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Build branch main with version main (a3cebc0)

Browse Source 
Build pipeline: viash-hub.toolbox.main-2kq6h

Source commit: a3cebc0315

Source message: Bump Viash version to 0.9.0
This commit is contained in:
CI
2024-09-13 08:57:53 +00:00
parent e3aee2f8b4
commit 39a745c398
10 changed files with 248 additions and 126 deletions
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6
target/executable/bgzip/.config.vsh.yaml
View File

@@ -224,15 +224,15 @@ build_info:
engine: "docker|native"
output: "target/executable/bgzip"
executable: "target/executable/bgzip/bgzip"
viash_version: "0.9.0-RC6"
git_commit: "7cec5cac6937b310c9f172d4c5655a5f20d2442f"
viash_version: "0.9.0"
git_commit: "a3cebc0315249e08a4a39d175670f29a800c1c5f"
git_remote: "https://github.com/viash-hub/toolbox"
package_config:
name: "toolbox"
version: "main"
description: "A collection of command-line tools.\n"
info: null
viash_version: "0.9.0-RC6"
viash_version: "0.9.0"
source: "src"
target: "target"
config_mods:

94
target/executable/bgzip/bgzip
View File

@@ -2,9 +2,9 @@
# bgzip main
#
# This wrapper script is auto-generated by viash 0.9.0-RC6 and is thus a
# derivative work thereof. This software comes with ABSOLUTELY NO WARRANTY from
# Data Intuitive.
# This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
# work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
# Intuitive.
#
# The component may contain files which fall under a different license. The
# authors of this component should specify the license in the header of such
@@ -54,24 +54,24 @@ function ViashRemoveFlags {
# $1 : Should always be set to ${BASH_SOURCE[0]}
# returns : The absolute path of the bash file
function ViashSourceDir {
SOURCE="$1"
while [ -h "$SOURCE" ]; do
DIR="$( cd -P "$( dirname "$SOURCE" )" >/dev/null 2>&1 && pwd )"
SOURCE="$(readlink "$SOURCE")"
[[ $SOURCE != /* ]] && SOURCE="$DIR/$SOURCE"
local source="$1"
while [ -h "$source" ]; do
local dir="$( cd -P "$( dirname "$source" )" >/dev/null 2>&1 && pwd )"
source="$(readlink "$source")"
[[ $source != /* ]] && source="$dir/$source"
done
cd -P "$( dirname "$SOURCE" )" >/dev/null 2>&1 && pwd
cd -P "$( dirname "$source" )" >/dev/null 2>&1 && pwd
}
# ViashFindTargetDir: return the path of the '.build.yaml' file, following symlinks
# usage : ViashFindTargetDir 'ScriptPath'
# $1 : The location from where to start the upward search
# returns : The absolute path of the '.build.yaml' file
function ViashFindTargetDir {
SOURCE="$1"
while [[ "$SOURCE" != "" && ! -e "$SOURCE/.build.yaml" ]]; do
SOURCE=${SOURCE%/*}
local source="$1"
while [[ "$source" != "" && ! -e "$source/.build.yaml" ]]; do
