Remove deprecated things (#833)

* wip deprecate things

* fix components

* fix test

* update tests and yamls

* fix test (recent versions of git require a message)

* remove test code for removed functionality

Author: Robrecht Cannoodt

CHANGELOG.md

@@ -8,13 +8,11 @@ TODO add summary
 
 ## BREAKING CHANGES
 
-* `Nextflow` runner: remove deprecated `map`, `mapId`, `mapData`, `mapPassthrough` and `renameKeys` (PR #792).
+* `Nextflow` runner: remove deprecated `map`, `mapId`, `mapData`, `mapPassthrough` and `renameKeys` arguments (PR #792).
 
-* `Nextflow` runner: remove helper functions: `setWorkflowArguments`, `getWorkflowArguments`, `strictMap`, `passthroughMap`, `passthroughFlatMap` and `passthroughFilter` (PR #792).
+* `Nextflow` runner: remove helper functions: `setWorkflowArguments`, `getWorkflowArguments`, `strictMap`, `passthroughMap`, `passthroughFlatMap`,  `passthroughFilter`, `channelFromParams`, `runComponents` (PRs #792, #811).
 
-* `Nextflow` runner: `channelFromParams` is now deprecated (PR #792).
-
-* `Nextflow` runner: remove deprecated `runComponents` (PR #811).
+* Deprecate `functionality` and `platforms`.
 
 ## BUG FIXES
 

…rs/nextflow/channel/channelFromParams.nf …s/nextflow/channel/_channelFromParams.nfsrc/main/resources/io/viash/runners/nextflow/channel/channelFromParams.nf renamed to src/main/resources/io/viash/runners/nextflow/channel/_channelFromParams.nf src/main/resources/io/viash/runners/nextflow/channel/channelFromParams.nf renamed to src/main/resources/io/viash/runners/nextflow/channel/_channelFromParams.nf

@@ -100,27 +100,3 @@ private _channelFromParams(Map params, Map config) {
   def processedParams = _paramsToParamSets(params, config)
   return Channel.fromList(processedParams)
 }
-
-/**
- * Parse nextflow parameters based on settings defined in a viash config 
- * and return a nextflow channel.
- * 
- * @param params Input parameters. Can optionaly contain a 'param_list' key that
- *               provides a list of arguments that can be split up into multiple events
- *               in the output channel possible formats of param_lists are: a csv file, 
- *               json file, a yaml file or a yaml blob. Each parameters set (event) must
- *               have a unique ID.
- * @param config A Map of the Viash configuration. This Map can be generated from the config file
- *               using the readConfig() function.
- * 
- * @return A nextflow Channel with events. Events are formatted as a tuple that contains 
- *         first contains the ID of the event and as second element holds a parameter map.
- *       
- *
- */
-def channelFromParams(Map params, Map config) {
-  log.warn "channelFromParams is deprecated and will be removed in Viash 0.10.0. ",
-    "Nextflow workflows can now be built into standalone components where parsed parameters ",
-    "are automatically provided to the input channel."
-  return _channelFromParams(params, config) 
-}

src/main/scala/io/viash/Main.scala

@@ -198,36 +198,6 @@ object Main extends Logging {
         }
       case _ => 
     }
-
-    // backwards compability for --platform
-    cli.subcommands.lastOption match {
-      case Some(x: ViashCommand) => 
-        if (x.platform.isDefined) {
-          if (x.runner.isDefined || x.engine.isDefined) {
-            throw new IllegalArgumentException("Error: --platform cannot be used together with --runner or --engine.")
-          }
-          warn("Warning: --platform is deprecated in Viash 0.9.0, will be removed in Viash 0.10.0. Use --runner or --engine instead.")
-        }
-      case Some(x: ViashNs) =>
-        if (x.platform.isDefined) {
-          if (x.runner.isDefined || x.engine.isDefined) {
-            throw new IllegalArgumentException("Error: --platform cannot be used together with --runner or --engine.")
-          }
-          warn("Warning: --platform is deprecated in Viash 0.9.0, will be removed in Viash 0.10.0. Use --runner or --engine instead.")
-        }
-      case _ => 
-    }
-    // backwards compability for --apply_platform
-    cli.subcommands match {
-      case List(cli.namespace, cli.namespace.exec) =>
-        if (cli.namespace.exec.applyPlatform()) {
-          if (cli.namespace.exec.applyRunner() || cli.namespace.exec.applyEngine()) {
-            throw new IllegalArgumentException("Error: --platform cannot be used together with --runner or --engine.")
-          }
-          warn("Warning: --apply_platform is deprecated in Viash 0.9.0, will be removed in Viash 0.10.0n. Use --apply_runner or --apply_engine instead.")
-        }
-      case _ =>
-    }
 
