Add Config parser v2 (and loader) (#4744)

Signed-off-by: Ben Sherman <bentshermann@gmail.com>
Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Co-authored-by: Chris Hakkaart <chris.hakkaart@seqera.io>
Co-authored-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>

Author: 3 people

.github/workflows/build.yml

@@ -133,7 +133,7 @@ jobs:
       fail-fast: false
       matrix:
         java_version: [17, 23]
-        test_mode: ["test_integration", "test_docs", "test_aws", "test_azure", "test_google", "test_wave"]
+        test_mode: ["test_integration", "test_parser_v2", "test_docs", "test_aws", "test_azure", "test_google", "test_wave"]
     steps:
       - name: Checkout
         uses: actions/checkout@v4

build.gradle

@@ -85,6 +85,10 @@ allprojects {
         maven { url 'https://oss.sonatype.org/content/repositories/snapshots' }
         maven { url = "https://s3-eu-west-1.amazonaws.com/maven.seqera.io/releases" }
         maven { url = "https://s3-eu-west-1.amazonaws.com/maven.seqera.io/snapshots" }
+        maven {
+            url 'https://jitpack.io'
+            content { includeGroup 'com.github.nextflow-io.language-server' }
+        }
     }
 
     configurations {

docs/config.md

@@ -254,13 +254,12 @@ With the above configuration:
 
 ## Config profiles
 
-Configuration files can contain the definition of one or more *profiles*. A profile is a set of configuration attributes that can be selected during pipeline execution by using the `-profile` command line option.
+Configuration files can define one or more *profiles*. A profile is a set of configuration settings that can be selected during pipeline execution using the `-profile` command line option.
 
-Configuration profiles are defined by using the special scope `profiles`, which group the attributes that belong to the same profile using a common prefix. For example:
+Configuration profiles are defined in the `profiles` scope. For example:
 
 ```groovy
 profiles {
-
     standard {
         process.executor = 'local'
     }
@@ -276,41 +275,47 @@ profiles {
         process.container = 'cbcrg/imagex'
         docker.enabled = true
     }
-
 }
 ```
 
-This configuration defines three different profiles: `standard`, `cluster`, and `cloud`, that each set different process
-configuration strategies depending on the target runtime platform. The `standard` profile is used by default when no profile is specified.
+The above configuration defines three profiles: `standard`, `cluster`, and `cloud`. Each profile provides a different configuration for a given execution environment. The `standard` profile is used by default when no profile is specified.
 
-:::{tip}
-Multiple configuration profiles can be specified by separating the profile names with a comma, for example:
+Configuration profiles can be specified at runtime as a comma-separated list:
 
 ```bash
 nextflow run <your script> -profile standard,cloud
 ```
 
 Config profiles are applied in the order in which they were defined in the config file, regardless of the order they are specified on the command line.
+
+:::{versionadded} 25.02.0-edge
+When using the {ref}`strict config syntax <updating-config-syntax>`, profiles are applied in the order in which they are specified on the command line.
 :::
 
 :::{danger}
-When using the `profiles` feature in your config file, do NOT set attributes in the same scope both inside and outside a `profiles` context. For example:
+When defining a profile in the config file, avoid using both the dot and block syntax for the same scope. For example:
 
 ```groovy
-process.cpus = 1
-
 profiles {
-  foo {
-    process.memory = '2 GB'
-  }
+    foo {
+        process.memory = '2 GB'
+        process {
+            cpus = 2
+        }
+    }
+}
+```
 
-  bar {
-    process.memory = '4 GB'
-  }
+Due to a limitation of the legacy config parser, the first setting will be overwritten by the second:
+
+```console
+$ nextflow config -profile foo
+process {
+   cpus = 2
 }
 ```
 
-In the above example, the `process.cpus` attribute is not correctly applied because the `process` scope is also used in the `foo` and `bar` profiles.
+This limitation can be avoided by using the {ref}`strict config syntax <updating-config-syntax>`.
 :::
 
 ## Workflow handlers

docs/reference/env-vars.md

@@ -182,6 +182,11 @@ The following environment variables control the configuration of the Nextflow ru
   :::
 : Enable the use of Spack recipes defined by using the {ref}`process-spack` directive. (default: `false`).
 
+`NXF_SYNTAX_PARSER`
+: :::{versionadded} 25.02.0-edge
+  :::
+: Set to `'v2'` to use the {ref}`strict syntax <updating-syntax-page>` for Nextflow config files (default: `'v1'`).
+
 `NXF_TEMP`
 : Directory where temporary files are stored
 

docs/updating-syntax.md

@@ -487,8 +487,14 @@ The process `when` section is deprecated. Use conditional logic, such as an `if`
 
 The process `shell` section is deprecated. Use the `script` block instead. The VS Code extension provides syntax highlighting and error checking to help distinguish between Nextflow variables and Bash variables.
 
+(updating-config-syntax)=
+
 ### Configuration syntax
 
+:::{versionadded} 25.02.0-edge
+The strict config syntax can be enabled in Nextflow by setting `NXF_SYNTAX_PARSER=v2`.
+:::
+
 See {ref}`Configuration <config-syntax>` for a comprehensive description of the configuration language.
 
 Currently, Nextflow parses config files as Groovy scripts, allowing the use of scripting constructs like variables, helper functions, try-catch blocks, and conditional logic for dynamic configuration:

modules/nextflow/build.gradle

@@ -20,6 +20,7 @@ compileGroovy {
 dependencies {
     api(project(':nf-commons'))
     api(project(':nf-httpfs'))
+    api 'com.github.nextflow-io.language-server:compiler:main-SNAPSHOT'
     api "org.apache.groovy:groovy:4.0.25"
     api "org.apache.groovy:groovy-nio:4.0.25"
     api "org.apache.groovy:groovy-xml:4.0.25"

modules/nextflow/src/main/groovy/nextflow/config/ConfigBuilder.groovy

@@ -71,8 +71,6 @@ class ConfigBuilder {
 
     List<Path> parsedConfigFiles = []
 
-    List<String> parsedProfileNames
-
     boolean showClosures
 
     boolean stripSecrets
@@ -347,7 +345,7 @@ class ConfigBuilder {
         assert env != null
 
         final ignoreIncludes = options ? options.ignoreConfigIncludes : false
-        final slurper = new ConfigParser()
+        final slurper = ConfigParserFactory.create()
                 .setRenderClosureAsString(showClosures)
                 .setStripSecrets(stripSecrets)
                 .setIgnoreIncludes(ignoreIncludes)
@@ -384,9 +382,8 @@ class ConfigBuilder {
                 }
             }
 
-            this.parsedProfileNames = new ArrayList<>(slurper.getProfileNames())
             if( validateProfile ) {
-                checkValidProfile(slurper.getConditionalBlockNames())
+                checkValidProfile(slurper.getProfiles())
             }
 
         }
@@ -421,7 +418,7 @@ class ConfigBuilder {
 
         log.debug "Applying config profile: `${profile}`"
         def allNames = profile.tokenize(',')
-        slurper.registerConditionalBlock('profiles', allNames)
+        slurper.setProfiles(allNames)
 
         def config = parse0(slurper,entry)
         validate(config,entry)