copick-web 0.1.5__tar.gz

copick_web-0.1.5/.dockerignore

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+.git
+__pycache__
+*.pyc
+*.egg-info
+.eggs
+dist
+build
+.venv
+.mypy_cache
+.pytest_cache
+.ruff_cache

copick_web-0.1.5/.gitignore

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+# =============================================================================
+# Python
+# =============================================================================
+
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py,cover
+.hypothesis/
+.pytest_cache/
+cover/
+
+# Translations
+*.mo
+*.pot
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+.pybuilder/
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# Environments
+.env*
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/
+
+# pytype static type analyzer
+.pytype/
+
+# Cython debug symbols
+cython_debug/
+
+# =============================================================================
+# Node.js / JavaScript / TypeScript
+# =============================================================================
+
+# Dependencies
+node_modules/
+.pnp
+.pnp.js
+
+# Build outputs
+dist/
+*.tsbuildinfo
+
+# Testing
+coverage/
+
+# Logs
+npm-debug.log*
+yarn-debug.log*
+yarn-error.log*
+lerna-debug.log*
+.pnpm-debug.log*
+
+# Runtime data
+pids
+*.pid
+*.seed
+*.pid.lock
+
+# Optional npm cache directory
+.npm
+
+# Optional eslint cache
+.eslintcache
+
+# Optional stylelint cache
+.stylelintcache
+
+# Microbundle cache
+.rpt2_cache/
+.rts2_cache_cjs/
+.rts2_cache_es/
+.rts2_cache_umd/
+
+# Optional REPL history
+.node_repl_history
+
+# Yarn v2
+.yarn/cache
+.yarn/unplugged
+.yarn/build-state.yml
+.yarn/install-state.gz
+.pnp.*
+
+# Vite
+*.local
+
+# =============================================================================
+# IDE / Editor
+# =============================================================================
+
+# JetBrains IDEs
+.idea/
+
+# VS Code (ignore all except shared config)
+.vscode/*
+!.vscode/tasks.json
+!.vscode/extensions.json
+*.code-workspace
+
+# WIP Scratch folder
+.scratch/
+
+# Claude
+.claude/
+CLAUDE.md
+
+# Vim
+*.swp
+*.swo
+*~
+
+# =============================================================================
+# OS
+# =============================================================================
+
+# macOS
+.DS_Store
+.AppleDouble
+.LSOverride
+._*
+
+# Windows
+Thumbs.db
+ehthumbs.db
+Desktop.ini
+
+# Linux
+*~
+
+# =============================================================================
+# Project-specific
+# =============================================================================
+
+# Built client files in server (generated by npm run build:server)
+# Keep .gitkeep but ignore actual build output
+server/src/copick_web/static/*
+!server/src/copick_web/static/.gitkeep
+
+# Local config files
+*.local.json
+copick_config.json
+
+# Test data
+.test/

