Run Python with the SDK using uvx:

# Quick start - run Python with the SDK available
uvx --with "diffuse-cli @ git+ssh://git@github.com/diff-use/webapp.git#subdirectory=cli" python

Or add to an existing project:

# uv
uv add "diffuse-cli @ git+ssh://git@github.com/diff-use/webapp.git#subdirectory=cli"

# pip
pip install "diffuse-cli @ git+ssh://git@github.com/diff-use/webapp.git#subdirectory=cli"

This example walks through authentication, creating an experiment with rich metadata, connecting related experiments, and searching.

1. Authentication

Option A: If you don't have a token, use the built-in device flow (opens browser):

from diffuse_cli import login, Diffuse

# First time: authenticate via GitHub device flow
login()  # Opens browser, prints code, waits for you to authorize

# Now create a client (uses stored token automatically)
diffuse = Diffuse()
print(diffuse.version())  # {'version': '0.2.1', ...}

Option B: If you already have a GitHub token:

from diffuse_cli import Diffuse

# Pass token directly (useful for CI/CD or existing tokens)
diffuse = Diffuse(token="ghp_xxxxxxxxxxxxxxxxxxxx")

# Or via environment variable
import os
diffuse = Diffuse(token=os.environ.get("GITHUB_TOKEN"))

2. Create an Experiment with Metadata

# Create a new experiment
exp = diffuse.experiments.create(
    title="Cryo-EM Structure of GPCR-Gαs Complex",
    summary="High-resolution structure determination using single-particle cryo-EM",
    tags=["cryo-em", "gpcr", "structural-biology", "2024-q4"],
)
print(f"Created: {exp['display_id']}")  # e.g., EXP-42

# Add detailed metadata (fields must be pre-configured by an admin)
diffuse.metadata.update(exp["display_id"], {
    "resolution_angstrom": 2.8,
    "particle_count": 1_250_000,
    "microscope": "Titan Krios G4",
    "detector": "Falcon 4i",
    "processing_software": "cryoSPARC v4.4",
    "pdb_id": None,  # To be deposited
})

3. Connect Related Experiments

# Find the data collection experiment to link
data_exps = diffuse.experiments.list(query="tag:data-collection AND tag:gpcr")

# Get the parent experiment
parent = data_exps[0] if data_exps else None

if parent:
    # Link experiments (requires relationships API - coming soon)
    print(f"Parent experiment: {parent['display_id']}")

4. Advanced Search

# Find high-resolution structures from this year
results = diffuse.experiments.list(
    query='tag:cryo-em AND resolution_angstrom:<3.0 AND created:>2024-01-01'
)

for exp in results:
    meta = diffuse.metadata.get(exp["display_id"])
    print(f"{exp['display_id']}: {exp['title']}")
    print(f"  Resolution: {meta.get('resolution_angstrom')} Å")
    print(f"  Particles: {meta.get('particle_count'):,}")
    print()

# Boolean operators and grouping
diffuse.experiments.list(
    query='(tag:xray OR tag:cryo-em) AND NOT tag:preliminary'
)

# Wildcard matching
diffuse.experiments.list(query='title:GPCR*')

# Exact phrase matching
diffuse.experiments.list(query='summary:"beta-arrestin complex"')

List Experiments

# List all experiments
experiments = diffuse.experiments.list()

# Filter with search query
experiments = diffuse.experiments.list(query="tag:crystal")
experiments = diffuse.experiments.list(query="tag:xray AND resolution:>1.5")

# Filter by visibility
public_exps = diffuse.experiments.list(public=True)
private_exps = diffuse.experiments.list(public=False)

# Sort results
experiments = diffuse.experiments.list(sort="recent")   # Default: most recently updated
experiments = diffuse.experiments.list(sort="oldest")   # Oldest first
experiments = diffuse.experiments.list(sort="title")    # Alphabetical

# Pagination
experiments = diffuse.experiments.list(limit=50, offset=100)

Get Experiment Details

# Get by display ID (recommended)
exp = diffuse.experiments.get("EXP-42")

# Get by UUID also works
exp = diffuse.experiments.get("550e8400-e29b-41d4-a716-446655440000")

print(exp["title"])
print(exp["summary"])
print(exp["tags"])
print(exp["artifact_count"])

Create Experiment

# Minimal creation
exp = diffuse.experiments.create(title="My New Experiment")

# With all options
exp = diffuse.experiments.create(
    title="Crystal Structure Analysis",
    summary="Analyzing X-ray diffraction patterns from sample batch A",
    tags=["xray", "crystal", "batch-a"],
    markdown="# Overview\n\nDetailed notes here...",
    type_id="protocol"  # Optional: experiment type
)

print(f"Created: {exp['display_id']}")

Update Experiment

# Update specific fields
exp = diffuse.experiments.update(
    "EXP-42",
    title="Updated Title",
    summary="New summary",
    tags=["new", "tags"]
)

# Update markdown content
exp = diffuse.experiments.update(
    "EXP-42",
    markdown="# Updated Content\n\nNew notes..."
)

