From a871abbd87111970cdc798993e711928f24fe426 Mon Sep 17 00:00:00 2001
From: Martin Larralde <martin.larralde@embl.de>
Date: Thu, 15 Feb 2024 16:14:03 +0100
Subject: [PATCH] Attempt fixing segmentation fault on MacOS in GitHub Actions

---
 .github/workflows/test.yml | 128 ++++++++++++++++++++++++-------------
 1 file changed, 83 insertions(+), 45 deletions(-)

diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
index 5c1b2b0..3e27e26 100644
--- a/.github/workflows/test.yml
+++ b/.github/workflows/test.yml
@@ -79,38 +79,38 @@ jobs:
         token: ${{ secrets.CODECOV_TOKEN }}
         verbose: true
 
-  test_linux_arm64:
-    name: Test (Linux, arm64)
-    runs-on: ubuntu-latest
-    strategy:
-      matrix:
-        python-tag:
-        - cp310-manylinux_aarch64
-        - cp311-manylinux_aarch64
-    steps:
-    - uses: actions/checkout@v3
-      with:
-        submodules: true
-    - name: Set up QEMU
-      id: qemu
-      uses: docker/setup-qemu-action@v2
-      with:
-        platforms: all
-    - name: Build manylinux wheels
-      uses: pypa/cibuildwheel@v2.11.3
-      env:
-        CIBW_ARCHS: aarch64
-        CIBW_BUILD: ${{ matrix.python-tag }}
-        CIBW_BUILD_VERBOSITY: 2
-        CIBW_BEFORE_BUILD: pip install cython
-        CIBW_TEST_COMMAND: python -m unittest pyhmmer.tests -vv
-        CIBW_TEST_REQUIRES: importlib-resources
-      with:
-        output-dir: dist
-    - uses: actions/upload-artifact@v3
-      with:
-        name: wheels
-        path: dist/*
+  # test_linux_arm64:
+  #   name: Test (Linux, arm64)
+  #   runs-on: ubuntu-latest
+  #   strategy:
+  #     matrix:
+  #       python-tag:
+  #       - cp310-manylinux_aarch64
+  #       - cp311-manylinux_aarch64
+  #   steps:
+  #   - uses: actions/checkout@v3
+  #     with:
+  #       submodules: true
+  #   - name: Set up QEMU
+  #     id: qemu
+  #     uses: docker/setup-qemu-action@v2
+  #     with:
+  #       platforms: all
+  #   - name: Build manylinux wheels
+  #     uses: pypa/cibuildwheel@v2.11.3
+  #     env:
+  #       CIBW_ARCHS: aarch64
+  #       CIBW_BUILD: ${{ matrix.python-tag }}
+  #       CIBW_BUILD_VERBOSITY: 2
+  #       CIBW_BEFORE_BUILD: pip install cython
+  #       CIBW_TEST_COMMAND: python -m unittest pyhmmer.tests -vv
+  #       CIBW_TEST_REQUIRES: importlib-resources
+  #     with:
+  #       output-dir: dist
+  #   - uses: actions/upload-artifact@v3
+  #     with:
+  #       name: wheels
+  #       path: dist/*
 
   test_osx_x86:
     name: Test (OSX)
@@ -174,16 +174,54 @@ jobs:
     - name: Install test requirements
       run: python -m pip install -r pyhmmer/tests/requirements.txt
       if: matrix.python-impl == 'CPython'
-    - name: Test with coverage
-      run: python -m coverage run -m unittest discover -vv
-    - name: Upload to Codecov
-      uses: codecov/codecov-action@v3
-      if: matrix.python-impl == 'CPython'
-      with:
-        flags: ${{ matrix.python-release }}
-        env_vars: OS
-        name: test-python-${{ matrix.python-version }}
-        fail_ci_if_error: false
-        token: ${{ secrets.CODECOV_TOKEN }}
-        codecov_curl_args: "--globoff"
-        verbose: true
+
+    - name: Test Plan7 Background
+      run: python -m unittest -vv pyhmmer.tests.test_plan7.test_background
+
+    - name: Test Plan7 Block
+      run: python -m unittest -vv pyhmmer.tests.test_plan7.test_block
+
+    - name: Test Plan7 Builder
+      run: python -m unittest -vv pyhmmer.tests.test_plan7.test_builder
+
+    - name: Test Plan7 Hit
+      run: python -m unittest -vv pyhmmer.tests.test_plan7.test_hit
+
+    - name: Test Plan7 HMM
+      run: python -m unittest -vv pyhmmer.tests.test_plan7.test_hmm
+
+    - name: Test Plan7 HMMFile
+      run: python -m unittest -vv pyhmmer.tests.test_plan7.test_hmmfile
+
+    - name: Test Plan7 OptimizedProfile
+      run: python -m unittest -vv pyhmmer.tests.test_plan7.test_optimizedprofile
+
+    - name: Test Plan7 Pipeline
+      run: python -m unittest -vv pyhmmer.tests.test_plan7.test_pipeline
+
+    - name: Test Plan7 Profile
+      run: python -m unittest -vv pyhmmer.tests.test_plan7.test_profile
+
+    - name: Test Plan7 TopHits
+      run: python -m unittest -vv pyhmmer.tests.test_plan7.test_tophits
+
+    - name: Test Plan7 TraceAligner
+      run: python -m unittest -vv pyhmmer.tests.test_plan7.test_tracealigner
+
+    - name: Test Plan7 Traces
+      run: python -m unittest -vv pyhmmer.tests.test_plan7.test_traces
+
+    - name: Test HMMER
+      run: python -m unittest -vv pyhmmer.tests.test_hmmer
+    #   run: python -m coverage run -m unittest discover -vv
+    # - name: Upload to Codecov
+    #   uses: codecov/codecov-action@v3
+    #   if: matrix.python-impl == 'CPython'
+    #   with:
+    #     flags: ${{ matrix.python-release }}
+    #     env_vars: OS
+    #     name: test-python-${{ matrix.python-version }}
+    #     fail_ci_if_error: false
+    #     token: ${{ secrets.CODECOV_TOKEN }}
+    #     codecov_curl_args: "--globoff"
+    #     verbose: true