Adopt the Organization Repository Standards

[PSchmiedmayer]

♻️ Current situation & Problem

SchmiedmayerLab/.github defines the organization repository standard in REPOSITORY_STANDARDS.md and enforces it in repository-standards.yml. This repository does not call that workflow yet.

No related issue was identified.

⚙️ Release Notes

• Call repository-standards.yml@v0.5 from a new .github/workflows/repository-standards.yml.
• Pin every shared workflow reference to v0.5.
• Complete CITATION.cff with the fields Zenodo reads, and bring CONTRIBUTORS.md to the documented shape.
• Add the badge block and the Contributing, License, Citation and Our Research sections to the README.
• Group Dependabot updates into a single weekly pull request.
• Name the same project in every SPDX header.

📚 Documentation

The standard is documented in REPOSITORY_STANDARDS.md.

✅ Testing

• actionlint, yamllint and reuse lint
• repository-standards.yml@v0.5 runs on this pull request

Code of Conduct & Contributing Guidelines

By creating and submitting this pull request, you agree to follow our Code of Conduct and Contributing Guidelines:

• I agree to follow the Code of Conduct and Contributing Guidelines.

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[coderabbitai]

No actionable comments were generated in the recent review. 🎉

ℹ️ Recent review info

⚙️ Run configuration

Configuration used: Organization UI

Review profile: CHILL

Plan: Pro Plus

Run ID: 9a903591-60c4-4693-bd8e-a6794a5a4f3f

📥 Commits

Reviewing files that changed from the base of the PR and between ae5dadf and 7306155.

📒 Files selected for processing (1)

• README.md

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📝 Walkthrough

Walkthrough

The PR adds a repository standards workflow and upgrades reusable validation workflows to v0.5. It adds a link-checker exception for Terra support URLs. It adds MIT license and citation metadata. It updates README badges, links, citation guidance, contributor text, and footer images. It removes CONTRIBUTING.md and SECURITY.md. Compliance tests now match the updated policies and workflow version.

Possibly related PRs

• SchmiedmayerLab/heartwood#1: Modifies the same validation workflow and link-checker configuration.
• SchmiedmayerLab/heartwood#30: Overlaps with the workflow-version changes and compliance-test updates.
• SchmiedmayerLab/heartwood#92: Modifies SECURITY.md and related support-policy checks.

🚥 Pre-merge checks | ✅ 4 | ❌ 1

❌ Failed checks (1 warning)

Check name	Status	Explanation	Resolution
Docstring Coverage	⚠️ Warning	Docstring coverage is 0.00% which is insufficient. The required threshold is 80.00%.	Write docstrings for the functions missing them to satisfy the coverage threshold.

✅ Passed checks (4 passed)

Check name	Status	Explanation
Title check	✅ Passed	The title clearly describes the primary change: adopting the organization repository standards.
Description check	✅ Passed	The description directly explains the repository standards adoption and lists the related workflow, documentation, and validation changes.
Linked Issues check	✅ Passed	Check skipped because no linked issues were found for this pull request.
Out of Scope Changes check	✅ Passed	Check skipped because no linked issues were found for this pull request.

---

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[coderabbitai]

Actionable comments posted: 1

🧹 Nitpick comments (1)

packages/compliance/tests/test_release_governance.py (1)

330-331: 🎯 Functional Correctness | 🔵 Trivial | ⚡ Quick win

Cover the new standards workflow in the version assertion.

This test validates only the three references in .github/workflows/validate.yml. The PR also adds repository-standards.yml@v0.5 in .github/workflows/repository-standards.yml. A future downgrade of that reference could pass this test.

Add an assertion for the new workflow.

Proposed test update

     validation = Path(".github/workflows/validate.yml").read_text(encoding="utf-8")
+    standards = Path(
+        ".github/workflows/repository-standards.yml"
+    ).read_text(encoding="utf-8")

     assert validation.count("SchmiedmayerLab/.github/.github/workflows/") == 3
     assert validation.count("`@v0.5`") == 3
+    assert standards.count(
+        "SchmiedmayerLab/.github/.github/workflows/"
+    ) == 1
+    assert standards.count("`@v0.5`") == 1

🤖 Prompt for AI Agents

Verify each finding against current code. Fix only still-valid issues, skip the
rest with a brief reason, keep changes minimal, and validate.

In `@packages/compliance/tests/test_release_governance.py` around lines 330 - 331,
Update the version assertions in the relevant release-governance test to also
verify the `@v0.5` reference in repository-standards.yml, ensuring the new
standards workflow is covered alongside the existing three workflow references.

🤖 Prompt for all review comments with AI agents

Verify each finding against current code. Fix only still-valid issues, skip the
rest with a brief reason, keep changes minimal, and validate.

Inline comments:
In `@README.md`:
- Line 15: Update the license badge link in README.md to use the
repository-relative LICENSE.md target, matching the existing reference used
elsewhere in the document, instead of the main-branch GitHub URL.

---

Nitpick comments:
In `@packages/compliance/tests/test_release_governance.py`:
- Around line 330-331: Update the version assertions in the relevant
release-governance test to also verify the `@v0.5` reference in
repository-standards.yml, ensuring the new standards workflow is covered
alongside the existing three workflow references.

🪄 Autofix

Fix all unresolved CodeRabbit comments on this PR:

• Push a commit to this branch (recommended)
• Create a new PR with the fixes

---

ℹ️ Review info

⚙️ Run configuration

Configuration used: Organization UI

Review profile: CHILL

Plan: Pro Plus

Run ID: dd45b29b-5e99-44df-a6e1-d223613cf72f

📥 Commits

Reviewing files that changed from the base of the PR and between c3d484e and ae5dadf.

📒 Files selected for processing (10)

• .github/workflows/repository-standards.yml
• .github/workflows/validate.yml
• .linkspector.yml
• CITATION.cff
• CONTRIBUTING.md
• CONTRIBUTORS.md
• LICENSE.md
• README.md
• SECURITY.md
• packages/compliance/tests/test_release_governance.py

💤 Files with no reviewable changes (2)

• CONTRIBUTING.md
• SECURITY.md