copick_web-0.1.5/CHANGELOG.md

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+# Changelog
+
+## [0.1.5](https://github.com/copick/copick-web/compare/server-v0.1.4...server-v0.1.5) (2026-10-26)
+
+
+### Features
+
+* publish copick-web to PyPI with the web UI bundled ([#39](https://github.com/copick/copick-web/issues/39)) ([6323e7c](https://github.com/copick/copick-web/commit/6323e7c7873385f76d3302e51aa78e7f265111e6))
+
+
+### Bug Fixes
+
+* require Python 3.11 for the server, so Dependabot can update uv.lock ([#69](https://github.com/copick/copick-web/issues/69)) ([a150289](https://github.com/copick/copick-web/commit/a150289cc03b4c5259cce438cba828919f9dbda0))
+
+
+### Continuous Integration
+
+* set up Dependabot, with a server uv.lock ([#43](https://github.com/copick/copick-web/issues/43)) ([0f0dc7d](https://github.com/copick/copick-web/commit/0f0dc7d68b6c9500c0f3c93217c600957ce5839f))
+
+## [0.1.4](https://github.com/copick/copick-web/compare/server-v0.1.3...server-v0.1.4) (2026-10-14)
+
+
+### Features
+
+* multi-tenant with embrella integration ([#10](https://github.com/copick/copick-web/issues/10)) ([5cbd935](https://github.com/copick/copick-web/commit/5cbd935dbd6002fa98936989e0542088c8042c41))
+
+## [0.1.3](https://github.com/copick/copick-web/compare/server-v0.1.2...server-v0.1.3) (2026-10-08)
+
+
+### Features
+
+* multi-panel viewer, filaments, instance and panoptic segmentations ([#20](https://github.com/copick/copick-web/issues/20)) ([ff48363](https://github.com/copick/copick-web/commit/ff48363349f6b523801bd5c19866ab90de189873))
+* reload the project from the sidebar ([#22](https://github.com/copick/copick-web/issues/22)) ([05d043d](https://github.com/copick/copick-web/commit/05d043d08db674e807895311249ec78b102380c5))
+* serve under any URL prefix, set at runtime ([#26](https://github.com/copick/copick-web/issues/26)) ([bb77a09](https://github.com/copick/copick-web/commit/bb77a09d631562e2e1a98c6ce3bddfbec30d7ef9))
+
+## [0.1.2](https://github.com/copick/copick-web/compare/server-v0.1.1...server-v0.1.2) (2026-07-24)
+
+
+### Features
+
+* containerize app ([#4](https://github.com/copick/copick-web/issues/4)) ([1b57cb4](https://github.com/copick/copick-web/commit/1b57cb40e51ce6553f47ea896802725e31e850bc))
+
+## [0.1.1](https://github.com/copick/copick-web/compare/server-v0.1.0...server-v0.1.1) (2026-02-25)
+
+
+### Features
+
+* Particle picking! ([26113f8](https://github.com/copick/copick-web/commit/26113f8257592c57df5f01444e4b6064c2f0ae13))
+
+
+### Bug Fixes
+
+* add missing files for particle picking. ([821f7aa](https://github.com/copick/copick-web/commit/821f7aa6f43cfea4aa2e7db111d5ff5098b76ff9))

copick_web-0.1.5/Dockerfile

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+FROM python:3.11-slim
+RUN apt-get update && apt-get install -y --no-install-recommends gcc libc6-dev && rm -rf /var/lib/apt/lists/*
+WORKDIR /app
+COPY . .
+RUN pip install --no-cache-dir .
+CMD ["uvicorn", "copick_web.app.main:app", "--host", "0.0.0.0", "--port", "8000"]

copick_web-0.1.5/Dockerfile.dev

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+FROM python:3.11-slim
+
+RUN apt-get update && apt-get install -y --no-install-recommends gcc libc6-dev && rm -rf /var/lib/apt/lists/*
+
+WORKDIR /app
+
+COPY pyproject.toml .
+RUN mkdir -p src/copick_web && touch src/copick_web/__init__.py && \
+    pip install --no-cache-dir -e ".[dev]"
+
+CMD ["sh", "-c", "pip install -e '.[dev]' && uvicorn copick_web.app.main:app --reload --host 0.0.0.0 --port 8000"]

copick_web-0.1.5/PKG-INFO

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+Metadata-Version: 2.5
+Name: copick-web
+Version: 0.1.5
+Summary: Web visualization for copick datasets
+Requires-Python: >=3.11
+Requires-Dist: click>=8.1.8
+Requires-Dist: copick>=0.8.0
+Requires-Dist: fastapi>=0.109.0
+Requires-Dist: httpx>=0.27.0
+Requires-Dist: pydantic-settings>=2.0.0
+Requires-Dist: pydantic>=2.5.0
+Requires-Dist: python-dotenv>=1.0.0
+Requires-Dist: sshfs>=2024.0.0
+Requires-Dist: uvicorn>=0.25.0
+Provides-Extra: dev
+Requires-Dist: black>=25.1.0; extra == 'dev'
+Requires-Dist: pre-commit>=4.0.0; extra == 'dev'
+Requires-Dist: pytest>=8.0.0; extra == 'dev'
+Requires-Dist: ruff>=0.12.0; extra == 'dev'

