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Fix CI #243

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merged 3 commits into from
Mar 3, 2025
Merged

Fix CI #243

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358f697
fix: use venv in all CI.
paquiteau Mar 3, 2025
67ece18
more isolation.
paquiteau Mar 3, 2025
d79e284
update ci
paquiteau Mar 3, 2025
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78 changes: 49 additions & 29 deletions .github/workflows/test-ci.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -16,6 +16,9 @@ env:
PYTHON_VERSION: "3.10"
BART_VERSION: "0.8.00"
ref_backend: "finufft"
create_venv: "python -m venv $RUNNER_WORKSPACE/venv"
activate_venv: "source $RUNNER_WORKSPACE/venv/bin/activate"
setup_cuda: "export CUDA_BIN_PATH=/usr/local/cuda-12.1/;export PATH=/usr/local/cuda-12.1/bin/:${PATH};export LD_LIBRARY_PATH=/usr/local/cuda-12.1/lib64/:${LD_LIBRARY_PATH}"

jobs:
test-cpu:
Expand Down Expand Up @@ -44,28 +47,38 @@ jobs:
- name: Install Python Deps
shell: bash
run: |
python --version
${{ env.create_venv }}
${{ env.activate_venv }}
python -m pip install --upgrade pip
python -m pip install -e .[test]

- name: Install pynfft
if: ${{ matrix.backend == 'pynfft' || env.ref_backend == 'pynfft' }}
shell: bash
run: |
${{ env.activate_venv }}
python -m pip install "pynfft2>=1.4.3"

- name: Install pynufft
if: ${{ matrix.backend == 'pynufft-cpu' || env.ref_backend == 'pynufft-cpu' }}
run: python -m pip install pynufft
run: |
${{ env.activate_venv }}
python -m pip install pynufft

- name: Install finufft
if: ${{ matrix.backend == 'finufft' || env.ref_backend == 'finufft'}}
shell: bash
run: python -m pip install finufft
run: |
${{ env.activate_venv }}
python -m pip install finufft

- name: Install Sigpy
if: ${{ matrix.backend == 'sigpy' || env.ref_backend == 'sigpy'}}
shell: bash
run: python -m pip install sigpy
run: |
${{ env.activate_venv }}
python -m pip install sigpy

- name: Install BART
if: ${{ matrix.backend == 'bart' || env.ref_backend == 'bart'}}
Expand All @@ -81,14 +94,17 @@ jobs:

- name: Install torchkbnufft-cpu
if: ${{ matrix.backend == 'torchkbnufft-cpu' || env.ref_backend == 'torchkbnufft-cpu'}}
run: python -m pip install torchkbnufft
run: |
${{ env.activate_venv }}
python -m pip install torchkbnufft


- name: Run Tests
shell: bash
run: |
${{ env.activate_venv }}
export COVERAGE_FILE=coverage_${{ matrix.backend }}
pytest -k='operators' --backend ${{ matrix.backend }} --ref ${{ env.ref_backend }} --cov --disable-pytest-warnings --cov-branch --cov-report=term
python -m pytest -k='operators' --backend ${{ matrix.backend }} --ref ${{ env.ref_backend }} --cov --disable-pytest-warnings --cov-branch --cov-report=term
- name: Upload coverage
uses: actions/upload-artifact@v4
with:
Expand All @@ -111,43 +127,39 @@ jobs:
- name: Install mri-nufft and finufft
shell: bash
run: |
cd $RUNNER_WORKSPACE
python --version
python -m venv venv
source $RUNNER_WORKSPACE/venv/bin/activate
pip install --upgrade pip wheel
pip install -e mri-nufft[test]
pip install cupy-cuda12x finufft "numpy<2.0"
${{ env.create_venv }}
${{ env.activate_venv }}
python -m pip install --upgrade pip wheel
python -m pip install -e .[test]
python -m pip install cupy-cuda12x finufft "numpy<2.0"

- name: Install torch with CUDA 12.1
shell: bash
if: ${{ matrix.backend != 'tensorflow'}}
run: |
source $RUNNER_WORKSPACE/venv/bin/activate
pip install torch
${{ env.activate_venv }}
python -m pip install torch

