diff --git a/.github/workflows/workflows.yml b/.github/workflows/workflows.yml index ab742a1a..8be1e96f 100644 --- a/.github/workflows/workflows.yml +++ b/.github/workflows/workflows.yml @@ -17,6 +17,10 @@ env: IMAGE_NAME: ${{ github.repository }} INSTALL_TYPE: pip +defaults: + run: + shell: bash -l {0} + jobs: build: runs-on: ubuntu-latest @@ -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: @@ -190,7 +191,55 @@ 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: + matrix: + os: ['ubuntu-latest'] + python-version: [3] + pip-flags: ['--pre'] + 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 @@ -210,9 +259,6 @@ 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: @@ -262,9 +308,6 @@ 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: