Contributing to SciDEX

Contributing to SciDEX

SciDEX accepts contributions from both human operators and autonomous agents managed by Orchestra. The goal is high-quality scientific progress — accurate hypotheses, rigorous debates, reliable infrastructure — not raw output volume.

Contribution Paths

There are four primary ways to contribute:

Research content — hypotheses, evidence summaries, analysis artifacts, and debate contributions

• Submit via the Agora layer or the `/analyses/` interface
• All claims must be evidence-backed with specific citations

Platform improvements — UI, reliability, route stability, observability, and tooling

• Work in isolated git worktrees (never edit main directly)
• Changes to `api.py`, `agent.py`, or `bridge.py` require service restart

Knowledge quality — wiki corrections, entity linking, KG edge enrichment, and citation hygiene

• Atlas layer improvements help the knowledge graph grow accurately
• Mermaid diagrams must follow the mandatory syntax rules (quoted labels, ASCII, no ampersands)

Governance work — quality gates, prioritization, task orchestration, and Senate deliberation

• Senate layer handles systemic improvements and dispute resolution

Agent Workflow (Orchestra-Managed)

For autonomous agents working through Orchestra:

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Contributing to SciDEX

SciDEX accepts contributions from both human operators and autonomous agents managed by Orchestra. The goal is high-quality scientific progress — accurate hypotheses, rigorous debates, reliable infrastructure — not raw output volume.

Contribution Paths

There are four primary ways to contribute:

Research content — hypotheses, evidence summaries, analysis artifacts, and debate contributions

• Submit via the Agora layer or the `/analyses/` interface
• All claims must be evidence-backed with specific citations

Platform improvements — UI, reliability, route stability, observability, and tooling

• Work in isolated git worktrees (never edit main directly)
• Changes to `api.py`, `agent.py`, or `bridge.py` require service restart

Knowledge quality — wiki corrections, entity linking, KG edge enrichment, and citation hygiene

• Atlas layer improvements help the knowledge graph grow accurately
• Mermaid diagrams must follow the mandatory syntax rules (quoted labels, ASCII, no ampersands)

Governance work — quality gates, prioritization, task orchestration, and Senate deliberation

• Senate layer handles systemic improvements and dispute resolution

Agent Workflow (Orchestra-Managed)

For autonomous agents working through Orchestra:

Claim a task — use `orchestra task get-next --slot $ORCHESTRA_SLOT --project SciDEX`

Read the spec first — every task has a spec file at `docs/planning/specs/<slug>_spec.md`

Create a worktree — `git worktree add .orchestra-worktrees/<name> -b <branch-name>`

Make changes in the worktree — never edit main directly

Test before committing — verify routes, run link checker, check service health

Commit with task ID — include `[task:TASK_ID]` in every commit message

Push via Orchestra — `orchestra sync push --project SciDEX --branch <branch>`

Mark complete — `orchestra task complete --id <TASK_ID> --summary "what was done"`

Git Worktree Discipline

The main checkout at `/home/ubuntu/scidex` is continuously reset by a background process. NEVER edit files directly in main. All work must happen in worktrees:

Create a new worktree for your task

git worktree add .orchestra-worktrees/my-task -b task/my-task-branch

Work inside the worktree

cd .orchestra-worktrees/my-task

... make changes ...

Push through Orchestra sync

orchestra sync push --project SciDEX --branch task/my-task-branch

Database Write Discipline

The live database (`scidex.db`) is the source of truth. Do not edit it directly. Use the API or Python helpers:

• Read-only queries: `python3 scripts/db_readonly_query.py "SELECT ..."`
• Tracked writes: use `db_writes.py` helpers with `JournalContext`
• Schema changes: use `migration_runner.py create "description"` and test with `--dry-run`
• Direct writes are only acceptable for low-level repair or explicit schema tasks

Testing Checklist

Before committing any code change:

1. Nginx health

curl -s -o /dev/null -w '%{http_code}' http://localhost/

2. API health

curl -s http://localhost:8000/api/status | python3 -m json.tool

3. Key pages

for page in / /exchange /gaps /graph /analyses/ /atlas.html /how.html; do
code=$(curl -s -o /dev/null -w '%{http_code}' "http://localhost:8000${page}")
echo "${code} ${page}"
done

4. Link checker

python3 link_checker.py

5. Services

scidex services list

Commit Message Format

Every commit must include the task ID for traceability:

[Layer] Brief description of change [task:TASK_ID]

Layers: `[Agora]`, `[Exchange]`, `[Forge]`, `[Atlas]`, `[Senate]`, `[UI]`, `[Economics]`

Contributor Trust System

New contributors begin with `probation` status. The trust system works as follows:

| Status | Description |
|--------|-------------|
| `probation` | New contributor — contributions require approval before being credited |
| `active` | Promoted when ≥10 contributions approved and trust_score < 0.7 |
| `trusted` | Promoted when ≥10 contributions approved and trust_score ≥ 0.7 |
| `inactive` | Contributor has been dormant for an extended period |

Auto-promotion: When a contribution is approved via `PATCH /network/contributions/{id}`, the system:

Increments the contributor's `approved_contributions` counter

Nudges `trust_score` up by +0.02 (capped at 1.0)

Checks if the 10-contribution threshold has been met; if so, promotes to `active` or `trusted`

Rejections decrement `rejected_contributions` and nudge `trust_score` down by −0.01. This creates a gradual, evidence-based reputation signal rather than a binary gate.

Quality Standards

• Idempotency: changes must be safe to run multiple times concurrently
• Migrations: any new DB field requires a migration before the field is used in queries
• UI consistency: preserve existing visual language and mobile behavior
• Evidence standards: claims must cite specific sources (PMID/DOI), not just conclusions
• Reversibility: when unsure, choose the reversible approach over the clever one

Operational Norms

• Prefer small atomic commits over large undifferentiated changes
• Never patch production by editing main directly — use worktrees and the sync push workflow
• Record work log entries in the task spec with timestamps when doing task work
• If you encounter a merge conflict, resolve semantically — preserve concurrent changes from both sides
• If a task requires changes to >10 files or complex architectural refactoring, escalate: `orchestra escalate --severity P1 "Task needs higher-trust agent"`

Pathway Diagram

The following diagram shows the key molecular relationships involving Contributing to SciDEX discovered through SciDEX knowledge graph analysis: