From 2a9ecc81e10345e93008d5ff916414c17b9bf9d9 Mon Sep 17 00:00:00 2001
From: Robrecht Cannoodt <rcannood@gmail.com>
Date: Mon, 12 Aug 2024 09:56:24 +0200
Subject: [PATCH 01/18] first commit

---
 .../scala/io/viash/wrapper/BashWrapper.scala  | 55 +++++++++++--------
 1 file changed, 31 insertions(+), 24 deletions(-)

diff --git a/src/main/scala/io/viash/wrapper/BashWrapper.scala b/src/main/scala/io/viash/wrapper/BashWrapper.scala
index 0faefc48f..a0aa59eef 100644
--- a/src/main/scala/io/viash/wrapper/BashWrapper.scala
+++ b/src/main/scala/io/viash/wrapper/BashWrapper.scala
@@ -52,41 +52,48 @@ object BashWrapper {
   }
 
   def store(name: String, env: String, value: String, multiple_sep: Option[String]): Array[String] = {
+    // note: 'value' is split using multiple_sep into 'values' for backwards compatibility.
+    // todo: strip quotes and escape as suggested by https://github.com/viash-io/viash/issues/705#issuecomment-2208448576
     if (multiple_sep.isDefined) {
-      s"""if [ -z "$$$env" ]; then
-         |  $env=$value
-         |else
-         |  $env="$$$env${multiple_sep.get}"$value
-         |fi""".stripMargin.split("\n")
+      // note: 'values' is a global variable here!
+      s"""if [ "$value" == "UNDEFINED" ]; then
+        |  unset $value
+        |else
+        |  readarray -d $$';' -t values <<< $value
+        |  if [ -z "$$$env" ]; then
+        |    $env=( "$${values[@]}" )
+        |  else
+        |    $env+=( "$${values[@]}" )
+        |  fi
+        |fi""".stripMargin.split("\n")
     } else {
-      Array(
-        s"""[ -n "$$$env" ] && ViashError Bad arguments for option \\'$name\\': \\'$$$env\\' \\& \\'$$2\\' - you should provide exactly one argument for this option. && exit 1""",
-        env + "=" + value
-      )
+      s"""if [ "$value" == "UNDEFINED" ]; then
+        |  unset $value
+        |else
+        |  [ -n "$$$env" ] && ViashError Bad arguments for option \\'$name\\': \\'$$$env\\' \\& \\'$$2\\' - you should provide exactly one argument for this option. && exit 1
+        |  $env=$value
+        |fi""".stripMargin.split("\n")
     }
   }
 
   def argStore(
     name: String,
     plainName: String,
-    store: String,
+    value: String,
     argsConsumed: Int,
     multiple_sep: Option[String] = None
   ): String = {
-    argsConsumed match {
-      case num if num > 1 =>
-        s"""        $name)
-           |            ${this.store(name, plainName, store, multiple_sep).mkString("\n            ")}
-           |            [ $$# -lt $argsConsumed ] && ViashError Not enough arguments passed to $name. Use "--help" to get more information on the parameters. && exit 1
-           |            shift $argsConsumed
-           |            ;;""".stripMargin
-      case _ =>
-        s"""        $name)
-           |            ${this.store(name, plainName, store, multiple_sep).mkString("\n            ")}
-           |            shift $argsConsumed
-           |            ;;""".stripMargin
-    }
-    
+    val argmatchError =
+      if (argsConsumed > 1) {
+        s"""\n            [ $$# -lt $argsConsumed ] && ViashError Not enough arguments passed to $name. Use "--help" to get more information on the parameters. && exit 1"""
+      } else {
+        ""
+      }
+
+    s"""        $name)$argmatchError
+        |            ${this.store(name, plainName, value, multiple_sep).mkString("\n            ")}
+        |            shift $argsConsumed
+        |            ;;""".stripMargin
   }
 
   def argStoreSed(name: String, plainName: String, multiple_sep: Option[String] = None): String = {

From 77cd691e75ed36cd0d677f12b812dae393c3808c Mon Sep 17 00:00:00 2001
From: Robrecht Cannoodt <rcannood@gmail.com>
Date: Mon, 12 Aug 2024 10:29:07 +0200
Subject: [PATCH 02/18] fix usage of wrong varible

---
 src/main/scala/io/viash/wrapper/BashWrapper.scala | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/src/main/scala/io/viash/wrapper/BashWrapper.scala b/src/main/scala/io/viash/wrapper/BashWrapper.scala
index a0aa59eef..7358c1f06 100644
--- a/src/main/scala/io/viash/wrapper/BashWrapper.scala
+++ b/src/main/scala/io/viash/wrapper/BashWrapper.scala
@@ -56,8 +56,8 @@ object BashWrapper {
     // todo: strip quotes and escape as suggested by https://github.com/viash-io/viash/issues/705#issuecomment-2208448576
     if (multiple_sep.isDefined) {
       // note: 'values' is a global variable here!
-      s"""if [ "$value" == "UNDEFINED" ]; then
-        |  unset $value
+      s"""if [ "$env" == "UNDEFINED" ]; then
+        |  unset $env
         |else
         |  readarray -d $$';' -t values <<< $value
         |  if [ -z "$$$env" ]; then
@@ -67,8 +67,8 @@ object BashWrapper {
         |  fi
         |fi""".stripMargin.split("\n")
     } else {
-      s"""if [ "$value" == "UNDEFINED" ]; then
-        |  unset $value
+      s"""if [ "$env" == "UNDEFINED" ]; then
+        |  unset $env
         |else
         |  [ -n "$$$env" ] && ViashError Bad arguments for option \\'$name\\': \\'$$$env\\' \\& \\'$$2\\' - you should provide exactly one argument for this option. && exit 1
         |  $env=$value

From 8190a76f2009743a26f73ae04c4ccf9af806de04 Mon Sep 17 00:00:00 2001
From: Robrecht Cannoodt <rcannood@gmail.com>
Date: Mon, 12 Aug 2024 10:29:34 +0200
Subject: [PATCH 03/18] fix missing $

---
 src/main/scala/io/viash/wrapper/BashWrapper.scala | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/main/scala/io/viash/wrapper/BashWrapper.scala b/src/main/scala/io/viash/wrapper/BashWrapper.scala
index 7358c1f06..0d295b93d 100644
--- a/src/main/scala/io/viash/wrapper/BashWrapper.scala
+++ b/src/main/scala/io/viash/wrapper/BashWrapper.scala
@@ -56,7 +56,7 @@ object BashWrapper {
     // todo: strip quotes and escape as suggested by https://github.com/viash-io/viash/issues/705#issuecomment-2208448576
     if (multiple_sep.isDefined) {
       // note: 'values' is a global variable here!
-      s"""if [ "$env" == "UNDEFINED" ]; then
+      s"""if [ "$$$env" == "UNDEFINED" ]; then
         |  unset $env
         |else
         |  readarray -d $$';' -t values <<< $value
@@ -67,7 +67,7 @@ object BashWrapper {
         |  fi
         |fi""".stripMargin.split("\n")
     } else {
-      s"""if [ "$env" == "UNDEFINED" ]; then
+      s"""if [ "$$$env" == "UNDEFINED" ]; then
         |  unset $env
         |else
         |  [ -n "$$$env" ] && ViashError Bad arguments for option \\'$name\\': \\'$$$env\\' \\& \\'$$2\\' - you should provide exactly one argument for this option. && exit 1

From a0b8c622a2a2f06bdbc7e845f5ea36388c24accb Mon Sep 17 00:00:00 2001
From: Robrecht Cannoodt <rcannood@gmail.com>
Date: Mon, 12 Aug 2024 10:53:25 +0200
Subject: [PATCH 04/18] fix variables again

---
 src/main/scala/io/viash/wrapper/BashWrapper.scala | 12 +++++++-----
 1 file changed, 7 insertions(+), 5 deletions(-)

diff --git a/src/main/scala/io/viash/wrapper/BashWrapper.scala b/src/main/scala/io/viash/wrapper/BashWrapper.scala
index 0d295b93d..b2eb1e9d9 100644
--- a/src/main/scala/io/viash/wrapper/BashWrapper.scala
+++ b/src/main/scala/io/viash/wrapper/BashWrapper.scala
@@ -55,11 +55,12 @@ object BashWrapper {
     // note: 'value' is split using multiple_sep into 'values' for backwards compatibility.
     // todo: strip quotes and escape as suggested by https://github.com/viash-io/viash/issues/705#issuecomment-2208448576
     if (multiple_sep.isDefined) {
-      // note: 'values' is a global variable here!
-      s"""if [ "$$$env" == "UNDEFINED" ]; then
+      // note: 'value' and 'values' are global values!!
+      s"""value=$value
+        |if [ $$value == UNDEFINED ]; then
         |  unset $env
         |else
-        |  readarray -d $$';' -t values <<< $value
+        |  readarray -d $$';' -t values <<< $$value
         |  if [ -z "$$$env" ]; then
         |    $env=( "$${values[@]}" )
         |  else
@@ -67,11 +68,12 @@ object BashWrapper {
         |  fi
         |fi""".stripMargin.split("\n")
     } else {
-      s"""if [ "$$$env" == "UNDEFINED" ]; then
+      s"""value=$value
+        |if [ $$value == UNDEFINED ]; then
         |  unset $env
         |else
         |  [ -n "$$$env" ] && ViashError Bad arguments for option \\'$name\\': \\'$$$env\\' \\& \\'$$2\\' - you should provide exactly one argument for this option. && exit 1
-        |  $env=$value
+        |  $env=$$value
         |fi""".stripMargin.split("\n")
     }
   }

