From bcb4220697d3f3f6361e6027cf711f9592307717 Mon Sep 17 00:00:00 2001 From: Oscar Esteban Date: Thu, 16 May 2024 16:11:32 -0400 Subject: [PATCH 1/5] fix: update circleci machine image --- .circleci/config.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.circleci/config.yml b/.circleci/config.yml index 9f216d61..1a067007 100644 --- a/.circleci/config.yml +++ b/.circleci/config.yml @@ -2,7 +2,7 @@ version: 2 jobs: build_pytest: machine: - image: ubuntu-2004:202107-02 + image: default working_directory: /tmp/src/nitransforms environment: TZ: "/usr/share/zoneinfo/America/Los_Angeles" From 7cef99c5e18f99155d875687c54183243ae2e1d8 Mon Sep 17 00:00:00 2001 From: Oscar Esteban Date: Thu, 16 May 2024 16:11:44 -0400 Subject: [PATCH 2/5] fix: update python version in dockerfile --- Dockerfile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Dockerfile b/Dockerfile index ae270b45..e578d3ed 100644 --- a/Dockerfile +++ b/Dockerfile @@ -108,7 +108,7 @@ ENV PATH="/usr/local/miniconda/bin:$PATH" \ # Installing precomputed python packages RUN conda install -y -c anaconda -c conda-forge \ - python=3.7 \ + python=3.8 \ libxml2=2.9 \ libxslt=1.1 \ lxml \ From 4f59910eb272220c2d6c2d8548bf7c62cc5b8a3b Mon Sep 17 00:00:00 2001 From: Oscar Esteban Date: Thu, 16 May 2024 16:16:08 -0400 Subject: [PATCH 3/5] fix: clean up environment cache --- .circleci/config.yml | 42 +- Dockerfile | 282 +++++--- docker/files/freesurfer7.3.2-exclude.txt | 868 +++++++++++++++++++++++ docker/files/neurodebian.gpg | 71 -- env.yml | 42 ++ 5 files changed, 1096 insertions(+), 209 deletions(-) create mode 100644 docker/files/freesurfer7.3.2-exclude.txt delete mode 100644 docker/files/neurodebian.gpg create mode 100644 env.yml diff --git a/.circleci/config.yml b/.circleci/config.yml index 1a067007..8d0d6748 100644 --- a/.circleci/config.yml +++ b/.circleci/config.yml @@ -12,9 +12,9 @@ jobs: - checkout - restore_cache: keys: - - env-v3-{{ .Branch }}- - - env-v3-master- - - env-v3- + - env-v6-{{ .Branch }}- + - env-v6-master- + - env-v6- - run: name: Setup git-annex command: | @@ -29,17 +29,14 @@ jobs: - run: name: Setup DataLad command: | - export PY3=$(pyenv versions | grep '3\.' | - sed -e 's/.* 3\./3./' -e 's/ .*//') - pyenv local $PY3 - python -m pip install --no-cache-dir -U pip "setuptools >= 45.0" "setuptools_scm[toml] >= 3.4" - python -m pip install --no-cache-dir -U datalad datalad-osf + python3 -m pip install --no-cache-dir -U pip "setuptools >= 45.0" "setuptools_scm[toml] >= 6.2" + python3 -m pip install --no-cache-dir -U datalad datalad-osf - save_cache: - key: env-v3-{{ .Branch }}-{{ .BuildNum }} + key: env-v6-{{ .Branch }}-{{ .BuildNum }} paths: - /opt/circleci/git-annex.linux - - /opt/circleci/.pyenv/versions/3.9.4 + - /opt/circleci/.pyenv/versions - restore_cache: keys: @@ -49,10 +46,7 @@ jobs: - run: name: Install test data from GIN command: | - export PY3=$(pyenv versions | grep '3\.' | - sed -e 's/.* 3\./3./' -e 's/ .