Merge pull request #8 from nipreps/enh/add-dockerfile

ENH: Add ``Dockerfile``

.dockerignore

@@ -0,0 +1,33 @@
+# python cache
+.cache/
+__pycache__/**/*
+__pycache__
+*.pyc
+
+# python distribution
+build/**/*
+build
+dist/**/*
+dist
+mriqc.egg-info/**/*
+mriqc.egg-info
+.eggs/**/*
+.eggs
+src/**/*
+src/
+notebooks/
+.maint/
+
+# releasing
+Makefile
+
+# git
+.github/
+.gitignore
+.gitattributes
+.git/**/*
+.git
+
+
+# local build of book
+docs/_build

.github/workflows/docker.yml

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+
+name: Docker Image CI
+
+on:
+  push:
+    # Publish `main` as Docker `latest` image.
+    branches:
+      - main
+  release:
+    types: [published]
+
+  # Run tests for any PRs.
+  pull_request:
+
+env:
+  IMAGE_NAME: qc-book
+
+jobs:
+  # Push image to GitHub Packages.
+  # See also https://docs.docker.com/docker-hub/builds/
+  push:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v2
+
+      - name: Log into GitHub Container Registry
+        run: echo "${{ secrets.GITHUB_TOKEN }}" | docker login ghcr.io -u ${{ github.actor }} --password-stdin
+
+      - uses: satackey/[email protected]
+        # Ignore the failure of a step and avoid terminating the job.
+        continue-on-error: true
+
+      - name: Build image
+        run: docker build . --file Dockerfile --tag $IMAGE_NAME --build-arg GITHUB_PAT=${{ secrets.GITHUB_TOKEN }}
+
+      - name: Push image to GitHub Container Registry
+        if: github.event_name == 'release'
+        run: |
+          IMAGE_ID=ghcr.io/${{ github.repository_owner }}/$IMAGE_NAME
+          # Change all uppercase to lowercase
+          IMAGE_ID=$(echo $IMAGE_ID | tr '[A-Z]' '[a-z]')
+          # Strip git ref prefix from version
+          VERSION=$(echo "${{ github.ref }}" | sed -e 's,.*/\(.*\),\1,')
+          # Strip "v" prefix from tag name
+          [[ "${{ github.ref }}" == "refs/tags/"* ]] && VERSION=$(echo $VERSION | sed -e 's/^v//')
+          # Use Docker `latest` tag convention
+          [ "$VERSION" == "main" ] && VERSION=latest
+          echo IMAGE_ID=$IMAGE_ID
+          echo VERSION=$VERSION
+          docker tag $IMAGE_NAME $IMAGE_ID:$VERSION
+          docker push $IMAGE_ID:$VERSION
+      - name: Log into DockerHub Container Registry
+        run: echo "${{ secrets.DOCKER_TOKEN }}" | docker login -u niprepsbot --password-stdin
+
+      - name: Push image to DockerHub Container Registry
+        if: github.event_name == 'release'
+        run: |
+          IMAGE_ID=nipreps/${IMAGE_NAME}
+          # Change all uppercase to lowercase
+          IMAGE_ID=$(echo $IMAGE_ID | tr '[A-Z]' '[a-z]')
+          # Strip git ref prefix from version
+          VERSION=$(echo "${{ github.ref }}" | sed -e 's,.*/\(.*\),\1,')
+          # Strip "v" prefix from tag name
+          [[ "${{ github.ref }}" == "refs/tags/"* ]] && VERSION=$(echo $VERSION | sed -e 's/^v//')
+          # Use Docker `latest` tag convention
+          [ "$VERSION" == "main" ] && VERSION=latest
+          echo IMAGE_ID=$IMAGE_ID
+          echo VERSION=$VERSION
+          docker tag $IMAGE_NAME $IMAGE_ID:$VERSION
+          docker push $IMAGE_ID:$VERSION

Dockerfile

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+# NiPreps' QC-Book Docker Container Image distribution
+#
+# MIT License
+#
+# Copyright (c) 2021 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 jupyter/datascience-notebook:2022-03-02
+
+RUN arch=$(uname -m) && \
+    if [ "${arch}" == "aarch64" ]; then \
+        # Prevent libmamba from sporadically hanging on arm64 under QEMU
+        # <https://github.com/mamba-org/mamba/issues/1611>
+        export G_SLICE=always-malloc; \
+    fi && \
+    mamba install --quiet --yes 'r-rnifti' && \
+    mamba clean --all -f -y && \
+    fix-permissions "${CONDA_DIR}" && \
+    fix-permissions "/home/${NB_USER}"
+
+USER root
+
+# Prepare environment
+RUN apt-get update && \
+    apt-get install -y --no-install-recommends \
+                    ca-certificates \
+                    curl \
+                    dvipng \
+                    fontconfig \
+                    git \
+                    unzip && \
+    apt-get clean && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
+
+USER $NB_UID
+
+# Install Libre Franklin font
+RUN curl -sSL "https://fonts.google.com/download?family=Libre%20Franklin" -o /tmp/LibreFranklin.zip \
+    && mkdir -p /home/${NB_USER}/.fonts \
+    && pushd /home/${NB_USER}/.fonts \
+    && unzip -e /tmp/LibreFranklin.zip \
+    && popd \
+    && rm /tmp/LibreFranklin.zip \
+    && fix-permissions /home/${NB_USER}/.fonts
+
+RUN fc-cache -v
+
+ARG GITHUB_PAT
+RUN R -e "devtools::install_github('AWKruijt/eMergeR')"
+
+# Installing precomputed python packages
+RUN conda install -y -c conda-forge -c anaconda \
+                  attr \
+                  jupytext \
+                  nibabel \
+                  nilearn \
+                  matplotlib \
+                  numpy \
+                  pandas \
+                  pip \
+                  requests \
+                  scipy \
+                  scikit-learn \
+                  zlib && \
+    conda clean --all -f -y && \
+    fix-permissions "${CONDA_DIR}" && \
+    fix-permissions "/home/${NB_USER}"
+
+# Installing nipreps-book
+COPY requirements.txt /tmp/requirements.txt
+
+USER root
+RUN pip install --no-cache-dir -r /tmp/requirements.txt \
+    && fix-permissions "${CONDA_DIR}" \
+    && rm /tmp/requirements.txt
+
+USER $NB_UID
+
+# Precaching fonts, set 'Agg' as default backend for matplotlib
+RUN rm -rf /home/${NB_USER}/.cache/matplotlib \
+    && python -c "from matplotlib import font_manager" \
+    && sed -i 's/\(backend *: \).*$/\1Agg/g' $( python -c "import matplotlib; print(matplotlib.matplotlib_fname())" ) \
+    && mkdir -p /home/${NB_USER}/.config/ \
+    && echo 'notebook_extensions = "ipynb,Rmd"' >> /home/${NB_USER}/.config/jupytext.toml