diff --git a/.circleci/config.yml b/.circleci/config.yml index 562fa7b14..b82f1b539 100644 --- a/.circleci/config.yml +++ b/.circleci/config.yml @@ -40,6 +40,12 @@ _pull_from_registry: &pull_from_registry docker pull localhost:5000/fmriprep docker tag localhost:5000/fmriprep nipreps/fmriprep:latest +_pull_test_image_from_registry: &pull_test_image_from_registry + name: Pull and tag image from local registry + command: | + docker pull localhost:5000/fmriprep-test + docker tag localhost:5000/fmriprep-test nipreps/fmriprep:test + _check_skip_job: &check_skip_job name: Check commit message and determine if job should be skipped command: | @@ -172,7 +178,7 @@ jobs: name: Create named builder command: docker buildx create --use --name=builder --driver=docker-container - run: - name: Build Docker image + name: Build Docker image (production environment) no_output_timeout: 60m command: | pyenv local 3 @@ -194,11 +200,23 @@ jobs: --build-arg BUILD_DATE=`date -u +"%Y-%m-%dT%H:%M:%SZ"` \ --build-arg VCS_REF=`git rev-parse --short HEAD` \ --build-arg VERSION="${CIRCLE_TAG:-$THISVERSION}" . + - run: + name: Build Docker image (test environment) + no_output_timeout: 60m + command: | + docker buildx build --load --builder builder \ + --cache-from localhost:5000/fmriprep \ + --cache-from nipreps/fmriprep:latest \ + -t nipreps/fmriprep:test \ + --platform linux/amd64 \ + --target test . - run: command: docker images - run: - name: Check Docker image + name: Check Docker image (production) command: | + hatch version + docker run --rm nipreps/fmriprep:latest --version # Get version, update files. THISVERSION=$( hatch version ) BUILT_VERSION=$( docker run --rm nipreps/fmriprep:latest --version ) @@ -208,12 +226,19 @@ jobs: echo "BUILT: \"$BUILT_VERSION\"" set -e test "$BUILT_VERSION" = "$THISVERSION" + - run: + name: Check Docker image (test) + command: | + docker run --rm nipreps/fmriprep:test fmriprep --version + docker run --rm nipreps/fmriprep:test pytest --version - run: name: Docker push to local registry no_output_timeout: 40m command: | docker tag nipreps/fmriprep:latest localhost:5000/fmriprep + docker tag nipreps/fmriprep:test localhost:5000/fmriprep-test docker push localhost:5000/fmriprep + docker push localhost:5000/fmriprep-test - run: name: Docker registry garbage collection command: | @@ -368,7 +393,7 @@ jobs: - docker/install-docker-credential-helper - run: *docker_auth - run: *setup_docker_registry - - run: *pull_from_registry + - run: *pull_test_image_from_registry - run: name: Run fMRIPrep tests no_output_timeout: 2h diff --git a/.dockerignore b/.dockerignore index 9fdac0a3b..839c5bbce 100644 --- a/.dockerignore +++ b/.dockerignore @@ -12,3 +12,5 @@ fmriprep.egg-info/**/* fmriprep.egg-info .eggs/**/* .eggs + +.pixi diff --git a/.gitattributes b/.gitattributes index 00a7b00c9..9851bd8e5 100644 --- a/.gitattributes +++ b/.gitattributes @@ -1 +1,3 @@ .git_archival.txt export-subst +# SCM syntax highlighting & preventing 3-way merges +pixi.lock merge=binary linguist-language=YAML linguist-generated=true diff --git a/.gitignore b/.gitignore index 96fcdbb2f..fdd19da9d 100644 --- a/.gitignore +++ b/.gitignore @@ -81,3 +81,6 @@ local_settings.py *.swp _version.py +# pixi environments +.pixi/* +!.pixi/config.toml diff --git a/Dockerfile b/Dockerfile index ed4c594ac..38b70963c 100644 --- a/Dockerfile +++ b/Dockerfile @@ -23,15 +23,53 @@ # SOFTWARE. # Ubuntu 22.04 LTS - Jammy -ARG BASE_IMAGE=ubuntu:jammy-20240125 +ARG BASE_IMAGE=ubuntu:jammy-20250730 # -# Build wheel +# Build pixi environment +# The