Modular open publishing workflow

Maximising Openness & Contribution Acknowledgement

Summary of ChatGPT thread on building an open-first academic writing workflow where all contributors have their contributions acknowledged and cited. Digested and annotated by Claude, with occasional Dan edits.


Context

The core challenge: how to pursue an output as an endpoint of an ongoing, open research project — sharing work early for feedback (blog posts, LinkedIn, policymakers, ONS) — while making sure all contributors have their contributions acknowledged and cited. The workflow already in place: Obsidian (writing) -> Quarto (rendering) -> GitHub (versioning/hosting), with R functions handling link/YAML conversion. Code lives at the RegionalEconomicTools repo. The published blog is at coveredinbees.org, with the workflow itself described in Why Make Things Simple?.


Part 1: The "Open-First, Attribution-Clear" Workflow

Key Principle: Timestamped Public Disclosure = Clear Attribution

In academia, copyright protects expression (your text/code) but not ideas. What ensures contributions are properly acknowledged is public, timestamped, citable disclosure. The strategy is to shift from "I said it on LinkedIn" to "I have a citable record with a DOI that makes it easy for anyone to acknowledge and cite the contribution."

Preprint / Working Paper Venues for Economics & Policy

Venue Notes
SSRN (Economics Research Network) Widely used for early-stage econ papers; strong visibility
MPRA (Munich Personal RePEc Archive) Free; feeds into the RePEc ecosystem (IDEAS / EconPapers)
SocArXiv (OSF community preprints) Cross-social-science; good for policy-adjacent work

A practical pattern: MPRA (for RePEc discoverability) + SSRN (for network visibility), keeping the PDF identical so citations converge.

GitHub -> Zenodo DOI Pipeline

If code is part of the intellectual contribution:

  1. Connect GitHub -> Zenodo integration
  2. Create GitHub Releases (v0.1, v0.2...) at meaningful milestones
  3. Zenodo archives each release and mints a DOI automatically
  4. Add a CITATION.cff file so GitHub shows a "Cite this repository" widget

This gives: clear provenance, a stable citation target, and separation between public releases and working branches.

Licensing Strategy

Content Type Recommended Licence Notes
Paper/preprint text CC BY (most open) or CC BY-NC CC BY-ND often too restrictive for academic reuse
Code MIT / BSD / Apache (permissive) or GPL (copyleft) Put in README + LICENSE file
Data Separate licensing + data dictionary If restricted, share synthetic/example data + reproducible pipelines

Keeping Journal Doors Open

Most journals now allow preprints, but policies vary. Check target journals via Sherpa/RoMEO before posting.

Engaging Policymakers / ONS

Send a link to the working paper DOI + a 1-2 page policy note summary, inviting comments on specific questions. This anchors conversations to a citable artefact rather than scattered posts.

See part 5 below for more on policy engagement.


Part 2: Integrating With the Existing Obsidian/Quarto/GitHub Workflow

Two Parallel Tracks in Quarto

Add a second content type alongside existing blog posts:

posts/           # (existing) exploratory, conversational, feedback-seeking
working-papers/  # (new) stable, citable snapshots with version stamps

The Release Ritual

At each meaningful milestone:

  1. Update working-papers/paper.qmd with relevant modules
  2. Render to paper-v0.X.pdf
  3. Create GitHub Release v0.X with notes
  4. Zenodo mints DOI for that release
  5. Next blog post includes "Cite this version" with the DOI

Post Metadata for "Paper Modules"

Extend existing Quarto front-matter:

project: regional-accounts-uncertainty
module: measurement-claim-1
status: draft | stable | superseded
claims: [claim-a, claim-b]
evidence: [dataset-x, paper-y]

This lets posts be selected and assembled into the working paper rather than copy-pasted.

Each Relevant Post Gets a Citation Panel

Project: Regional Accounts Uncertainty
This post is: a working note / module
Canonical version: Working paper v0.3 (PDF)
How to cite: DOI link

Branch Strategy


Part 3: Zenodo DOI Options for a "Bucket" Repo

Can You DOI the Entire RegionalEconomicTools Repo?

