New upstream version 2.5.0

2 files changed, 80 insertions, 4 deletions

diff --git a/.github/workflows/random-tests.yml b/.github/workflows/random-tests.yml
new file mode 100644
index 0000000..2d15a9e
--- /dev/null
+++ b/.github/workflows/random-tests.yml
@@ -0,0 +1,67 @@
+name: Random Tests
+on:
+  push:
+    branches:
+      - 'bug_fixes'
+      - 'master'
+    paths:
+      - '**.h'
+      - '**.cpp'
+      - 'bowtie2'
+      - 'bowtie2-build'
+      - 'bowtie2-inspect'
+      - 'Makefile'
+      - 'scripts/sim/**'
+      - 'scripts/test/**'
+  pull_request:
+    branches:
+      - 'master'
+    paths:
+      - '**.h'
+      - '**.cpp'
+      - 'bowtie2'
+      - 'bowtie2-build'
+      - 'bowtie2-inspect'
+      - 'Makefile'
+      - 'scripts/sim/**'
+      - 'scripts/test/**'
+jobs:
+  setup:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Check out repository code
+        uses: actions/checkout@v2
+      - name: Install zlib development files
+        run: |
+          sudo apt-get update
+          sudo apt-get install zlib1g-dev
+  linux:
+    runs-on: ubuntu-latest
+    needs: setup
+    steps:
+      - uses: actions/checkout@v2
+      - name: Run random tests
+        run: |
+          make clean; make -j4 allall
+          export NUM_CORES=1
+          make random-test
+  linux-avx2:
+    runs-on: ubuntu-latest
+    needs: linux
+    steps:
+      - uses: actions/checkout@v2
+      - name: Run random tests using avx2
+        run: |
+          export SSE_AVX2=1
+          make clean; make -j4 allall
+          export NUM_CORES=1
+          make random-test
+  macos:
+    runs-on: macos-latest
+    steps:
+      - uses: actions/checkout@v2
+      - name: Run random tests
+        run: |
+          make clean; make -j4 allall
+          export NUM_CORES=1
+          make random-test
diff --git a/.github/workflows/bowtie2.yml b/.github/workflows/simple-tests.yml
index a64a8a3..b65054c 100644
--- a/.github/workflows/bowtie2.yml
+++ b/.github/workflows/simple-tests.yml
@@ -1,4 +1,4 @@
-name: Basic compile and test on Ubuntu and MacOS
+name: Simple Tests
 on:
   push:
     branches:
@@ -42,7 +42,17 @@ jobs:
       - uses: actions/checkout@v2
       - name: Run simple tests
         run: |
-          make allall
+          make clean; make -j4 allall
+          make simple-test
+  linux-avx2:
+    runs-on: ubuntu-latest
+    needs: linux
+    steps:
+      - uses: actions/checkout@v2
+      - name: Run simple tests using AVX2
+        run: |
+          export SSE_AVX2=1
+          make clean; make -j4 allall
           make simple-test
   macos:
     runs-on: macos-latest
@@ -50,6 +60,5 @@ jobs:
       - uses: actions/checkout@v2
       - name: Run simple tests
         run: |
-          make allall
+          make clean; make -j4 allall
           make simple-test
-          make random-test