@synsci/cli-darwin-x64-baseline 1.1.76 → 1.1.78

package/bin/skills/lamindb/references/setup-deployment.md

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+# LaminDB Setup & Deployment
+
+This document covers installation, configuration, instance management, storage options, and deployment strategies for LaminDB.
+
+## Installation
+
+### Basic Installation
+
+```bash
+# Install LaminDB
+pip install lamindb
+
+# Or with pip3
+pip3 install lamindb
+```
+
+### Installation with Extras
+
+Install optional dependencies for specific functionality:
+
+```bash
+# Google Cloud Platform support
+pip install 'lamindb[gcp]'
+
+# Flow cytometry formats
+pip install 'lamindb[fcs]'
+
+# Array storage and streaming (Zarr support)
+pip install 'lamindb[zarr]'
+
+# AWS S3 support (usually included by default)
+pip install 'lamindb[aws]'
+
+# Multiple extras
+pip install 'lamindb[gcp,zarr,fcs]'
+```
+
+### Module Plugins
+
+```bash
+# Biological ontologies (Bionty)
+pip install bionty
+
+# Wet lab functionality
+pip install lamindb-wetlab
+
+# Clinical data (OMOP CDM)
+pip install lamindb-clinical
+```
+
+### Verify Installation
+
+```python
+import lamindb as ln
+print(ln.__version__)
+
+# Check available modules
+import bionty as bt
+print(bt.__version__)
+```
+
+## Authentication
+
+### Creating an Account
+
+1. Visit https://lamin.ai
+2. Sign up for a free account
+3. Navigate to account settings to generate an API key
+
+### Logging In
+
+```bash
+# Login with API key
+lamin login
+
+# You'll be prompted to enter your API key
+# API key is stored locally at ~/.lamin/
+```
+
+### Authentication Details
+
+**Data Privacy:** LaminDB authentication only collects basic metadata (email, user information). Your actual data remains private and is not sent to LaminDB servers.
+
+**Local vs Cloud:** Authentication is required even for local-only usage to enable collaboration features and instance management.
+
+## Instance Initialization
+
+### Local SQLite Instance
+
+For local development and small datasets:
+
+```bash
+# Initialize in current directory
+lamin init --storage ./mydata
+
+# Initialize in specific directory
+lamin init --storage /path/to/data
+
+# Initialize with specific modules
+lamin init --storage ./mydata --modules bionty
+
+# Initialize with multiple modules
+lamin init --storage ./mydata --modules bionty,wetlab
+```
+
+### Cloud Storage with SQLite
+
+Use cloud storage but local SQLite database:
+
+```bash
+# AWS S3
+lamin init --storage s3://my-bucket/path
+
+# Google Cloud Storage
+lamin init --storage gs://my-bucket/path
+
+# S3-compatible (MinIO, Cloudflare R2)
+lamin init --storage 's3://bucket?endpoint_url=http://endpoint:9000'
+```
+
+### Cloud Storage with PostgreSQL
+
+For production deployments:
+
+```bash
+# S3 + PostgreSQL
+lamin init --storage s3://my-bucket/path \
+  --db postgresql://user:password@hostname:5432/dbname \
+  --modules bionty
+
+# GCS + PostgreSQL
+lamin init --storage gs://my-bucket/path \
+  --db postgresql://user:password@hostname:5432/dbname \
+  --modules bionty
+```
+
+### Instance Naming
+
+```bash
+# Specify instance name
+lamin init --storage ./mydata --name my-project
+
+# Default name uses directory name
+lamin init --storage ./mydata  # Instance name: "mydata"
+```
+
+## Connecting to Instances
+
+### Connect to Your Own Instance
+
+```bash
+# By name
+lamin connect my-project
+
+# By full path
+lamin connect account_handle/my-project
+```
+
+### Connect to Shared Instance
+
+```bash
+# Connect to someone else's instance
+lamin connect other-user/their-project
+
+# Requires appropriate permissions
+```
+
+### Switching Between Instances
+
+```bash
+# List available instances
+lamin info
+
+# Switch instance
+lamin connect another-instance
+
+# Close current instance
+lamin close
+```
+
+## Storage Configuration
+
+### Local Storage
+
+**Advantages:**
