Merge pull request #7 from tsalo/draft-contents

Copy over ICA-AROMA workflow from fMRIPrep 23.0.2

.codespellrc

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+[codespell]
+skip = .git,*.pdf,*.svg,*.html,dataset_description.json,*.bib
+# te - TE
+# Weill - name
+# reson - Reson. abbreviation in citation
+ignore-words-list = te,weill,reson

.dockerignore

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+# python cache
+__pycache__/**/*
+__pycache__
+*.pyc
+
+# python distribution
+build/**/*
+build
+dist/**/*
+dist
+fmripost_aroma.egg-info/**/*
+fmripost_aroma.egg-info
+.eggs/**/*
+.eggs

.gitattributes

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+.git_archival.txt  export-subst

.mailmap

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+Christopher J. Markiewicz <[email protected]>
+Christopher J. Markiewicz <[email protected]> <[email protected]>
+Christopher J. Markiewicz <[email protected]> <[email protected]>

.pre-commit-config.yaml

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+exclude: ".*/data/.*"
+repos:
+-   repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.4.0
+    hooks:
+    -   id: trailing-whitespace
+    -   id: end-of-file-fixer
+    -   id: check-yaml
+    -   id: check-added-large-files
+-   repo: https://github.com/psf/black
+    rev: 23.1.0
+    hooks:
+    -   id: black
+        files: ^fmriprep/|^wrapper/
+-   repo: https://github.com/pycqa/isort
+    rev: 5.12.0
+    hooks:
+    -   id: isort
+        files: ^fmriprep/|^wrapper/

.readthedocs.yml

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+version: 2
+
+build:
+  os: ubuntu-22.04
+  tools:
+    python: "3.10"
+  jobs:
+    post_checkout:
+      - git fetch --unshallow
+
+sphinx:
+  configuration: docs/conf.py
+
+python:
+  install:
+    - method: pip
+      path: .
+      extra_requirements:
+        - doc

.versions.json

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+{
+	"flagged": {
+	}
+}

.zenodo.json

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+{
+  "title": "fMRIPost-AROMA: a robust preprocessing pipeline for functional MRI",
+  "description": "<p>fMRIPost-AROMA is a robust and easy-to-use pipeline for running ICA-AROMA on preprocessed fMRI data organized in BIDS format.</p>",
+  "creators": [
+    {
+      "affiliation": "Department of Psychology, Stanford University",
+      "name": "Markiewicz, Christopher J.",
+      "orcid": "0000-0002-6533-164X"
+    },
+    {
+      "affiliation": "Department of Psychology, Florida International University",
+      "name": "Salo, Taylor",
+      "orcid": "0000-0001-9813-3167"
+    }
+  ],
+  "keywords": [
+    "neuroimaging",
+    "workflow",
+    "pipeline",
+    "preprocessing",
+    "fMRI",
+    "BIDS"
+  ],
+  "license": "Apache-2.0",
+  "related_identifiers": [
+    {
+      "identifier": "https://fmripost_aroma.org",
+      "relation": "documents",
+      "scheme": "url"
+    },
+    {
+      "identifier": "10.1038/s41592-018-0235-4",
+      "relation": "isPartOf",
+      "scheme": "doi"
+    }
+  ],
+  "upload_type": "software"
+}

CHANGES.rst

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+23.0.0 ()
+=========
+
+fMRIPost-AROMA's initial release.

CODE_OF_CONDUCT.md

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+# fMRIPost-AROMA Code of Conduct
+
+*fMRIPost-AROMA* is a project of the
+[*NiPreps* Community, and is under its code of conduct](https://www.nipreps.org/community/CODE_OF_CONDUCT/).

CONTRIBUTING.md

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+# Contributing to *fMRIPost-AROMA*
+
+*fMRIPost-AROMA* is a project of the
+[*NiPreps* Community, which specifies the contributing guidelines](https://www.nipreps.org/community/).

