Add citation and archiving support from open-research-data-template

.github/ISSUE_TEMPLATE/data_issue_report.yml

@@ -0,0 +1,50 @@
+name: 📊 Report Data Issue
+description: Report faulty or missing data
+title: '[DATE]: [TITLE]'
+labels: [data issue]
+body:
+  - type: markdown
+    attributes:
+      value: A clear and concise description of the data issue. Use this template to report problems with data files, datasets, or data quality.
+  - type: input
+    id: dataset
+    attributes:
+      label: 'Dataset Information'
+      description: 'Specify the file path or dataset name'
+      placeholder: 'e.g., data/users.csv or API endpoint /api/v1/data'
+    validations:
+      required: true
+  - type: textarea
+    id: expected_data
+    attributes:
+      label: 'Expected Data'
+      description: 'A clear and concise description of what the expected data should be.'
+      placeholder: 'Describe the expected data structure, values, or behavior.'
+    validations:
+      required: true
+  - type: textarea
+    id: actual_data
+    attributes:
+      label: 'Actual Data'
+      description: 'A clear and concise description of what the actual data is, including any discrepancies or errors.'
+      placeholder: 'Describe the actual data found, including specific errors, missing values, or incorrect formats.'
+    validations:
+      required: true
+  - type: input
+    id: screenshot
+    attributes:
+      label: 'Screenshot/Example (if applicable)'
+      description: 'Provide a link to a screenshot or example file demonstrating the issue'
+      placeholder: 'https://... or attach files below'
+  - type: textarea
+    id: impact
+    attributes:
+      label: 'Impact'
+      description: 'Describe the impact of this data issue on your work or the project'
+      placeholder: 'e.g., Cannot proceed with analysis, incorrect results generated, etc.'
+  - type: textarea
+    id: additional_context
+    attributes:
+      label: 'Additional Context'
+      description: 'Add any other context about the issue here.'
+      placeholder: 'Include steps to reproduce, when the issue was first noticed, or any potential causes.'

.husky/pre-commit

@@ -1 +1 @@
-pnpm check
+npm run check

.zenodo.json

@@ -0,0 +1,21 @@
+{
+	"title": "REPO_NAME",
+	"description": "SHORT_DESCRIPTION",
+	"license": "AGPL-3.0",
+	"upload_type": "software",
+	"creators": [
+		{
+			"name": "FULLNAME",
+			"affiliation": "Your Institution"
+		}
+	],
+	"keywords": ["github", "template"],
+	"related_identifiers": [
+		{
+			"scheme": "url",
+			"identifier": "https://github.com/USERNAME/REPO_NAME",
+			"relation": "isSupplementTo"
+		}
+	],
+	"contributors": []
+}

CITATION.cff

@@ -0,0 +1,18 @@
+# Go to https://citation-file-format.github.io/ to learn more about the Citation File Format.
+cff-version: 1.2.0
+title: REPO_NAME
+message: >-
+  If you use this software, please cite it using the
+  metadata from this file.
+type: software
+authors:
+  - family-names: FULLNAME
+    email: '[INSERT CONTACT METHOD]'
+repository-code: 'https://github.com/USERNAME/REPO_NAME'
+url: 'https://github.com/USERNAME/REPO_NAME'
+abstract: SHORT_DESCRIPTION
+keywords:
+  - github
+  - template
+license: AGPL-3.0
+version: 0.0.1

README.md

@@ -6,6 +6,7 @@ This is a GitHub template designed for small projects that is independent of the
 [![GitHub forks](https://img.shields.io/github/forks/maehr/github-template.svg)](https://github.com/maehr/github-template/network)
 [![GitHub stars](https://img.shields.io/github/stars/maehr/github-template.svg)](https://github.com/maehr/github-template/stargazers)
 [![GitHub license](https://img.shields.io/github/license/maehr/github-template.svg)](https://github.com/maehr/github-template/blob/main/LICENSE.md)
+[![DOI](https://zenodo.org/badge/DOI/YOUR_DOI_HERE.svg)](https://doi.org/YOUR_DOI_HERE)
 
 ## Why use a template (even for small projects)
 
@@ -14,6 +15,7 @@ This is a GitHub template designed for small projects that is independent of the
 - Increase [security](#security)
 - Follow recognized [ethical principles](#ethics)
 - Promote [Free and Open-source software](#foss)
+- Enable proper [academic citation](#citation) and archiving
 
