Merge pull request #1941 from veg/develop

spond · web-flow · commit 81a83c99c530 · 2025-12-21T10:34:15.000-05:00
2.5.91
diff --git a/.github/workflows/wasm-build.yml b/.github/workflows/wasm-build.yml
@@ -7,6 +7,9 @@ on:
   # Allows running this workflow manually from the Actions tab
   workflow_dispatch:
 
+permissions:
+  contents: write
+
 jobs:
   build-wasm:
     name: Build WebAssembly
@@ -25,31 +28,15 @@ jobs:
           
       - name: Configure and build with Emscripten
         run: |
-          # Build with Emscripten - but without preloading files to avoid issues with CMake tests
           mkdir -p build
           cd build
           
-          # Configure without preload files to avoid issues during compiler checks
-          emcmake cmake .. -DCMAKE_EXE_LINKER_FLAGS="-sTOTAL_STACK=2097152 -O2 -sASSERTIONS=1 -sMODULARIZE=1 -sALLOW_MEMORY_GROWTH -sFORCE_FILESYSTEM=1 -sEXIT_RUNTIME=0 -s EXPORTED_RUNTIME_METHODS=[\"callMain\",\"FS\",\"PROXYFS\",\"WORKERFS\",\"UTF8ToString\",\"getValue\",\"AsciiToString\"] -lworkerfs.js -lproxyfs.js -s INVOKE_RUN=0 -s ENVIRONMENT=\"web,worker\" -fwasm-exceptions"
+          # Configure with preload files to generate hyphy.data
+          # Map local ../res to /res in the virtual filesystem
+          emcmake cmake .. -DCMAKE_EXE_LINKER_FLAGS="-sTOTAL_STACK=2097152 -O2 -sASSERTIONS=1 -sMODULARIZE=1 -sALLOW_MEMORY_GROWTH -sFORCE_FILESYSTEM=1 -sEXIT_RUNTIME=0 -s EXPORTED_RUNTIME_METHODS=[\"callMain\",\"FS\",\"PROXYFS\",\"WORKERFS\",\"UTF8ToString\",\"getValue\",\"AsciiToString\"] -lworkerfs.js -lproxyfs.js -s INVOKE_RUN=0 -s ENVIRONMENT=\"web,worker\" -fwasm-exceptions --preload-file ../res@/res"
           
-          # Build without preloading files
           emmake make -j hyphy
           
-      - name: Package resource files
-        run: |
-          cd build
-          
-          # Instead of bundling resources, we'll package them separately for download
-          mkdir -p hyphy_resources
-          cp -r ../res hyphy_resources/
-          cp -r ../tests/hbltests hyphy_resources/tests
-          
-          # Create a README for the resources
-          echo "These resource files should be placed in the same directory as hyphy.js, hyphy.wasm, and hyphy.data" > hyphy_resources/README.txt
-          
-          # Create a zip file of the resources
-          tar -czvf hyphy_resources.tar.gz hyphy_resources
-          
       - name: Display build artifacts
         run: |
           cd build
@@ -63,5 +50,20 @@ jobs:
             build/hyphy.js
             build/hyphy.wasm
             build/hyphy.data
-            build/hyphy_resources.tar.gz
-          retention-days: 30
+          retention-days: 30
+
+      - name: Prepare for deployment
+        run: |
+          mkdir -p public
+          cp build/hyphy.js public/
+          cp build/hyphy.wasm public/
+          cp build/hyphy.data public/
+          echo "<html><body><h1>HyPhy WASM Build</h1><ul><li><a href='hyphy.wasm'>hyphy.wasm</a></li><li><a href='hyphy.js'>hyphy.js</a></li><li><a href='hyphy.data'>hyphy.data</a></li></ul></body></html>" > public/index.html
+
+      - name: Deploy to GitHub Pages
+        uses: peaceiris/actions-gh-pages@v3
+        if: github.ref == 'refs/heads/master'
+        with:
+          github_token: ${{ secrets.GITHUB_TOKEN }}
+          publish_dir: ./public
+          publish_branch: gh-pages
diff --git a/res/TemplateBatchFiles/SelectionAnalyses/BUSTED-PH.bf b/res/TemplateBatchFiles/SelectionAnalyses/BUSTED-PH.bf
@@ -119,7 +119,7 @@ if (!busted.run_background_test) {
                                                          "{terms.json.omega_ratio : busted.inferred_test_distribution_raw [_index_][0],
                                                            terms.json.proportion : busted.inferred_test_distribution_raw [_index_][1]}")};
 
