From c4ebc7494a12fc9c89ef882c7a06e62313f7d5c9 Mon Sep 17 00:00:00 2001 From: beanbean9339 Date: Fri, 18 Sep 2026 15:05:38 -0400 Subject: [PATCH 01/13] 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 02/13] 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 03/13] 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. From 7f71e598ae3c444691c87c321cb178fa7ead3443 Mon Sep 17 00:00:00 2001 From: beanbean9339 Date: Sat, 26 Sep 2026 23:41:24 -0400 Subject: [PATCH 04/13] docs: clarify OpenCite guidance --- docs/wiki-guide/GitHub-Repo-Guide.md | 14 +++++++++----- 1 file changed, 9 insertions(+), 5 deletions(-) diff --git a/docs/wiki-guide/GitHub-Repo-Guide.md b/docs/wiki-guide/GitHub-Repo-Guide.md index e5d4a99..ab01edb 100644 --- a/docs/wiki-guide/GitHub-Repo-Guide.md +++ b/docs/wiki-guide/GitHub-Repo-Guide.md @@ -22,7 +22,6 @@ 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 @@ -104,7 +103,7 @@ 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. Alternatively, you can use [OpenCite](https://imageomics.github.io/OpenCite/)[^2] to generate the citation and Zenodo metadata files from one form. +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. 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). @@ -117,7 +116,7 @@ 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). [OpenCite](https://imageomics.github.io/OpenCite/)[^2] can generate both files from one form, but review the information before using it. + Pair this citation file with a [`.zenodo.json`](#zenodo-metadata) for easier DOI metadata tracking (grants, references, associated papers). Generate both files from one form with [OpenCite](https://imageomics.github.io/OpenCite/)[^2]. ```yaml { py linenums="1" } abstract: "" @@ -151,7 +150,7 @@ 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. [OpenCite](https://imageomics.github.io/OpenCite/)[^2] can generate both files from one form, but review the information before using it. + 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. !!! info - Subcategories of `preferred-citation` do not get bullet points, but the first subcategory of `references` must be bulleted (as below). @@ -220,6 +219,8 @@ Providing this file is as simple as copying the below example and filling in you Check whether your citation renders correctly on a branch. When you push the `CITATION.cff` to a branch and browse the repository at that branch, you can select "Cite this repository" in the righthand sidebar to see if it is rendering as expected: ![Screenshot of "Cite this repository" pop-up on the Collaborative Distributed Science Guide repository. It shows APA and BibTeX 'content tabs' with the beginnings of a scrollable and copiable citation](images/GH-repo-guide/citation-cff-check.png) +[^2]: [OpenCite](https://imageomics.github.io/OpenCite/) creates standardized citation metadata through a guided form for project details, authors, identifiers, references, and funding, then exports `CITATION.cff` and `.zenodo.json` files. Review generated or imported information for accuracy before adding the files to a repository or publishing a DOI. + ## Recommended Files Though the following files are not included in every repository and do not have a simple selection process integrated into GitHub, they are extremely important (if not essential) to maintaining FAIR principles and reproducibility in projects, as well as ensuring proper attribution for your work. @@ -234,7 +235,10 @@ 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). -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. +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)), or copy the example below into a new file and update it with the appropriate information (comments should be removed prior to upload). + +!!! tip "Pro tip" + To create both metadata files from one form, use [OpenCite](https://imageomics.github.io/OpenCite/)[^2]. !!! note The `publication_date` and `version` will need to be updated along with the `CITATION.cff` for each release. From b3fa41965b45842716afa8681cf8563dd72ec6b5 Mon Sep 17 00:00:00 2001 From: beanbean9339 Date: Sun, 4 Oct 2026 20:24:14 -0400 Subject: [PATCH 05/13] docs: update OpenCite references and improve citation guidance in GitHub Repo Guide --- docs/wiki-guide/GitHub-Repo-Guide.md | 19 ++++++++++++++----- 1 file changed, 14 insertions(+), 5 deletions(-) diff --git a/docs/wiki-guide/GitHub-Repo-Guide.md b/docs/wiki-guide/GitHub-Repo-Guide.md index ab01edb..aca3d72 100644 --- a/docs/wiki-guide/GitHub-Repo-Guide.md +++ b/docs/wiki-guide/GitHub-Repo-Guide.md @@ -101,7 +101,9 @@ For more information on managing these environments and generating such files pr ### CITATION -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). +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) or use +[OpenCite](https://imageomics.github.io/OpenCite/)[^2]. 