Tests/circleci

.circleci/config.yml

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+version: 2.1
+
+.dockersetup: &dockersetup
+  docker:
+    - image: chenyingzhao/fsub_extractor_deps:0.0.1
+  working_directory: /fsub_extractor
+
+
+runinstall: &runinstall
+    name: Install fsub_extractor
+    command: |
+      VERSION=0+build
+      if [[ -n "$CIRCLE_TAG" ]]; then
+        VERSION="$CIRCLE_TAG"
+      fi
+      git checkout $CIRCLE_BRANCH
+      echo "${VERSION}" > /src/qsiprep/qsiprep/VERSION
+      echo "include qsiprep/VERSION" >> /src/qsiprep/MANIFEST.in
+      pip install . --progress-bar off
+      # Precaching fonts, set 'Agg' as default backend for matplotlib
+      python -c "from matplotlib import font_manager"
+      sed -i 's/\(backend *: \).*$/\1Agg/g' $( python -c "import matplotlib; print(matplotlib.matplotlib_fname())" )
+
+jobs:
+
+  build:
+    <<: *dockersetup
+    steps:
+      - checkout
+      - run: *runinstall
+  test_working:
+    <<: *dockersetup
+    steps: 
+      - checkout
+      - run: *runinstall
+      - run:
+          name: Test command extrator is working
+          command: |
+            extractor
+      # can add more runs for different commands if needed
+
+workflows:
+  version: 2
+  build_test_deploy:
+    jobs:
+
+      - build:
+          filters:
+            tags:
+              only: /.*/
+
+      - test_working:
+          requires:
+            - build
+          filters:
+            tags:
+              only: /.*/

Dockerfile_4circleci

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+# This Dockerfile is for CircleCI tests of this python package. Below we install necessary dependent packages.
+# This Dockerfile is NOT for building the docker image of this python package.
+
+# ref: https://github.com/PennLINC/qsiprep_build/blob/main/setup_build.sh
+# ref: https://github.com/PennLINC/qsiprep_build/blob/main/Dockerfile
+
+FROM pennbbl/qsiprep-freesurfer:22.2.0 as build_freesurfer
+FROM pennbbl/qsiprep-mrtrix3:22.1.0 as build_mrtrix3
+FROM pennbbl/qsiprep-miniconda:22.4.1 as build_miniconda
+# seems MRTRIX3_DEPS requires cuda:
+FROM nvidia/cuda:10.2-runtime-ubuntu18.04 as cuda10   
+
+FROM cuda10
+
+## MRtrix3
+COPY --from=build_mrtrix3 /opt/mrtrix3-latest /opt/mrtrix3-latest
+ENV PATH="$PATH:/opt/mrtrix3-latest/bin" \
+    MRTRIX3_DEPS="bzip2 ca-certificates curl libpng16-16 libblas3 liblapack3 libtiff5"
+
+
+## FreeSurfer
+COPY --from=build_freesurfer /opt/freesurfer /opt/freesurfer
+# Simulate SetUpFreeSurfer.sh
+ENV FSL_DIR="/opt/fsl-6.0.5.1" \
+    OS="Linux" \
+    FS_OVERRIDE=0 \
+    FIX_VERTEX_AREA="" \
+    FSF_OUTPUT_FORMAT="nii.gz" \
+    FREESURFER_HOME="/opt/freesurfer"
+ENV SUBJECTS_DIR="$FREESURFER_HOME/subjects" \
+    FUNCTIONALS_DIR="$FREESURFER_HOME/sessions" \
+    MNI_DIR="$FREESURFER_HOME/mni" \
+    LOCAL_DIR="$FREESURFER_HOME/local" \
+    MINC_BIN_DIR="$FREESURFER_HOME/mni/bin" \
+    MINC_LIB_DIR="$FREESURFER_HOME/mni/lib" \
+    MNI_DATAPATH="$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:$PATH" \
+    FREESURFER_DEPS="bc ca-certificates curl libgomp1 libxmu6 libxt6 tcsh perl"
+
+
+
+## Python, compiled dependencies
+# if the last FROM is miniconda, we don't need to COPY it.
+COPY --from=build_miniconda /usr/local/miniconda /usr/local/miniconda
+COPY --from=build_miniconda /home/qsiprep/.dipy /home/qsiprep/.dipy
+ENV PATH="/usr/local/miniconda/bin:$PATH"
+
+
+## Install deps:
+RUN apt-get update \
+    && apt install -y --no-install-recommends \
+    ${MRTRIX3_DEPS}
+
+## Install fury:
+RUN conda install -c conda-forge fury
+
+## Install datalad etc:
+RUN conda install -c conda-forge datalad git git-annex
+
+## Install antspy:
+# RUN pip install antspyx   # is this correct ????????????
+
+# ## Install the current python pacakge - this is not needed for Dockerfile for CIRCLECI !!!!!
+# RUN apt-get update && apt-get install -y --no-install-recommends \
+#     git
+
+# COPY . /fsub_extractor
+
+# better not to git clone, but do `COPY`
+# # RUN git clone https://github.com/smeisler/fsub_extractor.git
+# WORKDIR fsub_extractor
+# #RUN git checkout ${commitSHA_confixel}
+# RUN pip install .
+# # NOTE: there is something wrong in this installation: `extractor` wasn't installed successfully....
+# WORKDIR /

Dockerfile_4circleci_run.sh

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+# Steps of preparing the Docker images:
+
+# +++++++++++++++++++++++++++++++++++++++
+tag_version="0.0.1.9000"
+# +++++++++++++++++++++++++++++++++++++++
+
+
+## build the dockerfile for fsub_extractor:
+cmd="docker build -t chenyingzhao/fsub_extractor_deps:${tag_version} -f Dockerfile_4circleci ."
+echo $cmd
+$cmd
+
+cmd="docker push chenyingzhao/fsub_extractor_deps:${tag_version}"
+#echo $cmd
+#$cmd