-    busted.report_multi_hit  (busted.null_results, busted.distribution_for_json, "MultiHit", "null-mh",busted.branch_length_string, busted.model_parameters);
+    busted.report_multi_hit  (busted.background_null_results, busted.distribution_for_json, "MultiHit", "null-mh",busted.branch_length_string, busted.model_parameters);
     busted.null_distro_raw = parameters.GetStickBreakingDistribution (busted.distribution);
     
     if (busted.error_sink) {
diff --git a/res/TemplateBatchFiles/SelectionAnalyses/contrast-fel.bf b/res/TemplateBatchFiles/SelectionAnalyses/contrast-fel.bf
@@ -148,11 +148,11 @@ io.ReportProgressMessageMD('FEL',  'selector', 'Branches to use as the test set
 
 fel.branch_sets = {};
 
-utility.ForEachPair (fel.selected_branches[0], "_branch_", "_model_",
-"
+for (_branch_, _model_; in; fel.selected_branches[0]) {
     utility.EnsureKey (fel.branch_sets, _model_);
     fel.branch_sets[_model_] + _branch_;
-");
+}
+
 
 fel.branch_class_count = utility.Array1D (fel.branch_sets);
 fel.scaler_parameter_names = {};
@@ -164,23 +164,22 @@ fel.branches.testable = {};
 fel.branches.has_background = FALSE;
 
 
-utility.ForEachPair (fel.branch_sets, "_group_", "_branches_",
-    "
-     if (_group_ != terms.tree_attributes.background) {
-        fel.site_tested_classes [_group_] = 'Site relative non-synonymous rate (' + _group_ + ' branches)';
-        fel.branch_class_counter += 1;
-        fel.branches.testable + _group_;
-        fel.scaler_parameter_names [_group_] = 'fel.beta_scaler_group_' + fel.branch_class_counter;
-        io.ReportProgressMessageMD('FEL',  'selector', '* Selected ' + Abs(_branches_) + ' branches in group _' + _group_ + '_ : \\\`' + Join (', ',_branches_) + '\\\`')
-     } else {
-        fel.scaler_parameter_names [_group_] = 'fel.beta_scaler_background';
-        fel.site_tested_classes [_group_] = 'Site relative non-synonymous rate (reference branches)';
-        fel.branches.has_background = TRUE;
-        io.ReportProgressMessageMD('FEL',  'selector', '* ' + Abs(_branches_) + ' branches are in the background group : \\\`' + Join (', ',_branches_) + '\\\`')
-     }
-     "
-);
+for (_group_, _branches_; in; fel.branch_sets) {
+    if (_group_ != terms.tree_attributes.background) {
+            fel.site_tested_classes [_group_] = 'Site relative non-synonymous rate (' + _group_ + ' branches)';
+            fel.branch_class_counter += 1;
+            fel.branches.testable + _group_;
+            fel.scaler_parameter_names [_group_] = 'fel.beta_scaler_group_' + fel.branch_class_counter;
+            io.ReportProgressMessageMD('FEL',  'selector', '* Selected ' + Abs(_branches_) + ' branches in group _' + _group_ + '_ : \\\`' + Join (', ',_branches_) + '\\\`')
+         } else {
+            fel.scaler_parameter_names [_group_] = 'fel.beta_scaler_background';
+            fel.site_tested_classes [_group_] = 'Site relative non-synonymous rate (reference branches)';
+            fel.branches.has_background = TRUE;
+            io.ReportProgressMessageMD('FEL',  'selector', '* ' + Abs(_branches_) + ' branches are in the background group : \\\`' + Join (', ',_branches_) + '\\\`')
+         }
+}
 
+io.CheckAssertion  ("utility.Array1D(fel.branches.testable) > 0", "Must select  a non-empty testable branch set");
 
 
 fel.test_count = 1;
@@ -614,6 +613,7 @@ lfunction fel.select_branches(partition_info) {
             selectTheseForTesting[k][1] = "Set of " + available_models[list_models[k-3]] + " unlabeled branches";
         }
     }
+    
 
     ChoiceList(testSet, "Choose sets of branches to compare. If more than one set is chosen, pairwise comparisons will be carried out in addition to a group-level difference test.", 0, NO_SKIP, selectTheseForTesting);
     io.CheckAssertion ("`&testSet[0]` >= 0", "User cancelled branch selection; analysis terminating");
@@ -623,6 +623,7 @@ lfunction fel.select_branches(partition_info) {
     tree_for_analysis  = (partition_info[0])[utility.getGlobalValue("terms.data.tree")];
     branch_set_count   = utility.Array1D (testSet);
     test_sets          = {};
+    
 
     for (k = 0; k < branch_set_count; k+=1) {
         tag_test = selectTheseForTesting [testSet[k]][0];
@@ -632,6 +633,7 @@ lfunction fel.select_branches(partition_info) {
         test_sets[tag_test] = TRUE;
     }
     