Yes. Zenodo archives the repository snapshot associated with a Release tag. The unit of DOI is the repo snapshot, not a folder or sub-project.

Zenodo Constraints

Constraint Detail
Size limit 50GB total per record
File count Up to 100 files per record (archive helps)
DOI versioning Concept DOI (always resolves to latest) + version-specific DOIs
Pre-reservation Can't pre-reserve a DOI via GitHub integration; minted on release
Metadata clarity Your job to explain what inside the snapshot supports which paper

Four Options

Option Description Best When
A: Umbrella repo + Releases DOI the whole repo at milestones. Add a papers/paper_slug/README.md mapping scripts/data. Repo isn't huge; "bucket" model works
B: Umbrella + thin paper repo Paper repo imports toolbox (submodule/pinned commit). DOI both separately. Want clean per-paper packaging
C: Umbrella repo + separate manuscript deposit Manuscript to MPRA/SSRN; code to Zenodo via umbrella release. Minimal restructuring
D: Manual Zenodo deposits Curated zip of paper-relevant folders uploaded manually. Repo too large for automatic archiving

Recommended for this case: Option A (DOI the umbrella repo) as default, with a papers/paper_slug/ folder per paper containing paper.qmd, run.R, and a README listing exact dependencies.


Part 4: Pre-Preprint Modular Publishing

The Goal

Something before a preprint (defined as "a complete full draft manuscript shared publicly without peer review" — NTU Preprints FAQ). A more modular approach where components mature and get cited independently, and the paper is an eventual assembly.

Established Modular Frameworks

1. Research Objects (RO)

Treat scholarship as an aggregation of resources (data + code + workflows + narrative), not a single PDF. Each module can be versioned and archived; the "paper" becomes one view over the research object.

2. Reproducible Research Compendia

The scholarly unit is something that can be run and re-created, not just read. Release "analysis artefacts" as DOI'd snapshots (method + code + minimal example data + figures) with a light 1-2 page method note.

3. OSF Projects + Components

OSF Projects are explicitly designed as modular containers. OSF Registrations create timestamped records. Use as an "index card catalogue" pointing to GitHub/Zenodo DOIs for each component.

4. Open Notebook Science

Publish as you go — the most "continuous publishing" model. Adapted safely for policy/econ by adding status labels (speculation / working / stable) and only DOI'ing stable milestones.

5. Nanopublications / Micro-contributions

Publish individual claims as citable units. Not mainstream in econ/policy, but the philosophy maps onto "claim modules" with provenance and reproducible evidence.

Proposed Module Taxonomy

Module Type Stability DOI? Example
Method modules Stable Yes (Zenodo) Quarto doc explaining one method + reproducible example
Evidence modules Stable-ish Yes when confident Curated data extracts, codebooks, derived datasets
Interpretation modules Fluid No — link to stable modules Blog posts, LinkedIn threads, policy reflections

The Manifest File

A modules.yml or modules.csv in the repo listing:

- name: expected-vs-observed-flows
  slug: exp-obs-flows
  status: stable
  canonical_url: https://coveredinbees.org/posts/...
  doi: 10.5281/zenodo.XXXXXXX
  dependencies: [script-a.R, dataset-x]
  paper_section: methods-section-2

This is a lightweight "Research Object map" implemented with boring files.

Why This Ensures Contributions Are Acknowledged

Even without a full preprint, a DOI'd method module + DOI'd code snapshot makes it straightforward for anyone building on the work to cite and credit the contribution (method + implementation), while interpretation stays flexible. When you do preprint, it becomes an assembly of already-citable modules — and all contributors along the way have a clear citation trail.


Part 5: Aligning Modular Outputs With UK Regional Economic Policy Engagement

The Opportunity

UK regional economic policy is in a period of intense institutional development — devolution, the creation of combined authorities, ONS's subnational statistics programme, and a growing emphasis on evidence-based local decision-making. This creates a natural audience for modular, open research outputs: policymakers and analysts who need usable components (methods, data, code) more than they need finished papers. The modular approach described above is worth testing for building genuine research-policy feedback loops.

