Simplify

.env.example

@@ -0,0 +1,21 @@
+# .env.example - Optional environment file for AltarDocker
+#
+# docker-compose.yml has sensible defaults built-in!
+# You only need this .env file if you want to customize settings.
+#
+# To use: Copy this file to .env and modify the values below
+# Without .env: docker-compose.yml uses defaults (sacred, 27017, minio_admin, etc.)
+
+# MongoDB Configuration
+MONGO_DB=sacred
+MONGO_PORT=27017
+
+# MinIO Configuration (S3-compatible storage)
+MINIO_ROOT_USER=minio_admin
+MINIO_ROOT_PASSWORD=changeme123
+MINIO_S3_PORT=9000
+MINIO_CONSOLE_PORT=9001
+
+# Volume Paths (where data is stored)
+MONGO_DATA_PATH=./data/mongo/
+MINIO_DATA_PATH=./data/minio/

.github/workflows/validate.yml

@@ -0,0 +1,53 @@
+name: Validate Docker Compose
+
+on:
+  push:
+    branches: [ main, no_credentials ]
+  pull_request:
+    branches: [ main ]
+
+jobs:
+  validate-compose:
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v4
+
+      - name: Set up Docker Buildx
+        uses: docker/setup-buildx-action@v3
+
+      - name: Validate docker-compose.yml syntax
+        run: |
+          docker compose -f docker-compose.yml config > /dev/null
+          echo "✅ docker-compose.yml is valid"
+
+      - name: Check .env.example has all required variables
+        run: |
+          echo "Checking required variables in .env.example..."
+          grep -q "MONGO_DB=" .env.example || (echo "❌ Missing MONGO_DB" && exit 1)
+          grep -q "MONGO_PORT=" .env.example || (echo "❌ Missing MONGO_PORT" && exit 1)
+          grep -q "MINIO_ROOT_USER=" .env.example || (echo "❌ Missing MINIO_ROOT_USER" && exit 1)
+          grep -q "MINIO_ROOT_PASSWORD=" .env.example || (echo "❌ Missing MINIO_ROOT_PASSWORD" && exit 1)
+          grep -q "MONGO_DATA_PATH=" .env.example || (echo "❌ Missing MONGO_DATA_PATH" && exit 1)
+          grep -q "MINIO_DATA_PATH=" .env.example || (echo "❌ Missing MINIO_DATA_PATH" && exit 1)
+          echo "✅ All required variables present"
+
+      - name: Test docker-compose.yml with defaults (no .env)
+        run: |
+          # Test without .env file to verify defaults work
+          docker compose -f docker-compose.yml up --dry-run mongo
+          echo "✅ docker-compose.yml works with defaults (no .env)"
+
+      - name: Test docker-compose.yml with .env overrides
+        run: |
+          cp .env.example .env
+          # Test all services
+          docker compose -f docker-compose.yml up --dry-run
+          echo "✅ docker-compose.yml all services with .env valid"
+
+      - name: Pull Docker images to verify they exist
+        run: |
+          docker pull mongo:6
+          docker pull quay.io/minio/minio:latest
+          echo "✅ All Docker images are accessible"

DEPLOY.md

@@ -1,219 +1,81 @@
-# AltarDocker — Local Deployment Guide
+# AltarDocker — Deployment Guide
 
-This guide helps you start a minimal stack locally using Docker Compose:
+Complete guide for deploying MongoDB and MinIO infrastructure for Sacred experiment tracking.
+
+**Services included:**
 - MongoDB for experiment metadata
-- MinIO (S3-compatible) for raw data (optional)
-- Omniboard connected to MongoDB
-- AltarExtractor for browsing Sacred experiments (optional)
+- MinIO for S3-compatible object storage
+
+> **Note:** Omniboard is managed by [AltarViewer](../AltarViewer), AltarExtractor is [deployed separately](../AltarExtractor).
 