Pixi environment includes: +# - Python +# - Scientific Python stack (via conda-forge) +# - General Python dependencies (via PyPI) +# - NodeJS +# - bids-validator +# - svgo +# - FSL (via fslconda) +# - ants (via conda-forge) +# - connectome-workbench (via conda-forge) +# - ... # -FROM ghcr.io/astral-sh/uv:python3.12-alpine AS src -RUN apk add git -COPY . /src -RUN uvx --from build pyproject-build --installer uv -w /src +FROM ghcr.io/prefix-dev/pixi:0.53.0 AS build +RUN apt-get update && \ + apt-get install -y --no-install-recommends \ + ca-certificates \ + git && \ + apt-get clean && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/* +# Run post-link scripts during install, but use global to keep out of source tree +RUN pixi config set --global run-post-link-scripts insecure + +# Install dependencies before the package itself to leverage caching +RUN mkdir /app +COPY pixi.lock pyproject.toml /app +WORKDIR /app +RUN --mount=type=cache,target=/root/.cache/rattler pixi install -e fmriprep -e test --frozen --skip fmriprep +RUN --mount=type=cache,target=/root/.npm pixi run --as-is -e fmriprep npm install -g svgo@^3.2.0 bids-validator@1.14.10 +# Note that PATH gets hard-coded. Remove it and re-apply in final image +RUN pixi shell-hook -e fmriprep --as-is | grep -v PATH > /shell-hook.sh +RUN pixi shell-hook -e test --as-is | grep -v PATH > /test-shell-hook.sh + +# Finally, install the package +COPY . /app +RUN --mount=type=cache,target=/root/.cache/rattler pixi install -e fmriprep -e test --frozen + +# +# Pre-fetch templates +# +FROM ghcr.io/astral-sh/uv:python3.12-alpine AS templates +ENV TEMPLATEFLOW_HOME="/templateflow" +RUN uv pip install --system templateflow +COPY scripts/fetch_templates.py fetch_templates.py +RUN python fetch_templates.py # # Download stages @@ -39,8 +77,12 @@ RUN uvx --from build pyproject-build --installer uv -w /src # Utilities for downloading packages FROM ${BASE_IMAGE} AS downloader +ENV DEBIAN_FRONTEND="noninteractive" \ + LANG="en_US.UTF-8" \ + LC_ALL="en_US.UTF-8" + # Bump the date to current to refresh curl/certificates/etc -RUN echo "2023.07.20" +RUN echo "2025.08.20" RUN apt-get update && \ apt-get install -y --no-install-recommends \ binutils \ @@ -56,59 +98,15 @@ COPY docker/files/freesurfer7.3.2-exclude.txt /usr/local/etc/freesurfer7.3.2-exc RUN curl -sSL https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/7.3.2/freesurfer-linux-ubuntu22_amd64-7.3.2.tar.gz \ | tar zxv --no-same-owner -C /opt --exclude-from=/usr/local/etc/freesurfer7.3.2-exclude.txt -# AFNI -FROM downloader AS afni -# Bump the date to current to update AFNI -RUN echo "2023.07.20" -RUN mkdir -p /opt/afni-latest \ - && curl -fsSL --retry 5 https://afni.nimh.nih.gov/pub/dist/tgz/linux_openmp_64.tgz \ - | tar -xz -C /opt/afni-latest --strip-components 1 \ - --exclude "linux_openmp_64/*.gz" \ - --exclude "linux_openmp_64/funstuff" \ - --exclude "linux_openmp_64/shiny" \ - --exclude "linux_openmp_64/afnipy" \ - --exclude "linux_openmp_64/lib/RetroTS" \ - --exclude "linux_openmp_64/lib_RetroTS" \ - --exclude "linux_openmp_64/meica.libs" \ - # Keep only what we use - && find /opt/afni-latest -type f -not \( \ - -name "3dTshift" -or \ - -name "3dUnifize" -or \ - -name "3dAutomask" -or \ - -name "3dvolreg" \) -delete - -# 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 "2024.02.06" -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 - -# 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/fmriprep/bin:$PATH" \ - UV_USE_IO_URING=0 -RUN npm install -g svgo@^3.2.0 bids-validator@1.14.10 && \ - rm -r ~/.npm +# MSM HOCR (Nov 19, 2019 release) +FROM downloader AS msm +RUN curl -L -H "Accept: application/octet-stream" https://api.github.com/repos/ecr05/MSM_HOCR/releases/assets/16253707 -o /usr/local/bin/msm \ + && chmod +x /usr/local/bin/msm # # Main stage # -FROM ${BASE_IMAGE} AS fmriprep +FROM ${BASE_IMAGE} AS base # Configure apt ENV DEBIAN_FRONTEND="noninteractive" \ @@ -121,50 +119,36 @@ RUN apt-get update && \ bc \ ca-certificates \ curl \ - git \ - gnupg \ + libgomp1 \ + libopenblas0-openmp \ lsb-release \ netbase \ xvfb && \ apt-get clean && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/* -# Configure PPAs for libpng12 and libxp6 -RUN GNUPGHOME=/tmp gpg --keyserver hkps://keyserver.ubuntu.com --no-default-keyring --keyring /usr/share/keyrings/linuxuprising.gpg --recv 0xEA8CACC073C3DB2A \ - && GNUPGHOME=/tmp gpg --keyserver hkps://keyserver.ubuntu.com --no-default-keyring --keyring /usr/share/keyrings/zeehio.gpg --recv 0xA1301338A3A48C4A \ - && echo "deb [signed-by=/usr/share/keyrings/linuxuprising.gpg] https://ppa.launchpadcontent.net/linuxuprising/libpng12/ubuntu jammy main" > /etc/apt/sources.list.d/linuxuprising.list \ - && echo "deb [signed-by=/usr/share/keyrings/zeehio.gpg] https://ppa.launchpadcontent.net/zeehio/libxp/ubuntu jammy main" > /etc/apt/sources.list.d/zeehio.list - -# Dependencies for AFNI; requires a discontinued multiarch-support package from bionic (18.04) -RUN apt-get update -qq \ - && apt-get install -y -q --no-install-recommends \ - ed \ - gsl-bin \ - libglib2.0-0 \ - libglu1-mesa-dev \ - libglw1-mesa \ - libgomp1 \ - libjpeg62 \ - libpng12-0 \ - libxm4 \ - libxp6 \ - netpbm \ - tcsh \ - xfonts-base \ - xvfb \ - && curl -sSL --retry 5 -o /tmp/multiarch.deb http://archive.ubuntu.com/ubuntu/pool/main/g/glibc/multiarch-support_2.27-3ubuntu1.5_amd64.deb \ - && dpkg -i /tmp/multiarch.deb \ - && rm /tmp/multiarch.deb \ - && apt-get install -f \ - && apt-get clean && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/* \ - && gsl2_path="$(find / -name 'libgsl.so.19' || printf '')" \ - && if [ -n "$gsl2_path" ]; then \ - ln -sfv "$gsl2_path" "$(dirname $gsl2_path)/libgsl.so.0"; \ - fi \ - && ldconfig - -# Install files from stages -COPY --from=freesurfer /opt/freesurfer /opt/freesurfer -COPY --from=afni /opt/afni-latest /opt/afni-latest + +# Install downloaded files from stages +COPY --link --from=freesurfer /opt/freesurfer /opt/freesurfer +COPY --link --from=msm /usr/local/bin/msm /usr/local/bin/msm + +# Install AFNI from Docker container +# Find libraries with `ldd $BINARIES | grep afni` +COPY --link --from=afni/afni_cmake_build:AFNI_25.2.08 \ + /opt/afni/install/usr/local/lib/lib3DEdge.so \ + /opt/afni/install/usr/local/lib/libeispack.so \ + /opt/afni/install/usr/local/lib/libf2c.so \ + /opt/afni/install/usr/local/lib/libgiftiio.so.0 \ + /opt/afni/install/usr/local/lib/libmri.so \ + /opt/afni/install/usr/local/lib/libnifti2.so.2 \ + /opt/afni/install/usr/local/lib/libnifticdf.so.2 \ + /opt/afni/install/usr/local/lib/libznz.so.3 \ + /usr/local/lib +COPY --link --from=afni/afni_cmake_build:AFNI_25.2.08 \ + /opt/afni/install/usr/local/bin/3dAutomask \ + /opt/afni/install/usr/local/bin/3dTshift \ + /opt/afni/install/usr/local/bin/3dUnifize \ + /opt/afni/install/usr/local/bin/3dvolreg \ + /usr/local/bin # Simulate SetUpFreeSurfer.sh ENV OS="Linux" \ @@ -184,38 +168,19 @@ ENV PERL5LIB="$MINC_LIB_DIR/perl5/5.8.5" \ PATH="$FREESURFER_HOME/bin:$FREESURFER_HOME/tktools:$MINC_BIN_DIR:$PATH" # AFNI config -ENV PATH="/opt/afni-latest:$PATH" \ - AFNI_IMSAVE_WARNINGS="NO" \ - AFNI_PLUGINPATH="/opt/afni-latest" +ENV AFNI_IMSAVE_WARNINGS="NO" # Create a shared $HOME directory RUN useradd -m -s /bin/bash -G users fmriprep WORKDIR /home/fmriprep -ENV HOME="/home/fmriprep" \ - LD_LIBRARY_PATH="/usr/lib/x86_64-linux-gnu:$LD_LIBRARY_PATH" +ENV HOME="/home/fmriprep" -COPY --from=micromamba /bin/micromamba /bin/micromamba -COPY --from=micromamba /opt/conda/envs/fmriprep /opt/conda/envs/fmriprep - -ENV MAMBA_ROOT_PREFIX="/opt/conda" -RUN micromamba shell init -s bash && \ - echo "micromamba activate fmriprep" >> $HOME/.bashrc -ENV PATH="/opt/conda/envs/fmriprep/bin:$PATH" \ - CPATH="/opt/conda/envs/fmriprep/include:$CPATH" \ - LD_LIBRARY_PATH="/opt/conda/envs/fmriprep/lib:$LD_LIBRARY_PATH" - -# Precaching atlases -COPY scripts/fetch_templates.py fetch_templates.py -RUN python fetch_templates.py && \ - rm fetch_templates.py && \ - find $HOME/.cache/templateflow -type d -exec chmod go=u {} + && \ - find $HOME/.cache/templateflow -type f -exec chmod go=u {} + +COPY --link --from=templates /templateflow /home/fmriprep/.cache/templateflow # FSL environment ENV LANG="C.UTF-8" \ LC_ALL="C.UTF-8" \ PYTHONNOUSERSITE=1 \ - FSLDIR="/opt/conda/envs/fmriprep" \ FSLOUTPUTTYPE="NIFTI_GZ" \ FSLMULTIFILEQUIT="TRUE" \ FSLLOCKDIR="" \ @@ -228,24 +193,31 @@ ENV LANG="C.UTF-8" \ ENV MKL_NUM_THREADS=1 \ OMP_NUM_THREADS=1 -# MSM HOCR (Nov 19, 2019 release) -RUN curl -L -H "Accept: application/octet-stream" https://api.github.com/repos/ecr05/MSM_HOCR/releases/assets/16253707 -o /usr/local/bin/msm \ - && chmod +x /usr/local/bin/msm +WORKDIR /tmp + +FROM base AS test -# Installing FMRIPREP -COPY --from=src /src/dist/*.whl . -RUN pip install --no-cache-dir $( ls *.whl )[container,test] +COPY --link --from=build /app/.pixi/envs/test /app/.pixi/envs/test +COPY --link --from=build /test-shell-hook.sh /shell-hook.sh +RUN cat /shell-hook.sh >> $HOME/.bashrc +ENV PATH="/app/.pixi/envs/test/bin:$PATH" -RUN find $HOME -type d -exec chmod go=u {} + && \ - find $HOME -type f -exec chmod go=u {} + && \ - rm -rf $HOME/.npm $HOME/.conda $HOME/.empty +ENV FSLDIR="/app/.pixi/envs/test" + +FROM base AS fmriprep + +# Keep synced with wrapper's PKG_PATH +COPY --link --from=build /app/.pixi/envs/fmriprep /app/.pixi/envs/fmriprep +COPY --link --from=build /shell-hook.sh /shell-hook.sh +RUN cat /shell-hook.sh >> $HOME/.bashrc +ENV PATH="/app/.pixi/envs/fmriprep/bin:$PATH" + +ENV FSLDIR="/app/.pixi/envs/fmriprep" # For detecting the container ENV IS_DOCKER_8395080871=1 -RUN ldconfig -WORKDIR /tmp -ENTRYPOINT ["/opt/conda/envs/fmriprep/bin/fmriprep"] +ENTRYPOINT ["/app/.pixi/envs/fmriprep/bin/fmriprep"] ARG BUILD_DATE ARG VCS_REF diff --git a/constraints.txt b/constraints.txt deleted file mode 100644 index 4928cdc32..000000000 --- a/constraints.txt +++ /dev/null @@ -1,7 +0,0 @@ -# 25.1.x -nireports ~= 25.0.1 -nitransforms ~= 24.1.2 -niworkflows ~= 1.13.5 -sdcflows ~= 2.13.2 -smriprep ~= 0.18.0 -templateflow ~= 24.2.2 diff --git a/env.yml b/env.yml deleted file mode 100644 index 13fc97b78..000000000 --- a/env.yml +++ /dev/null @@ -1,44 +0,0 @@ -name: fmriprep -channels: - - https://fsl.fmrib.ox.ac.uk/fsldownloads/fslconda/public/ - - conda-forge -# Update this ~yearly; last updated Mar 2025 -dependencies: - - python=3.12 - # Needed for svgo and bids-validator; consider moving to deno - - nodejs=20 - # Intel Math Kernel Library for numpy - - mkl=2024.2.2 - - mkl-service=2.4.2 - # git-annex for templateflow users with DataLad superdatasets - - git-annex=*=alldep* - # Base scientific python stack; required