Fixes to pass check.

kanaverse · Jul 20, 2023 · 48aa8f1 · 48aa8f1
1 parent 38f85f3
commit 48aa8f1
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Showing 3 changed files with 12 additions and 14 deletions.
diff --git a/extern/CMakeLists.txt b/extern/CMakeLists.txt
@@ -77,14 +77,14 @@ FetchContent_MakeAvailable(umappp)
 FetchContent_Declare(
   scran 
   GIT_REPOSITORY https://github.com/LTLA/libscran
-  GIT_TAG 591bd6fabd573ad5762c8efea257a114821c92c9
+  GIT_TAG da495dad607bed894cbcbb7ed811fa8d4983d576
 )
 FetchContent_MakeAvailable(scran)
 
 FetchContent_Declare(
   kmeans 
   GIT_REPOSITORY https://github.com/LTLA/CppKmeans
-  GIT_TAG master
+  GIT_TAG 4c5aca44bffd8ed7d7243b2451105b572028e9d4
 )
 FetchContent_MakeAvailable(kmeans)
 

diff --git a/js/quickAdtSizeFactors.js b/js/quickAdtSizeFactors.js
@@ -33,7 +33,7 @@ export function quickAdtSizeFactors(x, { numberOfClusters = 20, numberOfPCs = 25
     let norm, pcs;
     try {
         norm = logNormCounts(x, { sizeFactors: totals, block: block });
-        pcs = runPca(norm, { numberOfPCs: Math.min(norm.numberOfRows() - 1, numberOfPCs), numberOfThreads: numberOfThreads, block: block, blockMethod: "weight" });
+        pcs = runPca(norm, { numberOfPCs: Math.min(norm.numberOfRows() - 1, numberOfPCs), numberOfThreads: numberOfThreads, block: block, blockMethod: "project" });
     } finally {
         utils.free(norm);
     }

diff --git a/tests/runPca.test.js b/tests/runPca.test.js
@@ -52,11 +52,14 @@ test("PCA works as expected with blocking", () => {
 
     var block = new Int32Array(ncells);
     var nblocks = 4;
-    for (var i = 0; i < ncells; i++) {
-        block[i] = Math.floor(Math.random() * nblocks);
-    }
-    for (var j = 0; j < nblocks; j++) {
-        block[j] = j;
+    var i = 0;
+    while (i < ncells) {
+        for (var b = 0; b < nblocks; b++) {
+            for (var j = 0; j <= b && i < ncells; j++) {
+                block[i] = b;
+                ++i;
+            }
+        }
     }
 
     var pca = scran.runPca(mat, { features: feat, numberOfPCs: 15 });
@@ -71,15 +74,10 @@ test("PCA works as expected with blocking", () => {
     expect(pca.numberOfCells()).toBe(weighted.numberOfCells());
     expect(compare.equalFloatArrays(pca.principalComponents(), weighted.principalComponents())).toBe(false);
 
-    var none = scran.runPca(mat, { features: feat, numberOfPCs: 15, block: block, blockMethod: "none" });
-    expect(pca.numberOfPCs()).toBe(none.numberOfPCs());
-    expect(pca.numberOfCells()).toBe(none.numberOfCells());
-    expect(compare.equalFloatArrays(pca.principalComponents(), none.principalComponents())).toBe(false);
-
     var none2 = scran.runPca(mat, { features: feat, numberOfPCs: 15, block: block, blockMethod: "none", blockWeights: false });
     expect(pca.numberOfPCs()).toBe(none2.numberOfPCs());
     expect(pca.numberOfCells()).toBe(none2.numberOfCells());
-    expect(compare.equalFloatArrays(pca.principalComponents(), none2.principalComponents())).toBe(true);
+    expect(compare.equalArrays(pca.principalComponents(), none2.principalComponents())).toBe(true); // should be exactly equal.
 
     expect(() => scran.runPca(mat, { features: feat, numberOfPCs: 15, block: block, blockMethod: "foobar" })).toThrow("should be one of");
 });