Delete Experiment

diffuse.experiments.delete("EXP-42")

Publish / Unpublish

# Make experiment publicly accessible
exp = diffuse.experiments.publish("EXP-42")
print(exp["is_public"])  # True

# Make experiment private again
exp = diffuse.experiments.unpublish("EXP-42")
print(exp["is_public"])  # False

List Experiment Types

types = diffuse.experiments.types()
for t in types:
    print(f"{t['slug']}: {t['name']}")

Activity Log

# Get recent activity for an experiment
activity = diffuse.experiments.activity("EXP-42", limit=20)
for event in activity:
    print(f"{event['created_at']}: {event['action']}")

Artifacts in DiffUSE Hub follow a many-to-many model: a single artifact can be connected to multiple experiments, and experiments can share artifacts. This enables data reuse without duplication.

List Artifacts

# List all artifacts
artifacts = diffuse.artifacts.list()

# Filter by experiment
artifacts = diffuse.artifacts.list(experiment_id="EXP-42")

# Pagination
artifacts = diffuse.artifacts.list(limit=100, offset=0)

Get Artifact Details

artifact = diffuse.artifacts.get("artifact-uuid")

print(artifact["filename"])
print(artifact["size_bytes"])
print(artifact["content_type"])
print(artifact["checksum_sha256"])
print(artifact["file_mtime"])  # Original file modification time (if available)

Connect Artifact to Experiment

# Connect an existing artifact to another experiment
diffuse.artifacts.connect(
    artifact_id="artifact-uuid",
    experiment_id="EXP-99"
)

# Optionally specify a display path
diffuse.artifacts.connect(
    artifact_id="artifact-uuid",
    experiment_id="EXP-99",
    path="data/shared-dataset.csv"
)

Disconnect Artifact

# Remove artifact from experiment (doesn't delete the artifact)
diffuse.artifacts.disconnect(
    artifact_id="artifact-uuid",
    experiment_id="EXP-42"
)

Delete Artifact

# Delete artifact (only works if connected to 0-1 experiments)
diffuse.artifacts.delete("artifact-uuid")

# Force delete even if connected to multiple experiments
diffuse.artifacts.delete("artifact-uuid", force=True)

Store arbitrary key-value metadata on experiments. Values can be strings, numbers, booleans, or nested objects.

Get Metadata

# Get all metadata for an experiment
metadata = diffuse.metadata.get("EXP-42")
print(metadata)  # {"resolution": 1.5, "temperature": 298, ...}

# Get a specific key
resolution = diffuse.metadata.get("EXP-42", key="resolution")
print(resolution)  # 1.5

Set Metadata

# Set a single key-value pair
diffuse.metadata.set("EXP-42", "resolution", 1.5)
diffuse.metadata.set("EXP-42", "temperature", 298)
diffuse.metadata.set("EXP-42", "validated", True)

# Complex values work too
diffuse.metadata.set("EXP-42", "parameters", {
    "wavelength": 0.154,
    "detector": "Pilatus 6M",
    "exposure_time": 0.1
})

Update Multiple Fields

# Update multiple metadata fields at once
diffuse.metadata.update("EXP-42", {
    "resolution": 1.8,
    "temperature": 310,
    "status": "complete"
})

Delete Metadata

# Remove a metadata field
diffuse.metadata.delete("EXP-42", "obsolete_field")

List Metadata Fields

# Get available metadata field definitions
fields = diffuse.metadata.fields()
for field in fields:
    print(f"{field['name']} ({field['field_type']})")

from diffuse_cli import Diffuse, DiffuseError

diffuse = Diffuse()

try:
    exp = diffuse.experiments.get("nonexistent")
except DiffuseError as e:
    print(f"Error: {e}")
    print(f"Status code: {e.status_code}")  # e.g., 404
    print(f"Detail: {e.detail}")            # Server error message

Authentication

Use the built-in device flow for interactive login, or pass a token directly:

from diffuse_cli import login, Diffuse

# Option 1: Device flow (interactive, opens browser)
login()
diffuse = Diffuse()

# Option 2: Pass token directly
diffuse = Diffuse(token="ghp_xxxxxxxxxxxxxxxxxxxx")

# Option 3: Environment variable
import os
diffuse = Diffuse(token=os.environ.get("GITHUB_TOKEN"))

Environment Variables

# Set the API URL directly
export DIFFUSE_API_URL="https://app.diffuse.science"

# Or use environment shortcuts
export DIFFUSE_ENV="prod"     # https://app.diffuse.science (default)
export DIFFUSE_ENV="staging"  # https://dev.diffuse.science
export DIFFUSE_ENV="local"    # http://127.0.0.1:8000

Context Manager

# Automatically close the HTTP client when done
with Diffuse(token=token) as diffuse:
    experiments = diffuse.experiments.list()
    # ... do work ...

Custom Timeout

# Set a longer timeout for slow connections
diffuse = Diffuse(token=token, timeout=60.0)  # 60 seconds