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Merge pull request #386 from effigies/ci/test_master
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CI: Add a build to test with unreleased pybids
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effigies authored Sep 8, 2022
2 parents 7757f9f + c4ec589 commit 753b588
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Showing 2 changed files with 56 additions and 11 deletions.
65 changes: 55 additions & 10 deletions .github/workflows/workflows.yml
Original file line number Diff line number Diff line change
Expand Up @@ -17,6 +17,10 @@ env:
IMAGE_NAME: ${{ github.repository }}
INSTALL_TYPE: pip

defaults:
run:
shell: bash -l {0}

jobs:
build:
runs-on: ubuntu-latest
Expand Down Expand Up @@ -153,9 +157,6 @@ jobs:
CHECK_TYPE: ${{ matrix.check }}
EXTRA_PIP_FLAGS: ${{ matrix.pip-flags }}
OS_TYPE: ${{ matrix.os }}
defaults:
run:
shell: bash -l {0}
steps:
- uses: actions/checkout@v3
with:
Expand Down Expand Up @@ -190,7 +191,57 @@ jobs:
run: tools/ci/install.sh
- name: Run tests
run: tools/ci/check.sh
if: ${{ matrix.check != 'skiptests' }}
- uses: codecov/codecov-action@v3
with:
verbose: true
if: ${{ always() }}

pre-release:
runs-on: ${{ matrix.os }}
strategy:
fail-fast: false
matrix:
os: ['ubuntu-latest']
python-version: [3]
# Check pre-release pybids and pre-release everything
pip-flags: ['', 'PRE_PIP_FLAGS']
check: ['test']
env:
CHECK_TYPE: ${{ matrix.check }}
EXTRA_PIP_FLAGS: ${{ matrix.pip-flags }}
OS_TYPE: ${{ matrix.os }}
steps:
- uses: actions/checkout@v3
with:
submodules: recursive
fetch-depth: 0
- uses: conda-incubator/setup-miniconda@v2
with:
activate-environment: fitlins-ci
environment-file: tools/ci/conda_environment.yml
python-version: ${{ matrix.python-version }}
- name: Test conda installation
run: |
conda info
conda list
conda env list
conda config --show-sources
conda config --show
- name: Install dependencies
run: |
conda install -y --channel leej3 "afni-minimal"
conda list | grep afni
- name: Display Python version
run: |
which python
which pip
python -c "import sys; print(sys.version)"
- name: Install fitlins
run: tools/ci/install.sh
- name: Install pybids from GitHub
run: pip install git+https://github.com/bids-standard/pybids.git
- name: Run tests
run: tools/ci/check.sh
- uses: codecov/codecov-action@v3
with:
verbose: true
Expand All @@ -210,9 +261,6 @@ jobs:
CHECK_TYPE: ${{ matrix.check }}
EXTRA_PIP_FLAGS: ${{ matrix.pip-flags }}
OS_TYPE: ${{ matrix.os }}
defaults:
run:
shell: bash -l {0}
steps:
- uses: actions/checkout@v3
with:
Expand Down Expand Up @@ -262,9 +310,6 @@ jobs:
CHECK_TYPE: ${{ matrix.check }}
EXTRA_PIP_FLAGS: ${{ matrix.pip-flags }}
OS_TYPE: ${{ matrix.os }}
defaults:
run:
shell: bash -l {0}
steps:
- uses: actions/checkout@v3
with:
Expand Down
2 changes: 1 addition & 1 deletion setup.cfg
Original file line number Diff line number Diff line change
Expand Up @@ -26,7 +26,7 @@ install_requires =
nipype>=1.3.2
seaborn>=0.10.0
numpy>=1.11
nilearn~=0.8.1
nilearn~=0.9.1
pandas>=0.19
tables>=3.2.1
pybids~=0.15.1
Expand Down

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