chore: run oxfmt and fix lint issues

Author: tim-hm

.github/workflows/cd-nildb-image.yaml

@@ -74,7 +74,7 @@ jobs:
   create-and-push-manifest:
     runs-on: ubuntu-latest
     timeout-minutes: 5
-    needs: [ setup, build-and-push-arch ]
+    needs: [setup, build-and-push-arch]
     steps:
       - name: Log in to GitHub Container Registry
         uses: docker/login-action@v3
@@ -97,7 +97,7 @@ jobs:
           IMAGE_BASE="ghcr.io/nillionnetwork/nildb"
           AMD64_IMAGE="${IMAGE_BASE}:${{ needs.setup.outputs.short_sha }}-amd64"
           ARM64_IMAGE="${IMAGE_BASE}:${{ needs.setup.outputs.short_sha }}-arm64"
-          
+
           echo "${{ steps.meta.outputs.tags }}" | while IFS= read -r tag; do
             if [ -n "$tag" ]; then
               echo "Creating and pushing manifest for tag: ${tag}"
@@ -107,13 +107,13 @@ jobs:
           done
 
   deploy-to-ci-cluster:
-    needs: [ setup, create-and-push-manifest ]
+    needs: [setup, create-and-push-manifest]
     runs-on: ubuntu-latest
     timeout-minutes: 5
     if: github.ref_name == 'main'
     strategy:
       matrix:
-        node: [ "ci-n1", "ci-n2", "ci-n3" ]
+        node: ["ci-n1", "ci-n2", "ci-n3"]
     steps:
       - name: Dispatch event to start nildb-infra/.github/workflows/ecs-${{ matrix.node }}.yaml workflow
         run: |

.spectral.yaml

@@ -1 +1 @@
-extends: [ "spectral:oas" ]
+extends: ["spectral:oas"]

CONTRIBUTING.md

@@ -11,6 +11,7 @@ This guide explains how to set up your development environment and contribute co
 ## Development Setup
 
 1. Clone the repository:
+
    ```shell
    git clone git@github.com:NillionNetwork/nildb.git
    cd nildb
@@ -42,6 +43,7 @@ pnpm test   # run the full test suite
 ```
 
 > [!NOTE]
+>
 > - Tests use isolated collections (test_nildb and test_nildb_data)
 > - The test database is dropped at the start of each test run
 

README.md

@@ -11,7 +11,7 @@ If you're unsure where to start, head over to [docs.nillion.com](https://docs.ni
 
 - [Run a local cluster for development](./docs/build-on-nildb.md)
 - [Help build nilDB](./CONTRIBUTING.md)
-- [nilDB overview and network basics](./docs/overview.md) 
+- [nilDB overview and network basics](./docs/overview.md)
 - [Want to be a node operator?](./docs/node-operator-questionnaire.md)
 - [Node admin guide](./docs/admin-guide.md)
 

commitlint.config.ts

@@ -3,11 +3,7 @@ import { RuleConfigSeverity, type UserConfig } from "@commitlint/types";
 const config: UserConfig = {
   extends: ["@commitlint/config-conventional"],
   rules: {
-    "body-max-line-length": [
-      RuleConfigSeverity.Disabled,
-      "always",
-      Number.POSITIVE_INFINITY,
-    ],
+    "body-max-line-length": [RuleConfigSeverity.Disabled, "always", Number.POSITIVE_INFINITY],
   },
 };
 

docs/admin-guide.md

@@ -18,29 +18,31 @@ This section provides task-oriented instructions for node administrators.
 
 The following environment variables are require:
 
-| Variable                 | Description                                                    | Example                                  |
-|--------------------------|----------------------------------------------------------------|------------------------------------------|
-| APP_DB_NAME_BASE         | Database name prefix                                           | nildb_data                               |
-| APP_DB_URI               | MongoDB connection string                                      | mongodb://node-xxxx-db:27017             |
-| APP_ENABLED_FEATURES     | Enable features                                                | openapi-spec,metrics,migrations,otel     |
-| APP_LOG_LEVEL            | Logging verbosity                                              | debug                                    |
-| APP_METRICS_PORT         | Prometheus metrics port                                        | 9091                                     |
-| APP_NILAUTH_INSTANCES    | Trusted nilauth instances (format: `baseUrl/publicKey,...`)    | [see below]                              |
-| APP_NILAUTH_CHAIN_ID     | Ethereum chain ID for payment validation                       | 1                                        |
-| APP_NODE_PUBLIC_ENDPOINT | Public URL of node                                             | https://nildb-xxxx.domain.com            |
-| APP_NODE_SECRET_KEY      | Node's private key                                             | [hex encoded secp256k1 private key]      |
-| APP_PORT                 | API service port                                               | 8080                                     |
+| Variable                 | Description                                                 | Example                              |
+| ------------------------ | ----------------------------------------------------------- | ------------------------------------ |
+| APP_DB_NAME_BASE         | Database name prefix                                        | nildb_data                           |
+| APP_DB_URI               | MongoDB connection string                                   | mongodb://node-xxxx-db:27017         |
+| APP_ENABLED_FEATURES     | Enable features                                             | openapi-spec,metrics,migrations,otel |
+| APP_LOG_LEVEL            | Logging verbosity                                           | debug                                |
+| APP_METRICS_PORT         | Prometheus metrics port                                     | 9091                                 |
+| APP_NILAUTH_INSTANCES    | Trusted nilauth instances (format: `baseUrl/publicKey,...`) | [see below]                          |
+| APP_NILAUTH_CHAIN_ID     | Ethereum chain ID for payment validation                    | 1                                    |
+| APP_NODE_PUBLIC_ENDPOINT | Public URL of node                                          | https://nildb-xxxx.domain.com        |
+| APP_NODE_SECRET_KEY      | Node's private key                                          | [hex encoded secp256k1 private key]  |
+| APP_PORT                 | API service port                                            | 8080                                 |
 
 ### Nilauth Configuration
 
 The `APP_NILAUTH_INSTANCES` variable configures which nilauth instances this node trusts for builder authentication. Each instance is specified as `baseUrl/publicKey`, with multiple instances separated by commas.
 
 **Single instance:**
+
 ```bash
 APP_NILAUTH_INSTANCES=http://nilauth:8080/03520e70bd97a5fa6d70c614d50ee47bf445ae0b0941a1d61ddd5afa022b97ab14
 ```
 
 **Multiple instances:**
+
 ```bash
 APP_NILAUTH_INSTANCES=http://nilauth-a:8080/03520e70bd97a5fa...,http://nilauth-b:8080/02abc123def456...
 ```
@@ -49,19 +51,18 @@ APP_NILAUTH_INSTANCES=http://nilauth-a:8080/03520e70bd97a5fa...,http://nilauth-b
 
 The following variables control the IP-based rate limiting feature.
 
-| Variable                        | Description                                     | Default |
-|---------------------------------|-------------------------------------------------|---------|
-| APP_RATE_LIMIT_ENABLED          | Enables the rate-limiting feature.              | `true`  |
-| APP_RATE_LIMIT_WINDOW_SECONDS   | The duration of the time window in seconds.     | `60`    |
-| APP_RATE_LIMIT_MAX_REQUESTS     | Max requests per IP within the time window.     | `60`    |
-
+| Variable                      | Description                                 | Default |
+| ----------------------------- | ------------------------------------------- | ------- |
+| APP_RATE_LIMIT_ENABLED        | Enables the rate-limiting feature.          | `true`  |
+| APP_RATE_LIMIT_WINDOW_SECONDS | The duration of the time window in seconds. | `60`    |
+| APP_RATE_LIMIT_MAX_REQUESTS   | Max requests per IP within the time window. | `60`    |
 
 ### OpenTelemetry
 
 When the `otel` feature is enabled in `APP_ENABLED_FEATURES`, the following variables configure OpenTelemetry instrumentation:
 
 | Variable                        | Description                             | Default          | Required |
-|---------------------------------|-----------------------------------------|------------------|----------|
+| ------------------------------- | --------------------------------------- | ---------------- | -------- |
 | OTEL_ENDPOINT                   | OTLP endpoint URL                       | http://localhost | No       |
 | OTEL_SERVICE_NAME               | Service name for telemetry              | nildb            | No       |
 | OTEL_TEAM_NAME                  | Team responsible for the service        | nildb            | No       |
@@ -95,6 +96,7 @@ Values set via `OTEL_RESOURCE_ATTRIBUTES` take precedence over programmatically
 **Disabling OpenTelemetry SDK:**
 
