-doi-with-zenodo). As with any other component of your project, this file may change over the project's lifespan (see [Digital Product Life Cycle](Digital-Product-Lifecycle.md) for details), but it should be present and updated before any release. +[OpenCite](https://imageomics.github.io/OpenCite/) is a tool researchers can use to create standardized citation metadata for research software. It guides you through entering project details, authors and ORCID iDs, version and release information, identifiers, references, and funding. It then validates the information and exports both `CITATION.cff` and `.zenodo.json` files, helping you avoid missing or inconsistent metadata when preparing a repository or release for GitHub and Zenodo. Always review the generated or imported information before using it, especially the names, ORCID iDs, repository URL, version, release date, DOI, license, references, and funding details. + +[Open OpenCite](https://imageomics.github.io/OpenCite/){ .md-button } + Providing this file is as simple as copying the below example and filling in your information before uploading it to your repo. More examples and information about the Citation File Format can be found on the [citation-file-format repo](https://github.com/citation-file-format/citation-file-format), including helpful [related tools](https://github.com/citation-file-format/citation-file-format#tools-to-work-with-citationcff-files-wrench). #### Citation Templates @@ -233,6 +237,10 @@ Contributing guidelines are important to maintain consistency across the way peo When using the Zenodo-GitHub integration for [automatic DOI generation](DOI-Generation.md#automatic-generation), tracking metadata beyond the basics (authors, keywords, title, etc.) requires manual updates to the Zenodo record. The solution for this is to include a `.zenodo.json` file to keep track of this information (e.g., grant funding and references). +Use [OpenCite](https://imageomics.github.io/OpenCite/) when preparing a release: enter your metadata once, check it for common problems, and download a `CITATION.cff` and `.zenodo.json` that can be added to your repository. This makes it easier for GitHub to display citation information and for Zenodo to create a complete DOI record without re-entering the same information in multiple places. Before adding the files or publishing a DOI, review every field and correct anything OpenCite imported or generated incorrectly. + +[Create GitHub and Zenodo Metadata with OpenCite](https://imageomics.github.io/OpenCite/){ .md-button } + A `.zenodo.json` can be created by applying [cffconvert](https://github.com/citation-file-format/cffconvert) to your `CITATION.cff` (without the references, as these are not supported). Then add the references and other metadata back in to the JSON (following the [Zenodo dev guide](https://developers.zenodo.org/#representation)). Alternatively, The example below can simply be copied into a new file and updated with the appropriate information (comments should be removed prior to upload). !!! note From 9d238e05c80d1208aa25f18cb6f6893e99a7c885 Mon Sep 17 00:00:00 2001 From: Isabella Lo <138078620+beanbean9339@users.noreply.github.com> Date: Fri, 18 Sep 2026 15:11:44 -0400 Subject: [PATCH 2/3] Fix link formatting for OpenCite in GitHub Repo Guide Updated the link formatting for OpenCite and improved clarity in the documentation. Co-authored-by: Copilot Autofix powered by AI <175728472+Copilot@users.noreply.github.com> --- docs/wiki-guide/GitHub-Repo-Guide.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/wiki-guide/GitHub-Repo-Guide.md b/docs/wiki-guide/GitHub-Repo-Guide.md index 30e2b03..8fe60b2 100644 --- a/docs/wiki-guide/GitHub-Repo-Guide.md +++ b/docs/wiki-guide/GitHub-Repo-Guide.md @@ -107,7 +107,7 @@ As with journal publications, we expect to be cited when someone uses our code. [OpenCite](https://imageomics.github.io/OpenCite/) is a tool researchers can use to create standardized citation metadata for research software. It guides you through entering project details, authors and ORCID iDs, version and release information, identifiers, references, and funding. It then validates the information and exports both `CITATION.cff` and `.zenodo.json` files, helping you avoid missing or inconsistent metadata when preparing a repository or release for GitHub and Zenodo. Always review the generated or imported information before using it, especially the names, ORCID iDs, repository URL, version, release date, DOI, license, references, and funding details. -[Open OpenCite](https://imageomics.github.io/OpenCite/){ .md-button } +[OpenCite](https://imageomics.github.io/OpenCite/){ .md-button } Providing this file is as simple as copying the below example and filling in your information before uploading it to your repo. More examples and information about the Citation File Format can be found on the [citation-file-format repo](https://github.com/citation-file-format/citation-file-format), including helpful [related tools](https://github.com/citation-file-format/citation-file-format#tools-to-work-with-citationcff-files-wrench). From 46df8d0d096ac62a142281a5c84f00cebc87ccd9 Mon Sep 17 00:00:00 2001 From: beanbean9339 Date: Sat, 19 Sep 2026 13:38:46 -0400 Subject: [PATCH 3/3] Enhance OpenCite integration details in GitHub Repo Guide --- docs/wiki-guide/GitHub-Repo-Guide.md | 17 +++++------------ 1 file changed, 5 insertions(+), 12 deletions(-) diff --git a/docs/wiki-guide/GitHub-Repo-Guide.md b/docs/wiki-guide/GitHub-Repo-Guide.md index 8fe60b2..e5d4a99 100644 --- a/docs/wiki-guide/GitHub-Repo-Guide.md +++ b/docs/wiki-guide/GitHub-Repo-Guide.md @@ -22,6 +22,7 @@ More [recommendations](#recommended-files) are discussed below. !!! tip "Pro tip" All these files, plus more essential and recommended elements for a comprehensive GitHub repo, are included in our [Code Checklist](Code-Checklist.md). Following the checklist ensures compliance with the FAIR Principles for research software.[^1] [^1]: Barker, M., Chue Hong, N. P., Katz, D. S., Lamprecht, A. L., Martinez-Ortiz, C., Psomopoulos, F., Harrow, J., Castro, L. J., Gruenpeter, M., Martinez, P. A., & Honeyman, T. (2022). Introducing the FAIR Principles for research software. _Scientific data_, 9(1), 622. [URL](https://doi.org/10.1038/s41597-022-01710-x). + [^2]: [OpenCite](https://imageomics.github.io/OpenCite/) is a tool for creating standardized citation metadata. It guides users through entering project details, authors, identifiers, references, and funding, then exports `CITATION.cff` and `.zenodo.json` files. Review all generated or imported information for accuracy before adding the files to a repository or publishing a DOI. ### README @@ -103,11 +104,7 @@ For more information on managing these environments and generating such files pr Make it easier for people to cite your project by including a [CITATION.cff file](https://docs.github.com/en/repositories/managing-your-repositorys-settings-and-features/customizing-your-repository/about-citation-files); you can copy-paste the [template below](#citation-templates). -As with journal publications, we expect to be cited when someone uses our code. To facilitate proper attribution, GitHub will automatically read a [CITATION.cff file](https://docs.github.com/en/repositories/managing-your-repositorys-settings-and-features/customizing-your-repository/about-citation-files) and display a link to "cite this repository". This file is also used to populate metadata fields in a [Zenodo](https://zenodo.org/) record when [auto-generating a DOI](DOI-Generation.md#2-generate-a-doi-with-zenodo). As with any other component of your project, this file may change over the project's lifespan (see [Digital Product Life Cycle](Digital-Product-Lifecycle.md) for details), but it should be present and updated before any release. - -[OpenCite](https://imageomics.github.io/OpenCite/) is a tool researchers can use to create standardized citation metadata for research software. It guides you through entering project details, authors and ORCID iDs, version and release information, identifiers, references, and funding. It then validates the information and exports both `CITATION.cff` and `.zenodo.json` files, helping you avoid missing or inconsistent metadata when preparing a repository or release for GitHub and Zenodo. Always review the generated or imported information before using it, especially the names, ORCID iDs, repository URL, version, release date, DOI, license, references, and funding details. - -[OpenCite](https://imageomics.github.io/OpenCite/){ .md-button } +As with journal publications, we expect to be cited when someone uses our code. To facilitate proper attribution, GitHub will automatically read a [CITATION.cff file](https://docs.github.com/en/repositories/managing-your-repositorys-settings-and-features/customizing-your-repository/about-citation-files) and display a link to "cite this repository". This file is also used to populate metadata fields in a [Zenodo](https://zenodo.org/) record when [auto-generating a DOI](DOI-Generation.md#2-generate-a-doi-with-zenodo). As with any other component of your project, this file may change over the project's lifespan (see [Digital Product Life Cycle](Digital-Product-Lifecycle.md) for details), but it should be present and updated before any release. Alternatively, you can