source=${source%/*}
done
echo $SOURCE
echo $source
}
# see https://en.wikipedia.org/wiki/Syslog#Severity_level
VIASH_LOGCODE_EMERGENCY=0
@@ -250,9 +250,9 @@ function ViashDockerInstallationCheck {
fi
ViashDebug "Checking whether the Docker daemon is running"
save=$-; set +e
docker_version=$(docker version --format '{{.Client.APIVersion}}' 2> /dev/null)
out=$?
local save=$-; set +e
local docker_version=$(docker version --format '{{.Client.APIVersion}}' 2> /dev/null)
local out=$?
[[ $save =~ e ]] && set -e
if [ $out -ne 0 ]; then
ViashCritical "Docker daemon does not seem to be running. Try one of the following:"
@@ -304,9 +304,9 @@ function ViashDockerPull {
if [ $VIASH_VERBOSITY -ge $VIASH_LOGCODE_INFO ]; then
docker pull $1 && return 0 || return 1
else
save=$-; set +e
local save=$-; set +e
docker pull $1 2> /dev/null > /dev/null
out=$?
local out=$?
[[ $save =~ e ]] && set -e
if [ $out -ne 0 ]; then
ViashWarning "Could not pull from '$1'. Docker image doesn't exist or is not accessible."
@@ -326,7 +326,8 @@ function ViashDockerPull {
# echo $? # returns '1'
function ViashDockerPush {
ViashNotice "Pushing image to '$1'"
save=$-; set +e
local save=$-; set +e
local out
if [ $VIASH_VERBOSITY -ge $VIASH_LOGCODE_INFO ]; then
docker push $1
out=$?
@@ -350,9 +351,9 @@ function ViashDockerPush {
# examples:
# ViashDockerPullElseBuild mynewcomponent
function ViashDockerPullElseBuild {
save=$-; set +e
local save=$-; set +e
ViashDockerPull $1
out=$?
local out=$?
[[ $save =~ e ]] && set -e
if [ $out -ne 0 ]; then
ViashDockerBuild $@
@@ -508,9 +509,9 @@ ENTRYPOINT []
RUN bgzip -h | grep 'Version:' 2>&1 | sed 's/Version:\s\(.*\)/bgzip: "\1"/' > /var/software_versions.txt
LABEL org.opencontainers.image.description="Companion container for running component bgzip"
LABEL org.opencontainers.image.created="2024-08-19T07:32:49Z"
LABEL org.opencontainers.image.created="2024-09-13T08:50:00Z"
LABEL org.opencontainers.image.source="https://github.com/samtools/htslib"
LABEL org.opencontainers.image.revision="7cec5cac6937b310c9f172d4c5655a5f20d2442f"
LABEL org.opencontainers.image.revision="a3cebc0315249e08a4a39d175670f29a800c1c5f"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER
@@ -537,6 +538,9 @@ function ViashDockerBuildArgs {
# ViashAbsolutePath /foo/bar/.. # returns /foo
function ViashAbsolutePath {
local thePath
local parr
local outp
local len
if [[ ! "$1" =~ ^/ ]]; then
thePath="$PWD/$1"
else
@@ -567,14 +571,17 @@ function ViashAbsolutePath {
)
}