The UK Institutional Landscape: Who to Connect With

ONS Centre for Subnational Analysis & ONS Local

The ONS Centre for Subnational Analysis leads on producing regional accounts, subnational GDP, GDHI, and experimental local statistics. They actively share prototypes and code via GitHub. ONS Local, established in 2023, provides dedicated analytical advisory services to local leaders — analysts embedded across the UK who need practical tools and methods.

The GSS Subnational Data Strategy explicitly centres collaboration with academia and the private sector. This is a direct route for feeding modular code/method outputs into the statistical production system.

ADR UK (Administrative Data Research UK)

ADR UK is a UK-wide ESRC-funded partnership transforming public sector data into research insights. Their model is explicitly about bringing government and academic groups together into collaborative partnerships — with a feedback loop between data owners and researchers. ADR UK runs research fellowships and community catalysts that could align well with modular, open outputs that demonstrate method on linked administrative data.

The Productivity Institute

The Productivity Institute runs Regional Productivity Forums across the UK — forums that bring together businesses, policymakers, and academics on regional productivity issues. Their research on regional inequality and binding constraints is directly adjacent to regional accounts work. They publish working papers and policy briefs and actively seek engaged research contributions.

What Works Centre for Local Economic Growth

The What Works Centre for Local Economic Growth (hosted at LSE / Centre for Cities) focuses on which policies are most effective for local economic growth, using rigorous impact evaluation. They help local and central government make growth policy more cost-effective through better use of evidence. Sharing reproducible method modules — especially around measurement and evaluation — maps directly onto their mission.

ESRC Local Policy Innovation Partnerships (LPIPs)

Local Policy Innovation Partnerships bring together devolved governments, local authorities, businesses, and communities to address local policy challenges through research and innovation. The programme explicitly supports co-production between researchers and local stakeholders. A strategic coordination hub links the partnerships together.

Areas of Research Interest (ARIs)

The ARI Database lists questions that UK government departments are actively seeking to answer. Checking ARIs for relevant regional economics / measurement questions gives you a direct line to "this is what government wants to know" — and lets you frame modular outputs as contributing to those questions.

ESRC P2R (Policymaker Engagement with Research)

The P2R programme funds projects that increase policymaker engagement with research. Worth tracking for funding opportunities and for understanding the institutional framing of research-policy collaboration. (Already funded projects about to start...)

Maximising Iteration, Feedback, and Conversation

1. Make Modules Legible to Non-Academic Partners

Policymakers and ONS analysts don't read working papers the same way academics do. For each module, produce a twin output:

The policy note should always link back to the technical module and its DOI. This is the "citable artefact + legible summary" pattern from Part 1, but oriented towards government partners.

2. Use the Blog as a "Conversation Starter" Layer

The coveredinbees.org blog already functions as an open notebook. To maximise feedback from non-academic partners:

3. Build a "Stakeholder Feedback" Loop Into the Manifest

Extend the modules.yml manifest (from Part 4) to track engagement:

- name: expected-vs-observed-flows
  slug: exp-obs-flows
  status: stable
  doi: 10.5281/zenodo.XXXXXXX
  feedback_from:
    - org: ONS Subnational
      date: 2025-03-15
      summary: "Confirmed LA-level data available from 2024"
    - org: Combined Authority X
      date: 2025-04-02
      summary: "Interested in applying method to transport flows"
  policy_note: papers/exp-obs-flows/policy-note.md

This creates a transparent record of who has engaged with what, which strengthens both the academic paper ("we tested this with practitioners") and the policy case ("researchers and local government co-developed this").

4. Offer Reproducible "Sandboxes" Not Just Finished Results

Government analysts (especially in ONS and combined authorities) increasingly work with R and Python. Sharing a runnable example they can adapt is more valuable than a PDF they can only read. For each stable method module:

5. Attend to the "Co-Production" Framing

UKRI and ESRC increasingly value co-production — research designed with stakeholders, not just for them. The modular approach naturally supports this: you can share a draft method module with ONS analysts or local authority economists, incorporate their feedback, and credit their contribution explicitly in the module metadata and the eventual paper.

This is distinct from traditional "impact" (where you do the research, then tell people about it). Co-production means the iteration loop is part of the research design. Document it as such — it strengthens both the intellectual case and the REF/impact case.

