flakey test

.github/workflows/compatibility_tests.yml

@@ -7,6 +7,10 @@ on:
     branches:
       - main
 
+  # For debug - uncomment below to run on all PRs
+  pull_request:
+    branches: "*"
+
 env:
   JEST_ENV: prod
 
@@ -28,13 +32,14 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
+        # note: The `macos-latest` is latest Catalina version, and not Big Sur. So we explicitly ask for Big Sur (`macos-11`)
         os: [ubuntu-latest, macos-latest, macos-13]
-        python-version: ["3.10", "3.11", "3.12"]
+        python-version: ["3.10", "3.11"]
         cellxgene_build: [main, latest]
         # add anndata pinned version test for subset of matrix configurations,
         # in order to reduce matrix cross-product explosion
         include:
-          - python-version: 3.12
+          - python-version: 3.11
             cellxgene_build: latest
             # TODO: dynamically use the literal version in requirements.txt,
             # to avoid having to update this in manually in the future
@@ -95,7 +100,7 @@ jobs:
           # keep same pip pkg versions as in the cxg release
           sed -i'' -e 's/-r requirements.txt//' server/requirements-dev.txt
           pip install -r server/requirements-dev.txt
-          pip install --force-reinstall numpy==2.0.1 numba>=0.60.0 pandas flatbuffers==2.0.7
+          pip install --force-reinstall numpy==2.0.1 numba>=0.60.0 pandas
       - name: Install anndata version per matrix variable
         run: pip install anndata${{ matrix.anndata_version }}
       - name: Install node

README.md

@@ -1,4 +1,4 @@
-<img src="./docs/cellxgene-logo.png" width="300">
+![](https://github.com/chanzuckerberg/cellxgene/raw/main/docs/cellxgene-logo.png)
 
 _an interactive explorer for single-cell transcriptomics data_
 
@@ -11,7 +11,8 @@ CZ CELLxGENE Annotate (pronounced "cell-by-gene") is an interactive data explore
 
 Whether you need to visualize one thousand cells or one million, CELLxGENE Annotate helps you gain insight into your single-cell data.
 
-<img src="https://github.com/chanzuckerberg/cellxgene/raw/main/docs/images/crossfilter.gif" width="350" height="200" hspace="30"><img src="https://github.com/chanzuckerberg/cellxgene/raw/main/docs/images/category-breakdown.gif" width="350" height="200" hspace="30">
+![](https://github.com/chanzuckerberg/cellxgene/raw/main/docs/images/crossfilter.gif)
+![](https://github.com/chanzuckerberg/cellxgene/raw/main/docs/images/category-breakdown.gif)
 
 # Getting started
 

client/__tests__/util/promiseLimit.test.js

@@ -76,7 +76,7 @@ describe("PromiseLimit", () => {
     const plimit = new PromiseLimit(1);
 
     let finishOrder = 0;
-    const callback = () => async () => {
+    const callback = async () => {
       await delay(100);
       const result = finishOrder;
       finishOrder += 1;
@@ -84,11 +84,11 @@ describe("PromiseLimit", () => {
     };
 
     const result = await Promise.all([
-      plimit.add(callback()),
-      plimit.priorityAdd(4, callback()),
-      plimit.priorityAdd(0, callback()),
-      plimit.priorityAdd(1, callback()),
-      plimit.priorityAdd(-1, callback()),
+      plimit.add(callback),
+      plimit.priorityAdd(4, callback),
+      plimit.priorityAdd(0, callback),
+      plimit.priorityAdd(1, callback),
+      plimit.priorityAdd(-1, callback),
     ]);
 
     expect(result).toEqual([0, 4, 2, 3, 1]);

client/package.json

@@ -10,8 +10,8 @@
     "dev": "npm run build -- configuration/webpack/webpack.config.dev.js",
     "e2e": "jest --config __tests__/e2e/e2eJestConfig.json e2e/e2e.test.js",
     "e2e-annotations": "jest --config __tests__/e2e/e2eJestConfig.json e2e/e2eAnnotations.test.js",
-    "fmt": "eslint --fix src __tests__",
-    "lint": "eslint --fix src __tests__",
+    "fmt": "eslint --fix __tests__",
+    "lint": "eslint --fix __tests__",
     "prod": "npm run build -- configuration/webpack/webpack.config.prod.js",
     "test": "jest --testPathIgnorePatterns e2e",
     "prepare": "cd .. && husky install client/.husky"