+- Fast access
+- No internet required
+- Simple setup
+
+**Setup:**
+```bash
+lamin init --storage ./data
+```
+
+### AWS S3 Storage
+
+**Advantages:**
+- Scalable
+- Collaborative
+- Durable
+
+**Setup:**
+```bash
+# Set credentials
+export AWS_ACCESS_KEY_ID=your_key_id
+export AWS_SECRET_ACCESS_KEY=your_secret_key
+export AWS_DEFAULT_REGION=us-east-1
+
+# Initialize
+lamin init --storage s3://my-bucket/project-data \
+  --db postgresql://user:pwd@host:5432/db
+```
+
+**S3 Permissions Required:**
+```json
+{
+  "Version": "2012-10-17",
+  "Statement": [
+    {
+      "Effect": "Allow",
+      "Action": [
+        "s3:GetObject",
+        "s3:PutObject",
+        "s3:DeleteObject",
+        "s3:ListBucket"
+      ],
+      "Resource": [
+        "arn:aws:s3:::my-bucket/*",
+        "arn:aws:s3:::my-bucket"
+      ]
+    }
+  ]
+}
+```
+
+### Google Cloud Storage
+
+**Setup:**
+```bash
+# Authenticate
+gcloud auth application-default login
+
+# Or use service account
+export GOOGLE_APPLICATION_CREDENTIALS=/path/to/credentials.json
+
+# Initialize
+lamin init --storage gs://my-bucket/project-data \
+  --db postgresql://user:pwd@host:5432/db
+```
+
+### S3-Compatible Storage
+
+For MinIO, Cloudflare R2, or other S3-compatible services:
+
+```bash
+# MinIO example
+export AWS_ACCESS_KEY_ID=minioadmin
+export AWS_SECRET_ACCESS_KEY=minioadmin
+
+lamin init --storage 's3://my-bucket?endpoint_url=http://minio.example.com:9000'
+
+# Cloudflare R2 example
+export AWS_ACCESS_KEY_ID=your_r2_access_key
+export AWS_SECRET_ACCESS_KEY=your_r2_secret_key
+
+lamin init --storage 's3://bucket?endpoint_url=https://account-id.r2.cloudflarestorage.com'
+```
+
+## Database Configuration
+
+### SQLite (Default)
+
+**Advantages:**
+- No separate database server
+- Simple setup
+- Good for development
+
+**Limitations:**
+- Not suitable for concurrent writes
+- Limited scalability
+
+**Setup:**
+```bash
+# SQLite is default
+lamin init --storage ./data
+# Database stored at ./data/.lamindb/
+```
+
+### PostgreSQL
+
+**Advantages:**
+- Production-ready
+- Concurrent access
+- Better performance at scale
+
+**Setup:**
+```bash
+# Full connection string
+lamin init --storage s3://bucket/path \
+  --db postgresql://username:password@hostname:5432/database
+
+# With SSL
+lamin init --storage s3://bucket/path \
+  --db "postgresql://user:pwd@host:5432/db?sslmode=require"
+```
+
+**PostgreSQL Versions:** Compatible with PostgreSQL 12+
+
+### Database Schema Management
+
+```bash
+# Check current schema version
+lamin migrate check
+
+# Upgrade schema
+lamin migrate deploy
+
+# View migration history
+lamin migrate history
+```
+
+## Cache Configuration
+
+### Cache Directory
+
+LaminDB maintains a local cache for cloud files:
+
+```python
+import lamindb as ln
+
+# View cache location
+print(ln.settings.cache_dir)
+```
+
+### Configure Cache Location
+
+```bash
+# Set cache directory
+lamin cache set /path/to/cache
+
+# View current cache settings
+lamin cache get
+```
+
+### System-Wide Cache (Multi-User)
+
+For shared systems with multiple users:
+
+```bash
+# Create system settings file
+sudo mkdir -p /system/settings
+sudo nano /system/settings/system.env
+```
+
+Add to `system.env`:
+```bash
+lamindb_cache_path=/shared/cache/lamindb
+```
+
+Ensure permissions:
+```bash
+sudo chmod 755 /shared/cache/lamindb
+sudo chown -R shared-user:shared-group /shared/cache/lamindb
+```
+
+### Cache Management
+
+```python
+import lamindb as ln
+
+# Clear cache for specific artifact
+artifact = ln.Artifact.get(key="data.h5ad")
+artifact.delete_cache()
+
+# Check if artifact is cached
+if artifact.is_cached():
+    print("Already cached")
+
+# Manually clear entire cache
+import shutil
+shutil.rmtree(ln.settings.cache_dir)
+```
+
+## Settings Management
+
+### View Current Settings
+
+```python
+import lamindb as ln
+
+# User settings