# ViashDockerAutodetectMount: auto configuring docker mounts from parameters
# $1 : The parameter value
# returns : New parameter
# $VIASH_DIRECTORY_MOUNTS : Added another parameter to be passed to docker
# $1 : The parameter value
# returns : New parameter
# $VIASH_DIRECTORY_MOUNTS : Added another parameter to be passed to docker
# $VIASH_DOCKER_AUTOMOUNT_PREFIX : The prefix to be used for the automounts
# examples:
# ViashDockerAutodetectMount /path/to/bar # returns '/viash_automount/path/to/bar'
# ViashDockerAutodetectMountArg /path/to/bar # returns '--volume="/path/to:/viash_automount/path/to"'
function ViashDockerAutodetectMount {
abs_path=$(ViashAbsolutePath "$1")
local abs_path=$(ViashAbsolutePath "$1")
local mount_source
local base_name
if [ -d "$abs_path" ]; then
mount_source="$abs_path"
base_name=""
@@ -582,7 +589,7 @@ function ViashDockerAutodetectMount {
mount_source=`dirname "$abs_path"`
base_name=`basename "$abs_path"`
fi
mount_target="/viash_automount$mount_source"
local mount_target="$VIASH_DOCKER_AUTOMOUNT_PREFIX$mount_source"
if [ -z "$base_name" ]; then
echo "$mount_target"
else
@@ -590,7 +597,9 @@ function ViashDockerAutodetectMount {
fi
}
function ViashDockerAutodetectMountArg {
abs_path=$(ViashAbsolutePath "$1")
local abs_path=$(ViashAbsolutePath "$1")
local mount_source
local base_name
if [ -d "$abs_path" ]; then
mount_source="$abs_path"
base_name=""
@@ -598,17 +607,22 @@ function ViashDockerAutodetectMountArg {
mount_source=`dirname "$abs_path"`
base_name=`basename "$abs_path"`
fi
mount_target="/viash_automount$mount_source"
local mount_target="$VIASH_DOCKER_AUTOMOUNT_PREFIX$mount_source"
ViashDebug "ViashDockerAutodetectMountArg $1 -> $mount_source -> $mount_target"
echo "--volume=\"$mount_source:$mount_target\""
}
function ViashDockerStripAutomount {
abs_path=$(ViashAbsolutePath "$1")
echo "${abs_path#/viash_automount}"
local abs_path=$(ViashAbsolutePath "$1")
echo "${abs_path#$VIASH_DOCKER_AUTOMOUNT_PREFIX}"
}
# initialise variables
VIASH_DIRECTORY_MOUNTS=()
# configure default docker automount prefix if it is unset
if [ -z "${VIASH_DOCKER_AUTOMOUNT_PREFIX+x}" ]; then
VIASH_DOCKER_AUTOMOUNT_PREFIX="/viash_automount"
fi
# initialise docker variables
VIASH_DOCKER_RUN_ARGS=(-i --rm)
@@ -804,6 +818,18 @@ while [[ $# -gt 0 ]]; do
VIASH_MODE='dockerfile'
shift 1
;;
---docker_run_args)
VIASH_DOCKER_RUN_ARGS+=("$2")
shift 2
;;
---docker_run_args=*)
VIASH_DOCKER_RUN_ARGS+=("$(ViashRemoveFlags "$1")")
shift 1
;;
---docker_image_id)
VIASH_MODE='docker_image_id'
shift 1
;;
---debug)
VIASH_MODE='debug'
shift 1
@@ -865,6 +891,10 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
if [ "$VIASH_MODE" == "dockerfile" ]; then
ViashDockerfile "$VIASH_ENGINE_ID"
exit 0
elif [ "$VIASH_MODE" == "docker_image_id" ]; then
echo "$VIASH_DOCKER_IMAGE_ID"
exit 0
# enter docker container
elif [[ "$VIASH_MODE" == "debug" ]]; then

