Map conda channels to prefix.dev mirrors for pixi builds

Enable sharded repodata for pixi-based container builds by automatically
mapping well-known conda channels to their prefix.dev mirrors:
- conda-forge -> https://prefix.dev/conda-forge
- bioconda -> https://prefix.dev/bioconda

This provides 50-100x faster package resolution according to:
https://prefix.dev/blog/sharded_repodata

The mapping is only applied when using the CONDA_PIXI_V1 build template,
leaving other build templates (micromamba v1/v2) unchanged.

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>

Author: pditommaso

src/main/groovy/io/seqera/wave/util/ContainerHelper.groovy

@@ -84,17 +84,22 @@ class ContainerHelper {
         if( req.packages.type != PackagesSpec.Type.CONDA )
             return null
 
+        // Map channels to prefix.dev mirrors for pixi builds (enables sharded repodata for faster resolution)
+        final channels = req.buildTemplate == CONDA_PIXI_V1
+                ? PixiHelper.mapChannelsToPixiServers(req.packages.channels)
+                : req.packages.channels
+
         if( req.packages.environment ) {
             // parse the attribute as a conda file path *and* append the base packages if any
             // note 'channel' is null, because they are expected to be provided in the conda file
             final decoded = decodeBase64OrFail(req.packages.environment, 'packages.envFile')
-            return condaEnvironmentToCondaYaml(decoded, req.packages.channels)
+            return condaEnvironmentToCondaYaml(decoded, channels)
         }
 
         if ( req.packages.entries && !CondaHelper.tryGetLockFile(req.packages.entries)) {
             // create a minimal conda file with package spec from user input
             final String packages = req.packages.entries.join(' ')
-            return condaPackagesToCondaYaml(packages, req.packages.channels)
+            return condaPackagesToCondaYaml(packages, channels)
         }
 
         return null;

src/main/groovy/io/seqera/wave/util/PixiHelper.groovy

@@ -34,6 +34,30 @@ import static TemplateUtils.condaFileToSingularityFileUsingPixi
 @CompileStatic
 class PixiHelper {
 
+    /**
+     * Map of well-known conda channels to their prefix.dev mirrors.
+     * Using prefix.dev mirrors enables sharded repodata which provides
+     * 50-100x faster package resolution.
+     * See: https://prefix.dev/blog/sharded_repodata
+     */
+    static final Map<String, String> CHANNEL_TO_PREFIX_DEV = Map.of(
+            'conda-forge', 'https://prefix.dev/conda-forge',
+            'bioconda', 'https://prefix.dev/bioconda'
+    )
+
+    /**
+     * Maps conda channels to their prefix.dev mirrors for faster package resolution.
+     * Channels that don't have a known prefix.dev mirror are left unchanged.
+     *
+     * @param channels List of conda channel names
+     * @return List of channels with known channels mapped to prefix.dev mirrors
+     */
+    static List<String> mapChannelsToPixiServers(List<String> channels) {
+        if( !channels )
+            return channels
+        return channels.collect { ch -> CHANNEL_TO_PREFIX_DEV.getOrDefault(ch, ch) }
+    }
+
     /**
      * Generate a container file (Dockerfile or Singularity) using the Pixi template.
      * Only supports CONDA package type. Lock files are not supported.

src/test/groovy/io/seqera/wave/util/ContainerHelperTest.groovy

@@ -896,4 +896,69 @@ class ContainerHelperTest extends Specification {
         e.message == "Unexpected or missing package type 'CONDA' or build template 'invalid-template'"
     }
 