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. @@ -116,7 +118,7 @@ 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). Generate both files from one form with [OpenCite](https://imageomics.github.io/OpenCite/)[^2]. + Pair this citation file with a [`.zenodo.json`](#zenodo-metadata) for easier DOI metadata tracking (grants, references, associated papers). ```yaml { py linenums="1" } abstract: "" @@ -150,7 +152,7 @@ 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. [OpenCite](https://imageomics.github.io/OpenCite/)[^2] can generate both files from one form. + Pair the [standard citation file](#__tabbed_1_1) with a [.zenodo.json file](#zenodo-metadata), which can track references, associated papers, and grant information. !!! info - Subcategories of `preferred-citation` do not get bullet points, but the first subcategory of `references` must be bulleted (as below). @@ -219,7 +221,13 @@ Providing this file is as simple as copying the below example and filling in you Check whether your citation renders correctly on a branch. When you push the `CITATION.cff` to a branch and browse the repository at that branch, you can select "Cite this repository" in the righthand sidebar to see if it is rendering as expected: ![Screenshot of "Cite this repository" pop-up on the Collaborative Distributed Science Guide repository. It shows APA and BibTeX 'content tabs' with the beginnings of a scrollable and copiable citation](images/GH-repo-guide/citation-cff-check.png) -[^2]: [OpenCite](https://imageomics.github.io/OpenCite/) creates standardized citation metadata through a guided form for project details, authors, identifiers, references, and funding, then exports `CITATION.cff` and `.zenodo.json` files. Review generated or imported information for accuracy before adding the files to a repository or publishing a DOI. +[^2]: [OpenCite](https://imageomics.github.io/OpenCite/) creates standardized citation + metadata through a guided form for project details, authors, identifiers, + references, and funding, which can be imported from a GitHub repository. It + previews the generated `CITATION.cff` and `.zenodo.json` files, helping to + avoid missing or inconsistent metadata when preparing for release and/or + archive to Zenodo. Always review the generated or imported information for + accuracy before adding the files to a repository or publishing a DOI. ## Recommended Files @@ -238,7 +246,8 @@ When using the Zenodo-GitHub integration for [automatic DOI generation](DOI-Gene 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)), or copy the example below into a new file and update it with the appropriate information (comments should be removed prior to upload). !!! tip "Pro tip" - To create both metadata files from one form, use [OpenCite](https://imageomics.github.io/OpenCite/)[^2]. + To create both metadata files from one form, use + [OpenCite](https://imageomics.github.io/OpenCite/)[^2]. !!! note The `publication_date` and `version` will need to be updated along with the `CITATION.cff` for each release. From 46c576ee339b54fde2a930d1d4dbbcb828ee3b89 Mon Sep 17 00:00:00 2001 From: beanbean9339 Date: Mon, 5 Oct 2026 10:30:27 -0400 Subject: [PATCH 06/13] docs: add OpenCite links for improved citation metadata generation --- 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 aca3d72..95d1ce2 100644 --- a/docs/wiki-guide/GitHub-Repo-Guide.md +++ b/docs/wiki-guide/GitHub-Repo-Guide.md @@ -247,7 +247,7 @@ A `.zenodo.json` can be created by applying [cffconvert](https://github.com/cita !!! tip "Pro tip" To create both metadata files from one form, use - [OpenCite](https://imageomics.github.io/OpenCite/)[^2]. + [OpenCite](https://imageomics.github.io/OpenCite/). !!! note The `publication_date` and `version` will need to be updated along with the `CITATION.cff` for each release. From b3ed2ed1549f852f17f98817c4e6cdebe552894d Mon Sep 17 00:00:00 2001 From: Isabella Lo <138078620+beanbean9339@users.noreply.github.com> Date: Thu, 8 Oct 2026 22:04:59 -0400 Subject: [PATCH 07/13] Update docs/wiki-guide/GitHub-Repo-Guide.md Co-authored-by: Elizabeth Campolongo <38985481+egrace479@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 95d1ce2..180ab08 100644 --- a/docs/wiki-guide/GitHub-Repo-Guide.md +++ b/docs/wiki-guide/GitHub-Repo-Guide.md @@ -118,7 +118,7 @@ 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/) can generate both files from one form with helpful previews to review the files before downloading them. ```yaml { py linenums="1" } abstract: "" From 48910a6ac125e82428d64083af7ea0f6d045b388 Mon Sep 17 00:00:00 