by FSL, so pinned here - - numpy=2.2 - - scipy=1.15 - - matplotlib=3.10 - - pandas=2.2 - - h5py=3.13 - # Dependencies compiled against numpy, best to stick with conda - - nitime=0.11 - - scikit-image=0.25 - - scikit-learn=1.6 - # Utilities - - graphviz=12.2 - - pandoc=3.7 - # Workflow dependencies: ANTs - - ants=2.6 - # Workflow dependencies: Connectome Workbench - - connectome-workbench-cli=2.0 - # Workflow dependencies: FSL (versions pinned in 6.0.7.17.20250415.fe1c582e) - - fsl-bet2=2111.8 - - fsl-flirt=2111.4 - - fsl-fast4=2111.3 - - fsl-fugue=2201.5 - - fsl-mcflirt=2111.0 - - fsl-miscmaths=2412.4 - - fsl-topup=2203.5 - - pip - - pip: - - -r requirements.txt -variables: - FSLOUTPUTTYPE: NIFTI_GZ diff --git a/pixi.lock b/pixi.lock new file mode 100644 index 000000000..f443ddee8 --- /dev/null +++ b/pixi.lock @@ -0,0 +1,8121 @@ +version: 6 +environments: + default: + channels: + - url: https://fsl.fmrib.ox.ac.uk/fsldownloads/fslconda/public/ + - url: https://conda.anaconda.org/conda-forge/ + indexes: + - https://pypi.org/simple + packages: + linux-64: + - conda: https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-3_kmp_llvm.conda + - conda: https://conda.anaconda.org/conda-forge/noarch/adwaita-icon-theme-48.1-unix_0.conda + - conda: https://conda.anaconda.org/conda-forge/linux-64/alsa-lib-1.2.14-hb9d3cd8_0.conda + - conda: https://conda.anaconda.org/conda-forge/linux-64/ants-2.6.2-h5f726e6_2.conda + - conda: https://conda.anaconda.org/conda-forge/linux-64/aom-3.9.1-hac33072_0.conda + - conda: https://conda.anaconda.org/conda-forge/linux-64/at-spi2-atk-2.38.0-h0630a04_3.tar.bz2 + - conda: https://conda.anaconda.org/conda-forge/linux-64/at-spi2-core-2.40.3-h0630a04_0.tar.bz2 + - conda: https://conda.anaconda.org/conda-forge/linux-64/atk-1.0-2.38.0-h04ea711_2.conda + - conda: https://conda.anaconda.org/conda-forge/linux-64/blosc-1.21.6-he440d0b_1.conda + - conda: https://conda.anaconda.org/conda-forge/linux-64/brotli-1.1.0-hb9d3cd8_3.conda + - conda: https://conda.anaconda.org/conda-forge/linux-64/brotli-bin-1.1.0-hb9d3cd8_3.conda + - conda: https://conda.anaconda.org/conda-forge/linux-64/brunsli-0.1-h9c3ff4c_0.tar.bz2 + - conda: https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-h4bc722e_7.conda + - conda: https://conda.anaconda.org/conda-forge/linux-64/c-ares-1.34.5-hb9d3cd8_0.conda + - conda: https://conda.anaconda.org/conda-forge/linux-64/c-blosc2-2.20.0-h4cfbee9_0.conda + - conda: https://conda.anaconda.org/conda-forge/noarch/ca-certificates-2025.8.3-hbd8a1cb_0.conda + - conda: https://conda.anaconda.org/conda-forge/noarch/cached-property-1.5.2-hd8ed1ab_1.tar.bz2 + - 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__glibc >=2.17,<3.0.a0 + - libgcc >=13 + - libstdcxx >=13 + - libzlib >=1.3.1,<2.0a0 + license: BSD-3-Clause + license_family: BSD + purls: [] + size: 567578 + timestamp: 1742433379869 diff --git a/pyproject.toml b/pyproject.toml index d83f07b0f..25930ea60 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -119,6 +119,63 @@ raw-options = { version_scheme = "nipreps-calver" } [tool.hatch.build.hooks.vcs] version-file = "fmriprep/_version.py" +[tool.pixi.workspace] +channels = ["https://fsl.fmrib.ox.ac.uk/fsldownloads/fslconda/public", "conda-forge"] +platforms = ["linux-64"] + +[tool.pixi.activation.env] +FSLDIR = "$CONDA_PREFIX" + +[tool.pixi.environments] +# Local installs will use editable +default = { features = ["editable"], solve-group = "default" } +dev = { features = ["dev"], solve-group = "default" } +doc = { features = ["doc"], solve-group = "default" } +test = { features = ["editable", "test"], solve-group = "default" } +# Use "fmriprep" feature for production environment, so it is identifiable +fmriprep = { features = ["production", "container", "telemetry"], solve-group = "production" } + +[tool.pixi.feature.editable.pypi-dependencies] +fmriprep = { path = ".", editable = true } +[tool.pixi.feature.production.pypi-dependencies] +fmriprep = { path = ".", editable = false } + +[tool.pixi.tasks] + +[tool.pixi.pypi-options.dependency-overrides] +numpy = ">=2.2" + +[tool.pixi.dependencies] +python = "3.12.*" +nodejs = "20.*" +mkl = "2024.2.2.*" +mkl-service = "2.4.2.*" +numpy = "2.2.*" +scipy = "1.15.*" +matplotlib = "3.10.*" +pandas = "2.2.*" +h5py = "3.13.*" +nitime = "0.11.*" +scikit-image = "0.25.*" +scikit-learn = "1.6.*" +ants = "2.6.*" +connectome-workbench-cli = "2.0.*" +fsl-bet2 = "2111.8.*" +fsl-flirt = "2111.4.*" +fsl-fast4 = "2111.3.*" +fsl-fugue = "2201.5.*" +fsl-mcflirt = "2111.0.*" +fsl-miscmaths = "2412.4.*" +fsl-topup = "2203.5.*" +graphviz = "12.2.*" +pandoc = "3.7.*" + +[tool.pixi.feature.container.dependencies] +git = "*" + +[tool.pixi.feature.container.pypi-dependencies] +git-annex = ">=10.20250721" + # # Developer tool configurations # diff --git a/requirements.txt b/requirements.txt deleted file mode 100644 index bdf3192a0..000000000 --- a/requirements.txt +++ /dev/null @@ -1,547 +0,0 @@ -# This file was autogenerated by uv via the following command: -# uv pip compile --extra=container --strip-extras pyproject.toml -c constraints.txt -o requirements.txt -p 3.12 -acres==0.3.0 - # via - # fmriprep (pyproject.toml) - # bidsschematools - # nipype - # nireports - # niworkflows - # sdcflows - # smriprep -annexremote==1.6.6 - # via - # datalad - # datalad-next - # datalad-osf -annotated-types==0.7.0 - # via pydantic -anyio==4.9.0 - # via httpx -apscheduler==3.11.0 - # via fmriprep (pyproject.toml) -arrow==1.3.0 - # via codecarbon -attrs==25.3.0 - # via - # niworkflows - # sdcflows -bids-validator==1.14.7.post0 - # via pybids -bidsschematools==1.0.10 - # via bids-validator -bokeh==3.6.3 - # via tedana -boto3==1.38.38 - # via datalad -botocore==1.38.38 - # via - # boto3 - # s3transfer -certifi==2025.6.15 - # via - # httpcore - # httpx - # requests - # sentry-sdk -cffi==1.17.1 - # via cryptography -chardet==5.2.0 - # via datalad -charset-normalizer==3.4.2 - # via requests -ci-info==0.3.0 - # via - # etelemetry - # migas -click==8.2.1 - # via - # bidsschematools - # codecarbon - # nipype - # pybids - # typer -codecarbon==3.0.2 - # via fmriprep (pyproject.toml) -contourpy==1.3.2 - # via - # bokeh - # matplotlib -cryptography==45.0.4 - # via jwcrypto -cycler==0.12.1 - # via matplotlib -datalad==1.2.0 - # via - # fmriprep (pyproject.toml) - # datalad-next - # datalad-osf -datalad-next==1.5.0 - # via datalad-osf -datalad-osf==0.3.0 - # via fmriprep (pyproject.toml) -distro==1.9.0 - # via datalad -docopt==0.6.2 - # via num2words -etelemetry==0.3.1 - # via nipype -fasteners==0.19 - # via datalad -fief-client==0.20.0 - # via codecarbon -filelock==3.18.0 - # via nipype -fonttools==4.58.4 - # via matplotlib -formulaic==1.1.1 - # via pybids -frozendict==2.4.6 - # via pybids -fsspec==2025.5.1 - # via universal-pathlib -h11==0.16.0 - # via httpcore -h5py==3.14.0 - # via nitransforms -httpcore==1.0.9 - # via httpx -httpx==0.27.2 - # via fief-client -humanize==4.12.3 - # via - # datalad - # datalad-next -idna==3.10 - # via - # anyio - # httpx - # requests -imageio==2.37.0 - # via scikit-image -indexed-gzip==1.9.5 - # via smriprep -interface-meta==1.3.0 - # via formulaic -iso8601==2.1.0 - # via datalad -jaraco-classes==3.4.0 - # via - # keyring - # keyrings-alt -jaraco-context==6.0.1 - # via - # keyring - # keyrings-alt -jaraco-functools==4.1.0 - # via keyring -jinja2==3.1.6 - # via - # bokeh - # niworkflows -jmespath==1.0.1 - # via - # boto3 - # botocore -joblib==1.5.1 - # via - # nilearn - # robustica - # scikit-learn -jwcrypto==1.5.6 - # via fief-client -keyring==25.6.0 - # via datalad -keyrings-alt==5.0.2 - # via datalad -kiwisolver==1.4.8 - # via matplotlib -latexcodec==3.0.1 - # via pybtex -lazy-loader==0.4 - # via scikit-image -lockfile==0.12.2 - # via smriprep -looseversion==1.3.0 - # via - # fmriprep (pyproject.toml) - # datalad - # nipype - # niworkflows - # smriprep -lxml==5.4.0 - # via - # nilearn - # nireports - # svgutils -mapca==0.0.5 - # via tedana -markdown-it-py==3.0.0 - # via rich -markupsafe==3.0.2 - # via jinja2 -matplotlib==3.10.3 - # via - # nireports - # nitime - # niworkflows - # seaborn - # smriprep - # tedana -mdurl==0.1.2 - # via markdown-it-py -migas==0.4.0 - # via - # fmriprep (pyproject.toml) - # sdcflows -more-itertools==10.7.0 - # via - # datalad-next - # jaraco-classes - # jaraco-functools -msgpack==1.1.1 - # via datalad -networkx==3.5 - # via - # nipype - # prov - # scikit-image -nibabel==5.3.2 - # via - # fmriprep (pyproject.toml) - # mapca - # nilearn - # nipype - # nireports - # nitransforms - # niworkflows - # pybids - # sdcflows - # smriprep - # tedana -nilearn==0.11.1 - # via - # mapca - # nireports - # niworkflows - # tedana -nipype==1.10.0 - # via - # fmriprep (pyproject.toml) - # nireports - # niworkflows - # sdcflows - # smriprep -nireports==25.2.0 - # via - # -c constraints.txt - # fmriprep (pyproject.toml) - # sdcflows -nitime==0.11 - # via fmriprep (pyproject.toml) -nitransforms==24.1.2 - # via - # -c constraints.txt - # fmriprep (pyproject.toml) - # niworkflows - # sdcflows -niworkflows==1.13.4 - # via - # -c constraints.txt - # fmriprep (pyproject.toml) - # sdcflows - # smriprep -num2words==0.5.14 - # via pybids -numpy==2.2.4 - # via - # fmriprep (pyproject.toml) - # bokeh - # contourpy - # formulaic - # h5py - # imageio - # mapca - # matplotlib - # nibabel - # nilearn - # nipype - # nireports - # nitime - # nitransforms - # niworkflows - # pandas - # pybids - # robustica - # scikit-image - # scikit-learn - # scipy - # sdcflows - # seaborn - # smriprep - # tedana - # tifffile - # transforms3d -nvidia-ml-py==12.575.51 - # via pynvml -osfclient==0.0.5 - # via datalad-osf -packaging==25.0 - # via - # fmriprep (pyproject.toml) - # bokeh - # datalad - # etelemetry - # lazy-loader - # matplotlib - # nibabel - # nilearn - # nipype - # niworkflows - # scikit-image - # smriprep -pandas==2.2.3 - # via - # fmriprep (pyproject.toml) - # bokeh - # codecarbon - # formulaic - # nilearn - # nireports - # niworkflows - # pybids - # robustica - # seaborn - # tedana -patool==4.0.1 - # via datalad -pillow==11.3.0 - # via - # bokeh - # imageio - # matplotlib - # scikit-image -platformdirs==4.3.8 - # via datalad -prometheus-client==0.22.1 - # via codecarbon -prompt-toolkit==3.0.51 - # via questionary -prov==2.0.2 - # via nipype -psutil==7.0.0 - # via - # fmriprep (pyproject.toml) - # codecarbon -puremagic==1.29 - # via nipype -py-cpuinfo==9.0.0 - # via codecarbon -pybids==0.19.0 - # via - # fmriprep (pyproject.toml) - # nireports - # niworkflows - # sdcflows - # smriprep - # templateflow -pybtex==0.24.0 - # via tedana -pybtex-apa-style==1.3 - # via tedana -pycparser==2.22 - # via cffi -pydantic==2.11.7 - # via codecarbon -pydantic-core==2.33.2 - # via pydantic -pydot==4.0.1 - # via - # nipype - # prov -pygments==2.19.1 - # via rich -pynvml==12.0.0 - # via codecarbon -pyparsing==3.2.3 - # via - # matplotlib - # pydot - # rdflib -python-dateutil==2.9.0.post0 - # via - # arrow - # botocore - # matplotlib - # nipype - # pandas - # prov -python-gitlab==6.0.0 - # via datalad -pytz==2025.2 - # via pandas -pyyaml==6.0.2 - # via - # bidsschematools - # bokeh - # nireports - # niworkflows - # pybtex - # smriprep -questionary==2.1.0 - # via codecarbon -rapidfuzz==3.13.0 - # via codecarbon -rdflib==7.1.4 - # via nipype -requests==2.32.4 - # via - # fmriprep (pyproject.toml) - # codecarbon - # datalad - # etelemetry - # nilearn - # osfclient - # python-gitlab - # requests-toolbelt - # templateflow -requests-toolbelt==1.0.0 - # via python-gitlab -rich==14.0.0 - # via - # codecarbon - # typer -robustica==0.1.4 - # via tedana -s3transfer==0.13.0 - # via boto3 -scikit-image==0.25.2 - # via - # niworkflows - # sdcflows -scikit-learn==1.6.1 - # via - # mapca - # nilearn - # robustica - # tedana -scipy==1.15.2 - # via - # formulaic - # mapca - # nilearn - # nipype - # nitime - # nitransforms - # niworkflows - # pybids - # robustica - # scikit-image - # scikit-learn - # sdcflows - # tedana -sdcflows==2.13.2 - # via - # -c constraints.txt - # fmriprep (pyproject.toml) -seaborn==0.13.2 - # via - # nireports - # niworkflows - # tedana -sentry-sdk==2.28.0 - # via fmriprep (pyproject.toml) -shellingham==1.5.4 - # via typer -simplejson==3.20.1 - # via nipype -six==1.17.0 - # via - # osfclient - # pybtex - # python-dateutil -smriprep==0.18.0 - # via - # -c constraints.txt - # fmriprep (pyproject.toml) -sniffio==1.3.1 - # via - # anyio - # httpx -sqlalchemy==2.0.41 - # via pybids -svgutils==0.3.4 - # via niworkflows -tedana==25.0.1 - # via fmriprep (pyproject.toml) -templateflow==24.2.2 - # via - # -c constraints.txt - # fmriprep (pyproject.toml) - # nireports - # niworkflows - # sdcflows - # smriprep -termcolor==2.3.0 - # via yaspin -threadpoolctl==3.6.0 - # via - # scikit-learn - # tedana -tifffile==2025.6.11 - # via scikit-image -toml==0.10.2 - # via - # fmriprep (pyproject.toml) - # sdcflows -tornado==6.5.1 - # via bokeh -tqdm==4.67.1 - # via - # datalad - # osfclient - # robustica - # tedana - # templateflow -traits==7.0.2 - # via nipype -transforms3d==0.4.2 - # via - # fmriprep (pyproject.toml) - # niworkflows -typer==0.16.0 - # via codecarbon -types-python-dateutil==2.9.0.20250516 - # via arrow -typing-extensions==4.14.0 - # via - # anyio - # formulaic - # jwcrypto - # nibabel - # pydantic - # pydantic-core - # sqlalchemy - # typer - # typing-inspection -typing-inspection==0.4.1 - # via pydantic -tzdata==2025.2 - # via pandas -tzlocal==5.3.1 - # via apscheduler -universal-pathlib==0.2.6 - # via pybids -urllib3==2.5.0 - # via - # botocore - # requests - # sentry-sdk -wcwidth==0.2.13 - # via prompt-toolkit -wrapt==1.17.2 - # via formulaic -xyzservices==2025.4.0 - # via bokeh -yaspin==3.1.0 - # via fief-client diff --git a/wrapper/src/fmriprep_docker/__main__.py b/wrapper/src/fmriprep_docker/__main__.py index 23f677a0d..9b92684ec 100755 --- a/wrapper/src/fmriprep_docker/__main__.py +++ b/wrapper/src/fmriprep_docker/__main__.py @@ -32,7 +32,7 @@ MISSING = """ Image '{}' is missing Would you like to download? [Y/n] """ -PKG_PATH = '/opt/conda/envs/fmriprep/lib/python3.12/site-packages' +PKG_PATH = '/app/.pixi/envs/container/lib/python3.12/site-packages' TF_TEMPLATES = ( 'MNI152Lin', 'MNI152NLin2009cAsym',