copick_web-0.1.5/pyproject.toml

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+[build-system]
+requires = ["hatchling"]
+build-backend = "hatchling.build"
+
+[project]
+name = "copick-web"
+version = "0.1.5"
+description = "Web visualization for copick datasets"
+requires-python = ">=3.11"
+dependencies = [
+    "fastapi>=0.109.0",
+    "uvicorn>=0.25.0",
+    "pydantic>=2.5.0",
+    "pydantic-settings>=2.0.0",
+    "copick>=0.8.0",
+    "python-dotenv>=1.0.0",
+    "click>=8.1.8",
+    "httpx>=0.27.0",
+    "sshfs>=2024.0.0",
+]
+
+[project.optional-dependencies]
+dev = [
+    "black>=25.1.0",
+    "ruff>=0.12.0",
+    "pytest>=8.0.0",
+    "pre-commit>=4.0.0",
+]
+
+[project.scripts]
+copick-web = "copick_web.cli:main"
+
+[tool.hatch.build]
+# The client build is gitignored; ship it anyway when present (`npm run build:server` in client/).
+artifacts = ["src/copick_web/static"]
+
+[tool.hatch.build.targets.wheel]
+packages = ["src/copick_web"]
+
+[tool.black]
+line-length = 120
+target-version = ['py311']
+
+[tool.ruff]
+line-length = 120
+target-version = "py311"
+
+[tool.ruff.lint]
+select = ["E", "W", "F", "I", "B", "C4"]
+ignore = ["E501"]
+
+[tool.ruff.lint.flake8-bugbear]
+# FastAPI's dependency-injection idiom is a call in the argument default.
+# B008 flags every route signature otherwise.
+extend-immutable-calls = [
+    "fastapi.Depends",
+    "fastapi.Query",
+    "fastapi.Path",
+    "fastapi.Body",
+    "fastapi.Header",
+    "fastapi.Form",
+]

copick_web-0.1.5/src/copick_web/__init__.py

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+"""Copick Web - Web visualization for copick datasets."""
+
+__version__ = "0.1.5"

copick_web-0.1.5/src/copick_web/app/__init__.py

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+# copick-web server app

copick_web-0.1.5/src/copick_web/app/config.py

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+"""Server configuration using pydantic-settings."""
+
+from pydantic_settings import BaseSettings
+
+
+class Settings(BaseSettings):
+    """Application settings loaded from environment variables."""
+
+    copick_config_paths: list[str] = []
+    registry_url: str | None = None
+    registry_refresh_seconds: int = 60
+    service_cache_size: int = 8
+    # Hard ceiling on a single zarr-chunk read. If exceeded, the request
+    # returns 504 and the underlying CopickService is evicted so the next
+    # request rebuilds with a fresh SSH connection.
+    zarr_read_timeout_seconds: float = 60.0
+    # Max concurrent zarr chunk reads per project. Bounds peak memory
+    # (≈ value × max_chunk_size) and avoids saturating a single asyncssh
+    # SFTP channel — past ~16 in flight, parallel reads stop helping.
+    zarr_concurrency_per_project: int = 8
+    slurm_user: str | None = None
+    slurm_keyfile: str | None = None
+    slurm_ssh_port: int = 22
+    # cluster_id -> SSH hostname/IP. Defaults mirror the umbrella seed
+    # (umbrella/stores/migrations/0010_seed_clusters.py). Override via env:
+    #   CLUSTER_HOSTS='{"bruno":"…","czii":"…"}'
+    cluster_hosts: dict[str, str] = {
+        "bruno": "192.168.98.229",
+        "czii": "10.50.120.90",
+    }
+    cors_origins: list[str] = [
+        "http://localhost:5173",
+        "http://127.0.0.1:5173",
+        "http://localhost:8000",
+        "http://127.0.0.1:8000",
+    ]
+    host: str = "0.0.0.0"
+    port: int = 8000
+    base_path: str = ""
+    # In-memory caches of derived data (env: THUMBNAIL_CACHE_MB, MEASUREMENT_CACHE_MB, CACHE_MAX_AGE_SECONDS,
+    # CACHE_SWEEP_SECONDS). Entries older than the max age are dropped by a sweep every CACHE_SWEEP_SECONDS.
+    thumbnail_cache_mb: int = 64
+    measurement_cache_mb: int = 512
+    cache_max_age_seconds: int = 3600
+    cache_sweep_seconds: int = 300
+
+    class Config:
+        env_file = ".env"
+        env_file_encoding = "utf-8"
+
+
+settings = Settings()

