From 5c4288e07829a6397ba21085780ca1520269dc95 Mon Sep 17 00:00:00 2001 From: Chris Markiewicz Date: Fri, 8 Mar 2024 13:02:42 -0500 Subject: [PATCH 01/15] DOC: 0.14.0 changelog --- CHANGES.rst | 15 +++++++++++++++ 1 file changed, 15 insertions(+) diff --git a/CHANGES.rst b/CHANGES.rst index 6d1fa38462..5a61cf35cd 100644 --- a/CHANGES.rst +++ b/CHANGES.rst @@ -1,3 +1,18 @@ +0.14.0 (March 08, 2024) +======================= +New feature release in the 0.14.x series. + +This release restores correct handling of cohort identifiers in templates. +A feature release is warranted due to changes in the workflow structure. + +* FIX: Fetch templates during workflow construction (#418) +* FIX: Re-add cohort identifier to template name (#416) +* FIX: Repair FreeSurfer Dependency in Dockerfile (tcsh) (#404) +* FIX: Invert result of skull-strip check in auto mode (#402) +* STY: Adopt ruff for linting and formatting (#397) +* CHORE: Update ruff, ignore certain rules (#419) + + 0.13.2 (December 08, 2023) ========================== Bug fix release in the 0.13.x series. From ec61b58e0712895fc23a8c7b61b8a0525c8ee5b0 Mon Sep 17 00:00:00 2001 From: Chris Markiewicz Date: Wed, 6 Mar 2024 14:52:51 -0500 Subject: [PATCH 02/15] Update pyproject requirements and env.yml --- env.yml | 18 +++++++++--------- pyproject.toml | 2 +- 2 files changed, 10 insertions(+), 10 deletions(-) diff --git a/env.yml b/env.yml index 2e99487e37..6c4d96c74c 100644 --- a/env.yml +++ b/env.yml @@ -2,29 +2,29 @@ name: smriprep channels: - https://fsl.fmrib.ox.ac.uk/fsldownloads/fslconda/public/ - conda-forge -# Update this ~yearly; last updated April 2023 +# Update this ~yearly; last updated March 2024 dependencies: - - python=3.10 + - python=3.11 # Needed for svgo and bids-validator; consider moving to deno - - nodejs=18 + - nodejs=20 # Intel Math Kernel Library for numpy - - mkl=2022.1 + - mkl=2023.2 - mkl-service=2.4 # Base scientific python stack; required by FSL, so pinned here - numpy=1.26 - scipy=1.11 - matplotlib=3.8 - - pandas=2.1 + - pandas=2.2 - h5py=3.10 # Dependencies compiled against numpy, best to stick with conda - scikit-image=0.22 - - scikit-learn=1.3 + - scikit-learn=1.4 # Utilities - - graphviz=6.0 + - graphviz=9.0 - pandoc=3.1 # Workflow dependencies: ANTs - - ants=2.5.0 - # Workflow dependencies: FSL (versions pinned in 6.0.6.2) + - ants=2.5 + # Workflow dependencies: FSL (versions pinned in 6.0.7.7) - fsl-bet2=2111.4 - fsl-flirt=2111.2 - fsl-fast4=2111.3 diff --git a/pyproject.toml b/pyproject.toml index 0bd878e582..b7b3e3a16b 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -25,7 +25,7 @@ dependencies = [ "matplotlib >= 2.2.0", "nibabel >= 4.0.1", "nipype >= 1.7.0", - "niworkflows @ git+https://github.com/nipreps/niworkflows.git@master", + "niworkflows >= 1.10.1", "numpy", "packaging", "pybids >= 0.11.1", From 61e55a832dc6369d2ba88e9d1715a60bc807be9d Mon Sep 17 00:00:00 2001 From: Chris Markiewicz Date: Wed, 6 Mar 2024 14:53:12 -0500 Subject: [PATCH 03/15] chore(pin): echo "scipy<1.12" | uv pip compile --upgrade pyproject.toml -c - -p 3.11 -o requirements.txt --- requirements.txt | 93 +++++++++++++++++++----------------------------- 1 file changed, 37 insertions(+), 56 deletions(-) diff --git a/requirements.txt b/requirements.txt index fe4fbe0067..2d90f82d01 100644 --- a/requirements.txt +++ b/requirements.txt @@ -1,16 +1,12 @@ -# -# This file is autogenerated