Merge branch 'dev' into chat_update

.devcontainer/devcontainer.json

@@ -12,7 +12,11 @@
                 "ms-toolsai.jupyter",
                 "github.vscode-github-actions",
                 "eamodio.gitlens"
-            ]
+            ],
+            "settings": {
+                "python.analysis.typeCheckingMode": "basic",
+                "python.defaultInterpreterPath": "/usr/local/bin/python"
+            }
         }
     },
     "postStartCommand": "git config --global --add safe.directory /app"

python/mdvtools/charts/view.py

@@ -0,0 +1,25 @@
+import sys
+
+# You may also pick one without version check, of course
+if sys.version_info < (3, 11):
+    from typing_extensions import TypedDict, Required
+else:
+    from typing import TypedDict, Required
+
+from typing import Literal, Any
+# from .chart_dicts import BaseChart
+
+
+class Panel(TypedDict, total=False):
+    """This describes a panel in a view."""
+
+    layout: Literal["gridstack", "absolute"]
+    panelWidth: int | float
+
+
+class View(TypedDict, total=False):
+    """This metadata of a view to be added to a project views.json file."""
+
+    initialCharts: Required[dict[str, list[Any]]]  # todo
+    dataSources: dict[str, Panel]
+    links: dict[str, list[Any]]  # todo

python/mdvtools/conversions.py

@@ -72,7 +72,8 @@ def convert_scanpy_to_mdv(
     current_views = None
     if not delete_existing:
         current_views = mdv.views
-
+    else:
+        current_views = {}
     # create datasource 'cells'
     cell_table = scanpy_object.obs
     cell_table["cell_id"] = cell_table.index

python/mdvtools/server.py

@@ -561,7 +561,7 @@ def combine_anndata():
             # Process and combine the file
             new_anndata = sc.read(temp_path)
             convert_scanpy_to_mdv(project.dir, new_anndata, delete_existing=False, label=f"{label}_")
-            new_anndata.write(os.path.join(project.dir, "anndata.h5ad"))
+            new_anndata.write(os.path.join(project.dir, "anndata.h5ad")) # type: ignore - str output from os.path.join should be reliably PathLike
             cleanup_folder(temp_folder)
 
             return jsonify({'status': 'success', 'message': 'File merged successfully'}), 200

src/charts/BaseChart.ts

@@ -223,6 +223,14 @@ class BaseChart<T> {
 
         //work out width and height based on container
         this._setDimensions();
+        setTimeout(() => {
+            try {
+                //some charts weren't properly initialising the color legend, so doing it here may help that to be more consistent.
+                //there is an implementation of the method here in BaseChart, but we wrap in a try/catch as it assumes other associated methods are also implemented.
+                //Calling this in a timeout helps ensure that the chart is fully constructed before we try to do this.
+                this.setColorLegend();
+            } catch (e) { }
+        });
         // provide some observable mobx state for useOuterContainer()
         this.observable = makeAutoObservable({
             container: this.__doc__.body,

src/charts/charts.d.ts

@@ -89,10 +89,10 @@ export type DataColumn<T extends DataType> = {
     sgtype?: "dense" | "sparse"; //?? any other options?
 };
 export type LoadedDataColumn<T extends DataType> = DataColumn<T> & Required<Pick<DataColumn<T>, "data">>;
-function test(column: LoadedDataColumn<"text">) {
-    column.data;
-    column.values; //why does this degrade to 'any'?
-}
+// function test(column: LoadedDataColumn<"text">) {
+//     column.data;
+//     column.values; //why does this degrade to 'any'?
+// }
 // export type DataStore = {
 //     size: number;
 //     filterSize: number;

src/charts/dialogs/ColumnPreview.tsx

@@ -53,8 +53,8 @@ export const ColumnPreview: React.FC<ColumnPreviewProps> = ({
                     </thead>
                     <tbody className="bg-white dark:bg-gray-900 divide-y divide-gray-200 dark:divide-gray-700">
                         {filteredColumns.length > 0 ? (
-                            filteredColumns.map((column, index) => (
-                                <tr key={index}>
+                            filteredColumns.map((column) => (
+                                <tr key={column.name}>
                                     <td className="px-6 py-4 whitespace-nowrap text-sm font-medium text-gray-900 dark:text-gray-100 select-text">
                                         {column.name}
                                     </td>

src/charts/dialogs/TiffMetadataTable.tsx

@@ -93,6 +93,7 @@ export const TiffMetadataTable: React.FC<TiffMetadataTableProps> = ({ metadata }
           <tbody className="bg-white dark:bg-gray-900 divide-y divide-gray-200 dark:divide-gray-700">
             {filteredMetadata.length > 0 ? (
               filteredMetadata.map((item, index) => (
+                // biome-ignore lint/suspicious/noArrayIndexKey: not sure if there's an appropriate key to use here - may need to add one.
                 <tr key={index}>
                   <td className="px-6 py-4 whitespace-nowrap text-sm font-medium text-gray-900 dark:text-gray-100 select-text w-1/4">
                     {item.element || 'N/A'}

src/charts/dialogs/utils/h5Processing.ts

@@ -692,5 +692,6 @@ const processH5File = async (
     }
 };
 
-export { NonAnnDataError, CompressionError, H5Metadata, MatrixValue, DatasetValue, ProcessOptions, H5DataType, TypedArray };
+export { NonAnnDataError, CompressionError };
+export type { H5Metadata, MatrixValue, DatasetValue, ProcessOptions, H5DataType, TypedArray };
 export default processH5File;

src/react/components/DebugJsonDialogComponent.tsx

@@ -84,6 +84,7 @@ export default function ({ json, header }: { json: any; header?: string }) {
                     fontSize: '0.875rem',
                     fontFamily: 'ui-monospace, SFMono-Regular, Menlo, Monaco, Consolas, monospace'
                 }}
+                collapsed={1}
             />
         </div>
     );

src/react/hooks.ts

@@ -249,7 +249,8 @@ export function useFilteredIndices() {
                     return;
                 }
             }
-            setFilteredIndices(indices as Uint32Array<ArrayBuffer>);
+            //@ts-ignore ! there seems to be a discrepancy here after ts upgrade???
+            setFilteredIndices(indices);
         });
         // should I have a cleanup function to cancel the promise if it's not resolved
         // by the time the effect is triggered again?

src/react/screen_state.tsx

@@ -2,7 +2,7 @@ import type BaseChart from "@/charts/BaseChart";
 import type { BaseDialog } from "@/utilities/Dialog";
 import { observer } from "mobx-react-lite";
 import { createContext, useContext, useEffect, useState } from "react";
-import { type createMdvPortal } from './react_utils';
+import type { createMdvPortal } from './react_utils';
 /** All charts and dialogs have this as an `observable` property that can be passed to
  * {@link createMdvPortal} to allow access to the container they should render things like
  * which allows Mobx Observer components to {@link useOuterContainer} for access to the container they should render things like