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Fix the correlation matrix computation in Stouffers and Reports #1178

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Fix the correlation matrix computation in Stouffers and Reports

Fix the correlation matrix computation in Stouffers and Reports #1178

Workflow file for this run

.github/workflows/testing.yml at e7f1e42
name: "Run Tests"
on:
push:
branches:
- "main"
pull_request:
branches:
- '*'
concurrency:
group: testing-${{ github.ref }}
cancel-in-progress: true
jobs:
# Determine if tests should be run based on commit message.
check_skip:
name: Determine if CI should be skipped
runs-on: ubuntu-latest
outputs:
skip: ${{ steps.result_step.outputs.ci-skip }}
steps:
- uses: actions/checkout@v2
with:
fetch-depth: 0
- id: result_step
uses: mstachniuk/ci-skip@master
with:
commit-filter: '[skip ci];[ci skip];[skip github]'
commit-filter-separator: ';'
run_unit_tests:
name: Unit tests
needs: check_skip
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"]
defaults:
run:
shell: bash
steps:
- uses: actions/checkout@v2
- name: 'Set up python'
uses: actions/setup-python@v2
with:
python-version: ${{ matrix.python-version }}
- name: 'Install NiMARE'
shell: bash {0}
run: pip install -e .[tests,cbmr]
- name: 'Run tests'
shell: bash {0}
run: make unittest
- name: Upload artifacts
uses: actions/upload-artifact@v2
with:
name: unit_${{ matrix.os }}_${{ matrix.python-version }}
path: coverage.xml
if: success()
run_unit_tests_with_minimum_dependencies:
name: Unit tests with minimum dependency versions
needs: check_skip
if: ${{ needs.check_skip.outputs.skip == 'false' }}
runs-on: ${{ matrix.os }}
strategy:
fail-fast: false
matrix:
os: ["ubuntu-latest"]
python-version: ["3.8"]
defaults:
run:
shell: bash
steps:
- uses: actions/checkout@v2
- name: 'Set up python'
uses: actions/setup-python@v2
with:
python-version: 3.8
- name: 'Install NiMARE'
shell: bash {0}
run: pip install -e .[minimum,tests,cbmr]
- name: 'Run tests'
shell: bash {0}
run: make unittest
- name: Upload artifacts
uses: actions/upload-artifact@v2
with:
name: unit_minimum
path: coverage.xml
if: success()
test_performance_estimators:
name: Estimator performance tests
needs: check_skip
if: ${{ needs.check_skip.outputs.skip == 'false' }}
runs-on: ${{ matrix.os }}
strategy:
fail-fast: false
matrix:
os: ["ubuntu-latest"]
python-version: ["3.8"]
defaults:
run:
shell: bash
steps:
- uses: actions/checkout@v2
- name: 'Set up python'
uses: actions/setup-python@v2
with:
python-version: ${{ matrix.python-version }}
- name: 'Install NiMARE'
shell: bash {0}
run: pip install -e .[tests,cbmr]
- name: 'Run tests'
shell: bash {0}
run: make test_performance_estimators
- name: Upload artifacts
uses: actions/upload-artifact@v2
with:
name: performance_estimator
path: coverage.xml
if: success()
test_performance_correctors:
name: Corrector performance tests
needs: check_skip
if: ${{ needs.check_skip.outputs.skip == 'false' }}
runs-on: ${{ matrix.os }}
strategy:
fail-fast: false
matrix:
os: ["ubuntu-latest"]
python-version: ["3.8"]
defaults:
run:
shell: bash
steps:
- uses: actions/checkout@v2
- name: 'Set up python'
uses: actions/setup-python@v2
with:
python-version: ${{ matrix.python-version }}
- name: 'Install NiMARE'
shell: bash {0}
run: pip install -e .[tests,cbmr]
- name: 'Run tests'
shell: bash {0}
run: make test_performance_correctors
- name: Upload artifacts
uses: actions/upload-artifact@v2
with:
name: performance_corrector
path: coverage.xml
if: success()
test_performance_smoke:
name: Smoke performance tests
needs: check_skip
if: ${{ needs.check_skip.outputs.skip == 'false' }}
runs-on: ${{ matrix.os }}
strategy:
fail-fast: false
matrix:
os: ["ubuntu-latest"]
python-version: ["3.8"]
defaults:
run:
shell: bash
steps:
- uses: actions/checkout@v2
- name: 'Set up python'
uses: actions/setup-python@v2
with:
python-version: ${{ matrix.python-version }}
- name: 'Install NiMARE'
shell: bash {0}
run: pip install -e .[tests,cbmr]
- name: 'Run tests'
shell: bash {0}
run: make test_performance_smoke
- name: Upload artifacts
uses: actions/upload-artifact@v2
with:
name: performance_smoke
path: coverage.xml
if: success()
test_cbmr_importerror:
name: CBMR ImportError tests
needs: check_skip
if: ${{ needs.check_skip.outputs.skip == 'false' }}
runs-on: ${{ matrix.os }}
strategy:
fail-fast: false
matrix:
os: ["ubuntu-latest"]
python-version: ["3.8"]
defaults:
run:
shell: bash
steps:
- uses: actions/checkout@v2
- name: 'Set up python'
uses: actions/setup-python@v2
with:
python-version: ${{ matrix.python-version }}
- name: 'Install NiMARE'
shell: bash {0}
run: pip install -e .[tests]
- name: 'Run tests'
shell: bash {0}
run: make test_cbmr_importerror
- name: Upload artifacts
uses: actions/upload-artifact@v2
with:
name: cbmr_importerror
path: coverage.xml
if: success()
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]
runs-on: "ubuntu-latest"
steps:
- name: Checkout
uses: actions/checkout@v2
- name: Download artifacts
uses: actions/download-artifact@v2
- name: Upload to CodeCov
uses: codecov/codecov-action@v4
with:
fail_ci_if_error: true
env:
CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}