From 5d5b065ba50e3143252dea4ef66368b145d87763 Mon Sep 17 00:00:00 2001 From: Jacob Zimmerman Date: Thu, 31 Oct 2024 04:32:40 -0700 Subject: [PATCH 1/6] FIX: Gracefully warn when no motion components are found (#83) --- .zenodo.json | 5 +++++ src/fmripost_aroma/interfaces/confounds.py | 2 +- 2 files changed, 6 insertions(+), 1 deletion(-) 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/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 From c69585a3be16b37fba23eb7a6de41f151190a850 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Sun, 17 Nov 2024 10:36:59 -0500 Subject: [PATCH 2/6] Bump docker/setup-buildx-action from 3.6.1 to 3.7.1 (#84) Signed-off-by: dependabot[bot] Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> --- .github/workflows/docker.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/docker.yml b/.github/workflows/docker.yml index 7f20d55..8378145 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 From 88a4f4149686f804b60d90611e173854f198e396 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Sun, 1 Dec 2024 10:38:53 -0500 Subject: [PATCH 3/6] Bump docker/metadata-action from 5.5.1 to 5.6.1 (#89) Signed-off-by: dependabot[bot] Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> --- .github/workflows/docker.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/docker.yml b/.github/workflows/docker.yml index 8378145..58986d8 100644 --- a/.github/workflows/docker.yml +++ b/.github/workflows/docker.yml @@ -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 From 24a026a85675dff2ef9291c61d72ba4c88c3d879 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Sun, 1 Dec 2024 10:41:45 -0500 Subject: [PATCH 4/6] Bump docker/build-push-action from 6.9.0 to 6.10.0 (#87) Signed-off-by: dependabot[bot] Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> --- .github/workflows/docker.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/docker.yml b/.github/workflows/docker.yml index 58986d8..cb8c60a 100644 --- a/.github/workflows/docker.yml +++ b/.github/workflows/docker.yml @@ -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 From 990d17527b7b05f0daca9a7b0a508cf642373cbd Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Sun, 1 Dec 2024 10:41:52 -0500 Subject: [PATCH 5/6] Bump codecov/codecov-action from 4 to 5 (#88) Signed-off-by: dependabot[bot] Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> --- .github/workflows/test.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) 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 From cf32223721b21c4f8c46cbca413d7c6bbeb6b8bb Mon Sep 17 00:00:00 2001 From: Taylor Salo Date: Tue, 10 Dec 2024 10:22:43 -0500 Subject: [PATCH 6/6] Allow run entity in transform filename (#90) --- src/fmripost_aroma/cli/run.py | 2 +- src/fmripost_aroma/config.py | 2 +- src/fmripost_aroma/data/io_spec.json | 1 - 3 files changed, 2 insertions(+), 3 deletions(-) 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 9d7507d..8b635a7 100644 --- a/src/fmripost_aroma/data/io_spec.json +++ b/src/fmripost_aroma/data/io_spec.json @@ -137,7 +137,6 @@ }, "anat2mni152nlin6asym": { "datatype": "anat", - "run": null, "from": ["anat", "T1w", "T2w"], "to": "MNI152NLin6Asym", "space": null,