From 8d96497854b712dc617c5aa36512499b20842cd3 Mon Sep 17 00:00:00 2001
From: Robrecht Cannoodt <rcannood@gmail.com>
Date: Mon, 12 Aug 2024 11:03:52 +0200
Subject: [PATCH 05/18] unset first, just in case

---
 src/main/scala/io/viash/wrapper/BashWrapper.scala | 7 +++++--
 1 file changed, 5 insertions(+), 2 deletions(-)

diff --git a/src/main/scala/io/viash/wrapper/BashWrapper.scala b/src/main/scala/io/viash/wrapper/BashWrapper.scala
index b2eb1e9d9..1fb356271 100644
--- a/src/main/scala/io/viash/wrapper/BashWrapper.scala
+++ b/src/main/scala/io/viash/wrapper/BashWrapper.scala
@@ -56,7 +56,9 @@ object BashWrapper {
     // todo: strip quotes and escape as suggested by https://github.com/viash-io/viash/issues/705#issuecomment-2208448576
     if (multiple_sep.isDefined) {
       // note: 'value' and 'values' are global values!!
-      s"""value=$value
+      // -> could rename them to `${env}_value` and `${env}_values` to avoid conflicts
+      s"""unset value values
+        |value=$value
         |if [ $$value == UNDEFINED ]; then
         |  unset $env
         |else
@@ -68,7 +70,8 @@ object BashWrapper {
         |  fi
         |fi""".stripMargin.split("\n")
     } else {
-      s"""value=$value
+      s"""unset value
+        |value=$value
         |if [ $$value == UNDEFINED ]; then
         |  unset $env
         |else

From 3b96160794b1b56a00e56ce329f06a7db58d2c70 Mon Sep 17 00:00:00 2001
From: Robrecht Cannoodt <rcannood@gmail.com>
Date: Mon, 12 Aug 2024 11:08:03 +0200
Subject: [PATCH 06/18] replace `IFS=... for var in $myarg` with `for i in
 ${!myarg[@]}`

---
 .../io/viash/runners/ExecutableRunner.scala   | 21 ++---
 .../scala/io/viash/wrapper/BashWrapper.scala  | 76 ++++++++++---------
 2 files changed, 44 insertions(+), 53 deletions(-)

diff --git a/src/main/scala/io/viash/runners/ExecutableRunner.scala b/src/main/scala/io/viash/runners/ExecutableRunner.scala
index 99f1fa3b8..53f3d87ba 100644
--- a/src/main/scala/io/viash/runners/ExecutableRunner.scala
+++ b/src/main/scala/io/viash/runners/ExecutableRunner.scala
@@ -395,20 +395,14 @@ final case class ExecutableRunner(
     val detectMounts = args.flatMap {
       case arg: FileArgument if arg.multiple =>
         // resolve arguments with multiplicity different from singular args
-        val viash_temp = "VIASH_TEST_" + arg.plainName.toUpperCase()
         val chownIfOutput = if (arg.direction == Output) "\n    VIASH_CHOWN_VARS+=( \"$var\" )" else ""
         Some(
           s"""
             |if [ ! -z "$$${arg.VIASH_PAR}" ]; then
-            |  $viash_temp=()
-            |  IFS='${Bash.escapeString(arg.multiple_sep, quote = true)}'
-            |  for var in $$${arg.VIASH_PAR}; do
-            |    unset IFS
-            |    VIASH_DIRECTORY_MOUNTS+=( "$$(ViashDockerAutodetectMountArg "$$var")" )
-            |    var=$$(ViashDockerAutodetectMount "$$var")
-            |    $viash_temp+=( "$$var" )$chownIfOutput
+            |  for i in "$${!${arg.VIASH_PAR}[@]}"; do
+            |    VIASH_DIRECTORY_MOUNTS+=( "$$(ViashDockerAutodetectMountArg $${${arg.VIASH_PAR}[$$i]})" )
+            |    ${arg.VIASH_PAR}[$$i]=$$(ViashDockerAutodetectMount $${${arg.VIASH_PAR}[$$i]})
             |  done
-            |  ${arg.VIASH_PAR}=$$(IFS='${Bash.escapeString(arg.multiple_sep, quote = true)}' ; echo "$${$viash_temp[*]}")
             |fi""".stripMargin
         )
       case arg: FileArgument =>
@@ -455,17 +449,12 @@ final case class ExecutableRunner(
     val stripAutomounts = args.flatMap {
       case arg: FileArgument if arg.multiple && arg.direction == Input =>
         // resolve arguments with multiplicity different from singular args
-        val viash_temp = "VIASH_TEST_" + arg.plainName.toUpperCase()
         Some(
           s"""
             |  if [ ! -z "$$${arg.VIASH_PAR}" ]; then
-            |    unset $viash_temp
-            |    IFS='${Bash.escapeString(arg.multiple_sep, quote = true)}'
-            |    for var in $$${arg.VIASH_PAR}; do
-            |      unset IFS
-            |      ${BashWrapper.store("ViashDockerStripAutomount", viash_temp, "\"$(ViashDockerStripAutomount \"$var\")\"", Some(arg.multiple_sep)).mkString("\n    ")}
+            |    for i in "$${!${arg.VIASH_PAR}[@]}"; do
+            |      ${arg.VIASH_PAR}[i]=$$(ViashDockerStripAutomount "$${${arg.VIASH_PAR}[i]}")
             |    done
-            |    ${arg.VIASH_PAR}="$$$viash_temp"
             |  fi""".stripMargin
         )
       case arg: FileArgument =>
diff --git a/src/main/scala/io/viash/wrapper/BashWrapper.scala b/src/main/scala/io/viash/wrapper/BashWrapper.scala
index 1fb356271..e69d6e3a3 100644
--- a/src/main/scala/io/viash/wrapper/BashWrapper.scala
+++ b/src/main/scala/io/viash/wrapper/BashWrapper.scala
@@ -484,10 +484,8 @@ object BashWrapper {
                  |fi""".stripMargin
             } else if (direction == Input) {
               s"""if [ ! -z "$$${param.VIASH_PAR}" ]; then
-                 |  IFS='${Bash.escapeString(param.multiple_sep, quote = true)}'
                  |  set -f
-                 |  for file in $$${param.VIASH_PAR}; do
-                 |    unset IFS
+                 |  for file in $${${param.VIASH_PAR}[@]}; do
                  |    if [ ! -e "$$file" ]; then
                  |      ViashError "$direction file '$$file' does not exist."
                  |      exit 1
@@ -520,10 +518,8 @@ object BashWrapper {
           createParentFiles.map { param =>
             if (param.multiple && param.direction == Input) {
               s"""if [ ! -z "$$${param.VIASH_PAR}" ]; then
-                 |  IFS='${Bash.escapeString(param.multiple_sep, quote = true)}'
                  |  set -f
-                 |  for file in $$${param.VIASH_PAR}; do
-                 |    unset IFS
+                 |  for file in $${${param.VIASH_PAR}[@]}; do
                  |    if [ ! -d "$$(dirname "$$file")" ]; then
                  |      mkdir -p "$$(dirname "$$file")"
                  |    fi
@@ -613,14 +609,12 @@ object BashWrapper {
         case param if param.multiple && param.direction == Input =>
           val checkStart = 
             s"""if [ -n "$$${param.VIASH_PAR}" ]; then
-               |  IFS='${Bash.escapeString(param.multiple_sep, quote = true)}'
                |  set -f
-               |  for val in $$${param.VIASH_PAR}; do
+               |  for val in $${${param.VIASH_PAR}[@]}; do
                |"""
           val checkEnd =
             s"""  done
                |  set +f
-               |  unset IFS
                |fi
                |""".stripMargin
           // TODO add extra spaces for typeCheck, minCheck, maxCheck
@@ -659,37 +653,47 @@ object BashWrapper {
       }
 
     def checkChoices[T](param: Argument[T], allowedChoices: List[T]) = {
-      val allowedChoicesString = allowedChoices.mkString(param.multiple_sep.toString)
+      val allowedChoicesString = allowedChoices.map("\"" + Bash.escapeString(_, quote = true) + "\"").mkString(" ")
 
