Dockerfile (#216)

* Cleaning software environement related files in the repository * Typo in data documentation * Codespell * CI workflow not considering setup.cfg anymore
Inria-Empenn · Nov 22, 2024 · 2e8843a · 2e8843a
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diff --git a/.github/workflows/unit_tests.yml b/.github/workflows/unit_tests.yml
@@ -9,14 +9,12 @@ on:
     paths:
       - 'narps_open/**'
       - 'setup.py'
-      - 'setup.cfg'
       - 'pytest.ini'
       - 'tests/conftest.py'
   pull_request:
     paths:
       - 'narps_open/**'
       - 'setup.py'
-      - 'setup.cfg'
       - 'pytest.ini'
       - 'tests/conftest.py'
 

diff --git a/CONTENT.md b/CONTENT.md
@@ -1,4 +1,4 @@
-### Contents overview
+# Contents overview
 
 - :snake: :package: `narps_open/` contains the Python package with all the pipelines logic.
 - :brain: `data/` contains data that is used by the pipelines, as well as the (intermediate or final) results data. Instructions to download data are available in [INSTALL.md](/INSTALL.md#data-download-instructions).

diff --git a/Dockerfile b/Dockerfile
@@ -1,319 +1,8 @@
-# Generated by: Neurodocker version 0.7.0+0.gdc97516.dirty
-# Latest release: Neurodocker version 0.7.0
-# Timestamp: 2021/11/09 11:04:47 UTC
-# 
-# Thank you for using Neurodocker. If you discover any issues
-# or ways to improve this software, please submit an issue or
-# pull request on our GitHub repository:
-# 
-#     https://github.com/ReproNim/neurodocker
+FROM nipype/nipype:py38
 
