Add support for publication size weighting. General refactoring of IBMA estimators #1125

Workflow file for this run

.github/workflows/testing.yml at 62e71b7

	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"]

	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 }}

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Add support for publication size weighting. General refactoring of IBMA estimators #1125

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Add support for publication size weighting. General refactoring of IBMA estimators #1125

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Workflow file for this run