*//') - pyenv local $PY3 - export PATH=/opt/circleci/git-annex.linux:$PATH + export PATH=/opt/circleci/.pyenv/versions/3.12.2/bin/:/opt/circleci/git-annex.linux:$PATH mkdir -p /tmp/data cd /tmp/data datalad install -r https://gin.g-node.org/oesteban/nitransforms-tests @@ -98,15 +92,12 @@ jobs: name: Build Docker image & push to registry no_output_timeout: 60m command: | - export PY3=$(pyenv versions | grep '3\.' | - sed -e 's/.* 3\./3./' -e 's/ .*//') - pyenv local $PY3 e=1 && for i in {1..5}; do docker build --rm --cache-from=nitransforms:latest \ -t nitransforms:latest \ --build-arg BUILD_DATE=`date -u +"%Y-%m-%dT%H:%M:%SZ"` \ --build-arg VCS_REF=`git rev-parse --short HEAD` \ - --build-arg VERSION=$( python3 setup.py --version ) . \ + --build-arg VERSION=$( python3 -m setuptools_scm ) . \ && e=0 && break || sleep 15 done && [ "$e" -eq "0" ] docker tag nitransforms:latest localhost:5000/nitransforms @@ -123,10 +114,7 @@ jobs: - run: name: Check version packaged in Docker image command: | - export PY3=$(pyenv versions | grep '3\.' | - sed -e 's/.* 3\./3./' -e 's/ .*//') - pyenv local $PY3 - THISVERSION=${CIRCLE_TAG:-$(python3 setup.py --version)} + THISVERSION=${CIRCLE_TAG:-$(python3 -m setuptools_scm)} INSTALLED_VERSION=$(\ docker run -it --rm --entrypoint=python nitransforms \ -c 'import nitransforms as nit; print(nit.__version__, end="")' ) @@ -186,7 +174,7 @@ jobs: command: | python3 -m venv /tmp/buildenv source /tmp/buildenv/bin/activate - python3 -m pip install "setuptools >= 45.0" wheel "setuptools_scm[toml] >= 3.4" \ + python3 -m pip install "setuptools >= 45.0" wheel "setuptools_scm[toml] >= 6.2" \ "pip>=10.0.1" twine docutils python setup.py sdist bdist_wheel twine check dist/nitransforms* @@ -200,9 +188,9 @@ jobs: command: | python3 -m venv /tmp/install_sdist source /tmp/install_sdist/bin/activate - python3 -m pip install "setuptools >= 45.0" "pip>=10.0.1" + python3 -m pip install "setuptools >= 45.0" "pip>=10.0.1" "setuptools_scm[toml] >= 6.2" - THISVERSION=$( python3 setup.py --version ) + THISVERSION=$( python3 -m setuptools_scm ) THISVERSION=${CIRCLE_TAG:-$THISVERSION} python3 -m pip install dist/nitransforms*.tar.gz INSTALLED_VERSION=$(python3 -c 'import nitransforms as nit; print(nit.__version__, end="")') @@ -214,9 +202,9 @@ jobs: command: | python3 -m venv /tmp/install_wheel source /tmp/install_wheel/bin/activate - python3 -m pip install "setuptools >= 45.0" "pip>=10.0.1" + python3 -m pip install "setuptools >= 45.0" "pip>=10.0.1" "setuptools_scm[toml] >= 6.2" - THISVERSION=$( python3 setup.py --version ) + THISVERSION=$( python3 -m setuptools_scm ) THISVERSION=${CIRCLE_TAG:-$THISVERSION} python3 -m pip install dist/nitransforms*.whl INSTALLED_VERSION=$(python3 -c 'import nitransforms as nit; print(nit.