6
target/executable/yq/.config.vsh.yaml
View File

@@ -254,15 +254,15 @@ build_info:
engine: "docker|native"
output: "target/executable/yq"
executable: "target/executable/yq/yq"
viash_version: "0.9.0-RC6"
git_commit: "7cec5cac6937b310c9f172d4c5655a5f20d2442f"
viash_version: "0.9.0"
git_commit: "a3cebc0315249e08a4a39d175670f29a800c1c5f"
git_remote: "https://github.com/viash-hub/toolbox"
package_config:
name: "toolbox"
version: "main"
description: "A collection of command-line tools.\n"
info: null
viash_version: "0.9.0-RC6"
viash_version: "0.9.0"
source: "src"
target: "target"
config_mods:

94
target/executable/yq/yq
View File

@@ -2,9 +2,9 @@
# yq main
#
# This wrapper script is auto-generated by viash 0.9.0-RC6 and is thus a
# derivative work thereof. This software comes with ABSOLUTELY NO WARRANTY from
# Data Intuitive.
# This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
# work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
# Intuitive.
#
# The component may contain files which fall under a different license. The
# authors of this component should specify the license in the header of such
@@ -54,24 +54,24 @@ function ViashRemoveFlags {
# $1 : Should always be set to ${BASH_SOURCE[0]}
# returns : The absolute path of the bash file
function ViashSourceDir {
SOURCE="$1"
while [ -h "$SOURCE" ]; do
DIR="$( cd -P "$( dirname "$SOURCE" )" >/dev/null 2>&1 && pwd )"
SOURCE="$(readlink "$SOURCE")"
[[ $SOURCE != /* ]] && SOURCE="$DIR/$SOURCE"
local source="$1"
while [ -h "$source" ]; do
local dir="$( cd -P "$( dirname "$source" )" >/dev/null 2>&1 && pwd )"
source="$(readlink "$source")"
[[ $source != /* ]] && source="$dir/$source"
done
cd -P "$( dirname "$SOURCE" )" >/dev/null 2>&1 && pwd
cd -P "$( dirname "$source" )" >/dev/null 2>&1 && pwd
}
# ViashFindTargetDir: return the path of the '.build.yaml' file, following symlinks
# usage : ViashFindTargetDir 'ScriptPath'
# $1 : The location from where to start the upward search
# returns : The absolute path of the '.build.yaml' file
function ViashFindTargetDir {
SOURCE="$1"
while [[ "$SOURCE" != "" && ! -e "$SOURCE/.build.yaml" ]]; do
SOURCE=${SOURCE%/*}
local source="$1"
while [[ "$source" != "" && ! -e "$source/.build.yaml" ]]; do
source=${source%/*}
done
echo $SOURCE
echo $source
}
# see https://en.wikipedia.org/wiki/Syslog#Severity_level
VIASH_LOGCODE_EMERGENCY=0
@@ -233,9 +233,9 @@ function ViashDockerInstallationCheck {
fi
ViashDebug "Checking whether the Docker daemon is running"
save=$-; set +e
docker_version=$(docker version --format '{{.Client.APIVersion}}' 2> /dev/null)
out=$?
local save=$-; set +e
local docker_version=$(docker version --format '{{.Client.APIVersion}}' 2> /dev/null)
local out=$?
[[ $save =~ e ]] && set -e
if [ $out -ne 0 ]; then
ViashCritical "Docker daemon does not seem to be running. Try one of the following:"
@@ -287,9 +287,9 @@ function ViashDockerPull {
if [ $VIASH_VERBOSITY -ge $VIASH_LOGCODE_INFO ]; then
docker pull $1 && return 0 || return 1
else
save=$-; set +e
local save=$-; set +e
docker pull $1 2> /dev/null > /dev/null
out=$?
local out=$?
[[ $save =~ e ]] && set -e
if [ $out -ne 0 ]; then
ViashWarning "Could not pull from '$1'. Docker image doesn't exist or is not accessible."
@@ -309,7 +309,8 @@ function ViashDockerPull {
# echo $? # returns '1'
function ViashDockerPush {
ViashNotice "Pushing image to '$1'"
save=$-; set +e
local save=$-; set +e
local out
if [ $VIASH_VERBOSITY -ge $VIASH_LOGCODE_INFO ]; then
docker push $1
out=$?
@@ -333,9 +334,9 @@ function ViashDockerPush {
# examples:
# ViashDockerPullElseBuild mynewcomponent
function ViashDockerPullElseBuild {
save=$-; set +e
local save=$-; set +e
ViashDockerPull $1
out=$?
local out=$?
[[ $save =~ e ]] && set -e
if [ $out -ne 0 ]; then
ViashDockerBuild $@