6. Align With the Subnational Statistics Calendar

ONS publishes regional accounts, subnational GDP, GDHI, and experimental statistics on a known schedule (see the ONS subnational work programme). Timing module releases and blog posts to coincide with relevant ONS publications maximises relevance and visibility — e.g., releasing a method module on measuring regional flows just as new regional accounts data drops.

7. Use Existing Forums and Networks

Rather than building an audience from scratch, plug into existing convening structures:

Forum / Network What It Does How to Engage
Regional Productivity Forums (Productivity Institute) Regional stakeholder convenings Present method modules; seek practitioner feedback
ONS Local Embedded analysts advising local leaders Share tools/methods directly with embedded analysts
UPEN (Universities Policy Engagement Network) Bridges academia and policymakers Use as a channel for policy notes; learn from their resources on regional collaboration
NIESR (National Institute of Economic and Social Research) Independent economic research Engage via seminars, working paper series
What Works Growth seminars & evidence reviews Evidence for local growth policy Submit evidence; attend practitioner events
ESRC Knowledge Exchange opportunities Funded place-based knowledge exchange Apply for collaborative funding with local partners

How This Feeds Back Into the Paper

The modular, open, engaged approach doesn't just generate feedback — it generates evidence of impact and co-production that strengthens the eventual academic output:

This is increasingly what funders (ESRC, UKRI) and assessment frameworks (REF impact case studies, DORA) want to see: research that was engaged from the start, not retrofitted with an "impact" narrative after publication.


Summary & Additional Notes

The Core Strategy in One Sentence

Publish modular, DOI'd components early and often; assemble the paper later from already-citable pieces.

Resource URL
SSRN https://www.ssrn.com/
MPRA https://mpra.ub.uni-muenchen.de/
SocArXiv https://osf.io/preprints/socarxiv
RePEc / IDEAS https://ideas.repec.org/
Zenodo https://zenodo.org/
Zenodo-GitHub Integration Guide https://docs.github.com/en/repositories/archiving-a-github-repository/referencing-and-citing-content
CITATION.cff Docs https://docs.github.com/en/repositories/managing-your-repositorys-settings-and-features/customizing-your-repository/about-citation-files
Sherpa/RoMEO (journal preprint policies) https://v2.sherpa.ac.uk/romeo/
Creative Commons Licences https://creativecommons.org/licenses/
OSF (Open Science Framework) https://osf.io/
Research Object / RO-Crate https://www.researchobject.org/ro-crate/
Open Notebook Science https://en.wikipedia.org/wiki/Open-notebook_science
Nanopublications https://nanopub.net/
RegionalEconomicTools repo https://github.com/DanOlner/RegionalEconomicTools
coveredinbees.org https://coveredinbees.org/
Workflow post https://coveredinbees.org/posts/why-make-things-simple/
ONS Centre for Subnational Analysis https://www.ons.gov.uk/aboutus/whatwedo/programmesandprojects/onscentres/centreforsubnationalanalysis
ONS Local https://www.ons.gov.uk/aboutus/whatwedo/programmesandprojects/onslocal
GSS Subnational Data Strategy https://analysisfunction.civilservice.gov.uk/policy-store/gss-subnational-data-strategy/
ADR UK https://www.adruk.org/
The Productivity Institute https://www.productivity.ac.uk/
What Works Centre for Local Economic Growth https://whatworksgrowth.org/
Local Policy Innovation Partnerships https://www.ukri.org/opportunity/developing-local-policy-innovation-partnerships/
ARI Database https://ari.org.uk/
ESRC P2R Programme https://www.ukri.org/opportunity/p2r-increasing-uk-policymaker-engagement-with-research/
UPEN (Universities Policy Engagement Network) https://upen.ac.uk/
NIESR https://niesr.ac.uk/
Binder (reproducible environments) https://mybinder.org/

Additional Considerations (Claude)


Part 6: Technical Setup — Configuring a GitHub Repo for Modular Outputs With DOIs

This section collates the practical, technical details for setting up a GitHub repository to support the modular publishing workflow described above: Zenodo integration, metadata files, repo structure, versioning, issue templates for feedback, and GitHub Discussions.