by pip-compile with Python 3.11 -# by the following command: -# -# pip-compile --strip-extras -# +# This file was autogenerated by uv via the following command: +# uv pip compile pyproject.toml -c - -p 3.11 -o requirements.txt astor==0.8.1 # via formulaic -attrs==23.1.0 +attrs==23.2.0 # via niworkflows -bids-validator==1.13.1 +bids-validator==1.14.1 # via pybids -certifi==2023.11.17 +certifi==2024.2.2 # via requests charset-normalizer==3.3.2 # via requests @@ -30,25 +26,24 @@ etelemetry==0.3.1 # via nipype filelock==3.13.1 # via nipype -fonttools==4.44.3 +fonttools==4.49.0 # via matplotlib formulaic==0.5.2 # via pybids -greenlet==3.0.1 +greenlet==3.0.3 # via sqlalchemy h5py==3.10.0 # via nitransforms -idna==3.4 +idna==3.6 # via requests -imageio==2.32.0 +imageio==2.34.0 # via scikit-image indexed-gzip==1.8.7 - # via smriprep (pyproject.toml) interface-meta==1.3.0 # via formulaic isodate==0.6.1 # via rdflib -jinja2==3.1.2 +jinja2==3.1.3 # via niworkflows joblib==1.3.2 # via @@ -59,50 +54,43 @@ kiwisolver==1.4.5 lazy-loader==0.3 # via scikit-image lockfile==0.12.2 - # via smriprep (pyproject.toml) looseversion==1.3.0 # via # nipype # niworkflows - # smriprep (pyproject.toml) -lxml==4.9.3 +lxml==5.1.0 # via # nilearn # prov # svgutils -markupsafe==2.1.3 +markupsafe==2.1.5 # via jinja2 -matplotlib==3.8.2 +matplotlib==3.8.3 # via # niworkflows # seaborn - # smriprep (pyproject.toml) networkx==3.2.1 # via # nipype # prov # scikit-image -nibabel==5.1.0 +nibabel==5.2.1 # via # nilearn # nipype # nitransforms # niworkflows # pybids - # smriprep (pyproject.toml) -nilearn==0.10.2 +nilearn==0.10.3 # via niworkflows nipype==1.8.6 - # via - # niworkflows - # smriprep (pyproject.toml) + # via niworkflows nitransforms==23.0.1 # via niworkflows -niworkflows==1.9.0 - # via smriprep (pyproject.toml) +niworkflows==1.10.1 num2words==0.5.13 # via pybids -numpy==1.26.2 +numpy==1.26.4 # via # contourpy # formulaic @@ -120,7 +108,6 @@ numpy==1.26.2 # scikit-learn # scipy # seaborn - # smriprep (pyproject.toml) # tifffile packaging==23.2 # via @@ -131,45 +118,41 @@ packaging==23.2 # nipype # niworkflows # scikit-image - # smriprep (pyproject.toml) -pandas==2.1.3 +pandas==2.2.1 # via # formulaic # nilearn # niworkflows # pybids # seaborn -pillow==10.0.1 +pillow==10.2.0 # via # imageio # matplotlib # scikit-image prov==2.0.0 # via nipype -pybids==0.16.3 +pybids==0.16.4 # via # niworkflows - # smriprep (pyproject.toml) # templateflow -pydot==1.4.2 +pydot==2.0.0 # via nipype -pyparsing==3.1.1 +pyparsing==3.1.2 # via # matplotlib # pydot # rdflib -python-dateutil==2.8.2 +python-dateutil==2.9.0.post0 # via # matplotlib # nipype # pandas # prov -pytz==2023.3.post1 +pytz==2024.1 # via pandas pyyaml==6.0.1 - # via - # niworkflows - # smriprep (pyproject.toml) + # via niworkflows rdflib==7.0.0 # via # nipype @@ -181,7 +164,7 @@ requests==2.31.0 # templateflow scikit-image==0.22.0 # via niworkflows -scikit-learn==1.3.2 +scikit-learn==1.4.1.post1 # via nilearn scipy==1.11.4 # via @@ -193,7 +176,7 @@ scipy==1.11.4 # pybids # scikit-image # scikit-learn -seaborn==0.13.0 +seaborn==0.13.2 # via niworkflows simplejson==3.19.2 # via nipype @@ -201,19 +184,17 @@ six==1.16.0 # via # isodate # python-dateutil -sqlalchemy==2.0.23 +sqlalchemy==2.0.28 # via pybids svgutils==0.3.4 # via niworkflows -templateflow==23.1.0 - # via - # niworkflows - # smriprep (pyproject.toml) -threadpoolctl==3.2.0 +templateflow==24.0.0 + # via niworkflows +threadpoolctl==3.3.0 # via scikit-learn -tifffile==2023.9.26 +tifffile==2024.2.12 # via scikit-image -tqdm==4.66.1 +tqdm==4.66.2 # via templateflow traits==6.3.2 # via @@ -221,13 +202,13 @@ traits==6.3.2 # niworkflows transforms3d==0.4.1 # via niworkflows -typing-extensions==4.8.0 +typing-extensions==4.10.0 # via # formulaic # sqlalchemy -tzdata==2023.3 +tzdata==2024.1 # via pandas -urllib3==2.1.0 +urllib3==2.2.1 # via requests wrapt==1.16.0 # via formulaic From 035c342d4e752df11ed64d1a309b8d23929ee3c6 Mon Sep 17 00:00:00 2001 From: Chris Markiewicz Date: Fri, 8 Mar 2024 13:47:41 -0500 Subject: [PATCH 04/15] chore(build): Sync Dockerfile to fmriprep --- Dockerfile | 31 ++++++++++++++++++++++--------- 1 file changed, 22 insertions(+), 9 deletions(-) diff --git a/Dockerfile b/Dockerfile index 359528bec6..986380a701 100644 --- a/Dockerfile +++ b/Dockerfile @@ -2,7 +2,7 @@ # # MIT License # -# Copyright (c) 2023 The NiPreps Developers +# Copyright (c) The NiPreps Developers # # Permission is hereby granted, free of charge, to any person obtaining a copy # of this software and associated documentation files (the "Software"), to deal @@ -23,17 +23,17 @@ # SOFTWARE. # Ubuntu 22.04 LTS - Jammy -ARG BASE_IMAGE=ubuntu:jammy-20230308 +ARG BASE_IMAGE=ubuntu:jammy-20240125 # -# sMRIPrep wheel +# Build wheel # FROM python:slim AS src RUN pip install build RUN apt-get update && \ apt-get install -y --no-install-recommends git -COPY . /src/smriprep -RUN python -m build /src/smriprep +COPY . /src +RUN python -m build /src # # Download stages @@ -41,6 +41,8 @@ RUN python -m build /src/smriprep # Utilities for downloading packages FROM ${BASE_IMAGE} as downloader +# Bump the date to current to refresh curl/certificates/etc +RUN echo "2023.07.20" RUN apt-get update && \ apt-get install -y --no-install-recommends \ binutils \ @@ -67,19 +69,30 @@ RUN mkdir /opt/workbench && \ # Micromamba FROM downloader as micromamba + +# Install a C compiler to build extensions when needed. +# traits<6.4 wheels are not available for Python 3.11+, but build easily. +RUN apt-get update && \ + apt-get install -y --no-install-recommends build-essential && \ + apt-get clean && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/* + WORKDIR / # Bump the date to current to force update micromamba -RUN echo "2023.04.05" +RUN echo "2024.03.08" RUN curl -Ls https://micro.mamba.pm/api/micromamba/linux-64/latest | tar -xvj bin/micromamba ENV MAMBA_ROOT_PREFIX="/opt/conda" COPY env.yml /tmp/env.yml COPY requirements.txt /tmp/requirements.txt +WORKDIR /tmp RUN micromamba create -y -f /tmp/env.yml && \ micromamba clean -y -a -ENV PATH="/opt/conda/envs/smriprep/bin:$PATH" -RUN /opt/conda/envs/smriprep/bin/npm install -g svgo@^3.0 bids-validator@^1.13 && \ +# UV_USE_IO_URING for apparent race-condition (https://github.com/nodejs/node/issues/48444) +# Check if this is still necessary when updating the base image. +ENV PATH="/opt/conda/envs/smriprep/bin:$PATH" \ + UV_USE_IO_URING=0 +RUN npm install -g svgo@^3.2.0 bids-validator@^1.14.0 && \ rm -r ~/.npm # @@ -179,7 +192,7 @@ ENV MKL_NUM_THREADS=1 \ OMP_NUM_THREADS=1 # Installing SMRIPREP -COPY --from=src /src/smriprep/dist/*.whl . +COPY --from=src /src/dist/*.whl . RUN pip install --no-cache-dir $( ls *.whl )[telemetry,test] RUN find $HOME -type d -exec chmod go=u {} + && \ From 61757da0e20564f25f5de6c0f2df56ca5934b976 Mon Sep 17 00:00:00 2001 From: mathiasg Date: Fri, 8 Mar 2024 15:32:42 -0500 Subject: [PATCH 05/15] CI: Bump cimg, simplify pyenv, reset cache --- .circleci/config.yml | 26 +++++++++++--------------- 1 file changed, 11 insertions(+), 15 deletions(-) diff --git a/.circleci/config.yml b/.circleci/config.yml index ace45f1b1a..3854847095 100644 --- a/.circleci/config.yml +++ b/.circleci/config.yml @@ -4,14 +4,14 @@ _machine_defaults: &machine_defaults TZ: "/usr/share/zoneinfo/America/Los_Angeles" SCRATCH: "/scratch" machine: - image: ubuntu-2204:2023.04.2 + image: default docker_layer_caching: true working_directory: /tmp/src/smriprep resource_class: large _python_defaults: &python_defaults docker: - - image: cimg/python:3.10.9 + - image: cimg/python:3.12.2 auth: username: $DOCKER_USER password: $DOCKER_PAT @@ -115,8 +115,7 @@ jobs: name: Build Docker image no_output_timeout: 60m command: | - export PY3=$( pyenv versions | awk '/^\* 3/ { print $2 }' ) - pyenv local $PY3 + pyenv local 3 pip install hatch # Get version, update files. THISVERSION=$( hatch version ) @@ -139,8 +138,7 @@ jobs: - run: name: Check Docker image command: | - export PY3=$( pyenv versions | awk '/^\* 3/ { print $2 }' ) - pyenv local $PY3 + pyenv local 3 # Get version, update files. THISVERSION=$( hatch version ) BUILT_VERSION=$( docker run --rm nipreps/smriprep:latest --version ) @@ -309,8 +307,7 @@ jobs: - run: name: Test smriprep-wrapper (Python 2) command: | - export PY2=$( pyenv versions | awk '/^\* 2/ { print $2 }' ) - pyenv local $PY2 + pyenv local 2.7 echo -n "Python version: " python --version pip install --upgrade "pip<21" @@ -322,8 +319,7 @@ jobs: - run: name: Test smriprep-wrapper (Python 3) command: | - export PY3=$( pyenv versions | awk '/^\* 3/ { print $2 }' ) - pyenv local $PY3 + pyenv local 3 echo -n "Python version: " python --version pip install --upgrade pip setuptools @@ -440,10 +436,10 @@ jobs: - run: *pull_from_registry - restore_cache: keys: - - ds005-anat-v0-{{ .Branch }}-{{ epoch }} - - ds005-anat-v0-{{ .Branch }} - - ds005-anat-v0-master - - ds005-anat-v0-next + - ds005-anat-v1-{{ .Branch }}-{{ epoch }} + - ds005-anat-v1-{{ .Branch }} + - ds005-anat-v1-master + - ds005-anat-v1-next - restore_cache: keys: - testdata-v2-{{ .Branch }}-{{ epoch }} @@ -500,7 +496,7 @@ jobs: rm -rf /tmp/ds005/work/reportlets rm -rf /tmp/ds005/work/smriprep_wf/fsdir_run_*/ - save_cache: - key: ds005-anat-v0-{{ .Branch }}-{{ epoch }} + key: ds005-anat-v1-{{ .Branch }}-{{ epoch }} paths: - /tmp/ds005/work From a2b76f9954007262fa9287f11da87b3bc8429a09 Mon Sep 17 00:00:00 2001 From: mathiasg Date: Fri, 8 Mar 2024 16:07:29 -0500 Subject: [PATCH 06/15] CI: Sort expected outputs for consistency --- .circleci/config.yml | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/.circleci/config.yml b/.circleci/config.yml index 3854847095..3c67a2d7ae 100644 --- a/.circleci/config.yml +++ b/.circleci/config.yml @@ -505,7 +505,8 @@ jobs: command: | mkdir -p /tmp/ds005/test find /tmp/ds005/derivatives -name "*" ! -path "*/figures*" -print | sed s+/tmp/ds005/derivatives/++ | sort > /tmp/ds005/test/outputs.out - diff /tmp/src/smriprep/.circleci/ds005_outputs.txt /tmp/ds005/test/outputs.out + sort /tmp/src/smriprep/.circleci/ds005_outputs.txt > /tmp/ds005/test/expected.out + diff /tmp/ds005/test/{expected,outputs}.out exit $? - store_artifacts: path: /tmp/ds005/derivatives @@ -636,7 +637,8 @@ jobs: command: | mkdir -p /tmp/ds054/test find /tmp/ds054/derivatives -path */figures -prune -o -name "*" -print | sed s+/tmp/ds054/derivatives/++ | sort > /tmp/ds054/test/outputs.out - diff /tmp/src/smriprep/.circleci/ds054_outputs.txt /tmp/ds054/test/outputs.out + sort /tmp/src/smriprep/.circleci/ds054_outputs.txt > /tmp/ds054/test/expected.out + diff /tmp/ds054/test/{expected,outputs}.out exit $? - run: name: Clean working directory From b82d14c00343d5d8b6ed6c3fd0ac64279e76a400 Mon Sep 17 00:00:00 2001 From: mathiasg Date: Mon, 11 Mar 2024 09:37:56 -0400 Subject: [PATCH 07/15] rel(0.14.0): update changes [skip ci] --- CHANGES.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CHANGES.rst b/CHANGES.rst index 5a61cf35cd..25155a24d1 100644 --- a/CHANGES.rst +++ b/CHANGES.rst @@ -1,4 +1,4 @@ -0.14.0 (March 08, 2024) +0.14.0 (March 11, 2024) ======================= New feature release in the 0.14.x series. From 1f3094388ce956a0b3abb9501491b512b1de02ce Mon Sep 17 00:00:00 2001 From: Dimitri Papadopoulos <3234522+DimitriPapadopoulos@users.noreply.github.com> Date: Thu, 21 Mar 2024 07:41:42 +0100 Subject: [PATCH 08/15] MNT: Apply Repo-Review suggestions PP302: Sets a minimum pytest to at least 6 Must have a minversion=, and must be at least 6 (first version to support pyproject.toml configuration). PP304: Sets the log level in pytest log_cli_level should be set. This will allow logs to be displayed on failures. PP305: Specifies xfail_strict xfail_strict should be set. You can manually specify if a check should be strict when setting each xfail. PP306: Specifies strict config --strict-config should be in addopts = [...]. This forces an error if a config setting is misspelled. PP307: Specifies strict markers --strict-markers should be in addopts = [...]. This forces all markers to be specified in config, avoiding misspellings. PP308: Specifies useful pytest summary An explicit summary flag like -ra should be in addopts = [...] (print summary of all fails/errors). RF201: Avoid using deprecated config settings extend-ignore deprecated, use ignore instead (identical) --- pyproject.toml | 7 +++++-- 1 file changed, 5 insertions(+), 2 deletions(-) diff --git a/pyproject.toml b/pyproject.toml index b7b3e3a16b..2809260143 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -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", From 440579be27d107fa74333e63b92228ecbe6a01ee Mon Sep 17 00:00:00 2001 From: Dimitri Papadopoulos <3234522+DimitriPapadopoulos@users.noreply.github.com> Date: Thu, 21 Mar 2024 07:47:46 +0100 Subject: [PATCH 09/15] MNT: Verbatim copy of Apache license 2.0 https://www.apache.org/licenses/LICENSE-2.0.txt --- LICENSE | 1 + 1 file changed, 1 insertion(+) 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/ From c7084cf827886519af7e56380f917ad0581fc2ab Mon Sep 17 00:00:00 2001 From: Chris Markiewicz Date: Fri, 22 Mar 2024 12:25:04 -0400 Subject: [PATCH 10/15] CI: Limit COMMIT_MSG to subject line --- .github/workflows/pythonpackage.yml | 2 ++ 1 file changed, 2 insertions(+) diff --git a/.github/workflows/pythonpackage.yml b/.github/workflows/pythonpackage.yml index 1d17c89d58..71238c97c2 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 From 19d7b3bba14a8b4938864d241712549210edb305 Mon Sep 17 00:00:00 2001 From: Chris Markiewicz Date: Fri, 22 Mar 2024 