+print(ln.setup.settings.user)
+# User(handle='username', email='user@email.com', name='Full Name')
+
+# Instance settings
+print(ln.setup.settings.instance)
+# Instance(name='my-project', storage='s3://bucket/path')
+```
+
+### Configure Settings
+
+```bash
+# Set development directory for relative keys
+lamin settings set dev-dir /path/to/project
+
+# Configure git sync
+lamin settings set sync-git-repo https://github.com/user/repo.git
+
+# View all settings
+lamin settings
+```
+
+### Environment Variables
+
+```bash
+# Cache directory
+export LAMIN_CACHE_DIR=/path/to/cache
+
+# Settings directory
+export LAMIN_SETTINGS_DIR=/path/to/settings
+
+# Git sync
+export LAMINDB_SYNC_GIT_REPO=https://github.com/user/repo.git
+```
+
+## Instance Management
+
+### Viewing Instance Information
+
+```bash
+# Current instance info
+lamin info
+
+# List all instances
+lamin ls
+
+# View instance details
+lamin instance details
+```
+
+### Instance Collaboration
+
+```bash
+# Set instance visibility (requires LaminHub)
+lamin instance set-visibility public
+lamin instance set-visibility private
+
+# Invite collaborators (requires LaminHub)
+lamin instance invite user@email.com
+```
+
+### Instance Migration
+
+```bash
+# Backup instance
+lamin backup create
+
+# Restore from backup
+lamin backup restore backup_id
+
+# Export instance metadata
+lamin export instance-metadata.json
+```
+
+### Deleting Instances
+
+```bash
+# Delete instance (preserves data, removes metadata)
+lamin delete --force instance-name
+
+# This only removes the LaminDB metadata
+# Actual data in storage location remains
+```
+
+## Production Deployment Patterns
+
+### Pattern 1: Local Development → Cloud Production
+
+**Development:**
+```bash
+# Local development
+lamin init --storage ./dev-data --modules bionty
+```
+
+**Production:**
+```bash
+# Cloud production
+lamin init --storage s3://prod-bucket/data \
+  --db postgresql://user:pwd@db-host:5432/prod-db \
+  --modules bionty \
+  --name production
+```
+
+**Migration:** Export artifacts from dev, import to prod
+```python
+# Export from dev
+artifacts = ln.Artifact.filter().all()
+for artifact in artifacts:
+    artifact.export("/tmp/export/")
+
+# Switch to prod
+lamin connect production
+
+# Import to prod
+for file in Path("/tmp/export/").glob("*"):
+    ln.Artifact(str(file), key=file.name).save()
+```
+
+### Pattern 2: Multi-Region Deployment
+
+Deploy instances in multiple regions for data sovereignty:
+
+```bash
+# US instance
+lamin init --storage s3://us-bucket/data \
+  --db postgresql://user:pwd@us-db:5432/db \
+  --name us-production
+
+# EU instance
+lamin init --storage s3://eu-bucket/data \
+  --db postgresql://user:pwd@eu-db:5432/db \
+  --name eu-production
+```
+
+### Pattern 3: Shared Storage, Personal Instances
+
+Multiple users, shared data:
+
+```bash
+# Shared storage with user-specific DB
+lamin init --storage s3://shared-bucket/data \
+  --db postgresql://user1:pwd@host:5432/user1_db \
+  --name user1-workspace
+
+lamin init --storage s3://shared-bucket/data \
+  --db postgresql://user2:pwd@host:5432/user2_db \
+  --name user2-workspace
+```
+
+## Performance Optimization
+
+### Database Performance
+
+```python
+# Use connection pooling for PostgreSQL
+# Configure in database server settings
+
+# Optimize queries with indexes
+# LaminDB creates indexes automatically for common queries
+```
+
+### Storage Performance
+
+```bash
+# Use appropriate storage classes
+# S3: STANDARD for frequent access, INTELLIGENT_TIERING for mixed access
+
+# Configure multipart upload thresholds
+export AWS_CLI_FILE_IO_BANDWIDTH=100MB
+```
+
+### Cache Optimization
+
+```python
+# Pre-cache frequently used artifacts
+artifacts = ln.Artifact.filter(key__startswith="reference/")
+for artifact in artifacts:
+    artifact.cache()  # Download to cache
+
+# Use backed mode for large arrays
