diff --git a/.github/workflows/docker.yml b/.github/workflows/docker.yml index 7f20d55..cb8c60a 100644 --- a/.github/workflows/docker.yml +++ b/.github/workflows/docker.yml @@ -21,7 +21,7 @@ jobs: uses: actions/checkout@v4 - name: Set up Docker Buildx - uses: docker/setup-buildx-action@v3.6.1 + uses: docker/setup-buildx-action@v3.7.1 - name: Log in to Docker Hub uses: docker/login-action@v3.3.0 @@ -31,7 +31,7 @@ jobs: - name: Extract metadata (tags, labels) for Docker id: meta - uses: docker/metadata-action@v5.5.1 + uses: docker/metadata-action@v5.6.1 with: images: nipreps/fmripost-aroma # generate Docker tags based on the following events/attributes @@ -40,7 +40,7 @@ jobs: type=semver,pattern={{version}} - name: Build and push Docker image - uses: docker/build-push-action@v6.9.0 + uses: docker/build-push-action@v6.10.0 with: context: . push: true diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml index dc8966d..94f9805 100644 --- a/.github/workflows/test.yml +++ b/.github/workflows/test.yml @@ -64,7 +64,7 @@ jobs: run: tox c - name: Run tox run: tox -v --exit-and-dump-after 1200 - - uses: codecov/codecov-action@v4 + - uses: codecov/codecov-action@v5 if: ${{ always() }} with: files: cov.xml diff --git a/.zenodo.json b/.zenodo.json index 7034140..bc905cb 100644 --- a/.zenodo.json +++ b/.zenodo.json @@ -18,6 +18,11 @@ }, { "name": "Caballero Gaudes, Cesar" + }, + { + "affiliation": "Department of Psychology, University of Southern California", + "name": "Zimmerman, Jacob C.", + "orcid": "0000-0002-6010-8086" } ], "creators": [ diff --git a/src/fmripost_aroma/cli/run.py b/src/fmripost_aroma/cli/run.py index 3bf621b..a27ecbf 100644 --- a/src/fmripost_aroma/cli/run.py +++ b/src/fmripost_aroma/cli/run.py @@ -223,7 +223,7 @@ def main(): if sentry_sdk is not None and failed_reports: sentry_sdk.capture_message( - 'Report generation failed for %d subjects' % failed_reports, + f'Report generation failed for {failed_reports} subjects', level='error', ) sys.exit(int((errno + len(failed_reports)) > 0)) diff --git a/src/fmripost_aroma/config.py b/src/fmripost_aroma/config.py index 624a098..098a9cd 100644 --- a/src/fmripost_aroma/config.py +++ b/src/fmripost_aroma/config.py @@ -149,7 +149,7 @@ # Just get so analytics track one hit from contextlib import suppress - from requests import ConnectionError, ReadTimeout + from requests import ConnectionError, ReadTimeout # noqa: A004 from requests import get as _get_url with suppress((ConnectionError, ReadTimeout)): diff --git a/src/fmripost_aroma/data/io_spec.json b/src/fmripost_aroma/data/io_spec.json index 164d960..d75a6bf 100644 --- a/src/fmripost_aroma/data/io_spec.json +++ b/src/fmripost_aroma/data/io_spec.json @@ -138,7 +138,6 @@ }, "anat2mni152nlin6asym": { "datatype": "anat", - "run": null, "from": ["anat", "T1w", "T2w"], "to": "MNI152NLin6Asym", "space": null, diff --git a/src/fmripost_aroma/interfaces/confounds.py b/src/fmripost_aroma/interfaces/confounds.py index fd6489f..6de5cd4 100644 --- a/src/fmripost_aroma/interfaces/confounds.py +++ b/src/fmripost_aroma/interfaces/confounds.py @@ -91,7 +91,7 @@ def _get_ica_confounds(mixing, aroma_features, skip_vols, newpath=None): # Return dummy list of ones if no noise components were found if motion_ics.size == 0: - config.loggers.interfaces.warning('No noise components were classified') + config.loggers.interface.warning('No noise components were classified') return None, mixing_out # return dummy lists of zeros if no signal components were found