+    // === Channel mapping tests for pixi builds ===
+
+    def 'should map channels to prefix.dev mirrors for pixi builds' () {
+        given:
+        def spec = new PackagesSpec(type: PackagesSpec.Type.CONDA, entries: ['bwa', 'samtools'], channels: ['conda-forge', 'bioconda'])
+        def req = new SubmitContainerTokenRequest(packages: spec, buildTemplate: BuildTemplate.CONDA_PIXI_V1)
+
+        when:
+        def result = ContainerHelper.condaFileFromRequest(req)
+
+        then:
+        result == '''\
+            channels:
+            - https://prefix.dev/conda-forge
+            - https://prefix.dev/bioconda
+            dependencies:
+            - bwa
+            - samtools
+            '''.stripIndent()
+    }
+
+    def 'should not map channels for non-pixi builds' () {
+        given:
+        def spec = new PackagesSpec(type: PackagesSpec.Type.CONDA, entries: ['bwa', 'samtools'], channels: ['conda-forge', 'bioconda'])
+        def req = new SubmitContainerTokenRequest(packages: spec, buildTemplate: BuildTemplate.CONDA_MICROMAMBA_V2)
+
+        when:
+        def result = ContainerHelper.condaFileFromRequest(req)
+
+        then:
+        result == '''\
+            channels:
+            - conda-forge
+            - bioconda
+            dependencies:
+            - bwa
+            - samtools
+            '''.stripIndent()
+    }
+
+    def 'should map channels in environment file for pixi builds' () {
+        given:
+        def CONDA = '''\
+            channels:
+            - conda-forge
+            dependencies:
+            - bwa
+            '''.stripIndent()
+        and:
+        def spec = new PackagesSpec(type: PackagesSpec.Type.CONDA, environment: CONDA.bytes.encodeBase64().toString(), channels: ['bioconda'])
+        def req = new SubmitContainerTokenRequest(packages: spec, buildTemplate: BuildTemplate.CONDA_PIXI_V1)
+
+        when:
+        def result = ContainerHelper.condaFileFromRequest(req)
+
+        then:
+        result == '''\
+            channels:
+            - conda-forge
+            - https://prefix.dev/bioconda
+            dependencies:
+            - bwa
+            '''.stripIndent()
+    }
+
 }

src/test/groovy/io/seqera/wave/util/PixiHelperTest.groovy

@@ -133,4 +133,62 @@ class PixiHelperTest extends Specification {
         def ex = thrown(BadRequestException)
         ex.message.contains("Conda lock file is not supported by 'conda/pixi:v1' template")
     }
+
+    // ---- Tests for channel mapping to prefix.dev mirrors ----
+
+    def 'should map conda-forge channel to prefix.dev mirror'() {
+        when:
+        def result = PixiHelper.mapChannelsToPixiServers(['conda-forge'])
+
+        then:
+        result == ['https://prefix.dev/conda-forge']
+    }
+
+    def 'should map bioconda channel to prefix.dev mirror'() {
+        when:
+        def result = PixiHelper.mapChannelsToPixiServers(['bioconda'])
+
+        then:
+        result == ['https://prefix.dev/bioconda']
+    }
+
+    def 'should map multiple known channels to prefix.dev mirrors'() {
+        when:
+        def result = PixiHelper.mapChannelsToPixiServers(['conda-forge', 'bioconda'])
+
+        then:
+        result == ['https://prefix.dev/conda-forge', 'https://prefix.dev/bioconda']
+    }
+
+    def 'should leave unknown channels unchanged'() {
+        when:
+        def result = PixiHelper.mapChannelsToPixiServers(['defaults', 'my-custom-channel'])
+
+        then:
+        result == ['defaults', 'my-custom-channel']
+    }
+
+    def 'should handle mixed known and unknown channels'() {
+        when:
+        def result = PixiHelper.mapChannelsToPixiServers(['conda-forge', 'defaults', 'bioconda', 'my-channel'])
+
+        then:
+        result == ['https://prefix.dev/conda-forge', 'defaults', 'https://prefix.dev/bioconda', 'my-channel']
+    }
+
+    def 'should handle null channel list'() {
+        when:
+        def result = PixiHelper.mapChannelsToPixiServers(null)
+
+        then:
+        result == null
+    }
+
+    def 'should handle empty channel list'() {
+        when:
+        def result = PixiHelper.mapChannelsToPixiServers([])
+
+        then:
+        result == []
+    }
 }