       param match {
         case _ if param.multiple && param.direction == Input =>
           s"""if [ ! -z "$$${param.VIASH_PAR}" ]; then
-             |  ${param.VIASH_PAR}_CHOICES=("$allowedChoicesString")
-             |  IFS='${Bash.escapeString(param.multiple_sep, quote = true)}'
-             |  set -f
-             |  for val in $$${param.VIASH_PAR}; do
-             |    if ! [[ "${param.multiple_sep}$${${param.VIASH_PAR}_CHOICES[*]}${param.multiple_sep}" =~ "${param.multiple_sep}$${val}${param.multiple_sep}" ]]; then
-             |      ViashError '${param.name}' specified value of \\'$${val}\\' is not in the list of allowed values. Use "--help" to get more information on the parameters.
-             |      exit 1
-             |    fi
-             |  done
-             |  set +f
-             |  unset IFS
-             |fi
-             |""".stripMargin
+            |  ${param.VIASH_PAR}_CHOICES=($allowedChoicesString)
+            |  set -f
+            |  for val in $${${param.VIASH_PAR}}[@]}; do
+            |    found=0
+            |    for choice in $${${param.VIASH_PAR}_CHOICES[@]}; do
+            |      if [ "$$val" == "$$choice" ]; then
+            |        found=1
+            |        break
+            |      fi
+            |    done
+            |    if [ $$found -eq 0 ]; then
+            |      ViashError '${param.name}' specified value of \\'$${val}\\' is not in the list of allowed values. Use "--help" to get more information on the parameters.
+            |      exit 1
+            |    fi
+            |  done
+            |  set +f
+            |fi
+            |""".stripMargin
         case _ =>
           s"""if [ ! -z "$$${param.VIASH_PAR}" ]; then
-             |  ${param.VIASH_PAR}_CHOICES=("$allowedChoicesString")
-             |  IFS='${Bash.escapeString(param.multiple_sep, quote = true)}'
-             |  set -f
-             |  if ! [[ "${param.multiple_sep}$${${param.VIASH_PAR}_CHOICES[*]}${param.multiple_sep}" =~ "${param.multiple_sep}$$${param.VIASH_PAR}${param.multiple_sep}" ]]; then
-             |    ViashError '${param.name}' specified value of \\'$$${param.VIASH_PAR}\\' is not in the list of allowed values. Use "--help" to get more information on the parameters.
-             |    exit 1
-             |  fi
-             |  set +f
-             |  unset IFS
-             |fi
-             |""".stripMargin
+            |  ${param.VIASH_PAR}_CHOICES=($allowedChoicesString)
+            |  found=0
+            |  for choice in $${${param.VIASH_PAR}_CHOICES[@]}; do
+            |    if [ "$$${param.VIASH_PAR}" == "$$choice" ]; then
+            |      found=1
+            |      break
+            |    fi
+            |  done
+            |  set -f
+            |  if [ $$found -eq 0 ]; then
+            |    ViashError '${param.name}' specified value of \\'$$${param.VIASH_PAR}\\' is not in the list of allowed values. Use "--help" to get more information on the parameters.
+            |    exit 1
+            |  fi
+            |  set +f
+            |fi
+            |""".stripMargin
       }
     }
     val choicesCheckList = 
@@ -818,10 +822,8 @@ object BashWrapper {
         if (param.multiple && param.direction == Input) {
           s"""
              |if [ ! -z "$$${param.VIASH_PAR}" ]; then
-             |  IFS='${Bash.escapeString(param.multiple_sep, quote = true)}'
              |  set -f
-             |  for val in $$${param.VIASH_PAR}; do
-             |    unset IFS
+             |  for val in $${${param.VIASH_PAR}[@]}; do
              |    VIASH_EXECUTABLE_ARGS="$$VIASH_EXECUTABLE_ARGS$flag '$$val'"
              |  done
              |  set +f

From 5aaa7dfe3a79018e7f987e367b401a0c03bc1c68 Mon Sep 17 00:00:00 2001
From: Robrecht Cannoodt <rcannood@gmail.com>
Date: Mon, 12 Aug 2024 11:33:43 +0200
Subject: [PATCH 07/18] fix type mismatch error

---
 src/main/scala/io/viash/wrapper/BashWrapper.scala | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/main/scala/io/viash/wrapper/BashWrapper.scala b/src/main/scala/io/viash/wrapper/BashWrapper.scala
index e69d6e3a3..01a31d25a 100644
--- a/src/main/scala/io/viash/wrapper/BashWrapper.scala
+++ b/src/main/scala/io/viash/wrapper/BashWrapper.scala
@@ -653,7 +653,7 @@ object BashWrapper {
       }
 
     def checkChoices[T](param: Argument[T], allowedChoices: List[T]) = {
-      val allowedChoicesString = allowedChoices.map("\"" + Bash.escapeString(_, quote = true) + "\"").mkString(" ")
+      val allowedChoicesString = allowedChoices.map(choice => "\"" + Bash.escapeString(choice.toString, quote = true) + "\"").mkString(" ")
 
       param match {
         case _ if param.multiple && param.direction == Input =>

From df650b1ec36384fb162be08e7c104aec5039635b Mon Sep 17 00:00:00 2001
From: Robrecht Cannoodt <rcannood@gmail.com>
Date: Mon, 12 Aug 2024 11:52:20 +0200
Subject: [PATCH 08/18] move dependencies to mods

---
 .../scala/io/viash/wrapper/BashWrapper.scala  | 47 ++++++++++++-------
 1 file changed, 29 insertions(+), 18 deletions(-)

diff --git a/src/main/scala/io/viash/wrapper/BashWrapper.scala b/src/main/scala/io/viash/wrapper/BashWrapper.scala
index 01a31d25a..eecc9f70e 100644
--- a/src/main/scala/io/viash/wrapper/BashWrapper.scala
+++ b/src/main/scala/io/viash/wrapper/BashWrapper.scala
@@ -233,29 +233,16 @@ object BashWrapper {
       case Some(_: Executable) => generateExecutableArgs(args)
       case _ => BashWrapperMods()
     }
+    val depMods = generateDependencies(config)
 
     // combine
-    val allMods = helpMods ++ parMods ++ mods ++ execMods ++ computationalRequirementMods
+    val allMods = helpMods ++ parMods ++ mods ++ execMods ++ computationalRequirementMods ++ depMods
 
     // generate header
     val header = Helper.generateScriptHeader(config)
       .map(h => Escaper(h, newline = true))
       .mkString("# ", "\n# ", "")
 
-    val (localDependencies, remoteDependencies) = config.dependencies
-      .partition(d => d.isLocalDependency)
-    val localDependenciesStrings = localDependencies.map{ d =>
-      // relativize the path of the main component to the local dependency
-      // TODO ideally we'd already have 'thisPath' precalculated but until that day, calculate it here
-      val thisPath = ViashNamespace.targetOutputPath("", "invalid_runner_name", config)
-      val relativePath = Paths.get(thisPath).relativize(Paths.get(d.configInfo.getOrElse("executable", "")))
-      s"${d.VIASH_DEP}=\"$$VIASH_META_RESOURCES_DIR/$relativePath\""
-    }
-    val remoteDependenciesStrings = remoteDependencies.map{ d =>
-      s"${d.VIASH_DEP}=\"$$VIASH_TARGET_DIR/dependencies/${d.subOutputPath.get}/${Paths.get(d.configInfo.getOrElse("executable", "not_found")).getFileName()}\""
-    }
-    val dependenciesStr = (localDependenciesStrings ++ remoteDependenciesStrings).mkString("\n")
-
     /* GENERATE BASH SCRIPT */
     s"""#!/usr/bin/env bash
        |
@@ -334,9 +321,6 @@ object BashWrapper {
        |eval set -- $$VIASH_POSITIONAL_ARGS
        |${spaceCode(allMods.postParse)}${spaceCode(allMods.preRun)}
        |
-       |# set dependency paths
-       |$dependenciesStr
-       |
        |ViashDebug "Running command: ${executor.replaceAll("^eval (.*)", "\\$(echo $1)")}"
        |$heredocStart$executor${escapePipes(executionCode)}$heredocEnd
        |${spaceCode(allMods.postRun)}${spaceCode(allMods.last)}
@@ -841,4 +825,31 @@ object BashWrapper {
     )
   }
 
+  def generateDependencies(
+    config: Config
+  ): BashWrapperMods = {
+    if (config.dependencies.isEmpty) {
+      return BashWrapperMods()
+    }
+
+    val (localDependencies, remoteDependencies) = config.dependencies
+      .partition(d => d.isLocalDependency)
+
+    val localDependenciesStrings = localDependencies.map{ d =>
+      // relativize the path of the main component to the local dependency
+      // TODO ideally we'd already have 'thisPath' precalculated but until that day, calculate it here
+      val thisPath = ViashNamespace.targetOutputPath("", "invalid_runner_name", config)
+      val relativePath = Paths.get(thisPath).relativize(Paths.get(d.configInfo.getOrElse("executable", "")))
+      s"${d.VIASH_DEP}=\"$$VIASH_META_RESOURCES_DIR/$relativePath\""
+    }
+    val remoteDependenciesStrings = remoteDependencies.map{ d =>
+      s"${d.VIASH_DEP}=\"$$VIASH_TARGET_DIR/dependencies/${d.subOutputPath.get}/${Paths.get(d.configInfo.getOrElse("executable", "not_found")).getFileName()}\""
+    }
+    val dependenciesStr = (localDependenciesStrings ++ remoteDependenciesStrings).mkString("\n")
+
+    BashWrapperMods(
+      preRun = "\n# set dependency paths\n" + dependenciesStr
+    )
+  }
+
 }

From 2b81cc95caf661f699f740c99c75ed07754404e7 Mon Sep 17 00:00:00 2001
From: Robrecht Cannoodt <rcannood@gmail.com>
Date: Mon, 12 Aug 2024 17:20:11 +0200
Subject: [PATCH 09/18] wip helper functions

