From c0968df8f94dd3abfea83b76aea34179d30c71b3 Mon Sep 17 00:00:00 2001 From: James Kent Date: Wed, 11 Sep 2024 11:51:33 -0500 Subject: [PATCH] update workflow and fix example --- .github/workflows/testing.yml | 126 ++++++++++-------- .../02_meta-analyses/12_plot_ibma_workflow.py | 2 +- 2 files changed, 68 insertions(+), 60 deletions(-) diff --git a/.github/workflows/testing.yml b/.github/workflows/testing.yml index 7c7e2e253..378ad438a 100644 --- a/.github/workflows/testing.yml +++ b/.github/workflows/testing.yml @@ -6,7 +6,7 @@ on: - "main" pull_request: branches: - - '*' + - "*" concurrency: group: testing-${{ github.ref }} @@ -26,8 +26,8 @@ jobs: - id: result_step uses: mstachniuk/ci-skip@master with: - commit-filter: '[skip ci];[ci skip];[skip github]' - commit-filter-separator: ';' + commit-filter: "[skip ci];[ci skip];[skip github]" + commit-filter-separator: ";" run_unit_tests: name: Unit tests @@ -35,28 +35,28 @@ jobs: if: ${{ needs.check_skip.outputs.skip == 'false' }} runs-on: ${{ matrix.os }} strategy: - fail-fast: false - matrix: - os: ["ubuntu-latest", "macos-latest"] - python-version: ["3.8", "3.9", "3.10", "3.11", "3.12"] + fail-fast: false + matrix: + os: ["ubuntu-latest", "macos-latest"] + python-version: ["3.8", "3.9", "3.10", "3.11", "3.12"] defaults: run: shell: bash steps: - uses: actions/checkout@v2 - - name: 'Set up python' + - name: "Set up python" uses: actions/setup-python@v2 with: - python-version: ${{ matrix.python-version }} - - name: 'Install NiMARE' + python-version: ${{ matrix.python-version }} + - name: "Install NiMARE" shell: bash {0} run: pip install -e .[tests,cbmr] - - name: 'Run tests' + - name: "Run tests" shell: bash {0} run: make unittest - name: Upload artifacts - uses: actions/upload-artifact@v2 + uses: actions/upload-artifact@v4 with: name: unit_${{ matrix.os }}_${{ matrix.python-version }} path: coverage.xml @@ -68,27 +68,27 @@ jobs: if: ${{ needs.check_skip.outputs.skip == 'false' }} runs-on: ${{ matrix.os }} strategy: - fail-fast: false - matrix: - os: ["ubuntu-latest"] - python-version: ["3.8"] + fail-fast: false + matrix: + os: ["ubuntu-latest"] + python-version: ["3.8"] defaults: run: shell: bash steps: - uses: actions/checkout@v2 - - name: 'Set up python' + - name: "Set up python" uses: actions/setup-python@v2 with: - python-version: 3.8 - - name: 'Install NiMARE' + python-version: 3.8 + - name: "Install NiMARE" shell: bash {0} run: pip install -e .[minimum,tests,cbmr] - - name: 'Run tests' + - name: "Run tests" shell: bash {0} run: make unittest - name: Upload artifacts - uses: actions/upload-artifact@v2 + uses: actions/upload-artifact@v4 with: name: unit_minimum path: coverage.xml @@ -100,27 +100,27 @@ jobs: if: ${{ needs.check_skip.outputs.skip == 'false' }} runs-on: ${{ matrix.os }} strategy: - fail-fast: false - matrix: - os: ["ubuntu-latest"] - python-version: ["3.8"] + fail-fast: false + matrix: + os: ["ubuntu-latest"] + python-version: ["3.8"] defaults: run: shell: bash steps: - uses: actions/checkout@v2 - - name: 'Set up python' + - name: "Set up python" uses: actions/setup-python@v2 with: - python-version: ${{ matrix.python-version }} - - name: 'Install NiMARE' + python-version: ${{ matrix.python-version }} + - name: "Install NiMARE" shell: bash {0} run: pip install -e .[tests,cbmr] - - name: 'Run tests' + - name: "Run tests" shell: bash {0} run: make test_performance_estimators - name: Upload artifacts - uses: actions/upload-artifact@v2 + uses: actions/upload-artifact@v4 with: name: performance_estimator path: coverage.xml @@ -132,27 +132,27 @@ jobs: if: ${{ needs.check_skip.outputs.skip == 'false' }} runs-on: ${{ matrix.os }} strategy: - fail-fast: false - matrix: - os: ["ubuntu-latest"] - python-version: ["3.8"] + fail-fast: false + matrix: + os: ["ubuntu-latest"] + python-version: ["3.8"] defaults: run: shell: bash steps: - uses: actions/checkout@v2 - - name: 'Set up python' + - name: "Set up python" uses: actions/setup-python@v2 with: - python-version: ${{ matrix.python-version }} - - name: 'Install NiMARE' + python-version: ${{ matrix.python-version }} + - name: "Install NiMARE" shell: bash {0} run: pip install -e .