 To disable OpenTelemetry SDK and prevent telemetry emission while keeping the `otel` feature flag enabled, set the following environment variable:
+
 ```bash
 OTEL_SDK_DISABLED=true
 ```
@@ -113,6 +115,7 @@ docker compose -f local/docker-compose.yaml up -d
 ```
 
 This stack includes:
+
 - **nilDB**: The main API service (port 40080, metrics port 40091)
 - **MongoDB**: Database backend (port 40017)
 - **nilauth**: Authentication service for NUC tokens (port 40921)
@@ -124,6 +127,7 @@ This stack includes:
 The nilDB API will be available at `http://localhost:40080`.
 
 The local stack is configured with `APP_ENABLED_FEATURES=openapi,otel,migrations`, which means:
+
 - Metrics, traces, and logs are sent to the OTel Collector (visible in `docker compose logs otel-collector`)
 - No `/metrics` endpoint is exposed (OTLP push only)
 
@@ -176,6 +180,7 @@ The following endpoints provide operational information:
 
 > ![NOTE]
 > The `/metrics` endpoint behavior depends on feature flags:
+>
 > - **`metrics` only**: Serves metrics at `:9091/metrics` using OpenTelemetry PrometheusExporter
 > - **`otel` enabled**: No `/metrics` endpoint; all telemetry pushed to OTLP collector
 >
@@ -225,8 +230,8 @@ For user-facing operations, there is an OpenAPI documentation interface hosted a
 
 Configure MongoDB with the following backup/snapshot policy. This policy applies to both MongoDB Atlas and self-hosted MongoDB. Details specific to each are mentioned further below.
 
-* Full hourly snapshots with 1-day retention
-* Full daily snapshots with 7-day retention; configured snapshot time: 04:00 UTC
+- Full hourly snapshots with 1-day retention
+- Full daily snapshots with 7-day retention; configured snapshot time: 04:00 UTC
 
 ### MongoDB Atlas
 

docs/build-on-nildb.md

@@ -6,7 +6,6 @@ This section outlines specific builder-related tasks and is deliberately utilita
 
 An OpenAPI documentation site is available at `{APP_NODE_PUBLIC_ENDPOINT}/openapi.json` when the node is running and the `openapi-spec` feature is enabled.
 
-
 ## Running nilDB Locally
 
 ### Quick Start
@@ -20,7 +19,7 @@ docker compose -f local/docker-compose.yaml up -d
 This starts a single nilDB node along with all required supporting services:
 
 - **nilDB API**: http://localhost:40080
-- **MongoDB**: localhost:40017  
+- **MongoDB**: localhost:40017
 - **nilauth**: http://localhost:40921 (authentication service)
 - **nilchain**: http://localhost:40648 (local blockchain)
 - **PostgreSQL**: localhost:40432 (nilauth database)

docs/overview.md

@@ -6,8 +6,8 @@ nilDb is a structured data persistence service that provides a robust, distribut
 
 - [Networks](#networks)
 - [Network topology](#network-topology)
-    - [Clusters](#clusters)
-    - [Node Architecture](#node-architecture)
+  - [Clusters](#clusters)
+  - [Node Architecture](#node-architecture)
 - [Clients](#clients)
 
 ## Networks
@@ -65,4 +65,4 @@ curl https://nildb-a50d.nillion.network/api/v1/data/create \
   -d @data.json
 ```
 
-> ![NOTE] Data encryption is applied using [nilQL-ts](https://github.com/nillionnetwork/nilql-ts) or [nilQL-py](https://github.com/nillionnetwork/nilql-py) before transmission. 
+> ![NOTE] Data encryption is applied using [nilQL-ts](https://github.com/nillionnetwork/nilql-ts) or [nilQL-py](https://github.com/nillionnetwork/nilql-py) before transmission.

