diff --git a/.circleci/config.yml b/.circleci/config.yml index d23179c850..20057a3500 100644 --- a/.circleci/config.yml +++ b/.circleci/config.yml @@ -376,7 +376,7 @@ jobs: command: | python -m venv /tmp/venv source /tmp/venv/bin/activate - python -m pip install -U pip setuptools_scm + python -m pip install -U pip setuptools setuptools_scm pip install --no-cache-dir -r docs/requirements.txt - run: name: Build only this commit diff --git a/CHANGES.rst b/CHANGES.rst index 0296835c88..783f0ba195 100644 --- a/CHANGES.rst +++ b/CHANGES.rst @@ -1,3 +1,14 @@ +2.5.2 (November 09, 2023) +========================= +Bug-fix release in the 2.5.x series. + +This release includes a fix for phasediff/direct fieldmaps that were previously +producing distortions outside the brain due to an incorrect masking of the fieldmap. + +* FIX: Mask fieldmap before fitting spline field [backport gh-396] (#398) +* DOC: Fix doc build for 2.5.x branch (#399) +* MAINT: Make call to scipy.stats.mode compatible with scipy 1.11.0 (#371) + 2.5.1 (June 08, 2023) ===================== Bug-fix release in the 2.5.x series. @@ -6,7 +17,6 @@ Bug-fix release in the 2.5.x series. * FIX: Ensure metadata is not present in entity query (#367) * RF/FIX: Prioritize sbref and shortest echo for SyN-SDC (#364) - 2.5.0 (June 01, 2023) ===================== New feature release in the 2.5.x series. diff --git a/Dockerfile b/Dockerfile index 01df6d801e..99204845d8 100644 --- a/Dockerfile +++ b/Dockerfile @@ -147,10 +147,12 @@ RUN echo "Downloading Convert3D ..." \ ENV C3DPATH="/opt/convert3d-1.0.0" \ PATH="/opt/convert3d-1.0.0/bin:$PATH" -# Configure PPA for libpng12 +# Configure PPAs for libpng12 and libxp6 RUN GNUPGHOME=/tmp gpg --keyserver hkps://keyserver.ubuntu.com --no-default-keyring --keyring /usr/share/keyrings/linuxuprising.gpg --recv 0xEA8CACC073C3DB2A \ - && echo "deb [signed-by=/usr/share/keyrings/linuxuprising.gpg] https://ppa.launchpadcontent.net/linuxuprising/libpng12/ubuntu jammy main" > /etc/apt/sources.list.d/linuxuprising.list -# AFNI latest (neurodocker build) + && GNUPGHOME=/tmp gpg --keyserver hkps://keyserver.ubuntu.com --no-default-keyring --keyring /usr/share/keyrings/zeehio.gpg --recv 0xA1301338A3A48C4A \ + && echo "deb [signed-by=/usr/share/keyrings/linuxuprising.gpg] https://ppa.launchpadcontent.net/linuxuprising/libpng12/ubuntu jammy main" > /etc/apt/sources.list.d/linuxuprising.list \ + && echo "deb [signed-by=/usr/share/keyrings/zeehio.gpg] https://ppa.launchpadcontent.net/zeehio/libxp/ubuntu jammy main" > /etc/apt/sources.list.d/zeehio.list +# Dependencies for AFNI; requires a discontinued multiarch-support package from bionic (18.04) RUN apt-get update -qq \ && apt-get install -y -q --no-install-recommends \ ed \ @@ -162,27 +164,23 @@ RUN apt-get update -qq \ libjpeg62 \ libpng12-0 \ libxm4 \ + libxp6 \ netpbm \ tcsh \ xfonts-base \ xvfb \ - && apt-get clean \ - && rm -rf /var/lib/apt/lists/* \ && curl -sSL --retry 5 -o /tmp/multiarch.deb http://archive.ubuntu.com/ubuntu/pool/main/g/glibc/multiarch-support_2.27-3ubuntu1.5_amd64.deb \ && dpkg -i /tmp/multiarch.deb \ && rm /tmp/multiarch.deb \ - && curl -sSL --retry 5 -o /tmp/libxp6.deb http://mirrors.kernel.org/debian/pool/main/libx/libxp/libxp6_1.0.2-2_amd64.deb \ - && dpkg -i /tmp/libxp6.deb \ - && rm /tmp/libxp6.deb \ && apt-get install -f \ - && apt-get clean \ - && rm -rf /var/lib/apt/lists/* \ + && apt-get clean && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/* \ && gsl2_path="$(find / -name 'libgsl.so.19' || printf '')" \ && if [ -n "$gsl2_path" ]; then \ ln -sfv "$gsl2_path" "$(dirname $gsl2_path)/libgsl.so.0"; \ fi \ - && ldconfig \ - && echo "Downloading AFNI ..." \ + && ldconfig +# AFNI latest +RUN echo "Downloading AFNI ..." \ && 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 \