-FROM neurodebian:stretch-non-free
+WORKDIR /work
 
-USER root
+COPY narps_open/ ./narps_open/
+COPY setup.py ./
 
-ARG DEBIAN_FRONTEND="noninteractive"
-
-ENV LANG="en_US.UTF-8" \
-    LC_ALL="en_US.UTF-8" \
-    ND_ENTRYPOINT="/neurodocker/startup.sh"
-RUN export ND_ENTRYPOINT="/neurodocker/startup.sh" \
-    && apt-get update -qq \
-    && apt-get install -y -q --no-install-recommends \
-           apt-utils \
-           bzip2 \
-           ca-certificates \
-           curl \
-           locales \
-           unzip \
-    && apt-get clean \
-    && rm -rf /var/lib/apt/lists/* \
-    && sed -i -e 's/# en_US.UTF-8 UTF-8/en_US.UTF-8 UTF-8/' /etc/locale.gen \
-    && dpkg-reconfigure --frontend=noninteractive locales \
-    && update-locale LANG="en_US.UTF-8" \
-    && chmod 777 /opt && chmod a+s /opt \
-    && mkdir -p /neurodocker \
-    && if [ ! -f "$ND_ENTRYPOINT" ]; then \
-         echo '#!/usr/bin/env bash' >> "$ND_ENTRYPOINT" \
-    &&   echo 'set -e' >> "$ND_ENTRYPOINT" \
-    &&   echo 'export USER="${USER:=`whoami`}"' >> "$ND_ENTRYPOINT" \
-    &&   echo 'if [ -n "$1" ]; then "$@"; else /usr/bin/env bash; fi' >> "$ND_ENTRYPOINT"; \
-    fi \
-    && chmod -R 777 /neurodocker && chmod a+s /neurodocker
-
-ENTRYPOINT ["/neurodocker/startup.sh"]
-
-RUN apt-get update -qq \
-    && apt-get install -y -q --no-install-recommends \
-           git \
-    && apt-get clean \
-    && rm -rf /var/lib/apt/lists/*
-
-ENV FSLDIR="/opt/fsl-6.0.3" \
-    PATH="/opt/fsl-6.0.3/bin:$PATH" \
-    FSLOUTPUTTYPE="NIFTI_GZ" \
-    FSLMULTIFILEQUIT="TRUE" \
-    FSLTCLSH="/opt/fsl-6.0.3/bin/fsltclsh" \
-    FSLWISH="/opt/fsl-6.0.3/bin/fslwish" \
-    FSLLOCKDIR="" \
-    FSLMACHINELIST="" \
-    FSLREMOTECALL="" \
-    FSLGECUDAQ="cuda.q"
-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-6.0.3 \
-    && curl -fsSL --retry 5 https://fsl.fmrib.ox.ac.uk/fsldownloads/fsl-6.0.3-centos6_64.tar.gz \
-    | tar -xz -C /opt/fsl-6.0.3 --strip-components 1 \
-    && sed -i '$iecho Some packages in this Docker container are non-free' $ND_ENTRYPOINT \
-    && sed -i '$iecho If you are considering commercial use of this container, please consult the relevant license:' $ND_ENTRYPOINT \
-    && sed -i '$iecho https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/Licence' $ND_ENTRYPOINT \
-    && sed -i '$isource $FSLDIR/etc/fslconf/fsl.sh' $ND_ENTRYPOINT \
-    && echo "Installing FSL conda environment ..." \
-    && bash /opt/fsl-6.0.3/etc/fslconf/fslpython_install.sh -f /opt/fsl-6.0.3
-
-ENV PATH="/opt/afni-latest:$PATH" \
-    AFNI_PLUGINPATH="/opt/afni-latest"
-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 \
-           libnlopt-dev \
-           libxm4 \
-           netpbm \
-           python \
-           python3 \
-           r-base \
-           r-base-dev \
-           tcsh \
-           xfonts-base \
-           xvfb \
-    && apt-get clean \
-    && rm -rf /var/lib/apt/lists/* \
-    && curl -sSL --retry 5 -o /tmp/toinstall.deb http://mirrors.kernel.org/debian/pool/main/libx/libxp/libxp6_1.0.2-2_amd64.deb \
-    && dpkg -i /tmp/toinstall.deb \
-    && rm /tmp/toinstall.deb \
-    && curl -sSL --retry 5 -o /tmp/toinstall.deb http://snapshot.debian.org/archive/debian-security/20160113T213056Z/pool/updates/main/libp/libpng/libpng12-0_1.2.49-1%2Bdeb7u2_amd64.deb \
-    && dpkg -i /tmp/toinstall.deb \
-    && rm /tmp/toinstall.deb \
-    && apt-get install -f \
-    && apt-get clean \
-    && rm -rf /var/lib/apt/lists/* \
-    && gsl2_path="$(find / -name 'libgsl.so.19' || printf '')" \
-    && if [ -n "$gsl2_path" ]; then \
-         ln -sfv "$gsl2_path" "$(dirname $gsl2_path)/libgsl.so.0"; \
-    fi \
-    && ldconfig \
-    && echo "Downloading AFNI ..." \
-    && mkdir -p /opt/afni-latest \
-    && curl -fsSL --retry 5 https://afni.nimh.nih.gov/pub/dist/tgz/linux_openmp_64.tgz \
-    | tar -xz -C /opt/afni-latest --strip-components 1 \
-    && PATH=$PATH:/opt/afni-latest rPkgsInstall -pkgs ALL
-
-ENV FORCE_SPMMCR="1" \
-    SPM_HTML_BROWSER="0" \
-    LD_LIBRARY_PATH="$LD_LIBRARY_PATH:/usr/lib/x86_64-linux-gnu:/opt/matlabmcr-2010a/v713/runtime/glnxa64:/opt/matlabmcr-2010a/v713/bin/glnxa64:/opt/matlabmcr-2010a/v713/sys/os/glnxa64:/opt/matlabmcr-2010a/v713/extern/bin/glnxa64" \
-    MATLABCMD="/opt/matlabmcr-2010a/v713/toolbox/matlab"
-RUN export TMPDIR="$(mktemp -d)" \
-    && apt-get update -qq \
-    && apt-get install -y -q --no-install-recommends \
-           bc \
-           libncurses5 \
-           libxext6 \
-           libxmu6 \
-           libxpm-dev \
-           libxt6 \
-    && apt-get clean \
-    && rm -rf /var/lib/apt/lists/* \
-    && echo "Downloading MATLAB Compiler Runtime ..." \
-    && curl -sSL --retry 5 -o /tmp/toinstall.deb http://mirrors.kernel.org/debian/pool/main/libx/libxp/libxp6_1.0.2-2_amd64.deb \
-    && dpkg -i /tmp/toinstall.deb \
-    && rm /tmp/toinstall.deb \
-    && apt-get install -f \
-    && apt-get clean \
-    && rm -rf /var/lib/apt/lists/* \
-    && curl -fsSL --retry 5 -o "$TMPDIR/MCRInstaller.bin" https://dl.dropbox.com/s/zz6me0c3v4yq5fd/MCR_R2010a_glnxa64_installer.bin \