---
 .../helpers/bashutils/ViashRenderYaml.sh      | 82 +++++++++++++++++++
 1 file changed, 82 insertions(+)
 create mode 100644 src/main/resources/io/viash/helpers/bashutils/ViashRenderYaml.sh

diff --git a/src/main/resources/io/viash/helpers/bashutils/ViashRenderYaml.sh b/src/main/resources/io/viash/helpers/bashutils/ViashRenderYaml.sh
new file mode 100644
index 000000000..d2599a904
--- /dev/null
+++ b/src/main/resources/io/viash/helpers/bashutils/ViashRenderYaml.sh
@@ -0,0 +1,82 @@
+
+
+function ViashRenderQuotedValue {
+  local key="$1"
+  local value="$2"
+  if [ "$value" == "UNDEFINED_ITEM" ]; then
+    echo "null"
+    return
+  fi
+  # escape quotes, backslashes and newlines, and then surround by quotes
+  echo "$value" | sed 's#"#\\"#g' | sed 's#\\#\\\\#g' | sed ':a;N;$!ba;s/\n/\\n/g' | sed 's#^#"#g' | sed 's#$#"#g'
+}
+
+function ViashRenderBooleanValue {
+  local key="$1"
+  local value="$2"
+  if [ "$value" == "UNDEFINED_ITEM" ]; then
+    echo "null"
+    return
+  fi
+  value=$(echo "$value" | tr '[:upper:]' '[:lower:]')
+  if [[ "$value" == "true" || "$value" == "yes" ]]; then
+    echo "true"
+  elif [[ "$value" == "false" || "$value" == "no" ]]; then
+    echo "false"
+  else
+    echo "Argument '$key' has to be a boolean, but got '$value'. Use '--help' to get more information on the parameters."
+  fi
+}
+
+# can be infinite too
+function ViashRenderUnquotedValue {
+  local key="$1"
+  local value="$2"
+  if [ "$value" == "UNDEFINED_ITEM" ]; then
+    echo "null"
+    return
+  fi
+  echo "$value"
+}
+
+function ViashRenderYamlKeyValue {
+  local key="$1"
+  local type="$2"
+  local multiple="$3"
+  shift 3
+  
+  local out="$key: "
+
+  if [ "$1" == "UNDEFINED" ]; then
+    out+="null"
+    echo $out
+    return
+  fi
+
+  if [ "$multiple" == "true" ]; then
+    out+="["
+  fi
+
+  first_elem=1
+
+  for value in "$@"; do
+    if [ $first_elem -eq 1 ]; then
+      first_elem=0
+    else
+      out+=", "
+    fi
+    if [[ "$type" == "string" || "$type" == "file" ]]; then
+      out+="$(ViashRenderQuotedValue "$key" "$value")"
+    elif [[ "$type" == "boolean" || "$type" == "boolean_true" || "$type" == "boolean_false" ]]; then
+      out+="$(ViashRenderBooleanValue "$key" "$value")"
+    else
+      out+="$(ViashRenderUnquotedValue "$key" "$value")"
+    fi
+  done
+
+  if [ "$multiple" == "true" ]; then
+    out+="]"
+  fi
+
+  echo "$out"
+}

From af2bf7f0ca8ab87efc4a93cfd93415e882b4b341 Mon Sep 17 00:00:00 2001
From: Robrecht Cannoodt <rcannood@gmail.com>
Date: Tue, 13 Aug 2024 08:57:42 +0200
Subject: [PATCH 10/18] rename helper functions

---
 .../io/viash/helpers/bashutils/ViashRenderYaml.sh    | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

diff --git a/src/main/resources/io/viash/helpers/bashutils/ViashRenderYaml.sh b/src/main/resources/io/viash/helpers/bashutils/ViashRenderYaml.sh
index d2599a904..639a9aae7 100644
--- a/src/main/resources/io/viash/helpers/bashutils/ViashRenderYaml.sh
+++ b/src/main/resources/io/viash/helpers/bashutils/ViashRenderYaml.sh
@@ -1,6 +1,6 @@
 
 
-function ViashRenderQuotedValue {
+function ViashRenderYamlQuotedValue {
   local key="$1"
   local value="$2"
   if [ "$value" == "UNDEFINED_ITEM" ]; then
@@ -11,7 +11,7 @@ function ViashRenderQuotedValue {
   echo "$value" | sed 's#"#\\"#g' | sed 's#\\#\\\\#g' | sed ':a;N;$!ba;s/\n/\\n/g' | sed 's#^#"#g' | sed 's#$#"#g'
 }
 
-function ViashRenderBooleanValue {
+function ViashRenderYamlBooleanValue {
   local key="$1"
   local value="$2"
   if [ "$value" == "UNDEFINED_ITEM" ]; then
@@ -29,7 +29,7 @@ function ViashRenderBooleanValue {
 }
 
 # can be infinite too
-function ViashRenderUnquotedValue {
+function ViashRenderYamlUnquotedValue {
   local key="$1"
   local value="$2"
   if [ "$value" == "UNDEFINED_ITEM" ]; then
@@ -66,11 +66,11 @@ function ViashRenderYamlKeyValue {
       out+=", "
     fi
     if [[ "$type" == "string" || "$type" == "file" ]]; then
-      out+="$(ViashRenderQuotedValue "$key" "$value")"
+      out+="$(ViashRenderYamlQuotedValue "$key" "$value")"
     elif [[ "$type" == "boolean" || "$type" == "boolean_true" || "$type" == "boolean_false" ]]; then
-      out+="$(ViashRenderBooleanValue "$key" "$value")"
+      out+="$(ViashRenderYamlBooleanValue "$key" "$value")"
     else
-      out+="$(ViashRenderUnquotedValue "$key" "$value")"
+      out+="$(ViashRenderYamlUnquotedValue "$key" "$value")"
     fi
   done
 

From 140d2f9f61d5d09e1ce617748e1ea8158d3da358 Mon Sep 17 00:00:00 2001
From: Robrecht Cannoodt <rcannood@gmail.com>
Date: Tue, 13 Aug 2024 08:57:53 +0200
Subject: [PATCH 11/18] fixes to generated code

---
 src/main/scala/io/viash/wrapper/BashWrapper.scala | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/src/main/scala/io/viash/wrapper/BashWrapper.scala b/src/main/scala/io/viash/wrapper/BashWrapper.scala
index eecc9f70e..75df0549d 100644
--- a/src/main/scala/io/viash/wrapper/BashWrapper.scala
+++ b/src/main/scala/io/viash/wrapper/BashWrapper.scala
@@ -59,10 +59,10 @@ object BashWrapper {
       // -> could rename them to `${env}_value` and `${env}_values` to avoid conflicts
       s"""unset value values
         |value=$value
-        |if [ $$value == UNDEFINED ]; then
+        |if [ "$$value" == UNDEFINED ]; then
         |  unset $env
         |else
-        |  readarray -d $$';' -t values <<< $$value
+        |  readarray -d ';' -t values < <(printf '%s' "$$value")
         |  if [ -z "$$$env" ]; then
         |    $env=( "$${values[@]}" )
         |  else
@@ -72,7 +72,7 @@ object BashWrapper {
     } else {
       s"""unset value
         |value=$value
-        |if [ $$value == UNDEFINED ]; then
+        |if [ "$$value" == UNDEFINED ]; then
         |  unset $env
         |else
         |  [ -n "$$$env" ] && ViashError Bad arguments for option \\'$name\\': \\'$$$env\\' \\& \\'$$2\\' - you should provide exactly one argument for this option. && exit 1

From b47957a46a97e7eb45e0ab55d21bd961272f145e Mon Sep 17 00:00:00 2001
From: Robrecht Cannoodt <rcannood@gmail.com>
Date: Tue, 13 Aug 2024 09:37:18 +0200
Subject: [PATCH 12/18] add more comments

---
 .../scala/io/viash/wrapper/BashWrapper.scala  | 41 ++++++++++---------
 1 file changed, 21 insertions(+), 20 deletions(-)

diff --git a/src/main/scala/io/viash/wrapper/BashWrapper.scala b/src/main/scala/io/viash/wrapper/BashWrapper.scala
index 75df0549d..0d4a44bb0 100644
--- a/src/main/scala/io/viash/wrapper/BashWrapper.scala
+++ b/src/main/scala/io/viash/wrapper/BashWrapper.scala
@@ -51,33 +51,34 @@ object BashWrapper {
     )
   }
 
+  // TODO: if argument is required, do not check for undefined
+  // TODO: if value is quoted, don't split by separator
+  // TODO: if the separator is escaped, don't split
   def store(name: String, env: String, value: String, multiple_sep: Option[String]): Array[String] = {
     // note: 'value' is split using multiple_sep into 'values' for backwards compatibility.
     // todo: strip quotes and escape as suggested by https://github.com/viash-io/viash/issues/705#issuecomment-2208448576
     if (multiple_sep.isDefined) {
       // note: 'value' and 'values' are global values!!
       // -> could rename them to `${env}_value` and `${env}_values` to avoid conflicts
-      s"""unset value values
-        |value=$value
-        |if [ "$$value" == UNDEFINED ]; then
-        |  unset $env
-        |else
-        |  readarray -d ';' -t values < <(printf '%s' "$$value")
-        |  if [ -z "$$$env" ]; then
-        |    $env=( "$${values[@]}" )
-        |  else
-        |    $env+=( "$${values[@]}" )
-        |  fi
-        |fi""".stripMargin.split("\n")
+      s"""value=$value
+         |if [ "$$value" == UNDEFINED ]; then
+         |  unset $env
+         |else
+         |  readarray -d '${multiple_sep.get}' -t values < <(printf '%s' "$$value")
+         |  if [ -z "$$$env" ]; then
+         |    $env=( "$${values[@]}" )
+         |  else
+         |    $env+=( "$${values[@]}" )
+         |  fi
+         |fi""".stripMargin.split("\n")
     } else {
-      s"""unset value
-        |value=$value
-        |if [ "$$value" == UNDEFINED ]; then
-        |  unset $env
-        |else
-        |  [ -n "$$$env" ] && ViashError Bad arguments for option \\'$name\\': \\'$$$env\\' \\& \\'$$2\\' - you should provide exactly one argument for this option. && exit 1
-        |  $env=$$value
-        |fi""".stripMargin.split("\n")
+      s"""value=$value
+         |if [ "$$value" == UNDEFINED ]; then
+         |  unset $env
+         |else
+         |  [ -n "$$$env" ] && ViashError Bad arguments for option \\'$name\\': \\'$$$env\\' \\& \\'$$2\\' - you should provide exactly one argument for this option. && exit 1
+         |  $env=$$value
+         |fi""".stripMargin.split("\n")
     }
   }
 

From 4e016be07188dcbf039c0b8e02448b051831bbec Mon Sep 17 00:00:00 2001
From: Robrecht Cannoodt <rcannood@gmail.com>
Date: Tue, 13 Aug 2024 09:57:47 +0200
Subject: [PATCH 13/18] remove unused code

---
 src/main/scala/io/viash/helpers/Bash.scala | 29 ----------------------
 1 file changed, 29 deletions(-)

diff --git a/src/main/scala/io/viash/helpers/Bash.scala b/src/main/scala/io/viash/helpers/Bash.scala
index aa472adea..fc8b3d1c7 100644
--- a/src/main/scala/io/viash/helpers/Bash.scala
+++ b/src/main/scala/io/viash/helpers/Bash.scala
@@ -37,35 +37,6 @@ object Bash {
   lazy val ViashDockerFuns: String = readUtils("ViashDockerFuns")
   lazy val ViashLogging: String = readUtils("ViashLogging")
 
-  def save(saveVariable: String, args: Seq[String]): String = {
-    saveVariable + "=\"$" + saveVariable + " " + args.mkString(" ") + "\""
-  }
-
-  // generate strings in the form of:
-  // SAVEVARIABLE="$SAVEVARIABLE $(Quote arg1) $(Quote arg2)"
-  def quoteSave(saveVariable: String, args: Seq[String]): String = {
-    saveVariable + "=\"$" + saveVariable +
-      args.map(" $(ViashQuote \"" + _ + "\")").mkString +
-      "\""
-  }
-
-  def argStore(name: String, plainName: String, store: String, argsConsumed: Int, storeUnparsed: Option[String]): String = {
-    val passStr =
-      if (storeUnparsed.isDefined) {
-        "\n            " + quoteSave(storeUnparsed.get, (1 to argsConsumed).map("$" + _))
-      } else {
-        ""
-      }
-    s"""         $name)
-       |            $plainName=$store$passStr
-       |            shift $argsConsumed
-       |            ;;""".stripMargin
-  }
-
-  def argStoreSed(name: String, plainName: String, storeUnparsed: Option[String]): String = {
-    argStore(name + "=*", plainName, "$(ViashRemoveFlags \"$1\")", 1, storeUnparsed)
-  }
-
   /** 
    * Access the parameters contents in a bash script,
    * taking into account that some characters need to be escaped.

From 6ffee9372cbfba8f7e11e4a813a55336a15bb680 Mon Sep 17 00:00:00 2001
From: Robrecht Cannoodt <rcannood@gmail.com>
Date: Tue, 13 Aug 2024 09:58:06 +0200
Subject: [PATCH 14/18] make certain BashWrapper functions private

---
 src/main/scala/io/viash/wrapper/BashWrapper.scala | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/src/main/scala/io/viash/wrapper/BashWrapper.scala b/src/main/scala/io/viash/wrapper/BashWrapper.scala
index 0d4a44bb0..e6154f97c 100644
--- a/src/main/scala/io/viash/wrapper/BashWrapper.scala
+++ b/src/main/scala/io/viash/wrapper/BashWrapper.scala
@@ -54,7 +54,7 @@ object BashWrapper {
   // TODO: if argument is required, do not check for undefined
   // TODO: if value is quoted, don't split by separator
   // TODO: if the separator is escaped, don't split
-  def store(name: String, env: String, value: String, multiple_sep: Option[String]): Array[String] = {
+  private def store(name: String, env: String, value: String, multiple_sep: Option[String]): Array[String] = {
     // note: 'value' is split using multiple_sep into 'values' for backwards compatibility.
     // todo: strip quotes and escape as suggested by https://github.com/viash-io/viash/issues/705#issuecomment-2208448576
     if (multiple_sep.isDefined) {
@@ -82,7 +82,7 @@ object BashWrapper {
     }
   }
 
-  def argStore(
+  private def argStore(
     name: String,
     plainName: String,
     value: String,
@@ -102,11 +102,11 @@ object BashWrapper {
         |            ;;""".stripMargin
   }
 
-  def argStoreSed(name: String, plainName: String, multiple_sep: Option[String] = None): String = {
+  private def argStoreSed(name: String, plainName: String, multiple_sep: Option[String] = None): String = {
     argStore(name + "=*", plainName, "$(ViashRemoveFlags \"$1\")", 1, multiple_sep)
   }
 
-  def spaceCode(str: String): String = {
+  private def spaceCode(str: String): String = {
     if (str != "") {
       "\n" + str + "\n"
     } else {
@@ -826,7 +826,7 @@ object BashWrapper {
     )
   }
 
-  def generateDependencies(
+  private def generateDependencies(
     config: Config
   ): BashWrapperMods = {
     if (config.dependencies.isEmpty) {

From 147290d78bf808c21fbbd29a3e009f6abbfd1fa0 Mon Sep 17 00:00:00 2001
From: Robrecht Cannoodt <rcannood@gmail.com>
Date: Wed, 14 Aug 2024 09:37:47 +0200
Subject: [PATCH 15/18] improve yaml rendering

---
 .../bashutils/ViashParseArgumentValue.sh      |  34 +++
 .../helpers/bashutils/ViashRenderYaml.sh      |  31 +-
 src/main/scala/io/viash/helpers/Bash.scala    |   3 +-
 .../scala/io/viash/wrapper/BashWrapper.scala  | 270 ++++++++++++------
 4 files changed, 234 insertions(+), 104 deletions(-)
 create mode 100644 src/main/resources/io/viash/helpers/bashutils/ViashParseArgumentValue.sh

diff --git a/src/main/resources/io/viash/helpers/bashutils/ViashParseArgumentValue.sh b/src/main/resources/io/viash/helpers/bashutils/ViashParseArgumentValue.sh
new file mode 100644
index 000000000..ea66225bb
--- /dev/null
+++ b/src/main/resources/io/viash/helpers/bashutils/ViashParseArgumentValue.sh
@@ -0,0 +1,34 @@
+function ViashParseArgumentValue {
+  local env_name="$1"
+  local multiple="$2"
+  local flag="$3"
+  local value="$4"
+
+  if [ $# -lt 4 ]; then
+    ViashError "Not enough arguments passed to ${flag}. Use '--help' to get more information on the parameters."
+    exit 1
+  fi
+
+  if [ "$multiple" == "false" ]; then
+    # check whether the variable is already set
+    if [ ! -z ${!env_name+x} ]; then
+      local -n prev_value="$env_name"
+      ViashError "Pass only one argument to argument '${flag}'. Found: ${prev_value@Q} & ${value@Q}"
+      exit 1
+    fi
+
+    # set the variable
+    declare -g "$env_name=${value}"
+  else
+    local new_values
+
+    local -n prev_values="$env_name"
+
+    # todo: allow escaping the delimiter
+    readarray -d ';' -t new_values < <(printf '%s' "$value")
+
+    combined_values=( "${prev_values[@]}" "${new_values[@]}" )
+
+    declare -g -a "$env_name=(\"\${combined_values[@]}\")"
+  fi
+}
diff --git a/src/main/resources/io/viash/helpers/bashutils/ViashRenderYaml.sh b/src/main/resources/io/viash/helpers/bashutils/ViashRenderYaml.sh
index 639a9aae7..e1a2eb3bd 100644
--- a/src/main/resources/io/viash/helpers/bashutils/ViashRenderYaml.sh
+++ b/src/main/resources/io/viash/helpers/bashutils/ViashRenderYaml.sh
@@ -1,23 +1,18 @@
-
-
 function ViashRenderYamlQuotedValue {
   local key="$1"
   local value="$2"
-  if [ "$value" == "UNDEFINED_ITEM" ]; then
-    echo "null"
-    return
-  fi
   # escape quotes, backslashes and newlines, and then surround by quotes
-  echo "$value" | sed 's#"#\\"#g' | sed 's#\\#\\\\#g' | sed ':a;N;$!ba;s/\n/\\n/g' | sed 's#^#"#g' | sed 's#$#"#g'
+  echo "$value" | \
+    sed 's#\\#\\\\#g' | \
+    sed 's#"#\\"#g' | \
+    sed ':a;N;$!ba;s/\n/\\n/g' | \
+    sed 's#^#"#g;s#$#"#g'
 }
 
 function ViashRenderYamlBooleanValue {
   local key="$1"
   local value="$2"
-  if [ "$value" == "UNDEFINED_ITEM" ]; then
-    echo "null"
-    return
-  fi
+  # convert to lowercase
   value=$(echo "$value" | tr '[:upper:]' '[:lower:]')
   if [[ "$value" == "true" || "$value" == "yes" ]]; then
     echo "true"
@@ -32,10 +27,6 @@ function ViashRenderYamlBooleanValue {
 function ViashRenderYamlUnquotedValue {
   local key="$1"
   local value="$2"
-  if [ "$value" == "UNDEFINED_ITEM" ]; then
-    echo "null"
-    return
-  fi
   echo "$value"
 }
 
