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Attempt fixing segmentation fault on MacOS in GitHub Actions
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@@ -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/[email protected] | ||
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/[email protected] | ||
# 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 |