 ## How this template helps you
 
@@ -24,14 +26,15 @@ This is a GitHub template designed for small projects that is independent of the
 - Automated [CHANGELOG.md](CHANGELOG.md) via [git-cliff](https://github.com/orhun/git-cliff)
 - [package.json](package.json) according to [npm docs](https://docs.npmjs.com/cli/v7/configuring-npm/package-json)
 - Accessible documentation via [gh-pages](https://help.github.com/en/articles/configuring-a-publishing-source-for-github-pages)
+- [TODO.md](TODO.md) checklist for project setup and customization
 
 ### Consistency
 
 - Consistent formatting via [Prettier](https://prettier.io/)
 - Consistent commit messages according to [Conventional Commits](https://www.conventionalcommits.org/en/v1.0.0/) via [husky](https://github.com/typicode/husky)
 - Consistent versioning via [Semantic Versioning](https://semver.org/spec/v2.0.0.html)
 - Consistent [fork and pull](https://gist.github.com/Chaser324/ce0505fbed06b947d962) workflow via [GitHub branch protection](https://docs.github.com/en/repositories/configuring-branches-and-merges-in-your-repository/defining-the-mergeability-of-pull-requests/managing-a-branch-protection-rule)
-- Consistent issues via [issue templates](https://docs.github.com/en/communities/using-templates-to-encourage-useful-issues-and-pull-requests/configuring-issue-templates-for-your-repository)
+- Consistent issues via [issue templates](https://docs.github.com/en/communities/using-templates-to-encourage-useful-issues-and-pull-requests/configuring-issue-templates-for-your-repository) including specialized templates for bugs, features, documentation, and data issues
 
 ### Security
 
@@ -48,6 +51,12 @@ This is a GitHub template designed for small projects that is independent of the
 
 - [LICENSE.md](LICENSE.md) according to [choosealicense.com](https://choosealicense.com/)
 
+### Citation
+
+- [CITATION.cff](CITATION.cff) according to [Citation File Format](https://citation-file-format.github.io/)
+- Automatic archiving with [Zenodo](https://zenodo.org/) via [.zenodo.json](.zenodo.json) for DOI generation
+- GitHub citation widget support for proper academic attribution
+
 ## Installation
 