copick_web-0.1.5/src/copick_web/app/dependencies.py

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+"""FastAPI dependency injection for project-scoped routes."""
+
+from fastapi import HTTPException, Path
+
+from .models import ProjectSummaryResponse
+from .services.copick_service import CopickService
+from .services.project_registry import ProjectRegistry, get_project_registry
+from .services.registry_client import RegistryError
+
+
+def get_registry() -> ProjectRegistry:
+    """Dependency: the application's ``ProjectRegistry``."""
+    return get_project_registry()
+
+
+def get_copick_service(project_id: str = Path(...)) -> CopickService:
+    """Dependency: resolve the ``CopickService`` for the path's ``project_id``."""
+    registry = get_project_registry()
+    try:
+        return registry.get_service(project_id)
+    except KeyError:
+        raise HTTPException(status_code=404, detail=f"Project '{project_id}' not found") from None
+    except RegistryError as e:
+        raise HTTPException(status_code=502, detail=str(e)) from e
+
+
+def get_project_meta(project_id: str = Path(...)) -> ProjectSummaryResponse:
+    """Dependency: resolve the ``ProjectSummaryResponse`` for the path's ``project_id``.
+
+    Used by routes that need to branch on ``source`` (local vs. registry) — e.g.
+    zarr URL construction, where registry projects skip the server-side proxy
+    and point the browser at ``data_url`` directly.
+    """
+    registry = get_project_registry()
+    try:
+        return registry.get_metadata(project_id)
+    except KeyError:
+        raise HTTPException(status_code=404, detail=f"Project '{project_id}' not found") from None