1. Connecting GitHub to Zenodo (One-Time Setup)

The Zenodo-GitHub integration is straightforward. Once connected, every GitHub Release you create is automatically archived on Zenodo and assigned a DOI.

Steps:

  1. Create a Zenodo account at zenodo.org. You can sign up with your GitHub account directly, which links the two.
  2. Go to Zenodo settings → GitHub tab, or navigate to zenodo.org/account/settings/github/.
  3. Click "Sync now" to refresh your repository list.
  4. Toggle on the repository you want to archive (e.g. DanOlner/RegionalEconomicTools). The slider turns green when connected.
  5. That's it. From now on, every GitHub Release on that repo will be automatically ingested and archived by Zenodo, with a DOI minted for each release.

For a detailed walkthrough with screenshots, see this guide from INBO or GitHub's own docs on referencing and citing content.

Important: You can also link your ORCID iD to your Zenodo account. This ties your DOI'd outputs to your persistent author identity across all platforms. See the INBO guide on setting up GitHub, Zenodo and ORCID together.

2. Metadata Files: CITATION.cff and .zenodo.json

Zenodo extracts metadata from your repo when it archives a release. It looks for files in this priority order:

  1. .zenodo.json (highest priority — if present, CITATION.cff is ignored by Zenodo)
  2. CITATION.cff
  3. LICENSE

You can use either or both, but be aware: if your repo contains both .zenodo.json and CITATION.cff, Zenodo will only use .zenodo.json. However, GitHub itself uses CITATION.cff for its "Cite this repository" widget, so there's a case for having both — .zenodo.json for Zenodo-specific metadata, CITATION.cff for GitHub display.

CITATION.cff

The Citation File Format is a YAML file that tells people how to cite your work. When placed in the root of your repo, GitHub renders a "Cite this repository" button on the landing page, with BibTeX and APA formats auto-generated.

A minimal example:

cff-version: 1.2.0
message: "If you use this software or analysis, please cite it using these metadata."
authors:
  - family-names: Olner
    given-names: Dan
    orcid: "https://orcid.org/XXXX-XXXX-XXXX-XXXX"
title: "RegionalEconomicTools"
version: 0.1.0
date-released: "2025-02-10"
license: MIT
url: "https://github.com/DanOlner/RegionalEconomicTools"
repository-code: "https://github.com/DanOlner/RegionalEconomicTools"
keywords:
  - regional economics
  - subnational statistics
  - R

You can generate one using the CFF initializer tool. The full schema guide is at citation-file-format/schema-guide.md. The Turing Way has an excellent guide on software citation with CITATION.cff.

.zenodo.json

The .zenodo.json file supports Zenodo-specific metadata that CITATION.cff doesn't, including:

An example tailored for a modular research project:

{
    "creators": [
        {
            "name": "Olner, Dan",
            "orcid": "0000-0000-0000-0000",
            "affiliation": "Your Affiliation"
        }
    ],
    "title": "RegionalEconomicTools",
    "version": "0.1.0",
    "access_right": "open",
    "license": "mit",
    "upload_type": "software",
    "language": "eng",
    "keywords": [
        "regional economics",
        "subnational statistics",
        "uncertainty",
        "R"
    ],
    "related_identifiers": [
        {
            "identifier": "https://coveredinbees.org/",
            "relation": "isDocumentedBy",
            "resource_type": "publication-other"
        }
    ],
    "communities": [
        {"identifier": "your-community-if-applicable"}
    ]
}

The .zenodo.json format is parsed as JSON5, which means you can include comments — useful for documenting why certain metadata choices were made.

The full metadata schema is at zenodraft/metadata-schema-zenodo.