2001 From: Isabella Lo <138078620+beanbean9339@users.noreply.github.com> Date: Thu, 8 Oct 2026 22:05:11 -0400 Subject: [PATCH 08/13] Update docs/wiki-guide/GitHub-Repo-Guide.md Co-authored-by: Elizabeth Campolongo <38985481+egrace479@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 180ab08..e846313 100644 --- a/docs/wiki-guide/GitHub-Repo-Guide.md +++ b/docs/wiki-guide/GitHub-Repo-Guide.md @@ -152,7 +152,7 @@ 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/) can generate both files from one form with helpful previews to review the files before downloading them. !!! info - Subcategories of `preferred-citation` do not get bullet points, but the first subcategory of `references` must be bulleted (as below). From 3e4f550f1ef4d2fefc2b76a3d61fafb9b4be0fc7 Mon Sep 17 00:00:00 2001 From: Isabella Lo <138078620+beanbean9339@users.noreply.github.com> Date: Thu, 8 Oct 2026 22:05:29 -0400 Subject: [PATCH 09/13] Update docs/wiki-guide/GitHub-Repo-Guide.md Co-authored-by: Elizabeth Campolongo <38985481+egrace479@users.noreply.github.com> --- docs/wiki-guide/GitHub-Repo-Guide.md | 6 +----- 1 file changed, 1 insertion(+), 5 deletions(-) diff --git a/docs/wiki-guide/GitHub-Repo-Guide.md b/docs/wiki-guide/GitHub-Repo-Guide.md index e846313..96a2d2c 100644 --- a/docs/wiki-guide/GitHub-Repo-Guide.md +++ b/docs/wiki-guide/GitHub-Repo-Guide.md @@ -243,11 +243,7 @@ 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). -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)), or copy the example below into a new file and update it with the appropriate information (comments should be removed prior to upload). - -!!! tip "Pro tip" - To create both metadata files from one form, use - [OpenCite](https://imageomics.github.io/OpenCite/). +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). !!! note The `publication_date` and `version` will need to be updated along with the `CITATION.cff` for each release. From 2fee7f2ef4750e74413a5db741977197350511e4 Mon Sep 17 00:00:00 2001 From: beanbean9339 Date: Thu, 8 Oct 2026 22:26:10 -0400 Subject: [PATCH 10/13] docs: enhance FAIR Guide with additional resources for citation and metadata --- docs/wiki-guide/FAIR-Guide.md | 1 + 1 file changed, 1 insertion(+) diff --git a/docs/wiki-guide/FAIR-Guide.md b/docs/wiki-guide/FAIR-Guide.md index 4081140..ddd0ddd 100644 --- a/docs/wiki-guide/FAIR-Guide.md +++ b/docs/wiki-guide/FAIR-Guide.md @@ -16,6 +16,7 @@ The last topic in this section discusses different methods of [DOI Generation](D - [The Turing Way](https://book.the-turing-way.org/): an open-source, community data science handbook. It provides a strong foundation on the guiding principles for _this_ Guide, providing accessible explanations and overviews of topics from [reproducibility](https://book.the-turing-way.org/reproducible-research/reproducible-research), to [collaboration](https://book.the-turing-way.org/collaboration/collaboration) and [communication](https://book.the-turing-way.org/communication/communication), to [project design](https://book.the-turing-way.org/project-design/project-design), to [ethical research](https://book.the-turing-way.org/ethical-research/ethical-research). _This is a particularly good resource for those [just starting to use `git` and GitHub](https://book.the-turing-way.org/reproducible-research/vcs/vcs-git). It builds motivation for use of version control through the lens of reproducibility._ + - The [GitHub Repo Guide](GitHub-Repo-Guide.md) covers recommended repository contents and includes guidance on citations, including [OpenCite](https://imageomics.github.io/OpenCite/) for creating a `CITATION.cff` file. - Go-FAIR Initiative: [The FAIR Principles](https://www.go-fair.org/fair-principles/) - Ozoani, Ezi and Gerchick, Marissa and Mitchell, Margaret. Model Card Guidebook. Hugging Face, 2022. [https://huggingface.co/docs/hub/en/model-card-guidebook](https://huggingface.co/docs/hub/en/model-card-guidebook). From cf988cee2186ce5a9058ce80b22f8cc98cc2067b Mon Sep 17 00:00:00 2001 From: Isabella Lo <138078620+beanbean9339@users.noreply.github.com> Date: Mon, 12 Oct 2026 11:00:55 -0400 Subject: [PATCH 11/13] Update docs/wiki-guide/FAIR-Guide.md Co-authored-by: Elizabeth Campolongo <38985481+egrace479@users.noreply.github.com> --- docs/wiki-guide/FAIR-Guide.md | 1 - 1 file changed, 1 deletion(-) diff --git a/docs/wiki-guide/FAIR-Guide.md b/docs/wiki-guide/FAIR-Guide.md index ddd0ddd..4081140 100644 --- a/docs/wiki-guide/FAIR-Guide.md +++ b/docs/wiki-guide/FAIR-Guide.md @@ -16,7 +16,6 @@ The last topic in this section discusses different methods of [DOI Generation](D - [The Turing Way](https://book.the-turing-way.org/): an open-source, community data science