 ---
 
 ## Prerequisites
-- Docker >= 24 and Docker Compose v2 installed (https://docs.docker.com/engine/install/)
-- At least 2 GB of free disk space (more depending on the size of your data)
+- Docker >= 24 and Docker Compose v2 installed
+- At least 2 GB free disk space
 
 ---
 
-## Project Layout
-```
-AltarDocker/
-├─ .env                  # Environment variables (create this)
-├─ docker-compose.yml    # Docker Compose configuration
-├─ DEPLOY.md             # This file
-├─ MANAGE_USERS.md       # User management guide
-└─ mongo_dump.sh         # Backup script example
-```
+## 1) (Optional) Customize Settings
 
----
+**The compose file works without a `.env` file!** It has built-in defaults:
+- MongoDB: `sacred` database on port `27017`
+- MinIO: `minio_admin` / `changeme123` on ports `9000` and `9001`
+- Data stored in `./data/mongo/` and `./data/minio/`
+
+**To customize**, copy `.env.example` to `.env` and modify the values:
 
-## 1) Create the `.env` file
+```bash
+cp .env.example .env
+# Edit .env with your preferred values
+```
 
-Create a `.env` file in this folder with strong passwords:
+The `.env.example` file contains:
 
 ```dotenv
-# MongoDB (root account for initial setup)
-MONGO_ROOT_USER=admin
-MONGO_ROOT_PASSWORD=change_me_mongo_password
+# MongoDB Configuration
 MONGO_DB=sacred
+MONGO_PORT=27017
 
-# MinIO (S3 + console)
+# MinIO Configuration
 MINIO_ROOT_USER=minio_admin
-MINIO_ROOT_PASSWORD=change_me_minio_password
-
-# Host port for Omniboard (internal port is 9000)
-OMNIBOARD_HOST_PORT=9004
+MINIO_ROOT_PASSWORD=your_secure_password
+MINIO_S3_PORT=9000
+MINIO_CONSOLE_PORT=9001
 
-# Host port for AltarExtractor (internal port is 8050)
-EXTRACTOR_HOST_PORT=8050
+# Volume Paths (where data is stored)
+MONGO_DATA_PATH=./data/mongo/
+MINIO_DATA_PATH=./data/minio/
 ```
 
 ---
 
-## 2) Edit `docker-compose.yml`
-
-The data for MinIO and MongoDB will be saved in the folders specified in `volumes` (outside the Docker container). Update the volume paths to your preferred locations:
-
-```yaml
-services:
-  mongo:
-    image: mongo:6
-    container_name: mongo
-    restart: unless-stopped
-    environment:
-      MONGO_INITDB_ROOT_USERNAME: ${MONGO_ROOT_USER}
-      MONGO_INITDB_ROOT_PASSWORD: ${MONGO_ROOT_PASSWORD}
-      MONGO_INITDB_DATABASE: ${MONGO_DB}
-    ports:
-      - "27017:27017"
-    volumes:
-      - /path/to/your/mongo_data:/data/db  # Change this path
-
-  minio:
-    image: quay.io/minio/minio:latest
-    container_name: minio
-    restart: unless-stopped
-    command: server /data --console-address ":9001"
-    environment:
-      MINIO_ROOT_USER: ${MINIO_ROOT_USER}
-      MINIO_ROOT_PASSWORD: ${MINIO_ROOT_PASSWORD}
-    ports:
-      - "9000:9000"   # S3 API
-      - "9001:9001"   # Web console
-    volumes:
-      - /path/to/your/minio_data:/data  # Change this path
-    profiles:
-      - minio
-
-  omniboard:
-    image: vivekratnavel/omniboard:latest
-    container_name: omniboard
-    restart: unless-stopped
-    depends_on:
-      - mongo
-    ports:
-      - "${OMNIBOARD_HOST_PORT}:9000"
-    command: [
-      "--mu",
-      "mongodb://${MONGO_ROOT_USER}:${MONGO_ROOT_PASSWORD}@mongo:27017/?authSource=admin&authMechanism=SCRAM-SHA-1",
-      "${MONGO_DB}"
-    ]
-
-  extractor:
-    build:
-      context: ../AltarExtractor
-      dockerfile: Dockerfile
-    container_name: altar-extractor
-    restart: unless-stopped
-    depends_on:
-      - mongo
-    ports:
-      - "${EXTRACTOR_HOST_PORT:-8050}:8050"
-    environment:
-      - PORT=8050
-      - SACRED_DB_NAME=${MONGO_DB}
-    profiles:
-      - extractor
-
-volumes:
-  mongo_data:
-  minio_data:
-```
-
----
+## 2) Start the Services
 
-## 3) Start the Docker containers
-
-### Basic stack (MongoDB + Omniboard)
 ```bash
 docker compose up -d
 docker ps
 ```
 
-### With MinIO
-```bash
-docker compose --profile minio up -d
-docker ps
-```
-
-### With AltarExtractor
-```bash
-docker compose --profile extractor up -d
-docker ps
-```
-
-### With both MinIO and AltarExtractor
-```bash
-docker compose --profile minio --profile extractor up -d
-docker ps
-```
-
 > **Note:** On Linux, you may need to prefix commands with `sudo`.
 