-    && chmod +x "$TMPDIR/MCRInstaller.bin" \
-    && "$TMPDIR/MCRInstaller.bin" -silent -P installLocation="/opt/matlabmcr-2010a" \
-    && rm -rf "$TMPDIR" \
-    && unset TMPDIR \
-    && echo "Downloading standalone SPM ..." \
-    && curl -fsSL --retry 5 -o /tmp/spm12.zip https://www.fil.ion.ucl.ac.uk/spm/download/restricted/utopia/previous/spm12_r7771_R2010a.zip \
-    && unzip -q /tmp/spm12.zip -d /tmp \
-    && mkdir -p /opt/spm12-r7771 \
-    && mv /tmp/spm12/* /opt/spm12-r7771/ \
-    && chmod -R 777 /opt/spm12-r7771 \
-    && rm -rf /tmp/spm* \
-    && /opt/spm12-r7771/run_spm12.sh /opt/matlabmcr-2010a/v713 quit \
-    && sed -i '$iexport SPMMCRCMD=\"/opt/spm12-r7771/run_spm12.sh /opt/matlabmcr-2010a/v713 script\"' $ND_ENTRYPOINT
-
-RUN test "$(getent passwd neuro)" || useradd --no-user-group --create-home --shell /bin/bash neuro
-USER neuro
-
-WORKDIR /home
-
-ENV CONDA_DIR="/opt/miniconda-latest" \
-    PATH="/opt/miniconda-latest/bin:$PATH"
-RUN export PATH="/opt/miniconda-latest/bin:$PATH" \
-    && echo "Downloading Miniconda installer ..." \
-    && conda_installer="/tmp/miniconda.sh" \
-    && curl -fsSL --retry 5 -o "$conda_installer" https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh \
-    && bash "$conda_installer" -b -p /opt/miniconda-latest \
-    && rm -f "$conda_installer" \
-    && conda update -yq -nbase conda \
-    && conda config --system --prepend channels conda-forge \
-    && conda config --system --set auto_update_conda false \
-    && conda config --system --set show_channel_urls true \
-    && sync && conda clean -y --all && sync \
-    && conda create -y -q --name neuro \
-    && conda install -y -q --name neuro \
-           "python=3.8" \
-           "traits" \
-           "jupyter" \
-           "nilearn" \
-           "graphviz" \
-           "nipype" \
-           "scikit-image" \
-    && sync && conda clean -y --all && sync \
-    && bash -c "source activate neuro \
-    &&   pip install --no-cache-dir  \
-             "matplotlib"" \
-    && rm -rf ~/.cache/pip/* \
-    && sync \
-    && sed -i '$isource activate neuro' $ND_ENTRYPOINT
-
-ENV LD_LIBRARY_PATH="/opt/miniconda-latest/envs/neuro:"
-
-RUN bash -c 'source activate neuro'
-
-USER root
-
-RUN chmod 777 -Rf /home
-
-RUN chown -R neuro /home
-
-USER neuro
-
-RUN mkdir -p ~/.jupyter && echo c.NotebookApp.ip = \"0.0.0.0\" > ~/.jupyter/jupyter_notebook_config.py
-
-RUN echo '{ \
-    \n  "pkg_manager": "apt", \
-    \n  "instructions": [ \
-    \n    [ \
-    \n      "base", \
-    \n      "neurodebian:stretch-non-free" \
-    \n    ], \
-    \n    [ \
-    \n      "install", \
-    \n      [ \
-    \n        "git" \
-    \n      ] \
-    \n    ], \
-    \n    [ \
-    \n      "fsl", \
-    \n      { \
-    \n        "version": "6.0.3" \
-    \n      } \
-    \n    ], \
-    \n    [ \
-    \n      "afni", \
-    \n      { \
-    \n        "version": "latest", \
-    \n        "method": "binaries", \
-    \n        "install_r": "true", \
-    \n        "install_r_pkgs": "true", \
-    \n        "install_python2": "true", \
-    \n        "install_python3": "true" \
-    \n      } \
-    \n    ], \
-    \n    [ \
-    \n      "spm12", \
-    \n      { \
-    \n        "version": "r7771", \
-    \n        "method": "binaries" \
-    \n      } \
-    \n    ], \
-    \n    [ \
-    \n      "user", \
-    \n      "neuro" \
-    \n    ], \
-    \n    [ \
-    \n      "workdir", \
-    \n      "/home" \
-    \n    ], \
-    \n    [ \
-    \n      "miniconda", \
-    \n      { \
-    \n        "create_env": "neuro", \
-    \n        "conda_install": [ \
-    \n          "python=3.8", \
-    \n          "traits", \
-    \n          "jupyter", \
-    \n          "nilearn", \
-    \n          "graphviz", \
-    \n          "nipype", \
-    \n          "scikit-image" \
-    \n        ], \
-    \n        "pip_install": [ \
-    \n          "matplotlib" \
-    \n        ], \
-    \n        "activate": true \
-    \n      } \
-    \n    ], \
-    \n    [ \
-    \n      "env", \
-    \n      { \
-    \n        "LD_LIBRARY_PATH": "/opt/miniconda-latest/envs/neuro:" \
-    \n      } \
-    \n    ], \
-    \n    [ \
-    \n      "run_bash", \
-    \n      "source activate neuro" \
-    \n    ], \
-    \n    [ \
-    \n      "user", \
-    \n      "root" \
-    \n    ], \
-    \n    [ \
-    \n      "run", \
-    \n      "chmod 777 -Rf /home" \
-    \n    ], \
-    \n    [ \
-    \n      "run", \
-    \n      "chown -R neuro /home" \
-    \n    ], \
-    \n    [ \
-    \n      "user", \
-    \n      "neuro" \
-    \n    ], \
-    \n    [ \
-    \n      "run", \
-    \n      "mkdir -p ~/.jupyter && echo c.NotebookApp.ip = \\\"0.0.0.0\\\" > ~/.jupyter/jupyter_notebook_config.py" \
-    \n    ] \
-    \n  ] \
-    \n}' > /neurodocker/neurodocker_specs.json
+RUN /neurodocker/startup.sh pip install .
diff --git a/docs/data.md b/docs/data.md
@@ -20,7 +20,7 @@ Tips for people using M1 MacBooks: `git-annex` is not yet available for M1 MacBo
 