@@ -493,9 +494,9 @@ RUN apk add --no-cache bash yq-go
RUN /usr/bin/yq --version | sed 's/.*version\sv\(.*\)/yq: "\1"/' > /var/software_versions.txt
LABEL org.opencontainers.image.description="Companion container for running component yq"
LABEL org.opencontainers.image.created="2024-08-19T07:32:48Z"
LABEL org.opencontainers.image.created="2024-09-13T08:49:59Z"
LABEL org.opencontainers.image.source="https://github.com/mikefarah/yq"
LABEL org.opencontainers.image.revision="7cec5cac6937b310c9f172d4c5655a5f20d2442f"
LABEL org.opencontainers.image.revision="a3cebc0315249e08a4a39d175670f29a800c1c5f"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER
@@ -522,6 +523,9 @@ function ViashDockerBuildArgs {
# ViashAbsolutePath /foo/bar/.. # returns /foo
function ViashAbsolutePath {
local thePath
local parr
local outp
local len
if [[ ! "$1" =~ ^/ ]]; then
thePath="$PWD/$1"
else
@@ -552,14 +556,17 @@ function ViashAbsolutePath {
)
}
# ViashDockerAutodetectMount: auto configuring docker mounts from parameters
# $1 : The parameter value
# returns : New parameter
# $VIASH_DIRECTORY_MOUNTS : Added another parameter to be passed to docker
# $1 : The parameter value
# returns : New parameter
# $VIASH_DIRECTORY_MOUNTS : Added another parameter to be passed to docker
# $VIASH_DOCKER_AUTOMOUNT_PREFIX : The prefix to be used for the automounts
# examples:
# ViashDockerAutodetectMount /path/to/bar # returns '/viash_automount/path/to/bar'
# ViashDockerAutodetectMountArg /path/to/bar # returns '--volume="/path/to:/viash_automount/path/to"'
function ViashDockerAutodetectMount {
abs_path=$(ViashAbsolutePath "$1")
local abs_path=$(ViashAbsolutePath "$1")
local mount_source
local base_name
if [ -d "$abs_path" ]; then
mount_source="$abs_path"
base_name=""
@@ -567,7 +574,7 @@ function ViashDockerAutodetectMount {
mount_source=`dirname "$abs_path"`
base_name=`basename "$abs_path"`
fi
mount_target="/viash_automount$mount_source"
local mount_target="$VIASH_DOCKER_AUTOMOUNT_PREFIX$mount_source"
if [ -z "$base_name" ]; then
echo "$mount_target"
else
@@ -575,7 +582,9 @@ function ViashDockerAutodetectMount {
fi
}
function ViashDockerAutodetectMountArg {
abs_path=$(ViashAbsolutePath "$1")
local abs_path=$(ViashAbsolutePath "$1")
local mount_source
local base_name
if [ -d "$abs_path" ]; then
mount_source="$abs_path"
base_name=""
@@ -583,17 +592,22 @@ function ViashDockerAutodetectMountArg {
mount_source=`dirname "$abs_path"`
base_name=`basename "$abs_path"`
fi
mount_target="/viash_automount$mount_source"
local mount_target="$VIASH_DOCKER_AUTOMOUNT_PREFIX$mount_source"
ViashDebug "ViashDockerAutodetectMountArg $1 -> $mount_source -> $mount_target"
echo "--volume=\"$mount_source:$mount_target\""
}
function ViashDockerStripAutomount {
abs_path=$(ViashAbsolutePath "$1")
echo "${abs_path#/viash_automount}"
local abs_path=$(ViashAbsolutePath "$1")
echo "${abs_path#$VIASH_DOCKER_AUTOMOUNT_PREFIX}"
}
# initialise variables
VIASH_DIRECTORY_MOUNTS=()
# configure default docker automount prefix if it is unset
if [ -z "${VIASH_DOCKER_AUTOMOUNT_PREFIX+x}" ]; then
VIASH_DOCKER_AUTOMOUNT_PREFIX="/viash_automount"
fi
# initialise docker variables
VIASH_DOCKER_RUN_ARGS=(-i --rm)
@@ -738,6 +752,18 @@ while [[ $# -gt 0 ]]; do
VIASH_MODE='dockerfile'
shift 1
;;
---docker_run_args)
VIASH_DOCKER_RUN_ARGS+=("$2")
shift 2
;;
---docker_run_args=*)
VIASH_DOCKER_RUN_ARGS+=("$(ViashRemoveFlags "$1")")
shift 1
;;
---docker_image_id)
VIASH_MODE='docker_image_id'
shift 1
;;
---debug)
VIASH_MODE='debug'
shift 1
@@ -799,6 +825,10 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
if [ "$VIASH_MODE" == "dockerfile" ]; then
ViashDockerfile "$VIASH_ENGINE_ID"
exit 0
elif [ "$VIASH_MODE" == "docker_image_id" ]; then
echo "$VIASH_DOCKER_IMAGE_ID"
exit 0
# enter docker container
elif [[ "$VIASH_MODE" == "debug" ]]; then