+adata = artifact.backed()  # Don't load into memory
+```
+
+## Security Best Practices
+
+1. **Credentials Management:**
+   - Use environment variables, not hardcoded credentials
+   - Use IAM roles on AWS/GCP instead of access keys
+   - Rotate credentials regularly
+
+2. **Access Control:**
+   - Use PostgreSQL for multi-user access control
+   - Configure storage bucket policies
+   - Enable audit logging
+
+3. **Network Security:**
+   - Use SSL/TLS for database connections
+   - Use VPCs for cloud deployments
+   - Restrict IP addresses when possible
+
+4. **Data Protection:**
+   - Enable encryption at rest (S3, GCS)
+   - Use encryption in transit (HTTPS, SSL)
+   - Implement backup strategies
+
+## Monitoring and Maintenance
+
+### Health Checks
+
+```python
+import lamindb as ln
+
+# Check database connection
+try:
+    ln.Artifact.filter().count()
+    print("✓ Database connected")
+except Exception as e:
+    print(f"✗ Database error: {e}")
+
+# Check storage access
+try:
+    test_artifact = ln.Artifact("test.txt", key="healthcheck.txt").save()
+    test_artifact.delete(permanent=True)
+    print("✓ Storage accessible")
+except Exception as e:
+    print(f"✗ Storage error: {e}")
+```
+
+### Logging
+
+```python
+# Enable debug logging
+import logging
+logging.basicConfig(level=logging.DEBUG)
+
+# LaminDB operations will produce detailed logs
+```
+
+### Backup Strategy
+
+```bash
+# Regular database backups (PostgreSQL)
+pg_dump -h hostname -U username -d database > backup_$(date +%Y%m%d).sql
+
+# Storage backups (S3 versioning)
+aws s3api put-bucket-versioning \
+  --bucket my-bucket \
+  --versioning-configuration Status=Enabled
+
+# Metadata export
+lamin export metadata_backup.json
+```
+
+## Troubleshooting
+
+### Common Issues
+
+**Issue: Cannot connect to instance**
+```bash
+# Check instance exists
+lamin ls
+
+# Verify authentication
+lamin login
+
+# Re-connect
+lamin connect instance-name
+```
+
+**Issue: Storage permissions denied**
+```bash
+# Check AWS credentials
+aws s3 ls s3://your-bucket/
+
+# Check GCS credentials
+gsutil ls gs://your-bucket/
+
+# Verify IAM permissions
+```
+
+**Issue: Database connection error**
+```bash
+# Test PostgreSQL connection
+psql postgresql://user:pwd@host:5432/db
+
+# Check database version compatibility
+lamin migrate check
+```
+
+**Issue: Cache full**
+```python
+# Clear cache
+import lamindb as ln
+import shutil
+shutil.rmtree(ln.settings.cache_dir)
+
+# Set larger cache location
+lamin cache set /larger/disk/cache
+```
+
+## Upgrade and Migration
+
+### Upgrading LaminDB
+
+```bash
+# Upgrade to latest version
+pip install --upgrade lamindb
+
+# Upgrade database schema
+lamin migrate deploy
+```
+
+### Schema Compatibility
+
+Check the compatibility matrix to ensure your database schema version is compatible with your installed LaminDB version.
+
+### Breaking Changes
+
+Major version upgrades may require migration:
+
+```bash
+# Check for breaking changes
+lamin migrate check
+
+# Review migration plan
+lamin migrate plan
+
+# Execute migration
+lamin migrate deploy
+```
+
+## Best Practices
+
+1. **Start local, scale cloud**: Develop locally, deploy to cloud for production
+2. **Use PostgreSQL for production**: SQLite is only for development
+3. **Configure appropriate cache**: Size cache based on working set
+4. **Enable versioning**: Use S3/GCS versioning for data protection
+5. **Monitor costs**: Track storage and compute costs in cloud deployments
+6. **Document configuration**: Keep infrastructure-as-code for reproducibility
+7. **Test backups**: Regularly verify backup and restore procedures
+8. **Set up monitoring**: Implement health checks and alerting
+9. **Use modules strategically**: Only install needed plugins to reduce complexity
+10. **Plan for scale**: Consider concurrent users and data growth