diff --git a/.github/dependabot.yml b/.github/dependabot.yml index dfd0e30861..cdd849b6ab 100644 --- a/.github/dependabot.yml +++ b/.github/dependabot.yml @@ -2,9 +2,12 @@ version: 2 updates: - - package-ecosystem: "github-actions" directory: "/" schedule: # Check for updates to GitHub Actions every week interval: "weekly" + groups: + actions-infrastructure: + patterns: + - "actions/*" diff --git a/.github/workflows/pythonpackage.yml b/.github/workflows/pythonpackage.yml index 1d17c89d58..2e37dd8637 100644 --- a/.github/workflows/pythonpackage.yml +++ b/.github/workflows/pythonpackage.yml @@ -35,6 +35,8 @@ jobs: run: | if [[ -z "$COMMIT_MSG" ]]; then COMMIT_MSG=$(git show -s --format=%s) + else + COMMIT_MSG=$(echo $COMMIT_MSG | head -n 1) fi echo $COMMIT_MSG echo "commit_message=$COMMIT_MSG" >> $GITHUB_OUTPUT @@ -55,7 +57,7 @@ jobs: run: pipx run build - name: Check distributions run: pipx run twine check dist/* - - uses: actions/upload-artifact@v3 + - uses: actions/upload-artifact@v4 with: name: dist path: dist/ @@ -77,12 +79,13 @@ jobs: env: INSTALL_TYPE: ${{ matrix.install }} + FSLOUTPUTTYPE: NIFTI_GZ steps: - uses: actions/checkout@v4 if: matrix.install == 'repo' || matrix.install == 'editable' - name: Fetch packages - uses: actions/download-artifact@v3 + uses: actions/download-artifact@v4 with: name: dist path: dist/ diff --git a/LICENSE b/LICENSE index 261eeb9e9f..d645695673 100644 --- a/LICENSE +++ b/LICENSE @@ -1,3 +1,4 @@ + Apache License Version 2.0, January 2004 http://www.apache.org/licenses/ diff --git a/pyproject.toml b/pyproject.toml index b7b3e3a16b..7730a84dd1 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -30,7 +30,7 @@ dependencies = [ "packaging", "pybids >= 0.11.1", "pyyaml", - "templateflow >= 0.6", + "templateflow >= 24.1", ] dynamic = ["version"] @@ -115,8 +115,11 @@ per-file-ignores = [ ] [tool.pytest.ini_options] +minversion = "7" +log_cli_level = "INFO" +xfail_strict = true norecursedirs = [".git"] -addopts = "-svx --doctest-modules" +addopts = ["-svx", "--doctest-modules", "-ra", "--strict-config", "--strict-markers"] doctest_optionflags = "ALLOW_UNICODE NORMALIZE_WHITESPACE ELLIPSIS" env = "PYTHONHASHSEED=0" filterwarnings = ["ignore::DeprecationWarning"] @@ -163,7 +166,7 @@ extend-select = [ "PT", "Q", ] -extend-ignore = [ +ignore = [ "S311", # We are not using random for cryptographic purposes "ISC001", "S603", diff --git a/requirements.txt b/requirements.txt index 2d90f82d01..4e14b12178 100644 --- a/requirements.txt +++ b/requirements.txt @@ -188,7 +188,7 @@ sqlalchemy==2.0.28 # via pybids svgutils==0.3.4 # via niworkflows -templateflow==24.0.0 +templateflow==24.2.0 # via niworkflows threadpoolctl==3.3.0 # via scikit-learn diff --git a/smriprep/cli/run.py b/smriprep/cli/run.py index 0eb6f2322b..5510bcbb65 100644 --- a/smriprep/cli/run.py +++ b/smriprep/cli/run.py @@ -420,7 +420,16 @@ def _warn_redirect(message, category, filename, lineno, file=None, line=None): from niworkflows.utils.misc import _copy_any from templateflow import api - dseg_tsv = str(api.get('fsaverage', suffix='dseg', extension=['.tsv'])) + dseg_tsv = str( + api.get( + 'fsaverage', + hemi=None, + atlas=None, + segmentation='aparc', + suffix='dseg', + extension=['.tsv'], + ) + ) _copy_any(dseg_tsv, str(Path(output_dir) / 'smriprep' / 'desc-aseg_dseg.tsv')) _copy_any(dseg_tsv, str(Path(output_dir) / 'smriprep' / 'desc-aparcaseg_dseg.tsv')) logger.log(25, 'sMRIPrep finished without errors')