-### URLs
+**All services start automatically:**
+- MongoDB on port 27017
+- MinIO S3 API on port 9000
+- MinIO Console on port 9001
+
+### Access URLs
 
 | Service        | URL                                                      |
 |----------------|----------------------------------------------------------|
-| MongoDB        | `mongodb://localhost:27017` (authenticate with root)     |
+| MongoDB        | `mongodb://localhost:27017`                              |
 | MinIO S3 API   | http://localhost:9000                                    |
 | MinIO Console  | http://localhost:9001                                    |
-| Omniboard      | http://localhost:9004 (or your `OMNIBOARD_HOST_PORT`)    |
-| AltarExtractor | http://localhost:8050 (or your `EXTRACTOR_HOST_PORT`)    |
-
----
-
-## 4) Connecting AltarExtractor to MongoDB
-
-When you open AltarExtractor in your browser, you need to configure the MongoDB connection:
-
-1. Open http://localhost:8050 (or your configured `EXTRACTOR_HOST_PORT`)
-2. In the "Database credentials" section, enter:
-   - **Host**: `mongo` (the Docker service name, not localhost)
-   - **Port**: `27017`
-   - **Username**: your `MONGO_ROOT_USER` value
-   - **Password**: your `MONGO_ROOT_PASSWORD` value
-   - **Auth source**: `admin`
-3. Enter your database name (e.g., `sacred`)
-4. Click "Connect"
-
-> **Tip:** Check "Save credentials" to remember your connection settings in browser local storage.
 
 ---
 
-## 5) (Recommended) Create an app-specific MongoDB user
 
-```bash
-docker exec -it mongo mongosh -u admin -p your_password --authenticationDatabase admin
-```
-
-Inside mongosh:
-```javascript
-use sacred
-db.createUser({
-  user: "sacred_rw",
-  pwd:  "change_me",
-  roles: [ { role: "readWrite", db: "sacred" } ]
-})
-```
-
-Then update Omniboard to use this user (edit `docker-compose.yml`):
-```yaml
-command: [
-  "--mu",
-  "mongodb://sacred_rw:change_me@mongo:27017/?authSource=sacred&authMechanism=SCRAM-SHA-1",
-  "sacred"
-]
-```
-
-Restart Omniboard:
-```bash
-docker compose up -d omniboard
-```
-
-> **Note:** On Linux, prefix with `sudo` if needed.
-
----
-
-## 6) Backups (Linux)
+## Backups (Linux)
 
 ### MongoDB backup script
 
@@ -222,7 +84,7 @@ Edit the `mongo_dump.sh` file:
 #!/bin/bash
 
 # Dumps root repository
-BASE_DIR="/home/user/mongodumps/dump"  # Change to your backup location
+BAS5_DIR="/home/user/mongodumps/dump"  # Change to your backup location
 
 # Timestamp (e.g., 2025-07-07)
 DATE_STR=$(date +%Y-%m-%d)
@@ -256,7 +118,7 @@ Add:
 0 2 * * * bash /path/to/mongo_dump.sh >> /path/to/cron.log 2>&1
 ```
 
----
+---6
 
 ## 7) Cleanup
 
@@ -270,14 +132,14 @@ docker compose down
 
 ## Troubleshooting
 
-- **Omniboard cannot connect?** Check the `--mu` URI (authSource, host, port) and that MongoDB is reachable.
-- **Port conflict?** Change `OMNIBOARD_HOST_PORT`, `EXTRACTOR_HOST_PORT`, or MinIO mappings in `docker-compose.yml`.
+- **Omniboard cannot connect?** Use [AltarViewer](../AltarViewer) to launch Omniboard properly configured for your database.
+- **Port conflict?** Change `MONGO_PORT` or MinIO port mappings in `docker-compose.yml`.
 - **S3 SDKs:** Use endpoint `http://localhost:9000` with MinIO credentials.
-- **AltarExtractor can't connect?** Make sure to use `mongo` as the host (Docker service name), not `localhost`.
 
 ---
 
 ## Related
 
-- [AltarExtractor](https://github.com/DreamRepo/AltarExtractor) — Browse and filter Sacred experiments in a web UI
+- [AltarExtractor](https://github.com/DreamRepo/AltarExtractor) — Browse and filter Sacred experiments (standalone deployment)
 - [AltarSender](https://github.com/DreamRepo/AltarSender) — GUI to send experiments to Sacred and MinIO
+- [AltarViewer](https://github.com/DreamRepo/AltarViewer) — Launch Omniboard configured for your database