From d9a9c9539c8d9b56d5a219465f0794abaefb195f Mon Sep 17 00:00:00 2001
From: Michael Blaschek <michael.blaschek@univie.ac.at>
Date: Tue, 31 Jan 2023 15:19:22 +0000
Subject: [PATCH] addedgitlab ci for singularity build and push to repo
---
.gitlab-ci.yml | 36 +++++++++
.gitlabci/build.sh | 177 +++++++++++++++++++++++++++++++++++++++++++++
2 files changed, 213 insertions(+)
create mode 100644 .gitlab-ci.yml
create mode 100644 .gitlabci/build.sh
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
new file mode 100644
index 0000000..536c61f
--- /dev/null
+++ b/.gitlab-ci.yml
@@ -0,0 +1,36 @@
+image:
+ name: quay.io/singularity/singularity:v3.7.3
+ entrypoint: ["/bin/sh", "-c"]
+
+build:
+ when: manual
+ script:
+ - /bin/bash .gitlabci/build.sh Singularity
+ # step 1. build the container!
+ # You can add any other sregistry push commands here, and specify a client
+ # (and make sure your define the encrypted environment credentials in gitlab
+ # to push to your storage locations of choice
+
+ - mkdir -p build && cp *.sif build
+ - mkdir -p build && cp Singularity* build
+
+ # Step 2. Take a look at "artifacts" below and add the paths you want added
+ # You can also add the entire build folder. You can also upload to storage
+ # clients defined by sregistry, here are some examples
+ # https://singularityhub.github.io/sregistry-cli/clients
+ # Environment variables must be defined in CI encrypted secrets/settings
+ # https://code.stanford.edu/help/ci/variables/README#variables).
+ #- /bin/bash build.sh --uri collection/container --cli google-storage Singularity
+ #- /bin/bash build.sh --uri collection/container --cli google-drive Singularity
+ #- /bin/bash build.sh --uri collection/container --cli globus Singularity
+ #- /bin/bash build.sh --uri collection/container --cli registry Singularity
+
+ # This is where you can save job artifacts
+ # https://docs.gitlab.com/ee/user/project/pipelines/job_artifacts.html
+ # You can specify the path to containers or the build folder to save.
+ # Don't forget to save your recipes too!
+ artifacts:
+ paths:
+ - build/Singularity.sif
+ - build/Singularity
+
diff --git a/.gitlabci/build.sh b/.gitlabci/build.sh
new file mode 100644
index 0000000..e605a4c
--- /dev/null
+++ b/.gitlabci/build.sh
@@ -0,0 +1,177 @@
+#!/bin/bash
+
+# build.sh will build a Singularity container. It's not overly complicated.
+#
+# USAGE: build.sh --uri collection-name/container-name --cli registry Singularity
+# build.sh --uri collection-name/container-name --cli registry
+# build.sh Singularity
+
+# Copyright (C) 2017-2020 Vanessa Sochat.
+
+# This program is free software: you can redistribute it and/or modify it
+# under the terms of the GNU Affero General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or (at your
+# option) any later version.
+
+# This program is distributed in the hope that it will be useful, but WITHOUT
+# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
+# FITNESS FOR A PARTICULAR PURPOSE. See the GNU Affero General Public
+# License for more details.
+
+# You should have received a copy of the GNU Affero General Public License
+# along with this program. If not, see <https://www.gnu.org/licenses/>.
+
+set -o errexit
+set -o nounset
+
+function usage() {
+
+ echo "USAGE: build [recipe] [options]"
+ echo ""
+ echo "OPTIONS:
+
+ Image Format
+ --uri -u if uploading, a uri to give to sregistry
+ --cli -c the sregistry client to use (if uploading)
+ --help -h show this help and exit
+ "
+}
+
+# --- Option processing --------------------------------------------------------
+
+uri=""
+cli=""
+tag=""
+
+while true; do
+ case ${1:-} in
+ -h|--help|help)
+ usage
+ exit 0
+ ;;
+ -u|--uri)
+ shift
+ uri="${1:-}"
+ shift
+ ;;
+ -t|--tag)
+ shift
+ tag="${1:-}"
+ shift
+ ;;
+ -c|--cli)
+ shift
+ cli="${1:-}"
+ shift
+ ;;
+ \?) printf "illegal option: -%s\n" "${1:-}" >&2
+ usage
+ exit 1
+ ;;
+ -*)
+ printf "illegal option: -%s\n" "${1:-}" >&2
+ usage
+ exit 1
+ ;;
+ *)
+ break;
+ ;;
+ esac
+done
+
+################################################################################
+### Recipe File ################################################################
+################################################################################
+
+
+if [ $# == 0 ] ; then
+ recipe="Singularity"
+else
+ recipe=$1
+fi
+
+echo ""
+echo "Image Recipe: ${recipe}"
+
+
+################################################################################
+### Storage Client #############################################################
+################################################################################
+
+is_valid_client () {
+ local e match="$1"
+ shift
+ for e; do [[ "$e" == "$match" ]] && return 0; done
+ return 1
+}
+
+# Test if client is valid
+
+clients=("google-storage" "registry" "globus" "dropbox" "google-drive")
+
+if [ "${cli}" != "" ]; then
+ is_valid_client "${cli}" "${clients[@]}"
+ if [ $? -ne 0 ]; then
+ echo "${cli} is not a valid choice! Choose from ${clients[@]}";
+ exit 1
+ fi
+ echo "Storage Client: ${cli}"
+else
+ echo "Storage Client: none"
+fi
+
+
+################################################################################
+### Build! #####################################################################
+################################################################################
+
+# Continue if the image recipe is found
+
+if [ -f "$recipe" ]; then
+
+ imagefile="${recipe}.sif"
+
+ echo "Creating $imagefile using $recipe..."
+ singularity build $imagefile $recipe
+
+ # If the image is successfully built, test it and upload (examples)
+
+ if [ -f "${imagefile}" ]; then
+
+ # Example testing using run (you could also use test command)
+
+ echo "Testing the image... Marco!"
+ singularity exec $imagefile echo "Polo!"
+
+ # Example sregistry commands to push to endpoints
+
+ if [ "${cli}" != "" ]; then
+
+ # If the uri isn't provided, he gets a robot name
+ if [ "${uri}" == "" ]; then
+ uri=$(python -c "from sregistry.logger.namer import RobotNamer; bot=RobotNamer(); print(bot.generate())")
+ fi
+
+ # If a tag is provided, add to uri
+ if [ "${tag}" != "" ]; then
+ uri="${uri}:${tag}"
+ fi
+
+ echo "Pushing ${uri} to ${cli}://"
+ # singularity
+ # echo "SREGISTRY_CLIENT=${cli} sregistry push --name ${uri} ${imagefile}"
+ # SREGISTRY_CLIENT="${cli}" sregistry push --name "${uri}" "${imagefile}"
+
+ else
+ echo "Skipping upload. Image $imagefile is finished!"
+ fi
+
+ fi
+
+else
+
+ echo "Singularity recipe ${recipe} not found!"
+ exit 1
+
+fi
+
--
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