     // see if there are package overrides passed to the viash command
     val packSrc = cli.subcommands.lastOption match {
@@ -337,8 +307,8 @@ object Main extends Logging {
           cli.namespace.list,
           packageConfig = pack1,
           addOptMainScript = false, 
-          applyRunner = cli.namespace.list.runner.isDefined || cli.namespace.list.platform.isDefined,
-          applyEngine = cli.namespace.list.engine.isDefined || cli.namespace.list.platform.isDefined
+          applyRunner = cli.namespace.list.runner.isDefined,
+          applyEngine = cli.namespace.list.engine.isDefined
         )
         val configs2 = namespaceDependencies(configs, None, pack1.rootDir)
         ViashNamespace.list(
@@ -351,8 +321,8 @@ object Main extends Logging {
         val configs = readConfigs(
           cli.namespace.exec, 
           packageConfig = pack1, 
-          applyRunner = cli.namespace.exec.applyRunner() || cli.namespace.exec.applyPlatform(),
-          applyEngine = cli.namespace.exec.applyEngine() || cli.namespace.exec.applyPlatform()
+          applyRunner = cli.namespace.exec.applyRunner(),
+          applyEngine = cli.namespace.exec.applyEngine()
         )
         ViashNamespace.exec(
           configs = configs,
@@ -371,7 +341,7 @@ object Main extends Logging {
           cli.config.view,
           packageConfig = pack1,
           addOptMainScript = false,
-          applyRunnerAndEngine = cli.config.view.platform.isDefined || cli.config.view.runner.isDefined || cli.config.view.engine.isDefined
+          applyRunnerAndEngine = cli.config.view.runner.isDefined || cli.config.view.engine.isDefined
         )
         val config2 = DependencyResolver.modifyConfig(config.config, None, pack1.rootDir)
         ViashConfig.view(
@@ -480,11 +450,8 @@ object Main extends Logging {
       viashPackage = Some(packageConfig)
     )
     if (applyRunnerAndEngine) {
-      val runnerStr = subcommand.runner.toOption orElse subcommand.platform.toOption
-      val engineStr = subcommand.engine.toOption orElse subcommand.platform.toOption
-      
-      val runner = config.findRunner(runnerStr)
-      val engines = config.findEngines(engineStr)
+      val runner = config.findRunner(subcommand.runner.toOption)
+      val engines = config.findEngines(subcommand.engine.toOption)
 
       processConfigWithRunnerAndEngine(
         appliedConfig = config,
@@ -509,8 +476,8 @@ object Main extends Logging {
     val queryNamespace = subcommand.query_namespace.toOption
     val queryName = subcommand.query_name.toOption
     val queryConfig = subcommand.query_config.toOption
-    val runnerStr = subcommand.runner.toOption orElse subcommand.platform.toOption
-    val engineStr = subcommand.engine.toOption orElse subcommand.platform.toOption
+    val runnerStr = subcommand.runner.toOption
+    val engineStr = subcommand.engine.toOption
     val configMods = packageConfig.config_mods
 
     val configs0 = Config.readConfigs(

src/main/scala/io/viash/ViashExport.scala

@@ -76,13 +76,7 @@ object ViashExport extends Logging {
   }
 
   def exportResource(input: String, output: Option[Path]): Unit = {
-    val input2 = if (input.startsWith("platforms/")) {
-      warn("WARNING: The 'platforms/' prefix is deprecated. Please use 'runners/' instead.")
-      input.replaceFirst("platforms/", "runners/")
-    } else {
-      input
-    }
-    val pth = getClass.getResource(s"/io/viash/$input2")
+    val pth = getClass.getResource(s"/io/viash/$input")
     val str = IO.read(pth.toURI())
     if (output.isDefined) {
       Files.write(output.get, str.getBytes())

src/main/scala/io/viash/ViashNamespace.scala

@@ -98,7 +98,6 @@ object ViashNamespace extends Logging {
           val funName = ac.config.name
           val ns = ac.config.namespace
           val runnerId = ac.runner.get.id
-          // val engineId = ac.platform.get.id
           val out = 
             if (flatten) {
               target