12:25:24 -0400 Subject: [PATCH 11/15] CI: Set FSLOUTPUTTYPE to avoid noise in tests --- .github/workflows/pythonpackage.yml | 1 + 1 file changed, 1 insertion(+) diff --git a/.github/workflows/pythonpackage.yml b/.github/workflows/pythonpackage.yml index 71238c97c2..54fbd840e5 100644 --- a/.github/workflows/pythonpackage.yml +++ b/.github/workflows/pythonpackage.yml @@ -79,6 +79,7 @@ jobs: env: INSTALL_TYPE: ${{ matrix.install }} + FSLOUTPUTTYPE: NIFTI_GZ steps: - uses: actions/checkout@v4 From 0ae3ff9dceef25df4052cf8501823a25dfbf5afb Mon Sep 17 00:00:00 2001 From: bpinsard Date: Wed, 20 Mar 2024 14:19:26 -0400 Subject: [PATCH 12/15] fix copy of dseg.tsv following templateflow update --- smriprep/cli/run.py | 11 ++++++++++- 1 file changed, 10 insertions(+), 1 deletion(-) diff --git a/smriprep/cli/run.py b/smriprep/cli/run.py index cb0c20f360..31cdef4dba 100644 --- a/smriprep/cli/run.py +++ b/smriprep/cli/run.py @@ -413,7 +413,16 @@ 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') From 39b796ba4e8e122fb578303c53391e01b2613a12 Mon Sep 17 00:00:00 2001 From: Chris Markiewicz Date: Fri, 22 Mar 2024 13:14:58 -0400 Subject: [PATCH 13/15] CI: Update dependabot.yml [skip ci] --- .github/dependabot.yml | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) 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/*" From fe56cc735d3886c8138673d8076677b17e118e59 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Fri, 22 Mar 2024 17:15:44 +0000 Subject: [PATCH 14/15] Build(deps): Bump the actions-infrastructure group with 2 updates Bumps the actions-infrastructure group with 2 updates: [actions/upload-artifact](https://github.com/actions/upload-artifact) and [actions/download-artifact](https://github.com/actions/download-artifact). Updates `actions/upload-artifact` from 3 to 4 - [Release notes](https://github.com/actions/upload-artifact/releases) - [Commits](https://github.com/actions/upload-artifact/compare/v3...v4) Updates `actions/download-artifact` from 3 to 4 - [Release notes](https://github.com/actions/download-artifact/releases) - [Commits](https://github.com/actions/download-artifact/compare/v3...v4) --- updated-dependencies: - dependency-name: actions/upload-artifact dependency-type: direct:production update-type: version-update:semver-major dependency-group: actions-infrastructure - dependency-name: actions/download-artifact dependency-type: direct:production update-type: version-update:semver-major dependency-group: actions-infrastructure ... Signed-off-by: dependabot[bot] --- .github/workflows/pythonpackage.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/pythonpackage.yml b/.github/workflows/pythonpackage.yml index 1d17c89d58..876fd5f422 100644 --- a/.github/workflows/pythonpackage.yml +++ b/.github/workflows/pythonpackage.yml @@ -55,7 +55,7 @@ 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/ @@ -82,7 +82,7 @@ jobs: - 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/ From ac0c57fc15293f8e8c7b98a88deee6821fca7e07 Mon Sep 17 00:00:00 2001 From: Chris Markiewicz Date: Fri, 22 Mar 2024 13:38:52 -0400 Subject: [PATCH 15/15] PIN: templateflow 24.1+ --- pyproject.toml | 2 +- requirements.txt | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/pyproject.toml b/pyproject.toml index b7b3e3a16b..03ecad03d8 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"] 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