+    
     if (test_sets / 'Random set of branches') {
         KeywordArgument ("random-subset", "How many branches in the random subset to test", (internal_count+leaf_count)$2);
         test_count = io.PromptUser ("How many branches in the test set", (internal_count+leaf_count)$2,1,(internal_count+leaf_count), TRUE);
diff --git a/src/core/global_things.cpp b/src/core/global_things.cpp
@@ -115,7 +115,7 @@ _String const kEmptyString, kPromptForFilePlaceholder("PROMPT_FOR_FILE"),
                     "\"ENV=TOLERATE_NUMERICAL_ERRORS=1;\" as the command line "
                     "argument. This often resolves the issue, which is "
                     "indicative of numerical instability."),
-    kHyPhyVersion = _String("2.5.90"),
+    kHyPhyVersion = _String("2.5.91"),
 
     kNoneToken = "None", kNullToken = "null",
     kNoKWMatch = "__input_value_not_given__",
diff --git a/src/core/matrix_kernels.cpp b/src/core/matrix_kernels.cpp
@@ -39,81 +39,7 @@
 
 #include "matrix_kernels.h"
 
-/**** START: ARM SVE CODE *****/
-
-#ifdef _SLKP_USE_ARM_SVE
-#include <arm_sve.h>
-
-void _matrix_kernel_multiply_by_compressed_sparse(hyFloat *resBase,
-                                                  const long *compIdx,
-                                                  const hyFloat *secondArgBase,
-                                                  const hyFloat *theDataPtr,
-                                                  long N) {
-  long currentXIndex = 0L;
-  hyFloat *res = resBase;
-
-  uint64_t vl = svcntd();
-
-  for (long i = 0; i < N; i++) {
-    long up = compIdx[i];
-
-    if (currentXIndex < up) {
-      long j = 0;
-      // Unrolled loop
-      while (j + 4 * vl <= N) {
-        svbool_t pgAll = svptrue_b64();
-        svfloat64_t acc0 = svld1(pgAll, res + j);
-        svfloat64_t acc1 = svld1(pgAll, res + j + vl);
-        svfloat64_t acc2 = svld1(pgAll, res + j + 2 * vl);
-        svfloat64_t acc3 = svld1(pgAll, res + j + 3 * vl);
-
-        for (long cxi = currentXIndex; cxi < up; cxi++) {
-          long currentXColumn = compIdx[cxi + N];
-          const hyFloat *secArg = secondArgBase + currentXColumn * N;
-          svfloat64_t valVec = svdup_f64(theDataPtr[cxi]);
-
-          svfloat64_t b0 = svld1(pgAll, secArg + j);
-          svfloat64_t b1 = svld1(pgAll, secArg + j + vl);
-          svfloat64_t b2 = svld1(pgAll, secArg + j + 2 * vl);
-          svfloat64_t b3 = svld1(pgAll, secArg + j + 3 * vl);
-
-          acc0 = svmla_f64_x(pgAll, acc0, valVec, b0);
-          acc1 = svmla_f64_x(pgAll, acc1, valVec, b1);
-          acc2 = svmla_f64_x(pgAll, acc2, valVec, b2);
-          acc3 = svmla_f64_x(pgAll, acc3, valVec, b3);
-        }
-
-        svst1(pgAll, res + j, acc0);
-        svst1(pgAll, res + j + vl, acc1);
-        svst1(pgAll, res + j + 2 * vl, acc2);
-        svst1(pgAll, res + j + 3 * vl, acc3);
-
-        j += 4 * vl;
-      }
-
-      // Tail loop
-      while (j < N) {
-        svbool_t pg = svwhilelt_b64(j, N);
-        svfloat64_t acc = svld1(pg, res + j);
-
-        for (long cxi = currentXIndex; cxi < up; cxi++) {
-          long currentXColumn = compIdx[cxi + N];
-          const hyFloat *secArg = secondArgBase + currentXColumn * N;
-          svfloat64_t valVec = svdup_f64(theDataPtr[cxi]);
-          svfloat64_t b = svld1(pg, secArg + j);
-          acc = svmla_f64_m(pg, acc, valVec, b);
-        }
-        svst1(pg, res + j, acc);
-        j += vl;
-      }
-    }
-
-    res += N;
-    currentXIndex = up;
-  }
-}
-
-#elif defined _SLKP_USE_ARM_NEON
+#if defined _SLKP_USE_ARM_NEON
 
 void _matrix_kernel_multiply_by_compressed_sparse(hyFloat *resBase,
                                                   const long *compIdx,
