WIP cris-l1b-ru utility in docker container

.gitattributes

 *.nc filter=lfs diff=lfs merge=lfs -text
 *.mat filter=lfs diff=lfs merge=lfs -text
+*.zip filter=lfs diff=lfs merge=lfs -text

.gitlab-ci.yml

+# Build a Docker image with CI/CD and push to the GitLab registry.
+# ref: https://docs.gitlab.com/ee/ci/docker/using_kaniko.html
+
+# Define environment variables for all stages
+variables:
+  GIT_SUBMODULE_STRATEGY: normal
+  GIT_DEPTH: 1
+  # additional path in image name, optional (leave empty if not desired)
+  IMAGE_PATH: ""
+
+docker-build:
+  image:
+    name: gcr.io/kaniko-project/executor:debug
+    entrypoint: [""]
+  tags:
+      - docker
+      - ssec_shared
+  stage: build
+  before_script:
+    - |
+      mkdir -p /kaniko/.docker
+      echo "{\"auths\":{\"$CI_REGISTRY\":{\"username\":\"$CI_REGISTRY_USER\",\"password\":\"$CI_REGISTRY_PASSWORD\"}}}" > /kaniko/.docker/config.json
+  # Default branch leaves tag empty (= latest tag)
+  # All other branches are tagged with the escaped branch name (commit ref slug)
+  script:
+    - |
+      revid=:g${CI_COMMIT_SHA:0:10}
+      if [[ "$CI_COMMIT_BRANCH" == "$CI_DEFAULT_BRANCH" ]]; then
+        tag=""
+        echo "Running on default branch '$CI_DEFAULT_BRANCH': tag = 'latest'"
+      else
+      # tag=":$CI_COMMIT_REF_SLUG"
+        IMAGE_PATH="$IMAGE_PATH/$CI_COMMIT_REF_SLUG"
+        tag=""
+        echo "Running on branch '$CI_COMMIT_BRANCH': image = $IMAGE_PATH"
+      fi
+    - /kaniko/executor --context $CI_PROJECT_DIR --dockerfile $CI_PROJECT_DIR/Dockerfile --push-retry 4 --destination "${CI_REGISTRY_IMAGE}${IMAGE_PATH}${tag}" --destination "${CI_REGISTRY_IMAGE}${IMAGE_PATH}${revid}"
+  # Run this job in a branch where a Dockerfile exists
+  rules:
+    - if: $CI_COMMIT_BRANCH
+      exists:
+        - Dockerfile
+

Dockerfile

+FROM gitlab.ssec.wisc.edu:5555/cris_l1b/glue/buildbucket:r20200324 as matlab
+RUN mkdir -p /opt /work
+COPY RU /opt/RU
+RUN cd /opt/RU \
+ && mcc -m cris_gran_RU_ncparam.m
+
+RUN mkdir /work/mcr \
+ && cd /work/mcr \
+ && curl -sSO https://ssd.mathworks.com/supportfiles/downloads/R2014b/deployment_files/R2014b/installers/glnxa64/MCR_R2014b_glnxa64_installer.zip \
+ && unzip MCR_R2014b_glnxa64_installer.zip \
+ && mkdir /opt/mcr \
+ && ./install -mode silent -agreeToLicense yes -destinationFolder /opt/mcr
+
+FROM centos:7 as shell
+RUN yum -y install libXext libXt
+ENV RU_HOME=/opt/RU
+ENV MCRROOT=/opt/mcr/v84
+COPY --from=matlab /opt /opt
+RUN ln -s /opt/RU/cris-l1b-ru /usr/local/bin/
+
+ENTRYPOINT ["/opt/RU/cris-l1b-ru"]

RU/cris-l1b-ru

+#!/bin/bash -e
+
+usagexit() {
+	echo >&2 "usage: cris-l1b-ru {SNPP,J1} L1B-FILENAME RU-FILENAME"
+	echo >&2 "docker usage: docker run --rm -v\$PWD:\$PWD -w\$PWD gitlab.ssec.wisc.edu:5555/cris_l1b/user cris-l1b-ru {SNPP,J1} L1B-FILENAME RU-FILENAME"
+	exit 1
+}
+
+abspath() {
+    python -c 'import sys,os; print("\n".join([os.path.abspath(x) for x in sys.argv[1:]]))' "$@"
+}
+
+
+test -d "$RU_HOME" || echo >&2 "${Oops:?RU_HOME is not set}"
+test -d "$MCRROOT" || echo >&2 "${Oops:?MCRROOT must point to Matlab runtime}"
+SAT="$1"
+INPUT_FILE="$(abspath "$2")"
+OUTPUT_FILE="$3"
+
+test -n "$SAT" || usagexit
+test -f "$INPUT_FILE" || usagexit
+test -n "$OUTPUT_FILE" || usagexit
+
+export MATLABPATH="$RU_HOME"
+# always limit the blast radius of LD_LIBRARY_PATH to as small a space as possible
+export LD_LIBRARY_PATH="$MCRROOT/runtime/glnxa64:$MCRROOT/bin/glnxa64:$MCRROOT/sys/os/glnxa64"
+exec "$RU_HOME/run_cris_gran_RU_ncparam_wrapper.sh" "$MCRROOT" "$SAT" "$INPUT_FILE" "1" "$OUTPUT_FILE"