Check for keyboard interrupt only on main thread

bacpop · Dec 19, 2023 · ee62c0c · ee62c0c
1 parent b5054ea
commit ee62c0c
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Showing 3 changed files with 8 additions and 6 deletions.
diff --git a/.github/workflows/azure_ci.yml b/.github/workflows/azure_ci.yml
@@ -40,11 +40,12 @@ jobs:
 
     ## For debugging
     - name: Install and run_test.py
+      if: failure()
       shell: bash -l {0}
       run: |
         python setup.py build_ext --debug install
-    
     - name: Setup tmate session
+      if: failure()
       uses: mxschmitt/action-tmate@v3
       with:
         limit-access-to-actor: true

diff --git a/src/api.cpp b/src/api.cpp
@@ -81,9 +81,7 @@ std::vector<Reference> create_sketches(
     std::vector<std::runtime_error> errors;
 #pragma omp parallel for schedule(dynamic, 5) num_threads(num_threads)
     for (unsigned int i = 0; i < names.size(); i++) {
-      if (interrupt || PyErr_CheckSignals() != 0) {
-        interrupt = true;
-      } else {
+      if (!interrupt) {
         try {
           SeqBuf seq_in(files[i], kmer_lengths.back());
           sketches[i] = Reference(names[i], seq_in, kmer_seeds, sketchsize64,
@@ -101,6 +99,9 @@ std::vector<Reference> create_sketches(
 
       if (omp_get_thread_num() == 0) {
         sketch_progress.tick_count(done_count);
+        if (PyErr_CheckSignals() != 0) {
+          interrupt = true;
+        }
       }
     }
     sketch_progress.finalise();

diff --git a/test/run_test.py b/test/run_test.py
@@ -27,8 +27,8 @@
 # create sketches
 sys.stderr.write("Sketch smoke test\n")
 subprocess.run("python ../sketchlib-runner.py sketch -l references.txt -o test_db -s 10000 -k 15,29,4 --cpus 1", shell=True, check=True)
-#os.remove("test_db.h5")
-#subprocess.run("python ../sketchlib-runner.py sketch -l references.txt -o test_db -s 10000 -k 15,29,4 --cpus 2", shell=True, check=True)
+os.remove("test_db.h5")
+subprocess.run("python ../sketchlib-runner.py sketch -l references.txt -o test_db -s 10000 -k 15,29,4 --cpus 2", shell=True, check=True)
 subprocess.run("python ../sketchlib-runner.py sketch -l references.txt -o test_db_phased --codon-phased --cpus 1", shell=True, check=True)
 subprocess.run("python ../sketchlib-runner.py sketch 12673_8#24.contigs_velvet.fa 12673_8#34.contigs_velvet.fa -o test_db_small -s 1000 --kmer 14", shell=True, check=True)
 subprocess.run("python ../sketchlib-runner.py add random test_db --cpus 2", shell=True, check=True)