 The `datalad install` command only downloaded the metadata associated with the dataset ; to download the actual files run the following command:
 
-> [! WARNING]
+> [!WARNING]
 > The following command lines will download **all** the data, which represents around :
 >  * 3 GB for `data/results/`
 >  * 880 GB for `data/original/`

diff --git a/docs/environment.md b/docs/environment.md
@@ -19,6 +19,25 @@ docker run -it \
            nipype/nipype:py38
 ``` 
 
+> [!NOTE]
+> The `Dockerfile` available in the root directory of the repository contains a recipe to build a docker image with the project installed, ready to be launched.
+> From the root directory:
+>
+> ```bash
+> # Replace IMAGE_NAME in the following command
+> docker build -t IMAGE_NAME .
+> 
+> # Check the image was created
+> docker images
+> 
+> # Use IMAGE_NAME again to refer to the newly created image
+> docker run -it IMAGE_NAME
+> ``` 
+
+> [!TIP]
+> Find useful information on the [Docker documentation page](https://docs.docker.com/get-started/). Here is a [cheat sheet with Docker commands](https://docs.docker.com/get-started/docker_cheatsheet.pdf)
+
+
 ## Use Jupyter with the container
 
 If you wish to use [Jupyter](https://jupyter.org/) to run the code, a port forwarding is needed :
@@ -43,7 +62,7 @@ You can now access Jupyter using the address provided by the command line.
 
 ## Create a custom Docker image
 
-The `elodiegermani/open_pipeline` Docker image is based on [Neurodocker](https://github.com/ReproNim/neurodocker). It was created using the following command line :
+If you wish to create your own custom environment, make changes to the parameters, software versions, you can build your custom image using [Neurodocker](https://github.com/ReproNim/neurodocker). Generate a Dockerfile using the following command line :
 
 ```bash
 docker run --rm repronim/neurodocker:0.7.0 generate docker \
@@ -67,7 +86,7 @@ docker run --rm repronim/neurodocker:0.7.0 generate docker \
            --run 'mkdir -p ~/.jupyter && echo c.NotebookApp.ip = \"0.0.0.0\" > ~/.jupyter/jupyter_notebook_config.py' > Dockerfile
 ```
 
-If you wish to create your own custom environment, make changes to the parameters, and build your custom image from the generated Dockerfile.
+And build a new image from the Dockerfile.
 
 ```bash
 # Replace IMAGE_NAME in the following command