Add support for anndata backed mode (#943)

* initial cut at backed mode

* make flask multithreading conditional on debug flag

* update X access to support backed mode

* lint

* improve help message for backed mode

* fix tests

* add MatrixProxy to normalize supported matrix types

* add FAQ entry for --backed

* remove use of matrix.T

* clean up

* add ability to disable diffexp from CLI; add hueristic to detect likely slow diffexp calculation, and warn user

* fix tests

* do not print diffexp speed warning if diffexp is disabled

* tweak wording of diffexp speed messages

* add FAQ entry on --disable-diffexp

* revise heuristic for warning about slow diffexp

* use quick tooltip delay on diffexp button

client/src/components/menubar/index.js

@@ -16,7 +16,10 @@ import CellSetButton from "./cellSetButtons";
 import InformationMenu from "./infoMenu";
 import UndoRedoReset from "./undoRedoReset";
 import Clip from "./clip";
-import { tooltipHoverOpenDelay } from "../../globals";
+import {
+  tooltipHoverOpenDelay,
+  tooltipHoverOpenDelayQuick
+} from "../../globals";
 
 @connect(state => ({
   universe: state.universe,
@@ -39,7 +42,9 @@ import { tooltipHoverOpenDelay } from "../../globals";
   libraryVersions: state.config?.library_versions, // eslint-disable-line camelcase
   undoDisabled: state["@@undoable/past"].length === 0,
   redoDisabled: state["@@undoable/future"].length === 0,
-  aboutLink: state.config?.links?.["about-dataset"]
+  aboutLink: state.config?.links?.["about-dataset"],
+  disableDiffexp: state.config?.parameters?.["disable-diffexp"] ?? false,
+  diffexpMayBeSlow: state.config?.parameters?.["diffexp-may-be-slow"] ?? false
 }))
 class MenuBar extends React.Component {
   static isValidDigitKeyEvent(e) {
@@ -255,6 +260,65 @@ class MenuBar extends React.Component {
     });
   };
 
+  renderDiffExp() {
+    /* diffexp-related buttons may be disabled */
+    const { disableDiffexp, differential, diffexpMayBeSlow } = this.props;
+    if (disableDiffexp) return null;
+
+    const haveBothCellSets =
+      !!differential.celllist1 && !!differential.celllist2;
+
+    const tipMessage =
+      "See top 10 differentially expressed genes" +
+      (diffexpMayBeSlow
+        ? " (CAUTION: large dataset - may take longer or fail)"
+        : "");
+
+    return (
+      <div className="bp3-button-group" style={{ marginRight: 10 }}>
+        <CellSetButton {...this.props} eitherCellSetOneOrTwo={1} />
+        <CellSetButton {...this.props} eitherCellSetOneOrTwo={2} />
+        {!differential.diffExp ? (
+          <Tooltip
+            content={tipMessage}
+            position="bottom"
+            hoverOpenDelay={tooltipHoverOpenDelayQuick}
+          >
+            <AnchorButton
+              disabled={!haveBothCellSets}
+              intent="primary"
+              data-testid="diffexp-button"
+              loading={differential.loading}
+              icon="left-join"
+              fill
+              type="button"
+              onClick={this.computeDiffExp}
+            >
+              Compute Differential Expression
+            </AnchorButton>
+          </Tooltip>
+        ) : null}
+
+        {differential.diffExp ? (
+          <Tooltip
+            content="Remove differentially expressed gene list and clear cell selections"
+            position="bottom"
+            hoverOpenDelay={tooltipHoverOpenDelayQuick}
+          >
+            <Button
+              type="button"
+              fill
+              intent="warning"
+              onClick={this.clearDifferentialExpression}
+            >
+              Clear Differential Expression
+            </Button>
+          </Tooltip>
+        ) : null}
+      </div>
+    );
+  }
+
   render() {
     const {
       dispatch,
@@ -273,9 +337,6 @@ class MenuBar extends React.Component {
     } = this.props;
     const { pendingClipPercentiles } = this.state;
 
-    const haveBothCellSets =
-      !!differential.celllist1 && !!differential.celllist2;
-
     // constants used to create selection tool button
     let selectionTooltip;
     let selectionButtonClass;
@@ -295,47 +356,7 @@ class MenuBar extends React.Component {
           top: 8
         }}
       >
-        <div className="bp3-button-group" style={{ marginRight: 10 }}>
-          <CellSetButton {...this.props} eitherCellSetOneOrTwo={1} />
-          <CellSetButton {...this.props} eitherCellSetOneOrTwo={2} />
-          {!differential.diffExp ? (
-            <Tooltip
-              content="Add two cells selections, see the top 15 differentially expressed genes between them"
-              position="bottom"
-              hoverOpenDelay={tooltipHoverOpenDelay}
-            >
-              <AnchorButton
-                disabled={!haveBothCellSets}
-                intent="primary"
-                data-testid="diffexp-button"
-                loading={differential.loading}
-                icon="left-join"
-                fill
-                type="button"
-                onClick={this.computeDiffExp}
-              >
-                Compute Differential Expression
-              </AnchorButton>
-            </Tooltip>
-          ) : null}
-
-          {differential.diffExp ? (
-            <Tooltip
-              content="Remove differentially expressed gene list and clear cell selections"
-              position="bottom"
-              hoverOpenDelay={tooltipHoverOpenDelay}
-            >
-              <Button
-                type="button"
-                fill
-                intent="warning"
-                onClick={this.clearDifferentialExpression}
-              >
-                Clear Differential Expression
-              </Button>
-            </Tooltip>
-          ) : null}
-        </div>
+        {this.renderDiffExp()}
         <Tooltip
           content="Show only metadata and cells which are currently selected"
           position="bottom"