 To initialize the template, [generate](https://github.com/maehr/github-template/generate) or [clone](https://docs.github.com/en/github/creating-cloning-and-archiving-repositories/cloning-a-repository) the repository to your local machine and follow this guide.
@@ -59,11 +68,11 @@ npm install
 npm run prepare
 ```
 
-2. Complete the following checklist of tasks to customize the template for your project:
+2. Complete the comprehensive setup checklist in [TODO.md](TODO.md) to customize the template for your project. This includes:
 
 - [ ] enable [GitHub security alerts](https://github.blog/2017-11-16-introducing-security-alerts-on-github/)
 - [ ] [protect](https://help.github.com/en/articles/configuring-protected-branches) the main branch to enforce a [fork and pull](https://gist.github.com/Chaser324/ce0505fbed06b947d962) workflow
-- [ ] search and replace `FULLNAME`, `USERNAME`, `REPO_NAME`, `SHORT_DESCRIPTION` `[INSERT CONTACT METHOD]` in [CODE_OF_CONDUCT.md](CODE_OF_CONDUCT.md), [package.json](package.json), [README.md](README.md), [SECURITY.md](SECURITY.md), [config.yml](.github/ISSUE_TEMPLATE/config.yml)
+- [ ] search and replace `FULLNAME`, `USERNAME`, `REPO_NAME`, `SHORT_DESCRIPTION`, `[INSERT CONTACT METHOD]` in [CITATION.cff](CITATION.cff), [CODE_OF_CONDUCT.md](CODE_OF_CONDUCT.md), [package.json](package.json), [README.md](README.md), [SECURITY.md](SECURITY.md), [config.yml](.github/ISSUE_TEMPLATE/config.yml), and [.zenodo.json](.zenodo.json)
 - [ ] add favicons to `./`, e.g. via [favicon.io](https://favicon.io/)
 - [ ] search for `TODO` in the project (mostly documentation) and fix it
 - [ ] delete [README.md](README.md)

README.template.md

@@ -6,6 +6,7 @@ SHORT_DESCRIPTION
 [![GitHub forks](https://img.shields.io/github/forks/USERNAME/REPO_NAME.svg)](https://github.com/USERNAME/REPO_NAME/network)
 [![GitHub stars](https://img.shields.io/github/stars/USERNAME/REPO_NAME.svg)](https://github.com/USERNAME/REPO_NAME/stargazers)
 [![GitHub license](https://img.shields.io/github/license/USERNAME/REPO_NAME.svg)](https://github.com/USERNAME/REPO_NAME/blob/main/LICENSE.md)
+[![DOI](https://zenodo.org/badge/DOI/YOUR_DOI_HERE.svg)](https://doi.org/YOUR_DOI_HERE)
 
 ## Installation
 
@@ -29,6 +30,7 @@ This project is maintained by [@USERNAME](https://github.com/USERNAME). Please u
 | Type                                   | Platforms                                                               |
 | -------------------------------------- | ----------------------------------------------------------------------- |
 | 🚨 **Bug Reports**                     | [GitHub Issue Tracker](https://github.com/USERNAME/REPO_NAME/issues)    |
+| 📊 **Data Issues**                     | [GitHub Issue Tracker](https://github.com/USERNAME/REPO_NAME/issues)    |
 | 📚 **Docs Issue**                      | [GitHub Issue Tracker](https://github.com/USERNAME/REPO_NAME/issues)    |
 | 🎁 **Feature Requests**                | [GitHub Issue Tracker](https://github.com/USERNAME/REPO_NAME/issues)    |
 | 🛡 **Report a security vulnerability** | See [SECURITY.md](SECURITY.md)                                          |

TODO.md

@@ -0,0 +1,41 @@
+# Project Setup Checklist
+
+Complete the following steps after creating your project from this template to customize and finalize your project.
+
+## Essential Setup Tasks
+
+- [ ] **Enable GitHub Security Alerts**: Navigate to your repository's "Security" tab on GitHub and enable Dependabot alerts and security updates to monitor vulnerabilities in dependencies.
+- [ ] **Protect the Main Branch**: In repository settings under "Branches", add a branch protection rule for `main` to require pull request reviews before merging and prevent force pushes.
+- [ ] **Update Project Details**: Replace all placeholder values in the following files with your actual project information:
+  - `FULLNAME` → Your full name (e.g., "Jane Doe")
+  - `USERNAME` → Your GitHub username (e.g., "janedoe")
+  - `REPO_NAME` → Your repository name (e.g., "my-awesome-project")
+  - `SHORT_DESCRIPTION` → Brief description of your project (e.g., "A template for small GitHub projects")
+  - `[INSERT CONTACT METHOD]` → Your contact email or preferred method
+  - Files to update: `.github/ISSUE_TEMPLATE/config.yml`, `CITATION.cff`, `CODE_OF_CONDUCT.md`, `package.json`, `README.template.md`, and `SECURITY.md`
+- [ ] **Add Favicons**: Generate and add favicon files to the root directory using [favicon.io](https://favicon.io/) or a similar service. Include `favicon.ico`, `favicon-16x16.png`, `favicon-32x32.png`, `apple-touch-icon.png`, and Android icons.
+- [ ] **Address TODO Comments**: Search for `TODO` comments throughout all project files using `grep -r "TODO" .` and complete or remove each task as appropriate for your project.
+- [ ] **Finalize README**: Once all customization is complete, delete the template README.md and rename `README.template.md` to `README.md` to make it your project's main README.
+- [ ] **Format Files**: Run `npm run format` to apply consistent formatting to all files using Prettier before committing changes.
+- [ ] **Commit Changes**: Use `npm run commit` to create a properly formatted commit message following Conventional Commits standards (e.g., "chore: initial project setup").
+- [ ] **Generate Changelog**: Run `npm run changelog` to generate changelog entries from your commit history, then copy the output into `CHANGELOG.md`.
+- [ ] **Enable GitHub Pages**: In repository settings under "Pages", set the source to "Deploy from a branch" and select the `gh-pages` branch and `/ (root)` folder (if using GitHub Pages for your project documentation).
+
+## Optional Enhancements
+
+- [ ] **Update Citation File**: Customize `CITATION.cff` with complete citation metadata including authors, version, DOI (after first release), and keywords relevant to your project.
+- [ ] **Add Zenodo Integration**: Follow the [GitHub guide for Zenodo integration](https://docs.github.com/en/repositories/archiving-a-github-repository/referencing-and-citing-content) to enable automatic archiving and obtain a DOI for your repository. Update `.zenodo.json` with custom metadata if needed.
+- [ ] **Customize Issue Templates**: Modify the existing issue templates or add new ones in `.github/ISSUE_TEMPLATE/` to match your project's specific needs.
+- [ ] **Add GitHub Actions**: Consider adding custom workflows for automated testing, linting, or deployment specific to your project's technology stack.
+- [ ] **Setup Project Board**: Create a GitHub project board to track issues and pull requests for better project management.
+
+## Verification Steps
+
+After completing the checklist:
+
+1. Run `npm run check` to verify all files are properly formatted
+2. Review your GitHub Pages site to confirm it displays as expected (if applicable)
+3. Test that all links in your README work correctly
+4. Verify that security alerts and branch protection are active
+5. Create a test issue and pull request to ensure templates work correctly
+6. Check that commit hooks are working by making a test commit