Build branch main with version main (cfefb99)

Build pipeline: viash-hub.demultiplex.main-ks8mz Source commit: cfefb99ef0 Source message: Bump Viash version to 0.9.0
2024-09-12 12:30:59 +00:00
parent 54d722dcb7
commit 6c37efac8f
17 changed files with 393 additions and 192 deletions
--- a/target/executable/io/interop_summary_to_csv/.config.vsh.yaml
+++ b/target/executable/io/interop_summary_to_csv/.config.vsh.yaml
@@ -140,8 +140,8 @@ build_info:
  engine: "docker|native"
  output: "target/executable/io/interop_summary_to_csv"
  executable: "target/executable/io/interop_summary_to_csv/interop_summary_to_csv"
-  viash_version: "0.9.0-RC6"
-  git_commit: "ed860bed30c98b981270f104cffbdb9b7f1ce141"
+  viash_version: "0.9.0"
+  git_commit: "cfefb99ef0d6eeeaf62a3f52654651bc59d06e0f"
  git_remote: "https://github.com/viash-hub/demultiplex"
 package_config:
  name: "demultiplex"
@@ -151,7 +151,7 @@ package_config:
    test_resources:
    - path: "https://raw.githubusercontent.com/nf-core/test-datasets/demultiplex/testdata/NovaSeq6000/200624_A00834_0183_BHMTFYDRXX.tar.gz"
      dest: "test_resources"
-  viash_version: "0.9.0-RC6"
+  viash_version: "0.9.0"
  source: "src"
  target: "target"
  config_mods:
--- a/target/executable/io/interop_summary_to_csv/interop_summary_to_csv
+++ b/target/executable/io/interop_summary_to_csv/interop_summary_to_csv
@@ -2,9 +2,9 @@

 # interop_summary_to_csv 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
@@ -205,9 +205,9 @@ 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:"
@@ -259,9 +259,9 @@ 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."
@@ -281,7 +281,8 @@ 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 $1
    out=$?
@@ -305,9 +306,9 @@ 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 $@
@@ -469,9 +470,9 @@ tar -C /tmp/ --no-same-owner --no-same-permissions -xvf /tmp/interop.tar.gz && \
 mv /tmp/interop-1.3.1-Linux-GNU/bin/index-summary /tmp/interop-1.3.1-Linux-GNU/bin/summary /usr/local/bin/

 LABEL org.opencontainers.image.description="Companion container for running component io interop_summary_to_csv"
-LABEL org.opencontainers.image.created="2024-06-24T12:46:52Z"
+LABEL org.opencontainers.image.created="2024-09-12T12:25:58Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/demultiplex"
-LABEL org.opencontainers.image.revision="ed860bed30c98b981270f104cffbdb9b7f1ce141"
+LABEL org.opencontainers.image.revision="cfefb99ef0d6eeeaf62a3f52654651bc59d06e0f"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
@@ -498,6 +499,9 @@ function ViashDockerBuildArgs {
 #   ViashAbsolutePath /foo/bar/..     # returns /foo
 function ViashAbsolutePath {
  local thePath
+  local parr
+  local outp
+  local len
  if [[ ! "$1" =~ ^/ ]]; then
    thePath="$PWD/$1"
  else
@@ -528,14 +532,17 @@ 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="$abs_path"
    base_name=""
@@ -543,7 +550,7 @@ function ViashDockerAutodetectMount {
    mount_source=`dirname "$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
@@ -551,7 +558,9 @@ 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="$abs_path"
    base_name=""
@@ -559,17 +568,22 @@ function ViashDockerAutodetectMountArg {
    mount_source=`dirname "$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)

@@ -653,6 +667,18 @@ 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 "$1")")
+            shift 1
+            ;;
+        ---docker_image_id)
+            VIASH_MODE='docker_image_id'
+            shift 1
+            ;;
        ---debug)
            VIASH_MODE='debug'
            shift 1
@@ -714,6 +740,10 @@ if [[ "$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
--- a/target/executable/io/untar/.config.vsh.yaml
+++ b/target/executable/io/untar/.config.vsh.yaml
@@ -147,8 +147,8 @@ build_info:
  engine: "docker|native"
  output: "target/executable/io/untar"
  executable: "target/executable/io/untar/untar"
-  viash_version: "0.9.0-RC6"
-  git_commit: "ed860bed30c98b981270f104cffbdb9b7f1ce141"
+  viash_version: "0.9.0"
+  git_commit: "cfefb99ef0d6eeeaf62a3f52654651bc59d06e0f"
  git_remote: "https://github.com/viash-hub/demultiplex"
 package_config:
  name: "demultiplex"
@@ -158,7 +158,7 @@ package_config:
    test_resources:
    - path: "https://raw.githubusercontent.com/nf-core/test-datasets/demultiplex/testdata/NovaSeq6000/200624_A00834_0183_BHMTFYDRXX.tar.gz"
      dest: "test_resources"
-  viash_version: "0.9.0-RC6"
+  viash_version: "0.9.0"
  source: "src"
  target: "target"
  config_mods:
--- a/target/executable/io/untar/untar
+++ b/target/executable/io/untar/untar
@@ -2,9 +2,9 @@

 # untar 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
@@ -215,9 +215,9 @@ 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:"
@@ -269,9 +269,9 @@ 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."
@@ -291,7 +291,8 @@ 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 $1
    out=$?
@@ -315,9 +316,9 @@ 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 $@
@@ -475,9 +476,9 @@ RUN apt-get update && \
  rm -rf /var/lib/apt/lists/*

 LABEL org.opencontainers.image.description="Companion container for running component io untar"
-LABEL org.opencontainers.image.created="2024-06-24T12:46:53Z"
+LABEL org.opencontainers.image.created="2024-09-12T12:25:58Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/demultiplex"
-LABEL org.opencontainers.image.revision="ed860bed30c98b981270f104cffbdb9b7f1ce141"
+LABEL org.opencontainers.image.revision="cfefb99ef0d6eeeaf62a3f52654651bc59d06e0f"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
@@ -504,6 +505,9 @@ function ViashDockerBuildArgs {
 #   ViashAbsolutePath /foo/bar/..     # returns /foo
 function ViashAbsolutePath {
  local thePath
+  local parr
+  local outp
+  local len
  if [[ ! "$1" =~ ^/ ]]; then
    thePath="$PWD/$1"
  else
@@ -534,14 +538,17 @@ 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="$abs_path"
    base_name=""
@@ -549,7 +556,7 @@ function ViashDockerAutodetectMount {
    mount_source=`dirname "$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
@@ -557,7 +564,9 @@ 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="$abs_path"
    base_name=""
@@ -565,17 +574,22 @@ function ViashDockerAutodetectMountArg {
    mount_source=`dirname "$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)

@@ -665,6 +679,18 @@ 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 "$1")")
+            shift 1
+            ;;
+        ---docker_image_id)
+            VIASH_MODE='docker_image_id'
+            shift 1
+            ;;
        ---debug)
            VIASH_MODE='debug'
            shift 1
@@ -726,6 +752,10 @@ if [[ "$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