Build branch main with version main (5705b88)
Build pipeline: viash-hub.craftbox.main-6n7js
Source commit: 5705b88fa2
Source message: Bump Viash and update CHANGELOG
This commit is contained in:
@@ -221,15 +221,15 @@ build_info:
|
||||
engine: "docker|native"
|
||||
output: "target/executable/csv2fasta"
|
||||
executable: "target/executable/csv2fasta/csv2fasta"
|
||||
viash_version: "0.9.0-RC6"
|
||||
git_commit: "373be82129c13f50558c0dae25c07afe0866a8ba"
|
||||
viash_version: "0.9.0-RC7"
|
||||
git_commit: "5705b88fa20f267475b5d0ae1ca25dbf55ff1295"
|
||||
git_remote: "https://github.com/viash-hub/craftbox"
|
||||
package_config:
|
||||
name: "craftbox"
|
||||
version: "main"
|
||||
description: "A collection of custom-tailored scripts and applied tools.\n"
|
||||
info: null
|
||||
viash_version: "0.9.0-RC6"
|
||||
viash_version: "0.9.0-RC7"
|
||||
source: "src"
|
||||
target: "target"
|
||||
config_mods:
|
||||
|
||||
@@ -2,7 +2,7 @@
|
||||
|
||||
# csv2fasta main
|
||||
#
|
||||
# This wrapper script is auto-generated by viash 0.9.0-RC6 and is thus a
|
||||
# This wrapper script is auto-generated by viash 0.9.0-RC7 and is thus a
|
||||
# derivative work thereof. This software comes with ABSOLUTELY NO WARRANTY from
|
||||
# Data Intuitive.
|
||||
#
|
||||
@@ -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 $source
|
||||
}
|
||||
# see https://en.wikipedia.org/wiki/Syslog#Severity_level
|
||||
VIASH_LOGCODE_EMERGENCY=0
|
||||
@@ -261,9 +261,9 @@ function ViashDockerInstallationCheck {
|
||||
fi
|
||||
|
||||
ViashDebug "Checking whether the Docker daemon is running"
|
||||
save=$-; 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:"
|
||||
@@ -315,9 +315,9 @@ 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."
|
||||
@@ -337,7 +337,8 @@ 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 $1
|
||||
out=$?
|
||||
@@ -361,9 +362,9 @@ 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 $@
|
||||
@@ -524,9 +525,9 @@ RUN pip install --upgrade pip && \
|
||||
pip install --upgrade --no-cache-dir "dnaio"
|
||||
|
||||
LABEL org.opencontainers.image.description="Companion container for running component csv2fasta"
|
||||
LABEL org.opencontainers.image.created="2024-08-19T07:26:26Z"
|
||||
LABEL org.opencontainers.image.created="2024-09-12T15:41:15Z"
|
||||
LABEL org.opencontainers.image.source="https://github.com/viash-hub/craftbox"
|
||||
LABEL org.opencontainers.image.revision="373be82129c13f50558c0dae25c07afe0866a8ba"
|
||||
LABEL org.opencontainers.image.revision="5705b88fa20f267475b5d0ae1ca25dbf55ff1295"
|
||||
LABEL org.opencontainers.image.version="main"
|
||||
|
||||
VIASHDOCKER
|
||||
@@ -553,6 +554,9 @@ function ViashDockerBuildArgs {
|
||||
# ViashAbsolutePath /foo/bar/.. # returns /foo
|
||||
function ViashAbsolutePath {
|
||||
local thePath
|
||||
local parr
|
||||
local outp
|
||||
local len
|
||||
if [[ ! "$1" =~ ^/ ]]; then
|
||||
thePath="$PWD/$1"
|
||||
else
|
||||
@@ -583,14 +587,17 @@ 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="$abs_path"
|
||||
base_name=""
|
||||
@@ -598,7 +605,7 @@ function ViashDockerAutodetectMount {
|
||||
mount_source=`dirname "$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
|
||||
@@ -606,7 +613,9 @@ 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="$abs_path"
|
||||
base_name=""
|
||||
@@ -614,17 +623,22 @@ function ViashDockerAutodetectMountArg {
|
||||
mount_source=`dirname "$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)
|
||||
|
||||
@@ -768,6 +782,18 @@ 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 "$1")")
|
||||
shift 1
|
||||
;;
|
||||
---docker_image_id)
|
||||
VIASH_MODE='docker_image_id'
|
||||
shift 1
|
||||
;;
|
||||
---debug)
|
||||
VIASH_MODE='debug'
|
||||
shift 1
|
||||
@@ -829,6 +855,10 @@ if [[ "$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
|
||||
|
||||
Reference in New Issue
Block a user