__version__, end="")') diff --git a/Dockerfile b/Dockerfile index e578d3ed..a804bf11 100644 --- a/Dockerfile +++ b/Dockerfile @@ -1,48 +1,144 @@ -FROM ubuntu:xenial-20200114 - -# Pre-cache neurodebian key -COPY docker/files/neurodebian.gpg /usr/local/etc/neurodebian.gpg - -# Prepare environment +# Ubuntu 22.04 LTS - Jammy +ARG BASE_IMAGE=ubuntu:jammy-20240125 + +# +# 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 +RUN python -m build /src + +# +# Download stages +# + +# 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 \ - curl \ + binutils \ bzip2 \ ca-certificates \ - xvfb \ - build-essential \ - autoconf \ - libtool \ - pkg-config \ - git && \ - curl -sL https://deb.nodesource.com/setup_10.x | bash - && \ + curl \ + unzip && \ + apt-get clean && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/* + +# FreeSurfer 7.3.2 +FROM downloader as freesurfer +COPY docker/files/freesurfer7.3.2-exclude.txt /usr/local/etc/freesurfer7.3.2-exclude.txt +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 + +# +# Main stage +# +FROM ${BASE_IMAGE} as nitransforms + +# Configure apt +ENV DEBIAN_FRONTEND="noninteractive" \ + LANG="en_US.UTF-8" \ + LC_ALL="en_US.UTF-8" + +# Some baseline tools; bc is needed for FreeSurfer, so don't drop it +RUN apt-get update && \ apt-get install -y --no-install-recommends \ - nodejs && \ + bc \ + ca-certificates \ + curl \ + git \ + gnupg \ + lsb-release \ + netbase \ + xvfb && \ apt-get clean && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/* -# Installing freesurfer -RUN curl -sSL https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.1/freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.1.tar.gz | tar zxv --no-same-owner -C /opt \ - --exclude='freesurfer/diffusion' \ - --exclude='freesurfer/docs' \ - --exclude='freesurfer/fsfast' \ - --exclude='freesurfer/lib/cuda' \ - --exclude='freesurfer/lib/qt' \ - --exclude='freesurfer/matlab' \ - --exclude='freesurfer/mni/share/man' \ - --exclude='freesurfer/subjects/fsaverage_sym' \ - --exclude='freesurfer/subjects/fsaverage3' \ - --exclude='freesurfer/subjects/fsaverage4' \ - --exclude='freesurfer/subjects/cvs_avg35' \ - --exclude='freesurfer/subjects/cvs_avg35_inMNI152' \ - --exclude='freesurfer/subjects/bert' \ - --exclude='freesurfer/subjects/lh.EC_average' \ - --exclude='freesurfer/subjects/rh.EC_average' \ - --exclude='freesurfer/subjects/sample-*.mgz' \ - --exclude='freesurfer/subjects/V1_average' \ - --exclude='freesurfer/trctrain' - -ENV FSL_DIR="/usr/share/fsl/5.0" \ - OS="Linux" \ +# 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 $gsl2_path)/libgsl.so.0"; \ + fi \ + && ldconfig + +# Install files from stages +COPY --from=freesurfer /opt/freesurfer /opt/freesurfer +COPY --from=afni /opt/afni-latest /opt/afni-latest + +# Simulate SetUpFreeSurfer.sh +ENV OS="Linux" \ FS_OVERRIDE=0 \ FIX_VERTEX_AREA="" \ FSF_OUTPUT_FORMAT="nii.gz" \ @@ -56,95 +152,59 @@ ENV SUBJECTS_DIR="$FREESURFER_HOME/subjects" \ MNI_DATAPATH="$FREESURFER_HOME/mni/data" ENV PERL5LIB="$MINC_LIB_DIR/perl5/5.8.5" \ MNI_PERL5LIB="$MINC_LIB_DIR/perl5/5.8.5" \ - PATH="$FREESURFER_HOME/bin:$FSFAST_HOME/bin:$FREESURFER_HOME/tktools:$MINC_BIN_DIR:$PATH" + PATH="$FREESURFER_HOME/bin:$FREESURFER_HOME/tktools:$MINC_BIN_DIR:$PATH" -# Installing Neurodebian packages (FSL, AFNI, git) -RUN curl -sSL "http://neuro.debian.net/lists/$( lsb_release -c | cut -f2 ).us-ca.full" >> /etc/apt/sources.list.d/neurodebian.sources.list && \ - apt-key add /usr/local/etc/neurodebian.gpg && \ - (apt-key adv --refresh-keys --keyserver hkp://ha.pool.sks-keyservers.net 0xA5D32F012649A5A9 || true) +# AFNI config +ENV PATH="/opt/afni-latest:$PATH" \ + AFNI_IMSAVE_WARNINGS="NO" \ + AFNI_PLUGINPATH="/opt/afni-latest" -RUN apt-get update && \ - apt-get install -y --no-install-recommends \ - fsl-core=5.0.9-5~nd16.04+1 \ - fsl-mni152-templates=5.0.7-2 \ - afni=16.2.07~dfsg.1-5~nd16.04+1 \ - convert3d \ - connectome-workbench=1.3.2-2~nd16.04+1 \ - git-annex-standalone && \ - apt-get clean && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/* +# Workbench config +ENV PATH="/opt/workbench/bin_linux64:$PATH" + +# Create a shared $HOME directory +RUN useradd -m -s /bin/bash -G users neuro +WORKDIR /home/neuro +ENV HOME="/home/neuro" \ + LD_LIBRARY_PATH="/usr/lib/x86_64-linux-gnu:$LD_LIBRARY_PATH" + +COPY --from=micromamba /bin/micromamba /bin/micromamba +COPY --from=micromamba /opt/conda/envs/nitransforms /opt/conda/envs/nitransforms -ENV FSLDIR="/usr/share/fsl/5.0" \ +ENV MAMBA_ROOT_PREFIX="/opt/conda" +RUN micromamba shell init -s bash && \ + echo "micromamba activate nitransforms" >> $HOME/.bashrc +ENV PATH="/opt/conda/envs/nitransforms/bin:$PATH" \ + CPATH="/opt/conda/envs/nitransforms/include:$CPATH" \ + LD_LIBRARY_PATH="/opt/conda/envs/nitransforms/lib:$LD_LIBRARY_PATH" + +# FSL environment +ENV LANG="C.UTF-8" \ + LC_ALL="C.UTF-8" \ + PYTHONNOUSERSITE=1 \ + FSLDIR="/opt/conda/envs/nitransforms" \ FSLOUTPUTTYPE="NIFTI_GZ" \ FSLMULTIFILEQUIT="TRUE" \ - POSSUMDIR="/usr/share/fsl/5.0" \ - LD_LIBRARY_PATH="/usr/lib/fsl/5.0:$LD_LIBRARY_PATH" \ - FSLTCLSH="/usr/bin/tclsh" \ - FSLWISH="/usr/bin/wish" \ - AFNI_MODELPATH="/usr/lib/afni/models" \ - AFNI_IMSAVE_WARNINGS="NO" \ - AFNI_TTATLAS_DATASET="/usr/share/afni/atlases" \ - AFNI_PLUGINPATH="/usr/lib/afni/plugins" -ENV PATH="/usr/lib/fsl/5.0:/usr/lib/afni/bin:$PATH" - -# Installing ANTs 2.3.3 (NeuroDocker build) -# Note: the URL says 2.3.4 but it is actually 2.3.3 -ENV ANTSPATH=/usr/lib/ants -RUN mkdir -p $ANTSPATH && \ - curl -sSL "https://dl.dropbox.com/s/gwf51ykkk5bifyj/ants-Linux-centos6_x86_64-v2.3.4.tar.gz" \ - | tar -xzC $ANTSPATH --strip-components 1 -ENV PATH=$ANTSPATH:$PATH - -# Installing and setting up miniconda -RUN curl -sSLO https://repo.continuum.io/miniconda/Miniconda3-4.5.11-Linux-x86_64.sh && \ - bash Miniconda3-4.5.11-Linux-x86_64.sh -b -p /usr/local/miniconda && \ - rm Miniconda3-4.5.11-Linux-x86_64.sh - -# Set CPATH for packages relying on compiled libs (e.g. indexed_gzip) -ENV PATH="/usr/local/miniconda/bin:$PATH" \ - CPATH="/usr/local/miniconda/include/:$CPATH" \ - LANG="C.UTF-8" \ - LC_ALL="C.UTF-8" \ - PYTHONNOUSERSITE=1 - -# Installing precomputed python packages -RUN conda install -y -c anaconda -c conda-forge \ - python=3.8 \ - libxml2=2.9 \ - libxslt=1.1 \ - lxml \ - mkl \ - mkl-service \ - numpy=1.20 \ - pip=21 \ - scipy=1.6 \ - setuptools \ - setuptools_scm \ - toml \ - zlib; sync && \ - chmod -R a+rX /usr/local/miniconda; sync && \ - chmod +x /usr/local/miniconda/bin/*; sync && \ - conda build purge-all; sync && \ - conda clean -tipsy && sync + FSLLOCKDIR="" \ + FSLMACHINELIST="" \ + FSLREMOTECALL="" \ + FSLGECUDAQ="cuda.q" # Unless otherwise specified each process should only use one thread - nipype # will handle parallelization ENV MKL_NUM_THREADS=1 \ OMP_NUM_THREADS=1 -# Create a shared $HOME directory -RUN useradd -m -s /bin/bash -G users neuro -WORKDIR /home/neuro -ENV HOME="/home/neuro" - # Install package # CRITICAL: Make sure python setup.py --version has been run at least once # outside the container, with access to the git history. -COPY . /src/nitransforms -RUN pip install --no-cache-dir "/src/nitransforms[all]" +COPY --from=src /src/dist/*.whl . +RUN python -m pip install --no-cache-dir $( ls /src/dist/*.whl )[all] -RUN find $HOME -type d -exec chmod go=u {} + && \ - find $HOME -type f -exec chmod go=u {} + +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 RUN ldconfig WORKDIR /tmp/ diff --git a/docker/files/freesurfer7.3.2-exclude.txt b/docker/files/freesurfer7.3.2-exclude.txt new file mode 100644 index 00000000..3b07a64e --- /dev/null +++ b/docker/files/freesurfer7.3.2-exclude.txt @@ -0,0 +1,868 @@ 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PGP PUBLIC KEY BLOCK----- diff --git a/env.yml b/env.yml new file mode 100644 index 00000000..721507ae --- /dev/null +++ b/env.yml @@ -0,0 +1,42 @@ +name: nitransforms +channels: + - https://fsl.fmrib.ox.ac.uk/fsldownloads/fslconda/public/ + - conda-forge +# Update this ~yearly; last updated Jan 2024 +dependencies: + - python=3.11 + # Needed for svgo and bids-validator; consider moving to deno + - nodejs=20 + # Intel Math Kernel Library for numpy + - mkl=2023.2.0 + - mkl-service=2.4.0 + # git-annex for templateflow users with DataLad superdatasets + - git-annex=*=alldep* + # Base scientific python stack; required by FSL, so pinned here + - numpy=1.26 + - scipy=1.11 + - matplotlib=3.8 + - pandas=2.2 + - h5py=3.10 + # Dependencies compiled against numpy, best to stick with conda + - nitime=0.10 + - scikit-image=0.22 + - scikit-learn=1.4 + # Utilities + - graphviz=9.0 + - pandoc=3.1 + # Workflow dependencies: ANTs + - 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 + - fsl-fugue=2201.4 + - fsl-mcflirt=2111.0 + - fsl-miscmaths=2203.2 + - fsl-topup=2203.2 + # - pip + # - pip: + # - -r requirements.txt +variables: + FSLOUTPUTTYPE: NIFTI_GZ \ No newline at end of file From 315aab9594eed979ed4479bf7830fe03ec44df8e Mon Sep 17 00:00:00 2001 From: Oscar Esteban Date: Fri, 17 May 2024 12:13:35 -0400 Subject: [PATCH 4/5] fix: select python without fiddling Co-authored-by: Mathias Goncalves --- .circleci/config.yml | 10 ++++++---- 1 file changed, 6 insertions(+), 4 deletions(-) diff --git a/.circleci/config.yml b/.circleci/config.yml index 8d0d6748..e5bb0a04 100644 --- a/.circleci/config.yml +++ b/.circleci/config.yml @@ -46,7 +46,9 @@ jobs: - run: name: Install test data from GIN command: | - export PATH=/opt/circleci/.pyenv/versions/3.12.2/bin/:/opt/circleci/git-annex.linux:$PATH + export PATH=/opt/circleci/git-annex.linux:$PATH + pyenv local 3 + eval "$(pyenv init --path)" mkdir -p /tmp/data cd /tmp/data datalad install -r https://gin.g-node.org/oesteban/nitransforms-tests @@ -129,7 +131,7 @@ jobs: echo "cHJpbnRmICJrcnp5c3p0b2YuZ29yZ29sZXdza2lAZ21haWwuY29tXG41MTcyXG4gKkN2dW12RVYzelRmZ1xuRlM1Si8yYzFhZ2c0RVxuIiA+IGxpY2Vuc2UudHh0Cg==" | base64 -d | sh - run: name: Get codecov - command: python -m pip install codecov + command: python3 -m pip install codecov - run: name: Run unit tests no_output_timeout: 2h @@ -147,7 +149,7 @@ jobs: name: Submit unit test coverage command: | cd /tmp/src/nitransforms - python -m codecov --file /tmp/tests/summaries/unittests.xml \ + python3 -m codecov --file /tmp/tests/summaries/unittests.xml \ --flags unittests -e CIRCLE_JOB - run: name: Clean up tests directory @@ -176,7 +178,7 @@ jobs: source /tmp/buildenv/bin/activate python3 -m pip install "setuptools >= 45.0" wheel "setuptools_scm[toml] >= 6.2" \ "pip>=10.0.1" twine docutils - python setup.py sdist bdist_wheel + python3 -m build twine check dist/nitransforms* - store_artifacts: path: /tmp/src/nitransforms/dist From c6b63b29b67307259e92d8eb6eb9bdd8613dc8eb Mon Sep 17 00:00:00 2001 From: Oscar Esteban Date: Fri, 17 May 2024 13:24:41 -0400 Subject: [PATCH 5/5] fix: path to wheel --- .circleci/config.yml | 5 +++-- Dockerfile | 2 +- 2 files changed, 4 insertions(+), 3 deletions(-) diff --git a/.circleci/config.yml b/.circleci/config.yml index e5bb0a04..47b0e00e 100644 --- a/.circleci/config.yml +++ b/.circleci/config.yml @@ -137,7 +137,8 @@ jobs: no_output_timeout: 2h command: | mkdir -p /tmp/tests/{artifacts,summaries} - docker run -u $( id -u ) -it --rm -w /src/nitransforms \ + docker run -u $( id -u ) -it --rm \ + -w /src/nitransforms -v $PWD:/src/nitransforms \ -v /tmp/data/nitransforms-tests:/data -e TEST_DATA_HOME=/data \ -e COVERAGE_FILE=/tmp/summaries/.pytest.coverage \ -v /tmp/fslicense/license.txt:/opt/freesurfer/license.txt:ro \ @@ -176,7 +177,7 @@ jobs: command: | python3 -m venv /tmp/buildenv source /tmp/buildenv/bin/activate - python3 -m pip install "setuptools >= 45.0" wheel "setuptools_scm[toml] >= 6.2" \ + python3 -m pip install "setuptools >= 45.0" build wheel "setuptools_scm[toml] >= 6.2" \ "pip>=10.0.1" twine docutils python3 -m build twine check dist/nitransforms* diff --git a/Dockerfile b/Dockerfile index a804bf11..57c526b7 100644 --- a/Dockerfile +++ b/Dockerfile @@ -199,7 +199,7 @@ ENV MKL_NUM_THREADS=1 \ # CRITICAL: Make sure python setup.py --version has been run at least once # outside the container, with access to the git history. COPY --from=src /src/dist/*.whl . -RUN python -m pip install --no-cache-dir $( ls /src/dist/*.whl )[all] +RUN python -m pip install --no-cache-dir $( ls *.whl )[all] RUN find $HOME -type d -exec chmod go=u {} + && \