Dockerfile

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+# fMRIPost-AROMA Docker Container Image distribution
+#
+# MIT License
+#
+# Copyright (c) 2023 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
+# in the Software without restriction, including without limitation the rights
+# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+# copies of the Software, and to permit persons to whom the Software is
+# furnished to do so, subject to the following conditions:
+#
+# The above copyright notice and this permission notice shall be included in all
+# copies or substantial portions of the Software.
+#
+# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+# SOFTWARE.
+
+FROM python:slim AS src
+RUN pip install build
+RUN apt-get update && \
+    apt-get install -y --no-install-recommends git
+COPY . /src/fmripost_aroma
+RUN python -m build /src/fmripost_aroma
+
+# Use Ubuntu 22.04 LTS
+FROM ubuntu:jammy-20221130
+
+# Prepare environment
+RUN apt-get update && \
+    apt-get install -y --no-install-recommends \
+                    apt-utils \
+                    autoconf \
+                    build-essential \
+                    bzip2 \
+                    ca-certificates \
+                    curl \
+                    git \
+                    gnupg \
+                    libtool \
+                    lsb-release \
+                    netbase \
+                    pkg-config \
+                    unzip \
+                    xvfb && \
+    apt-get clean && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
+
+ENV DEBIAN_FRONTEND="noninteractive" \
+    LANG="en_US.UTF-8" \
+    LC_ALL="en_US.UTF-8"
+
+# FSL 6.0.5.1
+RUN apt-get update -qq \
+    && apt-get install -y -q --no-install-recommends \
+           bc \
+           dc \
+           file \
+           libfontconfig1 \
+           libfreetype6 \
+           libgl1-mesa-dev \
+           libgl1-mesa-dri \
+           libglu1-mesa-dev \
+           libgomp1 \
+           libice6 \
+           libxcursor1 \
+           libxft2 \
+           libxinerama1 \
+           libxrandr2 \
+           libxrender1 \
+           libxt6 \
+           sudo \
+           wget \
+    && apt-get clean \
+    && rm -rf /var/lib/apt/lists/* \
+    && echo "Downloading FSL ..." \
+    && mkdir -p /opt/fsl-6.0.5.1 \
+    && curl -fsSL --retry 5 https://fsl.fmrib.ox.ac.uk/fsldownloads/fsl-6.0.5.1-centos7_64.tar.gz \
+    | tar -xz -C /opt/fsl-6.0.5.1 --strip-components 1 \
+    --exclude "fsl/config" \
+    --exclude "fsl/data/atlases" \
+    --exclude "fsl/data/first" \
+    --exclude "fsl/data/mist" \
+    --exclude "fsl/data/possum" \
+    --exclude "fsl/data/standard/bianca" \
+    --exclude "fsl/data/standard/tissuepriors" \
+    --exclude "fsl/doc" \
+    --exclude "fsl/etc/default_flobs.flobs" \
+    --exclude "fsl/etc/fslconf" \
+    --exclude "fsl/etc/js" \
+    --exclude "fsl/etc/luts" \
+    --exclude "fsl/etc/matlab" \
+    --exclude "fsl/extras" \
+    --exclude "fsl/include" \
+    --exclude "fsl/python" \
+    --exclude "fsl/refdoc" \
+    --exclude "fsl/src" \
+    --exclude "fsl/tcl" \
+    --exclude "fsl/bin/FSLeyes" \
+    && find /opt/fsl-6.0.5.1/bin -type f -not \( \
+        -name "applywarp" -or \
+        -name "bet" -or \
+        -name "bet2" -or \
+        -name "convert_xfm" -or \
+        -name "fast" -or \
+        -name "flirt" -or \
+        -name "fsl_regfilt" -or \
+        -name "fslhd" -or \
+        -name "fslinfo" -or \
+        -name "fslmaths" -or \
+        -name "fslmerge" -or \
+        -name "fslroi" -or \
+        -name "fslsplit" -or \
+        -name "fslstats" -or \
+        -name "imtest" -or \
+        -name "mcflirt" -or \
+        -name "melodic" -or \
+        -name "prelude" -or \
+        -name "remove_ext" -or \