- name: Install backend
shell: bash
run: |
source $RUNNER_WORKSPACE/venv/bin/activate
export CUDA_BIN_PATH=/usr/local/cuda-12.1/
export PATH=/usr/local/cuda-12.1/bin/:${PATH}
export LD_LIBRARY_PATH=/usr/local/cuda-12.1/lib64/:${LD_LIBRARY_PATH}
${{ env.activate_venv }}
${{ env.setup_cuda }}
if [[ ${{ matrix.backend }} == "torchkbnufft-gpu" ]]; then
pip install torchkbnufft
python -m pip install torchkbnufft
elif [[ ${{ matrix.backend }} == "tensorflow" ]]; then
pip install tensorflow-mri==0.21.0 tensorflow-probability==0.17.0 tensorflow-io==0.27.0 matplotlib==3.7
python -m pip install tensorflow-mri==0.21.0 tensorflow-probability==0.17.0 tensorflow-io==0.27.0 matplotlib==3.7
elif [[ ${{ matrix.backend }} == "cufinufft" ]]; then
pip install "cufinufft<2.3"
python -m pip install "cufinufft<2.3"
else
pip install ${{ matrix.backend }}
python -m pip install ${{ matrix.backend }}
fi

- name: Run Tests
shell: bash
run: |
${{ env.activate_venv }}
cd $RUNNER_WORKSPACE/mri-nufft
source $RUNNER_WORKSPACE/venv/bin/activate
export COVERAGE_FILE=coverage_${{ matrix.backend }}
python -m pytest -k='operators' --ref ${{ env.ref_backend }} --backend ${{ matrix.backend }} --disable-pytest-warnings --cov --cov-branch --cov-report=term

Expand Down Expand Up @@ -205,21 +217,23 @@ jobs:
- name: Install Python deps
shell: bash
run: |
${{ env.create_venv }}
${{ env.activate_venv }}
python -m pip install --upgrade pip
python -m pip install -e .[extra,test,dev]
python -m pip install finufft pooch brainweb-dl torch fastmri

- name: Install GPU related interfaces
run: |
export CUDA_BIN_PATH=/usr/local/cuda-12.1/
export PATH=/usr/local/cuda-12.1/bin/:${PATH}
export LD_LIBRARY_PATH=/usr/local/cuda-12.1/lib64/:${LD_LIBRARY_PATH}
${{ env.activate_venv }}
${{ env.setup_cuda }}
pip install cupy-cuda12x torch
python -m pip install gpuNUFFT "cufinufft<2.3" sigpy scikit-image fastmri

- name: Run examples
shell: bash
run: |
${{ env.activate_venv }}
export COVERAGE_FILE=coverage_plots
pytest examples tests -k="not operators" --cov --cov-branch --cov-report=term

Expand Down Expand Up @@ -260,12 +274,15 @@ jobs:
- name: add the coverage tool
shell: bash
run: |
${{ env.create_venv }}
${{ env.activate_venv }}
python -m pip install --upgrade pip
python -m pip install coverage[toml]
python -m pip install -e .

- name: Combine coverage
run: |
${{ env.activate_venv }}
export COVERAGE_FILE=coverage_combined
coverage combine -a coverage_data/*

Expand All @@ -277,6 +294,7 @@ jobs:

- name: Reports
run: |
${{ env.activate_venv }}
export COVERAGE_FILE=coverage_combined
coverage xml
coverage report
Expand Down Expand Up @@ -316,20 +334,22 @@ jobs:
- name: Install dependencies
shell: bash -l {0}
run: |
${{ env.create_venv }}
${{ env.activate_venv }}
python -m pip install --upgrade pip
python -m pip install .[doc]
python -m pip install finufft

- name: Install GPU related interfaces
run: |
export CUDA_BIN_PATH=/usr/local/cuda-12.1/
export PATH=/usr/local/cuda-12.1/bin/:${PATH}
export LD_LIBRARY_PATH=/usr/local/cuda-12.1/lib64/:${LD_LIBRARY_PATH}
${{ env.activate_venv }}
${{ env.setup_cuda }}
pip install cupy-cuda12x torch
python -m pip install gpuNUFFT "cufinufft<2.3"

- name: Build API documentation
run: |
${{ env.activate_venv }}
python -m sphinx docs docs_build

- name: Display data
Expand Down
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