@@ -44,12 +35,12 @@ function ViashRenderYamlKeyValue {
   local type="$2"
   local multiple="$3"
   shift 3
-  
-  local out="$key: "
+
+  local out="  ${key}: "
 
   if [ "$1" == "UNDEFINED" ]; then
     out+="null"
-    echo $out
+    echo "$out"
     return
   fi
 
@@ -65,7 +56,9 @@ function ViashRenderYamlKeyValue {
     else
       out+=", "
     fi
-    if [[ "$type" == "string" || "$type" == "file" ]]; then
+    if [ "$value" == "UNDEFINED_ITEM" ]; then
+      out+="null"
+    elif [[ "$type" == "string" || "$type" == "file" ]]; then
       out+="$(ViashRenderYamlQuotedValue "$key" "$value")"
     elif [[ "$type" == "boolean" || "$type" == "boolean_true" || "$type" == "boolean_false" ]]; then
       out+="$(ViashRenderYamlBooleanValue "$key" "$value")"
diff --git a/src/main/scala/io/viash/helpers/Bash.scala b/src/main/scala/io/viash/helpers/Bash.scala
index fc8b3d1c7..ad9753810 100644
--- a/src/main/scala/io/viash/helpers/Bash.scala
+++ b/src/main/scala/io/viash/helpers/Bash.scala
@@ -30,12 +30,11 @@ object Bash {
   lazy val ViashRemoveFlags: String = readUtils("ViashRemoveFlags")
   lazy val ViashAbsolutePath: String = readUtils("ViashAbsolutePath")
   lazy val ViashDockerAutodetectMount: String = readUtils("ViashDockerAutodetectMount")
-  // backwards compatibility, for now
-  lazy val ViashAutodetectMount: String = ViashDockerAutodetectMount.replace("ViashDocker", "Viash")
   lazy val ViashSourceDir: String = readUtils("ViashSourceDir")
   lazy val ViashFindTargetDir: String = readUtils("ViashFindTargetDir")
   lazy val ViashDockerFuns: String = readUtils("ViashDockerFuns")
   lazy val ViashLogging: String = readUtils("ViashLogging")
+  lazy val ViashParseArgumentValue: String = readUtils("ViashParseArgumentValue")
 
   /** 
    * Access the parameters contents in a bash script,
diff --git a/src/main/scala/io/viash/wrapper/BashWrapper.scala b/src/main/scala/io/viash/wrapper/BashWrapper.scala
index e6154f97c..1093c1ff6 100644
--- a/src/main/scala/io/viash/wrapper/BashWrapper.scala
+++ b/src/main/scala/io/viash/wrapper/BashWrapper.scala
@@ -51,59 +51,83 @@ object BashWrapper {
     )
   }
 
-  // TODO: if argument is required, do not check for undefined
-  // TODO: if value is quoted, don't split by separator
-  // TODO: if the separator is escaped, don't split
-  private def store(name: String, env: String, value: String, multiple_sep: Option[String]): Array[String] = {
-    // note: 'value' is split using multiple_sep into 'values' for backwards compatibility.
-    // todo: strip quotes and escape as suggested by https://github.com/viash-io/viash/issues/705#issuecomment-2208448576
-    if (multiple_sep.isDefined) {
-      // note: 'value' and 'values' are global values!!
-      // -> could rename them to `${env}_value` and `${env}_values` to avoid conflicts
-      s"""value=$value
-         |if [ "$$value" == UNDEFINED ]; then
-         |  unset $env
-         |else
-         |  readarray -d '${multiple_sep.get}' -t values < <(printf '%s' "$$value")
-         |  if [ -z "$$$env" ]; then
-         |    $env=( "$${values[@]}" )
-         |  else
-         |    $env+=( "$${values[@]}" )
-         |  fi
-         |fi""".stripMargin.split("\n")
-    } else {
-      s"""value=$value
-         |if [ "$$value" == UNDEFINED ]; then
-         |  unset $env
-         |else
-         |  [ -n "$$$env" ] && ViashError Bad arguments for option \\'$name\\': \\'$$$env\\' \\& \\'$$2\\' - you should provide exactly one argument for this option. && exit 1
-         |  $env=$$value
-         |fi""".stripMargin.split("\n")
-    }
-  }
-
-  private def argStore(
-    name: String,
-    plainName: String,
+  /**
+   * Generate a flag parser for arguments of the form --arg value (by default)
+   * 
+   * @param argName The name of the argument.
+   * @param envName The name of the environment variable to store the value in.
+   * @param value Where the value of the argument is stored during parsing.
+   * @param argsConsumed The number of arguments consumed by this argument.
+   * @param matchKey The key to match the argument with.
+   * @param multiple_sep The separator to use when splitting the value into multiple values.
+   */
+  private def generateParser(
+    matchKey: String,
+    argName: String,
+    envName: String,
     value: String,
     argsConsumed: Int,
     multiple_sep: Option[String] = None
   ): String = {
-    val argmatchError =
-      if (argsConsumed > 1) {
-        s"""\n            [ $$# -lt $argsConsumed ] && ViashError Not enough arguments passed to $name. Use "--help" to get more information on the parameters. && exit 1"""
-      } else {
-        ""
-      }
 
-    s"""        $name)$argmatchError
-        |            ${this.store(name, plainName, value, multiple_sep).mkString("\n            ")}
-        |            shift $argsConsumed
+    s"""        ${matchKey})
+        |            ViashParseArgumentValue "${argName}" "${envName}" "${multiple_sep.isDefined}" "${value}"
+        |            shift ${argsConsumed}
         |            ;;""".stripMargin
   }
 
-  private def argStoreSed(name: String, plainName: String, multiple_sep: Option[String] = None): String = {
-    argStore(name + "=*", plainName, "$(ViashRemoveFlags \"$1\")", 1, multiple_sep)
+  /**
+   * Helper function for generating a flag parser for arguments of the form --arg ...
+   */
+  private def generateFlagParser(
+    argName: String,
+    envName: String,
+    multiple_sep: Option[String] = None
+  ): String = {
+    generateParser(
+      argName = argName,
+      envName = envName,
+      matchKey = argName,
+      value = "$2",
+      argsConsumed = 2,
+      multiple_sep = multiple_sep
+    )
+  }
+
+  /**
+   * Helper function for generating a flag parser for arguments of the form --arg=...
+   */
+  private def generateFlagWithEqualsParser(
+    argName: String,
+    envName: String,
+    multiple_sep: Option[String] = None
+  ): String = {
+    generateParser(
+      argName = argName,
+      matchKey = argName + "=*", 
+      envName = envName,
+      value = "$(ViashRemoveFlags \"$1\")",
+      argsConsumed = 1,
+      multiple_sep = multiple_sep
+    )
+  }
+
+  /**
+   * Helper function for generating a flag parser for boolean arguments of the form --arg
+   */
+  private def generateBooleanFlagParser(
+    argName: String,
+    envName: String,
+    value: Boolean
+  ): String = {
+    generateParser(
+      argName = argName,
+      envName = envName,
+      matchKey = argName,
+      value = value.toString,
+      argsConsumed = 1,
+      multiple_sep = None
+    )
   }
 
   private def spaceCode(str: String): String = {
@@ -228,16 +252,17 @@ object BashWrapper {
 
     // generate script modifiers
     val helpMods = generateHelp(config)
-    val computationalRequirementMods = generateComputationalRequirements(config)
+    val reqMods = generateComputationalRequirements(config)
     val parMods = generateParsers(args)
     val execMods = mainResource match {
       case Some(_: Executable) => generateExecutableArgs(args)
       case _ => BashWrapperMods()
     }
     val depMods = generateDependencies(config)
+    val workDirMods = generateWorkDir(argsMetaAndDeps)
 
     // combine
-    val allMods = helpMods ++ parMods ++ mods ++ execMods ++ computationalRequirementMods ++ depMods
+    val allMods = helpMods ++ parMods ++ mods ++ execMods ++ reqMods ++ depMods ++ workDirMods
 