+        -name "susan" -or \
+        -name "topup" -or \
+        -name "zeropad" \) -delete \
+    && find /opt/fsl-6.0.5.1/data/standard -type f -not -name "MNI152_T1_2mm_brain.nii.gz" -delete
+ENV FSLDIR="/opt/fsl-6.0.5.1" \
+    PATH="/opt/fsl-6.0.5.1/bin:$PATH" \
+    FSLOUTPUTTYPE="NIFTI_GZ" \
+    FSLMULTIFILEQUIT="TRUE" \
+    FSLLOCKDIR="" \
+    FSLMACHINELIST="" \
+    FSLREMOTECALL="" \
+    FSLGECUDAQ="cuda.q" \
+    LD_LIBRARY_PATH="/opt/fsl-6.0.5.1/lib:$LD_LIBRARY_PATH"
+
+# Configure PPA for libpng12
+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
+
+# Installing and setting up ICA_AROMA
+WORKDIR /opt/ICA-AROMA
+RUN curl -sSL "https://github.com/oesteban/ICA-AROMA/archive/v0.4.5.tar.gz" \
+  | tar -xzC /opt/ICA-AROMA --strip-components 1 && \
+  chmod +x /opt/ICA-AROMA/ICA_AROMA.py
+ENV PATH="/opt/ICA-AROMA:$PATH" \
+    AROMA_VERSION="0.4.5"
+
+WORKDIR /opt
+RUN curl -sSLO https://www.humanconnectome.org/storage/app/media/workbench/workbench-linux64-v1.5.0.zip && \
+    unzip workbench-linux64-v1.5.0.zip && \
+    rm workbench-linux64-v1.5.0.zip && \
+    rm -rf /opt/workbench/libs_linux64_software_opengl /opt/workbench/plugins_linux64 && \
+    strip --remove-section=.note.ABI-tag /opt/workbench/libs_linux64/libQt5Core.so.5
+    # ABI tags can interfere when running on Singularity
+
+ENV PATH="/opt/workbench/bin_linux64:$PATH" \
+    LD_LIBRARY_PATH="/opt/workbench/lib_linux64:$LD_LIBRARY_PATH"
+
+# nipreps/miniconda:py39_4.12.0rc0
+COPY --from=nipreps/miniconda@sha256:5aa4d2bb46e7e56fccf6e93ab3ff765add74e79f96ffa00449504b4869790cb9 /opt/conda /opt/conda
+
+RUN ln -s /opt/conda/etc/profile.d/conda.sh /etc/profile.d/conda.sh && \
+    echo ". /opt/conda/etc/profile.d/conda.sh" >> ~/.bashrc && \
+    echo "conda activate base" >> ~/.bashrc
+
+# Set CPATH for packages relying on compiled libs (e.g. indexed_gzip)
+ENV PATH="/opt/conda/bin:$PATH" \
+    CPATH="/opt/conda/include:$CPATH" \
+    LD_LIBRARY_PATH="/opt/conda/lib:$LD_LIBRARY_PATH" \
+    LANG="C.UTF-8" \
+    LC_ALL="C.UTF-8" \
+    PYTHONNOUSERSITE=1
+
+RUN conda install -y -n base \
+    -c anaconda \
+    -c conda-forge \
+    convert3d=1.3.0 \
+    && sync \
+    && conda clean -afy; sync \
+    && rm -rf ~/.conda ~/.cache/pip/*; sync \
+    && ldconfig
+
+# 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 $HOME directory
+RUN useradd -m -s /bin/bash -G users fmripost_aroma
+WORKDIR /home/fmripost_aroma
+ENV HOME="/home/fmripost_aroma" \
+    LD_LIBRARY_PATH="/usr/lib/x86_64-linux-gnu:$LD_LIBRARY_PATH"
+
+RUN echo ". /opt/conda/etc/profile.d/conda.sh" >> $HOME/.bashrc && \
+    echo "conda activate base" >> $HOME/.bashrc
+
+RUN /opt/conda/bin/python -m pip install --no-cache-dir --upgrade templateflow
+
+# Precaching atlases
+COPY scripts/fetch_templates.py fetch_templates.py
+
+RUN /opt/conda/bin/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 {} +
+
+# Installing fMRIPost-AROMA
+COPY --from=src /src/fmripost_aroma/dist/*.whl .
+RUN /opt/conda/bin/python -m pip install --no-cache-dir $( ls *.whl )[all]
+
+RUN find $HOME -type d -exec chmod go=u {} + && \
+    find $HOME -type f -exec chmod go=u {} + && \
+    rm -rf $HOME/.npm $HOME/.conda $HOME/.empty
+
+ENV IS_DOCKER_8395080871=1
+
+RUN ldconfig
+WORKDIR /tmp
+ENTRYPOINT ["/opt/conda/bin/fmripost_aroma"]
+
+ARG BUILD_DATE
+ARG VCS_REF
+ARG VERSION
+LABEL org.label-schema.build-date=$BUILD_DATE \
+      org.label-schema.name="fMRIPost-AROMA" \
+      org.label-schema.description="fMRIPost-AROMA - robust fMRI preprocessing tool" \
+      org.label-schema.url="http://fmripost_aroma.org" \
+      org.label-schema.vcs-ref=$VCS_REF \
+      org.label-schema.vcs-url="https://github.com/nipreps/fmripost_aroma" \
+      org.label-schema.version=$VERSION \
+      org.label-schema.schema-version="1.0"