handbook. It provides a strong foundation on the guiding principles for _this_ Guide, providing accessible explanations and overviews of topics from [reproducibility](https://book.the-turing-way.org/reproducible-research/reproducible-research), to [collaboration](https://book.the-turing-way.org/collaboration/collaboration) and [communication](https://book.the-turing-way.org/communication/communication), to [project design](https://book.the-turing-way.org/project-design/project-design), to [ethical research](https://book.the-turing-way.org/ethical-research/ethical-research). _This is a particularly good resource for those [just starting to use `git` and GitHub](https://book.the-turing-way.org/reproducible-research/vcs/vcs-git). It builds motivation for use of version control through the lens of reproducibility._ - - The [GitHub Repo Guide](GitHub-Repo-Guide.md) covers recommended repository contents and includes guidance on citations, including [OpenCite](https://imageomics.github.io/OpenCite/) for creating a `CITATION.cff` file. - Go-FAIR Initiative: [The FAIR Principles](https://www.go-fair.org/fair-principles/) - Ozoani, Ezi and Gerchick, Marissa and Mitchell, Margaret. Model Card Guidebook. Hugging Face, 2022. [https://huggingface.co/docs/hub/en/model-card-guidebook](https://huggingface.co/docs/hub/en/model-card-guidebook). From b39b3a3a7fe379cb1ab7a41fae9f0eb9927d18a6 Mon Sep 17 00:00:00 2001 From: Isabella Lo <138078620+beanbean9339@users.noreply.github.com> Date: Mon, 12 Oct 2026 11:44:17 -0400 Subject: [PATCH 12/13] Update docs/wiki-guide/GitHub-Repo-Guide.md Co-authored-by: Elizabeth Campolongo <38985481+egrace479@users.noreply.github.com> --- docs/wiki-guide/GitHub-Repo-Guide.md | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) diff --git a/docs/wiki-guide/GitHub-Repo-Guide.md b/docs/wiki-guide/GitHub-Repo-Guide.md index 96a2d2c..ba2054d 100644 --- a/docs/wiki-guide/GitHub-Repo-Guide.md +++ b/docs/wiki-guide/GitHub-Repo-Guide.md @@ -101,9 +101,7 @@ For more information on managing these environments and generating such files pr ### CITATION -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) or use -[OpenCite](https://imageomics.github.io/OpenCite/)[^2]. +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) or use [OpenCite](https://imageomics.github.io/OpenCite/)[^2]. 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. From a694776c32fb3158be5c28249494842f7997ff6f Mon Sep 17 00:00:00 2001 From: Isabella Lo <138078620+beanbean9339@users.noreply.github.com> Date: Mon, 12 Oct 2026 11:52:46 -0400 Subject: [PATCH 13/13] Update docs/wiki-guide/GitHub-Repo-Guide.md Co-authored-by: Elizabeth Campolongo <38985481+egrace479@users.noreply.github.com> --- docs/wiki-guide/GitHub-Repo-Guide.md | 8 +------- 1 file changed, 1 insertion(+), 7 deletions(-) diff --git a/docs/wiki-guide/GitHub-Repo-Guide.md b/docs/wiki-guide/GitHub-Repo-Guide.md index ba2054d..dbeb843 100644 --- a/docs/wiki-guide/GitHub-Repo-Guide.md +++ b/docs/wiki-guide/GitHub-Repo-Guide.md @@ -219,13 +219,7 @@ Providing this file is as simple as copying the below example and filling in you Check whether your citation renders correctly on a branch. When you push the `CITATION.cff` to a branch and browse the repository at that branch, you can select "Cite this repository" in the righthand sidebar to see if it is rendering as expected: ![Screenshot of "Cite this repository" pop-up on the Collaborative Distributed Science Guide repository. It shows APA and BibTeX 'content tabs' with the beginnings of a scrollable and copiable citation](images/GH-repo-guide/citation-cff-check.png) -[^2]: [OpenCite](https://imageomics.github.io/OpenCite/) creates standardized citation - metadata through a guided form for project details, authors, identifiers, - references, and funding, which can be imported from a GitHub repository. It - previews the generated `CITATION.cff` and `.zenodo.json` files, helping to - avoid missing or inconsistent metadata when preparing for release and/or - archive to Zenodo. Always review the generated or imported information for - accuracy before adding the files to a repository or publishing a DOI. +[^2]: [OpenCite](https://imageomics.github.io/OpenCite/) creates standardized citation metadata through a guided form for project details, authors, identifiers, references, and funding, which can be imported from a GitHub repository. It previews the generated `CITATION.cff` and `.zenodo.json` files, helping to avoid missing or inconsistent metadata when preparing for release and/or archive to Zenodo. Always review the generated or imported information for accuracy before adding the files to a repository or publishing a DOI. ## Recommended Files