copick_web-0.1.5/src/copick_web/app/main.py

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+"""FastAPI application entry point."""
+
+import asyncio
+import logging
+from contextlib import asynccontextmanager
+from pathlib import Path
+
+from fastapi import FastAPI, HTTPException, Request
+from fastapi.middleware.cors import CORSMiddleware
+from fastapi.responses import FileResponse, RedirectResponse
+from fastapi.staticfiles import StaticFiles
+
+from .config import settings
+from .routes import config, filaments, projects, runs, zarr_proxy
+from .services.project_registry import ProjectRegistry, set_project_registry
+from .services.registry_client import RegistryClient
+
+logging.basicConfig(level=logging.DEBUG)
+logger = logging.getLogger(__name__)
+
+
+async def _refresh_loop(registry: ProjectRegistry, interval: int):
+    """Background loop that refreshes the registry list at a fixed cadence."""
+    while True:
+        try:
+            await asyncio.sleep(interval)
+            await registry.refresh_registry()
+        except asyncio.CancelledError:
+            raise
+        except Exception as e:
+            logger.exception("Registry refresh loop error: %s", e)
+
+
+@asynccontextmanager
+async def lifespan(app: FastAPI):
+    """Application lifespan handler."""
+    # Build registry
+    if not settings.copick_config_paths and not settings.registry_url:
+        raise RuntimeError(
+            "No project source configured. Provide local config paths via the CLI / "
+            "COPICK_CONFIG_PATHS, or set REGISTRY_URL."
+        )
+
+    client = RegistryClient(settings.registry_url) if settings.registry_url else None
+    registry = ProjectRegistry(registry_client=client, service_cache_size=settings.service_cache_size)
+
+    for path in settings.copick_config_paths:
+        try:
+            pid = registry.register_local(path)
+            logger.info(
+                "Registered local project '%s' (%s) from %s",
+                pid,
+                registry.get_metadata(pid).name or "unnamed",
+                path,
+            )
+        except FileNotFoundError as e:
+            logger.error("Local config not found, skipping: %s (%s)", path, e)
+
+    if client is not None:
+        try:
+            await registry.refresh_registry()
+        except Exception as e:
+            logger.warning("Initial registry refresh failed; continuing without registry projects: %s", e)
+
+    set_project_registry(registry)
+
+    tasks = [asyncio.create_task(_sweep_caches(registry, settings.cache_sweep_seconds))]
+    if client is not None:
+        tasks.append(asyncio.create_task(_refresh_loop(registry, settings.registry_refresh_seconds)))
+
+    logger.info("copick-web ready: %d project(s) listed.", len(registry.list_projects()))
+
+    try:
+        yield
+    finally:
+        for task in tasks:
+            task.cancel()
+            try:
+                await task
+            except asyncio.CancelledError:
+                pass
+        logger.info("Shutting down copick-web server")
+
+
+async def _sweep_caches(registry: ProjectRegistry, every: float) -> None:
+    """Drop expired cache entries of every open project regularly, so memory is released even when nothing is
+    requested."""
+    while True:
+        await asyncio.sleep(max(every, 1))
+        try:
+            dropped = registry.sweep_caches()
+            if dropped:
+                logger.info(f"Dropped {dropped} expired cache entries")
+        except Exception as e:  # never let the sweeper die
+            logger.warning(f"Cache sweep failed: {e}")
+
+
+app = FastAPI(
+    title="Copick Web Server",
+    description="API server for copick web visualization",
+    version="0.1.0",
+    lifespan=lifespan,
+    # A prefix the proxy forwards (e.g. /node/<host>/<port>); requests with or without it are routed alike.
+    root_path=settings.base_path.rstrip("/"),
+)
+
+
+@app.middleware("http")
+async def redirect_root_relatively(request: Request, call_next):
+    """Add the trailing slash to the app root under a forwarded prefix (``/node/<host>/<port>``) with a relative
+    redirect: Starlette's own is absolute and names the Host it was sent, which may be the backend behind the proxy."""
+    root = request.scope.get("root_path", "")
+    if root and request.url.path == root:
+        query = f"?{request.url.query}" if request.url.query else ""
+        return RedirectResponse(f"{root.rsplit('/', 1)[-1]}/{query}", status_code=307)
+    return await call_next(request)
+
+
+# Configure CORS
+app.add_middleware(
+    CORSMiddleware,
+    allow_origins=settings.cors_origins,
+    allow_credentials=True,
+    allow_methods=["*"],
+    allow_headers=["*"],
+)
+
+app.include_router(projects.router)
+app.include_router(config.router)
+app.include_router(runs.router)
+app.include_router(filaments.router)
+app.include_router(zarr_proxy.router)
+
+
+@app.get("/health")
+async def health_check():
+    """Liveness check. Async so a saturated threadpool can't make the server look dead."""
+    return {"status": "healthy"}
+
+
+# Serve the built SPA. Order matters: SPA catch-all must come BEFORE the
+# StaticFiles mount at "/" so it can intercept deep-link refreshes
+# (e.g. /projects/abc) and return index.html instead of 404.
+static_dir = Path(__file__).parent.parent / "static"
+
+
+def _has_static_files() -> bool:
+    if not static_dir.exists():
+        return False
+    return any(f.name != ".gitkeep" for f in static_dir.iterdir())
+
+
+if _has_static_files():
+    index_file = static_dir / "index.html"
+
+    @app.get("/projects/{full_path:path}", include_in_schema=False)
+    def spa_projects(full_path: str, request: Request):
+        """Serve the SPA index.html for client-side routes under /projects."""
+        if not index_file.exists():
+            raise HTTPException(status_code=404, detail="SPA index.html missing")
+        return FileResponse(index_file)
+
+    logger.info(f"Serving static files from: {static_dir}")
+    app.mount("/", StaticFiles(directory=static_dir, html=True), name="static")
+elif static_dir.exists():
+    logger.warning(
+        f"Static directory exists but is empty: {static_dir}. "
+        "Run 'npm run build:server' in the client directory to build the client."
+    )
+
+
+if __name__ == "__main__":
+    import uvicorn
+
+    uvicorn.run(
+        "copick_web.app.main:app",
+        host=settings.host,
+        port=settings.port,
+        reload=True,
+    )