     // generate header
     val header = Helper.generateScriptHeader(config)
@@ -268,6 +293,7 @@ object BashWrapper {
        |${Bash.ViashSourceDir}
        |${Bash.ViashFindTargetDir}
        |${Bash.ViashLogging}
+       |${Bash.ViashParseArgumentValue}
        |
        |# find source folder of this component
        |VIASH_META_RESOURCES_DIR=`ViashSourceDir $${BASH_SOURCE[0]}`
@@ -282,9 +308,12 @@ object BashWrapper {
        |VIASH_META_CONFIG="$$VIASH_META_RESOURCES_DIR/${ConfigMeta.metaFilename}"
        |VIASH_META_TEMP_DIR="$$VIASH_TEMP"
        |
+       |# preparse bashwrapper mods start ------------------------------
        |${spaceCode(allMods.preParse)}
+       |# preparse bashwrapper mods end --------------------------------
+       |
        |# initialise array
-       |VIASH_POSITIONAL_ARGS=''
+       |VIASH_POSITIONAL_ARGS=()
        |
        |while [[ $$# -gt 0 ]]; do
        |    case "$$1" in
@@ -309,22 +338,36 @@ object BashWrapper {
        |            exit
        |            ;;
        |${allMods.parsers}
-       |        *)  # positional arg or unknown option
-       |            # since the positional args will be eval'd, can we always quote, instead of using ViashQuote
-       |            VIASH_POSITIONAL_ARGS="$$VIASH_POSITIONAL_ARGS '$$1'"
-       |            [[ $$1 == -* ]] && ViashWarning $$1 looks like a parameter but is not a defined parameter and will instead be treated as a positional argument. Use "--help" to get more information on the parameters.
+       |        *)
+       |            # positional arg or unknown option
+       |            VIASH_POSITIONAL_ARGS+=("$$1")
+       |            [[ $$1 == -* ]] && ViashWarning "Value '$$1' looks like a parameter but is not a defined parameter and will instead be treated as a positional argument. Use \\"--help\\" to get more information on the parameters."
        |            shift # past argument
        |            ;;
        |    esac
        |done
        |
        |# parse positional parameters
-       |eval set -- $$VIASH_POSITIONAL_ARGS
-       |${spaceCode(allMods.postParse)}${spaceCode(allMods.preRun)}
+       |set -- "$${VIASH_POSITIONAL_ARGS[@]}"
+       |
+       |# postparse bashwrapper mods start -----------------------------
+       |${spaceCode(allMods.postParse)}
+       |# postparse bashwrapper mods end -------------------------------
+       |
+       |# prerun bashwrapper mods start --------------------------------
+       |${spaceCode(allMods.preRun)}
+       |# prerun bashwrapper mods end ----------------------------------
        |
        |ViashDebug "Running command: ${executor.replaceAll("^eval (.*)", "\\$(echo $1)")}"
        |$heredocStart$executor${escapePipes(executionCode)}$heredocEnd
-       |${spaceCode(allMods.postRun)}${spaceCode(allMods.last)}
+       |
+       |# postrun bashwrapper mods start -------------------------------
+       |${spaceCode(allMods.postRun)}
+       |# postrun bashwrapper mods end ---------------------------------
+       |
+       |# last bashwrapper mods start ----------------------------------
+       |${spaceCode(allMods.last)}
+       |# last bashwrapper mods end ------------------------------------
        |
        |exit 0
        |""".stripMargin
@@ -347,22 +390,32 @@ object BashWrapper {
   }
 
   private def generateParsers(params: List[Argument[_]]) = {
-    // gather parse code for params
+    // no parsers should be generated for positional arguments, so remove these first
     val wrapperParams = params.filterNot(_.flags == "")
+    
+    // gather parse code for params
     val parseStrs = wrapperParams.map {
-      case bo: BooleanArgumentBase if bo.flagValue.isDefined =>
-        val fv = bo.flagValue.get
+      case param: BooleanArgumentBase if param.flagValue.isDefined =>
+        val flagValue = param.flagValue.get
 
         // params of the form --param
-        val part1 = argStore(bo.name, bo.VIASH_PAR, fv.toString, 1)
+        val part1 = generateBooleanFlagParser(
+          argName = param.name,
+          envName = param.VIASH_PAR,
+          value = flagValue
+        )
         // Alternatives
-        val moreParts = bo.alternatives.map(alt => {
-          argStore(alt, bo.VIASH_PAR, fv.toString, 1)
+        val moreParts = param.alternatives.map(alt => {
+          generateBooleanFlagParser(
+            argName = alt,
+            envName = param.VIASH_PAR,
+            value = flagValue
+          )
         })
 
         (part1 :: moreParts).mkString("\n")
       case param =>
-        val multisep =
+        val multiple_sep =
           if (param.multiple && param.direction == Input) {
             Some(param.multiple_sep)
           } else {
@@ -370,18 +423,31 @@ object BashWrapper {
           }
 
         // params of the form --param ...
-        val part1 = param.flags match {
-          case "---" | "--" | "-" => argStore(param.name, param.VIASH_PAR, "\"$2\"", 2, multisep)
-          case "" => Nil
-        }
+        val part1 = generateFlagParser(
+          argName = param.name,
+          envName = param.VIASH_PAR,
+          multiple_sep = multiple_sep
+        )
+
         // params of the form --param=..., except -param=... is not allowed
         val part2 = param.flags match {
-          case "---" | "--" => List(argStoreSed(param.name, param.VIASH_PAR, multisep))
-          case "-" | "" => Nil
+          case "---" | "--" =>
+            List(
+              generateFlagWithEqualsParser(
+                argName = param.name,
+                envName = param.VIASH_PAR,
+                multiple_sep = multiple_sep
+              )
+            )
+          case "-" => Nil
         }
         // Alternatives
-        val moreParts = param.alternatives.map(alt => {
-          argStore(alt, param.VIASH_PAR, "\"$2\"", 2, multisep)
+        val moreParts = param.alternatives.map(alternativeFlag => {
+          generateFlagParser(
+            argName = alternativeFlag,
+            envName = param.VIASH_PAR,
+            multiple_sep = multiple_sep
+          )
         })
 
         (part1 :: part2 ::: moreParts).mkString("\n")
@@ -395,17 +461,21 @@ object BashWrapper {
       } else {
         "\n# storing leftover values in positionals\n" +
         positionals.map { param =>
-          if (param.multiple && param.direction == Input) {
-            s"""while [[ $$# -gt 0 ]]; do
-              |  ${store("positionalArg", param.VIASH_PAR, "\"$1\"", Some(param.multiple_sep)).mkString("\n  ")}
-              |  shift 1
-              |done""".stripMargin
-          } else {
-            s"""if [[ $$# -gt 0 ]]; then
-              |  ${param.VIASH_PAR}="$$1"
-              |  shift 1
-              |fi"""
-          }
+          val storeStr =
+            s"""ViashParseArgumentValue "${param.name}" "${param.VIASH_PAR}" "${param.multiple}" "$$1""""
+
+          val (begin, end) =
+            if (param.multiple && param.direction == Input) {
+              ("while", "done")
+            } else {
+              ("if", "fi")
+            }
+
+          s"""# processing positional values for '${param.name}'
+             |${begin} [[ $$# -gt 0 ]]; do
+             |  ${storeStr}
+             |  shift 1
+             |${end}""".stripMargin
         }.mkString("\n")
       }
 
@@ -720,8 +790,8 @@ object BashWrapper {
     val parsers = 
       compArgs.flatMap{ case (flag, env, _) => 
         List(
-          argStore(flag, env, "\"$2\"", 2),
-          argStoreSed(flag, env)
+          generateFlagParser(argName = flag, envName = env),
+          generateFlagWithEqualsParser(argName = flag, envName = env)
         )
       }.map("\n" + _).mkString
 
@@ -852,5 +922,39 @@ object BashWrapper {
       preRun = "\n# set dependency paths\n" + dependenciesStr
     )
   }
+  
+  private def generateWorkDir(argsMetaAndDeps: Map[String, List[Argument[_]]]): BashWrapperMods = {
+    def renderStrs = argsMetaAndDeps.map{case (key, args) =>
+      def renderYamlStrs = args.map(arg => {
+        s"""ViashRenderYamlKeyValue '${arg.name}' '${arg.`type`}' "${arg.multiple}" "$${${arg.VIASH_PAR}:-UNDEFINED}" >> "$$VIASH_WORK_PARAMS""""
+      })
+      s"""echo '${key}:' >> "$$VIASH_WORK_PARAMS"
+         |${renderYamlStrs.mkString("\n")}""".stripMargin
+    }
 
+    def preRun = 
+      s"""VIASH_WORK_DIR=$$(mktemp -d "$$VIASH_META_TEMP_DIR/viash-run-testbash-XXXXXX")
+         |function clean_up {
+         |  rm -rf "$$VIASH_WORK_DIR"
+         |}
+         |function interrupt {
+         |  echo -e "\nCTRL-C Pressed..."
+         |  exit 1
+         |}
+         |trap clean_up EXIT
+         |trap interrupt INT SIGINT
+         |
+         |# Create params yaml
+         |VIASH_WORK_PARAMS="$$VIASH_WORK_DIR/params.yaml"
+         |touch "$$VIASH_WORK_PARAMS"
+         |
+         |${renderStrs.mkString("\n\n")}
+         |
+         |cat "$$VIASH_WORK_PARAMS" # cat it for now
+         |""".stripMargin
+    // todo: generate script here as well?
+    BashWrapperMods(
+      preRun = preRun
+    )
+  }
 }