lefthook.yml

@@ -1,11 +1,11 @@
 pre-commit:
   commands:
-    biome-format:
+    oxfmt:
       glob: "*.{ts,json,jsonc}"
       # Uses pnpm directly (not justfile) because:
       # - Requires lefthook's {staged_files} variable for incremental formatting
       # - Uses stage_fixed to auto-stage formatted files (lefthook-specific)
-      run: pnpm exec biome format --write --no-errors-on-unmatched --files-ignore-unknown=true --colors=off {staged_files}
+      run: pnpm exec oxfmt {staged_files}
       stage_fixed: true
 
 commit-msg:

packages/api/UPGRADING.md

@@ -5,7 +5,7 @@ This document explains how to upgrade nilDB between major versions.
 ## Version Compatibility
 
 | From Version  | To Version | Upgrade Path                  |
-|---------------|------------|-------------------------------|
+| ------------- | ---------- | ----------------------------- |
 | Fresh install | 1.2.0+     | Direct install                |
 | 1.1.2         | 1.2.0+     | Direct upgrade                |
 | < 1.1.2       | 1.2.0+     | **Two-step upgrade required** |
@@ -15,6 +15,7 @@ This document explains how to upgrade nilDB between major versions.
 ### Overview
 
 Version 1.2.0 consolidates the database migration system:
+
 - **Migration library**: Changed from `mongo-migrate-ts` to `migrate-mongo`
 - **Changelog collection**: Renamed from `migrations_changelog` to `_migrations`
 - **Migration count**: Reduced from 5 migrations to 1 consolidated migration
@@ -37,31 +38,37 @@ mongosh <connection-string> --eval "db.migrations_changelog.count()"
 ### Upgrade Steps
 
 1. **Backup your database**
+
    ```bash
    mongodump --uri="<your-mongodb-uri>" --out=/path/to/backup
    ```
 
 2. **Stop the current nilDB instance**
+
    ```bash
    docker stop <nildb-container>
    ```
 
 3. **Pull the new version**
+
    ```bash
    docker pull <nildb-image>:1.2.0
    ```
 
 4. **Start the new version**
+
    ```bash
    docker start <nildb-container>
    ```
 
 5. **Monitor the migration**
+
    ```bash
    docker logs -f <nildb-container>
    ```
 
    You should see:
+
    ```
    ! Running consolidated init migration
    ! Detected upgrade from v1.1.2
@@ -72,6 +79,7 @@ mongosh <connection-string> --eval "db.migrations_changelog.count()"
    ```
 
 6. **Verify the upgrade**
+
    ```bash
    # Check new changelog format
    mongosh <connection-string> --eval "db._migrations.findOne()"
@@ -85,6 +93,7 @@ mongosh <connection-string> --eval "db.migrations_changelog.count()"
 ### What Happens During Upgrade
 
 The migration automatically:
+
 1. Detects the old `migrations_changelog` collection from v1.1.2
 2. Validates it contains exactly 5 expected migrations
 3. Drops the old `migrations_changelog` collection
@@ -111,6 +120,7 @@ Follow the [v1.1.2 → v1.2.0 upgrade steps](#upgrading-from-v112-to-v120) above
 ## Fresh Installation
 
 For new installations, simply start the latest version. The migration will:
+
 1. Create all 7 collections (`builders`, `users`, `collections`, `queries`, `query_runs`, `config`, `data`)
 2. Create required indexes:
    - `builders.did` (unique)
@@ -126,6 +136,7 @@ For new installations, simply start the latest version. The migration will:
 **Cause**: Your database is not from v1.1.2.
 
 **Solution**:
+
 - If you're on an older version, first upgrade to v1.1.2
 - If migrations are incomplete, manually run v1.1.2 migrations to completion
 - If uncertain, restore from backup and contact support
@@ -135,6 +146,7 @@ For new installations, simply start the latest version. The migration will:
 **Cause**: The migration files in your v1.1.2 installation don't match expected names.
 
 **Solution**:
+
 - Verify you're running official v1.1.2 release
 - Check for custom or modified migrations
 - Restore from backup if migrations were tampered with
@@ -144,6 +156,7 @@ For new installations, simply start the latest version. The migration will:
 **Cause**: The old migration system didn't create a `migrations_changelog` collection.
 
 **Solution**:
+
 - This is expected for fresh installations (not an error)
 - For upgrades, verify you actually had v1.1.2 running previously
 - If uncertain, treat as fresh install (will recreate collections)
@@ -153,11 +166,13 @@ For new installations, simply start the latest version. The migration will:
 If you need to rollback after upgrading:
 
 1. **Stop the new version**
+
    ```bash
    docker stop <nildb-container>
    ```
 
 2. **Restore from backup**
+
    ```bash
    mongorestore --uri="<your-mongodb-uri>" --drop /path/to/backup
    ```