Initial pixi support

Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>

Author: pditommaso

settings.gradle

@@ -10,4 +10,4 @@ rootProject.name="wave"
 // only for development
 // clone https://github.com/seqeralabs/libseqera
 // in a sibling directory and include the build below
-//includeBuild('../libseqera')
+includeBuild('../libseqera')

src/main/groovy/io/seqera/wave/controller/ContainerController.groovy

@@ -85,7 +85,7 @@ import static io.seqera.wave.service.builder.BuildFormat.SINGULARITY
 import static io.seqera.wave.service.pairing.PairingService.TOWER_SERVICE
 import static io.seqera.wave.util.ContainerHelper.checkContainerSpec
 import static io.seqera.wave.util.ContainerHelper.condaFileFromRequest
-import static io.seqera.wave.util.ContainerHelper.containerFileFromPackages
+import static io.seqera.wave.util.ContainerHelper.containerFileFromRequest
 import static io.seqera.wave.util.ContainerHelper.decodeBase64OrFail
 import static io.seqera.wave.util.ContainerHelper.makeContainerId
 import static io.seqera.wave.util.ContainerHelper.makeResponseV1
@@ -248,7 +248,7 @@ class ContainerController {
 
         if( v2 && req.packages ) {
             // generate the container file required to assemble the container
-            final generated = containerFileFromPackages(req.packages, req.formatSingularity())
+            final generated = containerFileFromRequest(req)
             req = req.copyWith(containerFile: generated.bytes.encodeBase64().toString())
         }
 

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

@@ -27,6 +27,7 @@ import io.seqera.wave.api.PackagesSpec
 import io.seqera.wave.api.SubmitContainerTokenRequest
 import io.seqera.wave.api.SubmitContainerTokenResponse
 import io.seqera.wave.config.CondaOpts
+import io.seqera.wave.config.PixiOpts
 import io.seqera.wave.core.ContainerPlatform
 import io.seqera.wave.exception.BadRequestException
 import io.seqera.wave.service.builder.BuildFormat
@@ -36,6 +37,7 @@ import org.yaml.snakeyaml.Yaml
 import static io.seqera.wave.service.builder.BuildFormat.SINGULARITY
 import static io.seqera.wave.util.DockerHelper.condaEnvironmentToCondaYaml
 import static io.seqera.wave.util.DockerHelper.condaFileToDockerFile
+import static io.seqera.wave.util.DockerHelper.condaFileToDockerFileUsingPixi
 import static io.seqera.wave.util.DockerHelper.condaFileToSingularityFile
 import static io.seqera.wave.util.DockerHelper.condaPackagesToCondaYaml
 import static io.seqera.wave.util.DockerHelper.condaPackagesToDockerFile
@@ -76,10 +78,34 @@ class ContainerHelper {
             }
             return result
         }
-
         throw new BadRequestException("Unexpected packages spec type: $spec.type")
     }
 
+    static String containerFileFromRequest(SubmitContainerTokenRequest req) {
+        if( !req.buildTemplate )
+            return containerFileFromPackages(req.packages, req.formatSingularity())
+        // build the container using the pixi template
+        if( req.buildTemplate=='pixi/v1') {
+            // check the type of the packages and apply
+            if( req.packages.type == PackagesSpec.Type.CONDA ) {
+                final lockFile = condaLockFile(req.packages.entries)
+                final opts = req.packages.pixiOpts ?: new PixiOpts()
+                if( req.containerImage )
+                    opts.baseImage = req.containerImage
+                if( lockFile )
+                    throw new BadRequestException("Conda lock file is not supported by '${req}' template")
+                if( req.formatSingularity() )
+                    throw new BadRequestException("Singularity is not supported by '${req.buildTemplate}' template")
+                final result = condaFileToDockerFileUsingPixi(opts)
+                return result
+            }
+            else
+                throw new BadRequestException("Package type '${req.packages.type}' not supported by build template: ${req.buildTemplate}")
+
+        }
+        throw new BadRequestException("Unexpected build template: ${req.buildTemplate}")
+    }
+
     static String condaFileFromRequest(SubmitContainerTokenRequest req) {
         if( !req.packages )
             return decodeBase64OrFail(req.condaFile, 'condaFile')

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

@@ -28,6 +28,7 @@ import io.seqera.wave.api.ImageNameStrategy
 import io.seqera.wave.api.PackagesSpec
 import io.seqera.wave.api.SubmitContainerTokenRequest
 import io.seqera.wave.config.CondaOpts
+import io.seqera.wave.config.PixiOpts
 import io.seqera.wave.exception.BadRequestException
 import io.seqera.wave.service.request.ContainerRequest
 import io.seqera.wave.service.builder.BuildFormat
@@ -603,4 +604,97 @@ class ContainerHelperTest extends Specification {
 
     }
 
+
+    // === build with pixi tests
+
+    def 'should create conda docker file with packages and pixi'() {
+        given:
+        def CHANNELS = ['conda-forge', 'defaults']
+        def PACKAGES = ['bwa=0.7.15', 'salmon=1.1.1']
+        def packages = new PackagesSpec(
+                type: PackagesSpec.Type.CONDA,
+                entries:  PACKAGES,
+                channels: CHANNELS)
+        and:
+        def req = new SubmitContainerTokenRequest(packages:packages, buildTemplate: 'pixi/v1')
+        when:
+        def result = ContainerHelper.containerFileFromRequest(req)
+
+        then:
+        result =='''\
+                FROM ghcr.io/prefix-dev/pixi:latest AS build
+                 
+                COPY conda.yml /opt/wave/conda.yml
+                WORKDIR /opt/wave
+                 
+                RUN pixi init --import /opt/wave/conda.yml \\
+                    && pixi add conda-forge::procps-ng \\
+                    && pixi shell-hook > /shell-hook.sh \\
+                    && echo 'exec "$@"' >> /shell-hook.sh \\
+                    && echo ">> CONDA_LOCK_START" \\
+                    && cat /opt/wave/pixi.lock \\
+                    && echo "<< CONDA_LOCK_END"
+                 
+                FROM ubuntu:24.04 AS prod
+                 
+                # copy the pixi environment in the final container
+                COPY --from=build /opt/wave/.pixi/envs/default /opt/wave/.pixi/envs/default
+                COPY --from=build /shell-hook.sh /shell-hook.sh
+                 
+                # set the entrypoint to the shell-hook script (activate the environment and run the command)
+                # no more pixi needed in the prod container
+                ENTRYPOINT ["/bin/bash", "/shell-hook.sh"]
+                 
+                # Default command for "docker run"
+                CMD ["/bin/bash"]
+                '''.stripIndent()
+    }
+
+    def 'should create conda docker file with packages and pixi custom image'() {
+        given:
+        def CHANNELS = ['conda-forge', 'defaults']
+        def PIXI_OPTS = new PixiOpts(
+                basePackages: 'foo::one bar::two',
+                baseImage: 'base/image',
+                pixiImage: 'ghcr.io/prefix-dev/pixi:0.47.0-jammy-cuda-12.8.1')
+        def PACKAGES = ['bwa=0.7.15', 'salmon=1.1.1']
+        def packages = new PackagesSpec(
+                type: PackagesSpec.Type.CONDA,
+                entries:  PACKAGES,
+                channels: CHANNELS,
+                pixiOpts: PIXI_OPTS)
+        and:
+        def req = new SubmitContainerTokenRequest(packages:packages, buildTemplate: 'pixi/v1')
+        when:
+        def result = ContainerHelper.containerFileFromRequest(req)
+
+        then:
+        result =='''\
+                FROM ghcr.io/prefix-dev/pixi:0.47.0-jammy-cuda-12.8.1 AS build
+                 
+                COPY conda.yml /opt/wave/conda.yml
+                WORKDIR /opt/wave
+                 
+                RUN pixi init --import /opt/wave/conda.yml \\
+                    && pixi add foo::one bar::two \\
+                    && pixi shell-hook > /shell-hook.sh \\
+                    && echo 'exec "$@"' >> /shell-hook.sh \\
+                    && echo ">> CONDA_LOCK_START" \\
+                    && cat /opt/wave/pixi.lock \\
+                    && echo "<< CONDA_LOCK_END"
+                 
+                FROM base/image AS prod
+                 
+                # copy the pixi environment in the final container
+                COPY --from=build /opt/wave/.pixi/envs/default /opt/wave/.pixi/envs/default
+                COPY --from=build /shell-hook.sh /shell-hook.sh
+                 
+                # set the entrypoint to the shell-hook script (activate the environment and run the command)
+                # no more pixi needed in the prod container
+                ENTRYPOINT ["/bin/bash", "/shell-hook.sh"]
+                 
+                # Default command for "docker run"
+                CMD ["/bin/bash"]
+                '''.stripIndent()
+    }
 }