[tests,cbmr] - - name: 'Run tests' + - name: "Run tests" shell: bash {0} run: make test_performance_correctors - name: Upload artifacts - uses: actions/upload-artifact@v2 + uses: actions/upload-artifact@v4 with: name: performance_corrector path: coverage.xml @@ -164,27 +164,27 @@ jobs: if: ${{ needs.check_skip.outputs.skip == 'false' }} runs-on: ${{ matrix.os }} strategy: - fail-fast: false - matrix: - os: ["ubuntu-latest"] - python-version: ["3.8"] + fail-fast: false + matrix: + os: ["ubuntu-latest"] + python-version: ["3.8"] defaults: run: shell: bash steps: - uses: actions/checkout@v2 - - name: 'Set up python' + - name: "Set up python" uses: actions/setup-python@v2 with: - python-version: ${{ matrix.python-version }} - - name: 'Install NiMARE' + python-version: ${{ matrix.python-version }} + - name: "Install NiMARE" shell: bash {0} run: pip install -e .[tests,cbmr] - - name: 'Run tests' + - name: "Run tests" shell: bash {0} run: make test_performance_smoke - name: Upload artifacts - uses: actions/upload-artifact@v2 + uses: actions/upload-artifact@v4 with: name: performance_smoke path: coverage.xml @@ -196,27 +196,27 @@ jobs: if: ${{ needs.check_skip.outputs.skip == 'false' }} runs-on: ${{ matrix.os }} strategy: - fail-fast: false - matrix: - os: ["ubuntu-latest"] - python-version: ["3.8"] + fail-fast: false + matrix: + os: ["ubuntu-latest"] + python-version: ["3.8"] defaults: run: shell: bash steps: - uses: actions/checkout@v2 - - name: 'Set up python' + - name: "Set up python" uses: actions/setup-python@v2 with: - python-version: ${{ matrix.python-version }} - - name: 'Install NiMARE' + python-version: ${{ matrix.python-version }} + - name: "Install NiMARE" shell: bash {0} run: pip install -e .[tests] - - name: 'Run tests' + - name: "Run tests" shell: bash {0} run: make test_cbmr_importerror - name: Upload artifacts - uses: actions/upload-artifact@v2 + uses: actions/upload-artifact@v4 with: name: cbmr_importerror path: coverage.xml @@ -224,13 +224,21 @@ jobs: upload_to_codecov: name: Upload coverage - needs: [run_unit_tests,run_unit_tests_with_minimum_dependencies,test_performance_estimators,test_performance_correctors,test_performance_smoke,test_cbmr_importerror] + needs: + [ + run_unit_tests, + run_unit_tests_with_minimum_dependencies, + test_performance_estimators, + test_performance_correctors, + test_performance_smoke, + test_cbmr_importerror, + ] runs-on: "ubuntu-latest" steps: - name: Checkout uses: actions/checkout@v2 - name: Download artifacts - uses: actions/download-artifact@v2 + uses: actions/download-artifact@v4 - name: Upload to CodeCov uses: codecov/codecov-action@v4 with: diff --git a/examples/02_meta-analyses/12_plot_ibma_workflow.py b/examples/02_meta-analyses/12_plot_ibma_workflow.py index ea0899a39..95c5459be 100644 --- a/examples/02_meta-analyses/12_plot_ibma_workflow.py +++ b/examples/02_meta-analyses/12_plot_ibma_workflow.py @@ -78,7 +78,7 @@ ############################################################################### # Contribution table # `````````````````````````````````````````````````````````````````````````````` -result.tables["z_corr-FDR_method-indep_diag-Jackknife_tab-counts_tail-positive"] +result.tables["z_corr-FDR_method-indep_diag-Jackknife_tab-counts"] ############################################################################### # Report