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Add CI github actions workflow #1034
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bebdd49
Add CI github actions workflow
sethaxen 3b7544f
Correctly reference environmental variable
sethaxen a846c35
Fix boost package name
sethaxen 46f9023
Use same form of setup
sethaxen 10c5ec0
Remove regex arg to ctest
sethaxen c5a84f0
Make ctest output on failure
sethaxen 0a3dfe1
Install more dependencies
sethaxen f102355
Make build directory in imp directory
sethaxen d2b07cc
Replace ctest with nosetests
sethaxen b18174a
Don't run codecov action verbosely
sethaxen 37f4121
Fix package name
sethaxen e8272d6
Execute from build directory
sethaxen 15ba0e7
Add nose as dependency
sethaxen 28d19b9
Change comment indentation
sethaxen c875f3a
Create test directory
sethaxen 1b1a065
Don't install both Python 2 and 3
sethaxen 53c0161
Remove extraneous python install step
sethaxen c3d942e
Install codecov
sethaxen 232dfcd
Fix check for Python 2 env
benmwebb cefd848
Set correct Python 3 version
benmwebb 844eb15
Use correct pip binary
benmwebb 0554bd9
Use correct nosetests
benmwebb c2d0e0c
Help CMake to find CGAL
benmwebb 000ee17
Run just IMP.kernel tests for now
benmwebb ca909b7
Add missing "then" to if statement
benmwebb 6569ce8
Merge branch 'develop' into githubactionsci
sethaxen b101763
Add coverage module
sethaxen 3cd828b
Remove duplicated Python package installation
sethaxen d4e40a6
Compile only a few modules for faster iteration
sethaxen 0b376a0
Only test kernel for now
sethaxen c677c62
Use pytest instead of nose
benmwebb 4334497
There are no "medium" tests in IMP.kernel
benmwebb ef05987
Run each test in a separate process
benmwebb 02c3de0
Many kernel tests use IMP.core/algebra classes
benmwebb bbe1122
Don't cancel others if one build fails
benmwebb e4b18c1
Use older py.test binary
benmwebb a75a4af
Run test via unittest
benmwebb 6018f19
Install .deb packages for pytest, not pip
benmwebb 4039666
Need IMP.container to run some kernel tests
benmwebb ecc8e65
Fix pytest name
benmwebb 1db30a4
Increase fetch-depth
sethaxen 8ffe8da
Explicitly output xml coverage report
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,47 @@ | ||
| name: CI | ||
| on: | ||
| push: | ||
| branches: [develop] | ||
| pull_request: | ||
|
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||
| env: | ||
| CXXFLAGS: "-fprofile-arcs -ftest-coverage" | ||
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||
| jobs: | ||
| test: | ||
| name: "Python ${{ matrix.python-version }} / ${{ matrix.os }}" | ||
| runs-on: ${{ matrix.os }} | ||
| strategy: | ||
| matrix: | ||
| python-version: ["2.7", "3.8"] | ||
| os: [ubuntu-latest] | ||
| compiler: [gcc] | ||
| env: | ||
| CC: ${{ matrix.compiler }} | ||
| PY2: ${{ startsWith(matrix.python-version, 2) && 'on' || 'off' }} | ||
| steps: | ||
| - uses: actions/checkout@v2 | ||
| - name: Install dependencies | ||
| run: | | ||
| sudo apt-get update -qq | ||
| sudo apt-get install -qq libboost-all-dev swig libhdf5-serial-dev libeigen3-dev | ||
| - name: Set up python | ||
| uses: actions/setup-python@v2 | ||
| with: | ||
| python-version: ${{ matrix.python-version }} | ||
| architecture: 'x64' | ||
| - name: Set up git | ||
| run: ./setup_git.py | ||
| - name: Build IMP | ||
| run: | | ||
| mkdir ../build | ||
| cd ../build | ||
| cmake ../imp -DUSE_PYTHON2=${{ env.PY2 }} -DCMAKE_CXX_FLAGS="${{ env.CXXFLAGS }}" | ||
| make -k -j 2 | ||
| - name: Run tests | ||
| run: ctest -j 2 --output-on-failure | ||
| - name: Upload coverage to Codecov | ||
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|
||
| uses: codecov/codecov-action@v1 | ||
| with: | ||
| fail_ci_if_error: false | ||
| verbose: true | ||
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You're missing a lot of IMP build deps here - if you look at the logs you'll see that many modules are not building. On my Ubuntu build images I also install
python-numpy python3-biopython python3-numpy cmake libcgal-dev libcgal-qt5-dev libfftw3-dev libopencv-dev libgsl0-dev python2-dev python3-dev libann-dev libprotobuf-dev protobuf-compiler python-protobuf python3-protobuf libopenmpi-dev.There was a problem hiding this comment.
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I adapted this from Travis. Why don't we need these dependencies over there?
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Travis just does a very basic build of some of the low-level modules, not all of IMP, just to see if things compile. And it doesn't run any of the tests.