Limit dependencies (#444)

* Limit dependencies

* Move imports

* Space

Author: keller-mark

pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "hatchling.build"
 
 [project]
 name = "vitessce"
-version = "3.6.1"
+version = "3.6.2"
 authors = [
   { name="Mark Keller", email="mark_keller@hms.harvard.edu" },
 ]
@@ -26,20 +26,11 @@ classifiers = [
 ]
 dependencies = [
   'scipy>=1.2.1',
-  'negspy>=0.2.24',
   'pandas>=1.1.2',
   'black>=21.11b1',
   'numpy>=1.21.2',
   'zarr>=2.5.0,<3',
   'numcodecs>=0.5.7,<0.16.0',
-  'anndata>=0.7.8',
-  # scanpy < 1.10.3 does not support numpy >= 2.0.0 and does not
-  # Reference: https://github.com/scverse/scanpy/pull/3115/files
-  'scanpy>=1.10.2',
-  'ome-zarr<0.10.3',
-  'tifffile>=2020.10.1',
-  'jsonschema>=3.2',
-  'tqdm>=4.1.0',
 ]
 
 [project.optional-dependencies]
@@ -68,6 +59,15 @@ docs = [
   'jinja2',
 ]
 all = [
+  # For data_utils
+  'negspy>=0.2.24',
+  'anndata>=0.7.8',
+  # scanpy < 1.10.3 does not support numpy >= 2.0.0 and does not
+  # Reference: https://github.com/scverse/scanpy/pull/3115/files
+  'scanpy>=1.10.2',
+  'ome-zarr<0.10.3',
+  'tifffile>=2020.10.1',
+
   'jupyter-server-proxy>=1.5.2',
   'oxc-py>=0.1.1',
   'anywidget>=0.9.10',
@@ -92,6 +92,7 @@ notebook = [
   'dask[dataframe]==2024.11.1',
   'marimo',
   'starlette>=0.42.0',
+  'tqdm>=4.1.0',
 ]
 demos = [
   "pulp==2.7.0",

src/vitessce/__init__.py

@@ -27,11 +27,6 @@
     BASE_URL_PLACEHOLDER,
 )
 
-from .config_converter import (
-    CellBrowserToAnndataZarrConverter,  # only exported for testing.
-    convert_cell_browser_project_to_anndata,
-)
-
 from .wrappers import AbstractWrapper
 
 # We allow installation without all of the dependencies that the widget requires.

src/vitessce/widget.py

@@ -2,21 +2,11 @@
 from urllib.parse import quote_plus
 import json
 import sys
-
-# Widget dependencies
-import anywidget
-from traitlets import Unicode, Dict, List, Int, Bool
 import time
 import uuid
+import anywidget
+from traitlets import Unicode, Dict, List, Int, Bool
 
-# Server dependencies
-from uvicorn import Config, Server
-
-from starlette.applications import Starlette
-from starlette.middleware import Middleware
-from starlette.middleware.cors import CORSMiddleware
-from threading import Thread
-import socket
 
 MAX_PORT_TRIES = 1000
 DEFAULT_PORT = 8000
@@ -25,6 +15,10 @@
 class BackgroundServer:
     # Reference: https://github.com/gosling-lang/gos/blob/main/gosling/data/_background_server.py#L10
     def __init__(self, routes):
+        from starlette.applications import Starlette
+        from starlette.middleware import Middleware
+        from starlette.middleware.cors import CORSMiddleware
+
         middleware = [
             Middleware(CORSMiddleware, allow_origins=[
                        '*'], allow_methods=["OPTIONS", "GET"], allow_headers=['Range'])
@@ -47,6 +41,9 @@ def stop(self):
         return self
 
     def start(self, port=None, timeout=1, daemon=True, log_level="warning"):
+        from uvicorn import Config, Server
+        from threading import Thread
+
         if self.thread is not None:
             return self
 
@@ -87,6 +84,7 @@ def register(self, config):
 
 
 def is_port_in_use(port):
+    import socket
     with socket.socket(socket.AF_INET, socket.SOCK_STREAM) as s:
         return s.connect_ex(('localhost', port)) == 0
 

tests/test_config_converter.py

@@ -2,7 +2,7 @@
 from unittest.mock import patch, Mock
 from copy import deepcopy
 
-from vitessce import (
+from vitessce.config_converter import (
     CellBrowserToAnndataZarrConverter,
     convert_cell_browser_project_to_anndata,
 )