3. Versioning and Release Strategy

Semantic versioning uses the format MAJOR.MINOR.PATCH (e.g. v1.2.3):

For a research project (rather than production software), a pragmatic adaptation:

Version Meaning When to Use
v0.x.y Pre-publication development All work before the first formal working paper release
v0.1.0 First meaningful public release Enough content for others to engage with
v0.2.0, v0.3.0... Module milestones Each time a new method/evidence module reaches "stable"
v1.0.0 First working paper / preprint release The assembled paper is ready for external feedback
v1.1.0, v1.2.0... Post-feedback revisions Incorporating reviewer/practitioner feedback

Creating a release in GitHub:

  1. Go to your repo → "Releases" (right sidebar) → "Draft a new release"
  2. Create a new tag (e.g. v0.2.0)
  3. Write release notes — describe what changed, which modules are new/updated, link to relevant blog posts
  4. Click "Publish release"
  5. Zenodo automatically archives and mints a DOI (if integration is enabled)

Note: you can use GitKraken to create tags before drafting the release in the GitHub web interface. See GitKraken's guide on semantic versioning with git tags.

After a release, paste the new Zenodo DOI into:

4. Suggested Repository Structure

Drawing on the research compendium tradition (see also rcompendium and the CodeRefinery guide on organising projects), here's a structure that supports the modular workflow:

RegionalEconomicTools/
├── README.md                    # Project overview, how to cite, link to Zenodo DOI
├── CITATION.cff                 # Citation metadata (GitHub display)
├── .zenodo.json                 # Zenodo-specific metadata
├── LICENSE                      # Code licence (e.g. MIT)
├── modules.yml                  # Manifest of all modules (from Part 4)
├── FEEDBACK.md                  # Guide for giving feedback (or link to it)
│
├── R/                           # Reusable R functions
│   ├── data_processing.R
│   ├── flow_analysis.R
│   └── ...
│
├── data/                        # Small/example/synthetic data only
│   ├── README.md                # Data dictionary, sources, licences
│   └── ...
│
├── modules/                     # Modular analysis components
│   ├── expected-vs-observed/
│   │   ├── README.md            # What this module does, dependencies, status
│   │   ├── method.qmd           # Quarto doc: full method + reproducible example
│   │   ├── policy-note.md       # 1-2 page summary for non-academic audiences
│   │   ├── run.R                # Entrypoint script to reproduce results
│   │   └── outputs/             # Generated figures, tables
│   ├── another-module/
│   │   └── ...
│   └── ...
│
├── papers/                      # Assembled working papers
│   ├── paper-1/
│   │   ├── paper.qmd            # Working paper pulling from modules
│   │   ├── README.md            # Which modules/scripts/data this paper uses
│   │   └── paper-v0.1.pdf       # Rendered PDF for deposit
│   └── ...
│
├── posts/                       # Blog post drafts (if co-located)
│   └── ...
│
├── .github/                     # GitHub configuration
│   ├── ISSUE_TEMPLATE/          # Issue templates (see below)
│   │   ├── feedback.yml
│   │   ├── method-question.yml
│   │   └── config.yml
│   └── DISCUSSION_TEMPLATE/     # Discussion category templates (if using)
│       └── ...
│
└── renv/                        # R environment lockfile (if using renv)
    └── ...

Each modules/ subfolder is a self-contained unit that can be DOI'd as part of the repo release, referenced from blog posts, and assembled into papers. The README.md in each module folder acts as a lightweight metadata record (status, dependencies, which paper section it maps to).

5. Issue Templates for Structured Feedback

GitHub lets you create issue templates so that when someone opens an issue, they get a structured form rather than a blank text box. Templates live in .github/ISSUE_TEMPLATE/ as YAML files.

An example feedback template (.github/ISSUE_TEMPLATE/feedback.yml):

name: Feedback on a module or post
description: Share feedback, questions, or suggestions about a specific piece of work
title: "[Feedback] "
labels: ["external-feedback"]
body:
  - type: dropdown
    id: module
    attributes:
      label: Which module or post is this about?
      options:
        - Expected vs Observed Flows
        - Regional Accounts Method
        - General / cross-cutting
        - Other (please specify below)
    validations:
      required: true
  - type: textarea
    id: feedback
    attributes:
      label: Your feedback
      description: Questions, suggestions, corrections, or anything else
      placeholder: Tell us what you think...
    validations:
      required: true
  - type: dropdown
    id: role
    attributes:
      label: Your background (optional, helps us understand context)
      options:
        - Academic researcher
        - Government analyst / policymaker
        - ONS / statistical producer
        - Local authority / combined authority
        - Other
    validations:
      required: false
  - type: checkboxes
    id: attribution
    attributes:
      label: Attribution
      options:
        - label: I'm happy to be credited by name in any resulting work
          required: false