src/main/scala/io/viash/cli/CLIConf.scala

@@ -24,18 +24,6 @@ import io.viash.helpers.Logging
 
 trait ViashCommand {
   this: DocumentedSubcommand =>
-  val platform = registerOpt[String](
-    name = "platform",
-    short = Some('p'),
-    default = None,
-    descr =
-      "Deprecated. Use --runner and --engine instead. " +
-      "Specifies which platform amongst those specified in the config to use. " +
-      "If this is not provided, the first platform will be used. " +
-      "If no platforms are defined in the config, the native platform will be used. " +
-      "In addition, the path to a platform yaml file can also be specified.",
-    required = false
-  )
   val runner = registerOpt[String](
     name = "runner",
     default = None,
@@ -113,18 +101,6 @@ trait ViashNs {
     descr = "A source directory containing viash config files, possibly structured in a hierarchical folder structure. Default: src/.",
     default = None
   )
-  val platform = registerOpt[String](
-    name = "platform",
-    short = Some('p'),
-    descr =
-      "Deprecated. Use --runner and --engine instead. " +
-      "Acts as a regular expression to filter the platform ids specified in the found config files. " +
-        "If this is not provided, all platforms will be used. " +
-        "If no platforms are defined in a config, the native platform will be used. " +
-        "In addition, the path to a platform yaml file can also be specified.",
-    default = None,
-    required = false
-  )
   val runner = registerOpt[String](
     name = "runner",
     default = None,
@@ -440,7 +416,6 @@ class CLIConf(arguments: Seq[String]) extends ScallopConf(arguments) with Loggin
           | * `{main-script}`: path to the main script (if any)
           | * `{abs-main-script}`: absolute path to the main script (if any)
           | * `{name}`: name of the component
-          | * `{functionality-name}`: name of the component (deprecated)
           | * `{namespace}`: namespace of the component
           | * `{runner}`: selected runner id (only when --apply_runner is used)
           | * `{engine}`: selected engine id (only when --apply_engine is used)
@@ -453,16 +428,6 @@ class CLIConf(arguments: Seq[String]) extends ScallopConf(arguments) with Loggin
         """viash ns exec 'echo {path} \\;'
           |viash ns exec 'chmod +x {main-script} +'""".stripMargin
       )
-      val applyPlatform = registerOpt[Boolean] (
-        name = "apply_platform",
-        short = Some('a'),
-        default = Some(false),
-        descr = 
-          """Deprecated. Use --apply_runner and --apply_engine instead.
-            |Fills in the {platform} and {output} field by applying each platform to the
-            |config separately. Note that this results in the provided command being applied
-            |once for every platform that matches the --platform regex.""".stripMargin
-      )
       val applyRunner = registerOpt[Boolean] (
         name = "apply_runner",
         short = Some('r'),

src/main/scala/io/viash/config/Config.scala

@@ -21,8 +21,6 @@ import io.viash.config_mods.ConfigModParser
 import arguments._
 import resources._
 import dependencies._
-import io.viash.functionality.Functionality
-import io.viash.platforms.Platform
 import io.viash.helpers.{Git, GitInfo, IO, Logging}
 import io.viash.helpers.circe._
 import io.viash.helpers.{status => BuildStatus};
@@ -384,14 +382,6 @@ case class Config(
   @undocumented
   package_config: Option[PackageConfig] = None,
 ) {
-  @description(
-    """The @[functionality](functionality) describes the behaviour of the script in terms of arguments and resources.
-      |By specifying a few restrictions (e.g. mandatory arguments) and adding some descriptions, Viash will automatically generate a stylish command-line interface for you.
-      |""")
-  @deprecated("Functionality level is deprecated, all functionality fields are now located on the top level of the config file.", "0.9.0", "0.10.0")
-  @default("")
-  private val functionality: Functionality = Functionality("foo")
-
   @description(
     """A list of @[arguments](argument) for this component. For each argument, a type and a name must be specified. Depending on the type of argument, different properties can be set. See these reference pages per type for more information:  
       |
@@ -414,17 +404,6 @@ case class Config(
   @example("__merge__: ../api/common_interface.yaml", "yaml")
   @since("Viash 0.6.3")
   private val `__merge__`: Option[File] = None
-
-  @description(
-  """A list of platforms to generate target artifacts for.
-    |
-    | - @[Native](platform_native)
-    | - @[Docker](platform_docker)
-    | - @[Nextflow](platform_nextflow)
-    |""")
-  @default("Empty")
-  @deprecated("Use 'engines' and 'runners' instead.", "0.9.0", "0.10.0")
-  private val platforms: List[Platform] = Nil
 
   /**
     * Find the runner