Merge branch 'main' of github.com:vitessce/vitessce-python into keller-mark/kpmp

Author: keller-mark

.github/workflows/test_widget.yml

@@ -32,6 +32,8 @@ jobs:
         run: uv run jupyter nbconvert --to=html --execute docs/notebooks/widget_from_dict.ipynb
       - name: Export Marimo notebook to HTML
         run: uv run marimo export html docs/notebooks/marimo.py -o docs/notebooks/marimo.html
+      - name: Export Marimo notebook to HTML-WASM
+        run: uv run marimo export html-wasm docs/notebooks/marimo-wasm.py -o docs/notebooks/marimo-wasm.html --mode edit
       - name: Check that widget renders in HTML output using Playwright
         run: pnpm exec playwright test
         working-directory: ./tests-widget

.gitignore

@@ -11,6 +11,7 @@ tests/data/*
 !tests/data/test.ome.tif
 ./notebooks/
 docs/notebooks/data/
+docs/notebooks/*.html
 __pycache__/
 .snakemake/
 .coverage

docs/notebooks/marimo-wasm.py

@@ -0,0 +1,92 @@
+import marimo
+
+__generated_with = "0.13.15"
+app = marimo.App()
+
+
+@app.cell
+def _():
+    import marimo as mo
+    return (mo,)
+
+
+@app.cell
+def _():
+    import anywidget
+    from vitessce import (
+        VitessceConfig,
+        ViewType as vt,
+        CoordinationType as ct,
+        ImageOmeTiffWrapper,
+        ImageOmeZarrWrapper,
+        AnnDataWrapper,
+        SpatialDataWrapper,
+        CoordinationLevel as CL,
+        get_initial_coordination_scope_prefix,
+        hconcat,
+        vconcat,
+    )
+    return VitessceConfig, ImageOmeTiffWrapper, get_initial_coordination_scope_prefix
+
+
+@app.cell
+def _(VitessceConfig, ImageOmeTiffWrapper, get_initial_coordination_scope_prefix):
+    vc = VitessceConfig(
+        schema_version="1.0.17",
+        name='My configuration',
+        description='Data from https://portal.hubmapconsortium.org/browse/collection/6a6efd0c1a2681dc7d2faab8e4ab0bca'
+    )
+    dataset = vc.add_dataset(name='My dataset').add_object(
+        ImageOmeTiffWrapper(
+            img_url="https://assets.hubmapconsortium.org/f4188a148e4c759092d19369d310883b/ometiff-pyramids/processedMicroscopy/VAN0006-LK-2-85-PAS_images/VAN0006-LK-2-85-PAS_registered.ome.tif"
+        )
+    )
+
+    spatial = vc.add_view("spatialBeta", dataset=dataset)
+    lc = vc.add_view("layerControllerBeta", dataset=dataset)
+
+    vc.link_views_by_dict([spatial, lc], {
+        "photometricInterpretation": "RGB"
+    }, meta=True, scope_prefix=get_initial_coordination_scope_prefix("A", "image"))
+
+    vc.layout(spatial | lc);
+    return (vc,)
+
+
+@app.cell
+def _(mo, vc):
+    vw = mo.ui.anywidget(vc.widget())
+    vw
+    return (vw,)
+
+
+@app.cell(hide_code=True)
+def _(mo):
+    mo.md(r"""As you interact with the widget above, watch as the Vitessce configuration below dynamically updates. For instance, as you zoom in the spatial view, check the value of `coordinationSpace.spatialZoom`""")
+    return
+
+
+@app.cell
+def _(vw):
+    vw.config
+    return
+
+
+@app.cell
+def _(vw):
+    vw.config["coordinationSpace"]["spatialZoom"]
+    return
+
+@app.cell
+def _(vc):
+    import json
+    print(json.dumps(vc.to_dict(), indent=2))
+    return
+
+@app.cell
+def _():
+    return
+
+
+if __name__ == "__main__":
+    app.run()

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="[email protected]" },
 ]
@@ -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
 
@@ -602,7 +600,7 @@ class VitessceWidget(anywidget.AnyWidget):
 
     next_port = DEFAULT_PORT
 
-    js_package_version = Unicode('3.6.2').tag(sync=True)
+    js_package_version = Unicode('3.6.3').tag(sync=True)
     js_dev_mode = Bool(False).tag(sync=True)
     custom_js_url = Unicode('').tag(sync=True)
     plugin_esm = List(trait=Unicode(''), default_value=[]).tag(sync=True)
@@ -614,7 +612,7 @@ class VitessceWidget(anywidget.AnyWidget):
 
     store_urls = List(trait=Unicode(''), default_value=[]).tag(sync=True)
 
-    def __init__(self, config, height=600, theme='auto', uid=None, port=None, proxy=False, js_package_version='3.6.2', js_dev_mode=False, custom_js_url='', plugins=None, remount_on_uid_change=True, prefer_local=True, invoke_timeout=300000, invoke_batched=True, page_mode=False, page_esm=None):
+    def __init__(self, config, height=600, theme='auto', uid=None, port=None, proxy=False, js_package_version='3.6.3', js_dev_mode=False, custom_js_url='', plugins=None, remount_on_uid_change=True, prefer_local=True, invoke_timeout=300000, invoke_batched=True, page_mode=False, page_esm=None):
         """
         Construct a new Vitessce widget.
 
@@ -749,7 +747,7 @@ def _plugin_command(self, params, buffers):
 # Launch Vitessce using plain HTML representation (no ipywidgets)
 
 
-def ipython_display(config, height=600, theme='auto', base_url=None, host_name=None, uid=None, port=None, proxy=False, js_package_version='3.6.2', js_dev_mode=False, custom_js_url='', plugins=None, remount_on_uid_change=True, page_mode=False, page_esm=None):
+def ipython_display(config, height=600, theme='auto', base_url=None, host_name=None, uid=None, port=None, proxy=False, js_package_version='3.6.3', js_dev_mode=False, custom_js_url='', plugins=None, remount_on_uid_change=True, page_mode=False, page_esm=None):
     from IPython.display import display, HTML
     uid_str = "vitessce" + get_uid_str(uid)
 

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,
 )