A method-question template (.github/ISSUE_TEMPLATE/method-question.yml):

name: Method question
description: Ask a technical question about a method or analysis
title: "[Method] "
labels: ["method-question"]
body:
  - type: textarea
    id: question
    attributes:
      label: Your question
      description: What would you like to understand about the method?
    validations:
      required: true
  - type: textarea
    id: context
    attributes:
      label: Context (optional)
      description: Any context that helps — e.g. you're trying to apply this to a different dataset or geography
    validations:
      required: false

You can also add a config.yml to control the template chooser:

blank_issues_enabled: true
contact_links:
  - name: Email feedback
    url: mailto:your@email.com
    about: Prefer to give feedback by email? That's fine too.
  - name: Project blog
    url: https://coveredinbees.org/
    about: Read the latest posts and context for this work.

Suggested issue labels (create these in the repo under Settings → Labels):

Label Colour Purpose
external-feedback blue Feedback from outside contributors
method-question purple Technical questions about methods
data-request green Questions about data availability/access
policy-implication orange Feedback on policy relevance
from-email grey Logged by you from email correspondence
from-linkedin grey Logged by you from LinkedIn comments
module:exp-obs-flows teal Tagged to a specific module
addressed light green Issue has been incorporated into the work

6. GitHub Discussions (Alternative/Complement to Issues)

GitHub Discussions provides a more forum-like space — less "bug tracker", more open-ended conversation. It uses the same GitHub account as Issues but feels more inviting for non-developers. You can enable it under Settings → General → Features → Discussions.

Discussions support categories with different formats:

Category Format Purpose
Methods & data Open-ended discussion Conversation about approaches, data sources, assumptions
Policy implications Open-ended discussion What the findings mean for practice
Questions Question & Answer Specific questions with markable answers
Announcements Announcement New releases, new modules, new blog posts (only you can post)

Discussions can coexist with Issues: use Issues for specific, actionable feedback tied to modules, and Discussions for broader conversation about direction, interpretation, and policy relevance.

7. README as the Landing Page

The repo README is the first thing anyone sees. For a modular research project, it should include:

You can add a Zenodo DOI badge to the README that always resolves to the latest version:

[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.XXXXXXX.svg)](https://doi.org/10.5281/zenodo.XXXXXXX)

(Zenodo provides this badge markdown automatically when your first release is archived.)

8. Putting It All Together: The Release Checklist

A concrete checklist for each milestone release:

Technical References

Resource Link
Zenodo: Enable a repository help.zenodo.org
Zenodo: Describe your software help.zenodo.org
Zenodo: .zenodo.json reference help.zenodo.org
Zenodo: CITATION.cff reference help.zenodo.org
Zenodo FAQ: GitHub integration support.zenodo.org
Zenodo-GitHub integration documentation (community) rue-a.github.io
INBO: Setting up GitHub + Zenodo + ORCID inbo.github.io
INBO: Zenodo-GitHub integration tutorial tutorials.inbo.be
Citation File Format specification citation-file-format.github.io
CFF initializer tool citation-file-format.github.io
CFF schema guide github.com
The Turing Way: Software citation with CFF book.the-turing-way.org
GitHub Docs: About CITATION files docs.github.com
GitHub Docs: Referencing and citing content docs.github.com
GitHub Docs: Configuring issue templates docs.github.com
GitHub Docs: About Discussions docs.github.com
GitHub Docs: Managing discussion categories docs.github.com
Semantic Versioning 2.0.0 semver.org
GitKraken: Semantic versioning with git tags gitkraken.com
rrtools: R research compendium tools github.com/benmarwick/rrtools
rcompendium: R package for research compendium structure frbcesab.github.io
CodeRefinery: Organising reproducible projects coderefinery.github.io
GitHub for collaborative documentation: Zenodo integration cassgvp.github.io
Zenodo .zenodo.json metadata schema github.com/zenodraft

Generated from ChatGPT conversation (Parts 1-4), with Parts 5-6 and additional context/links added by Claude. February 2025.