From 921fa8b975ec3ee5739e80db6d4f2775d1399242 Mon Sep 17 00:00:00 2001
From: Robrecht Cannoodt <rcannood@gmail.com>
Date: Wed, 14 Aug 2024 09:47:01 +0200
Subject: [PATCH 16/18] fixes

---
 .../helpers/bashutils/ViashParseArgumentValue.sh   |  6 +++---
 src/main/scala/io/viash/helpers/Bash.scala         |  1 +
 src/main/scala/io/viash/wrapper/BashWrapper.scala  | 14 ++++++++------
 3 files changed, 12 insertions(+), 9 deletions(-)

diff --git a/src/main/resources/io/viash/helpers/bashutils/ViashParseArgumentValue.sh b/src/main/resources/io/viash/helpers/bashutils/ViashParseArgumentValue.sh
index ea66225bb..c54d8cfe1 100644
--- a/src/main/resources/io/viash/helpers/bashutils/ViashParseArgumentValue.sh
+++ b/src/main/resources/io/viash/helpers/bashutils/ViashParseArgumentValue.sh
@@ -1,7 +1,7 @@
 function ViashParseArgumentValue {
-  local env_name="$1"
-  local multiple="$2"
-  local flag="$3"
+  local flag="$1"
+  local env_name="$2"
+  local multiple="$3"
   local value="$4"
 
   if [ $# -lt 4 ]; then
diff --git a/src/main/scala/io/viash/helpers/Bash.scala b/src/main/scala/io/viash/helpers/Bash.scala
index ad9753810..1fea9b62a 100644
--- a/src/main/scala/io/viash/helpers/Bash.scala
+++ b/src/main/scala/io/viash/helpers/Bash.scala
@@ -34,6 +34,7 @@ object Bash {
   lazy val ViashFindTargetDir: String = readUtils("ViashFindTargetDir")
   lazy val ViashDockerFuns: String = readUtils("ViashDockerFuns")
   lazy val ViashLogging: String = readUtils("ViashLogging")
+  lazy val ViashRenderYaml: String = readUtils("ViashRenderYaml")
   lazy val ViashParseArgumentValue: String = readUtils("ViashParseArgumentValue")
 
   /** 
diff --git a/src/main/scala/io/viash/wrapper/BashWrapper.scala b/src/main/scala/io/viash/wrapper/BashWrapper.scala
index 1093c1ff6..f186e7bc1 100644
--- a/src/main/scala/io/viash/wrapper/BashWrapper.scala
+++ b/src/main/scala/io/viash/wrapper/BashWrapper.scala
@@ -287,13 +287,15 @@ object BashWrapper {
        |  VIASH_TEMP=$${VIASH_TEMP:-/tmp}
        |fi
        |
-       |# define helper functions
+       |# bash helper functions start -----------------------------------
        |${Bash.ViashQuote}
        |${Bash.ViashRemoveFlags}
        |${Bash.ViashSourceDir}
        |${Bash.ViashFindTargetDir}
        |${Bash.ViashLogging}
        |${Bash.ViashParseArgumentValue}
+       |${Bash.ViashRenderYaml}
+       |# bash helper functions end -------------------------------------
        |
        |# find source folder of this component
        |VIASH_META_RESOURCES_DIR=`ViashSourceDir $${BASH_SOURCE[0]}`
@@ -464,15 +466,15 @@ object BashWrapper {
           val storeStr =
             s"""ViashParseArgumentValue "${param.name}" "${param.VIASH_PAR}" "${param.multiple}" "$$1""""
 
-          val (begin, end) =
+          val (begin, mid, end) =
             if (param.multiple && param.direction == Input) {
-              ("while", "done")
+              ("while", "do", "done")
             } else {
-              ("if", "fi")
+              ("if", "then", "fi")
             }
 
           s"""# processing positional values for '${param.name}'
-             |${begin} [[ $$# -gt 0 ]]; do
+             |${begin} [[ $$# -gt 0 ]]; ${mid}
              |  ${storeStr}
              |  shift 1
              |${end}""".stripMargin
@@ -926,7 +928,7 @@ object BashWrapper {
   private def generateWorkDir(argsMetaAndDeps: Map[String, List[Argument[_]]]): BashWrapperMods = {
     def renderStrs = argsMetaAndDeps.map{case (key, args) =>
       def renderYamlStrs = args.map(arg => {
-        s"""ViashRenderYamlKeyValue '${arg.name}' '${arg.`type`}' "${arg.multiple}" "$${${arg.VIASH_PAR}:-UNDEFINED}" >> "$$VIASH_WORK_PARAMS""""
+        s"""ViashRenderYamlKeyValue '${arg.plainName}' '${arg.`type`}' "${arg.multiple}" "$${${arg.VIASH_PAR}:-UNDEFINED}" >> "$$VIASH_WORK_PARAMS""""
       })
       s"""echo '${key}:' >> "$$VIASH_WORK_PARAMS"
          |${renderYamlStrs.mkString("\n")}""".stripMargin

From 653b3284418dd68ee166002cb802034ca4328319 Mon Sep 17 00:00:00 2001
From: Robrecht Cannoodt <rcannood@gmail.com>
Date: Wed, 14 Aug 2024 09:50:25 +0200
Subject: [PATCH 17/18] more fixes

---
 src/main/scala/io/viash/wrapper/BashWrapper.scala | 14 ++++++++++----
 1 file changed, 10 insertions(+), 4 deletions(-)

diff --git a/src/main/scala/io/viash/wrapper/BashWrapper.scala b/src/main/scala/io/viash/wrapper/BashWrapper.scala
index f186e7bc1..150e297f4 100644
--- a/src/main/scala/io/viash/wrapper/BashWrapper.scala
+++ b/src/main/scala/io/viash/wrapper/BashWrapper.scala
@@ -926,15 +926,21 @@ object BashWrapper {
   }
   
   private def generateWorkDir(argsMetaAndDeps: Map[String, List[Argument[_]]]): BashWrapperMods = {
-    def renderStrs = argsMetaAndDeps.map{case (key, args) =>
-      def renderYamlStrs = args.map(arg => {
-        s"""ViashRenderYamlKeyValue '${arg.plainName}' '${arg.`type`}' "${arg.multiple}" "$${${arg.VIASH_PAR}:-UNDEFINED}" >> "$$VIASH_WORK_PARAMS""""
+    val renderStrs = argsMetaAndDeps.map{case (key, args) =>
+      val renderYamlStrs = args.map(arg => {
+        val value =
+          if (arg.multiple) {
+            s"$${${arg.VIASH_PAR}[@]}"
+          } else {
+            s"$${${arg.VIASH_PAR}:-UNDEFINED}"
+          }
+        s"""ViashRenderYamlKeyValue '${arg.plainName}' '${arg.`type`}' "${arg.multiple}" "${value}" >> "$$VIASH_WORK_PARAMS""""
       })
       s"""echo '${key}:' >> "$$VIASH_WORK_PARAMS"
          |${renderYamlStrs.mkString("\n")}""".stripMargin
     }
 
-    def preRun = 
+    val preRun = 
       s"""VIASH_WORK_DIR=$$(mktemp -d "$$VIASH_META_TEMP_DIR/viash-run-testbash-XXXXXX")
          |function clean_up {
          |  rm -rf "$$VIASH_WORK_DIR"

From 18f594b4a3612acf083edde2178b0b1cdd2ba9bc Mon Sep 17 00:00:00 2001
From: Robrecht Cannoodt <rcannood@gmail.com>
Date: Wed, 14 Aug 2024 09:57:30 +0200
Subject: [PATCH 18/18] only input multiples are arrays

---
 src/main/scala/io/viash/wrapper/BashWrapper.scala | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/src/main/scala/io/viash/wrapper/BashWrapper.scala b/src/main/scala/io/viash/wrapper/BashWrapper.scala
index 150e297f4..ee8b4b42c 100644
--- a/src/main/scala/io/viash/wrapper/BashWrapper.scala
+++ b/src/main/scala/io/viash/wrapper/BashWrapper.scala
@@ -928,13 +928,14 @@ object BashWrapper {
   private def generateWorkDir(argsMetaAndDeps: Map[String, List[Argument[_]]]): BashWrapperMods = {
     val renderStrs = argsMetaAndDeps.map{case (key, args) =>
       val renderYamlStrs = args.map(arg => {
+        val multiple = arg.multiple && arg.direction == Input
         val value =
-          if (arg.multiple) {
+          if (multiple) {
             s"$${${arg.VIASH_PAR}[@]}"
           } else {
             s"$${${arg.VIASH_PAR}:-UNDEFINED}"
           }
-        s"""ViashRenderYamlKeyValue '${arg.plainName}' '${arg.`type`}' "${arg.multiple}" "${value}" >> "$$VIASH_WORK_PARAMS""""
+        s"""ViashRenderYamlKeyValue '${arg.plainName}' '${arg.`type`}' "${multiple}" "${value}" >> "$$VIASH_WORK_PARAMS""""
       })
       s"""echo '${key}:' >> "$$VIASH_WORK_PARAMS"
          |${renderYamlStrs.mkString("\n")}""".stripMargin