use [OpenCite](https://imageomics.github.io/OpenCite/)[^2] to generate the citation and Zenodo metadata files from one form. Providing this file is as simple as copying the below example and filling in your information before uploading it to your repo. More examples and information about the Citation File Format can be found on the [citation-file-format repo](https://github.com/citation-file-format/citation-file-format), including helpful [related tools](https://github.com/citation-file-format/citation-file-format#tools-to-work-with-citationcff-files-wrench). @@ -120,7 +117,7 @@ Providing this file is as simple as copying the below example and filling in you === "Standard Citation File (Recommended)" !!! tip "Pro tip" - Pair this citation file with a [`.zenodo.json`](#zenodo-metadata) for easier DOI metadata tracking (grants, references, associated papers). + Pair this citation file with a [`.zenodo.json`](#zenodo-metadata) for easier DOI metadata tracking (grants, references, associated papers). [OpenCite](https://imageomics.github.io/OpenCite/)[^2] can generate both files from one form, but review the information before using it. ```yaml { py linenums="1" } abstract: "" @@ -154,7 +151,7 @@ Providing this file is as simple as copying the below example and filling in you This is generally intended as a **reference for your code**. Preferred citation can be used for the paper, though it is better to ask in the `README` that someone cites _both_ and provide the paper reference there (only the `preferred-citation` will show up to be copied from the citation box if it is included). !!! success "Simplify version tracking for you code" - Pair the [standard citation file](#__tabbed_1_1) with a [.zenodo.json file](#zenodo-metadata), which can track references, associated papers, and grant information. + Pair the [standard citation file](#__tabbed_1_1) with a [.zenodo.json file](#zenodo-metadata), which can track references, associated papers, and grant information. [OpenCite](https://imageomics.github.io/OpenCite/)[^2] can generate both files from one form, but review the information before using it. !!! info - Subcategories of `preferred-citation` do not get bullet points, but the first subcategory of `references` must be bulleted (as below). @@ -237,11 +234,7 @@ Contributing guidelines are important to maintain consistency across the way peo When using the Zenodo-GitHub integration for [automatic DOI generation](DOI-Generation.md#automatic-generation), tracking metadata beyond the basics (authors, keywords, title, etc.) requires manual updates to the Zenodo record. The solution for this is to include a `.zenodo.json` file to keep track of this information (e.g., grant funding and references). -Use [OpenCite](https://imageomics.github.io/OpenCite/) when preparing a release: enter your metadata once, check it for common problems, and download a `CITATION.cff` and `.zenodo.json` that can be added to your repository. This makes it easier for GitHub to display citation information and for Zenodo to create a complete DOI record without re-entering the same information in multiple places. Before adding the files or publishing a DOI, review every field and correct anything OpenCite imported or generated incorrectly. - -[Create GitHub and Zenodo Metadata with OpenCite](https://imageomics.github.io/OpenCite/){ .md-button } - -A `.zenodo.json` can be created by applying [cffconvert](https://github.com/citation-file-format/cffconvert) to your `CITATION.cff` (without the references, as these are not supported). Then add the references and other metadata back in to the JSON (following the [Zenodo dev guide](https://developers.zenodo.org/#representation)). Alternatively, The example below can simply be copied into a new file and updated with the appropriate information (comments should be removed prior to upload). +A `.zenodo.json` can be created by applying [cffconvert](https://github.com/citation-file-format/cffconvert) to your `CITATION.cff` (without the references, as these are not supported). Then add the references and other metadata back in to the JSON (following the [Zenodo dev guide](https://developers.zenodo.org/#representation)). Alternatively, you can use [OpenCite](https://imageomics.github.io/OpenCite/)[^2] to generate both files together, or copy the example below into a new file and update it with the appropriate information (comments should be removed prior to upload). Before adding the files or publishing a DOI, review every field and correct anything OpenCite imported or generated incorrectly. !!! note The `publication_date` and `version` will need to be updated along with the `CITATION.cff` for each release.