Remove seqera from default Conda channels (#67)

Signed-off-by: Paolo Di Tommaso <[email protected]>

Author: pditommaso

README.md

@@ -117,7 +117,6 @@ docker run $container sh -c 'bamtools --version && samtools --version'
     cat << EOF > ./conda.yaml
     name: my-conda
     channels:
-    - defaults
     - bioconda
     - conda-forge
     dependencies:

app/src/main/java/io/seqera/wave/cli/App.java

@@ -158,7 +158,7 @@ public class App implements Runnable {
     private List<String> condaRunCommands;
 
     @Option(names = {"--conda-channels"}, paramLabel = "''", description = "Conda channels used to build the container (default: ${DEFAULT-VALUE}).")
-    private String condaChannels = "seqera,conda-forge,bioconda,defaults";
+    private String condaChannels = "conda-forge,bioconda";
 
     @Option(names = {"--spack-file"}, paramLabel = "''",  description = "A Spack file used to build the container e.g. /some/path/spack.yaml.")
     private String spackFile;

app/src/main/java/io/seqera/wave/cli/util/GptHelper.java

@@ -117,7 +117,7 @@ static protected PackagesSpec jsonToPackageSpec(String json) {
                 throw new IllegalArgumentException("Unable to resolve packages from json response: " + json);
             List<String> channels = (List<String>) object.get("channels");
             if( Checkers.isEmpty(channels) )
-                channels = List.of("bioconda","conda-forge","defaults");
+                channels = List.of("bioconda","conda-forge");
             return new PackagesSpec()
                     .withType(PackagesSpec.Type.CONDA)
                     .withEntries(packages)

app/src/test/groovy/io/seqera/wave/cli/AppCondaOptsTest.groovy

@@ -141,7 +141,7 @@ class AppCondaOptsTest extends Specification {
             '''.stripIndent(true)
         and:
         req.packages.condaOpts == new CondaOpts(mambaImage: CondaOpts.DEFAULT_MAMBA_IMAGE, basePackages: CondaOpts.DEFAULT_PACKAGES)
-        req.packages.channels == ['seqera', 'conda-forge', 'bioconda', 'defaults']
+        req.packages.channels == ['conda-forge', 'bioconda']
         and:
         !req.packages.entries
         and:
@@ -166,7 +166,7 @@ class AppCondaOptsTest extends Specification {
         req.packages.entries == ['foo']
         and:
         req.packages.condaOpts == new CondaOpts(mambaImage: CondaOpts.DEFAULT_MAMBA_IMAGE, basePackages: CondaOpts.DEFAULT_PACKAGES)
-        req.packages.channels == ['seqera', 'conda-forge', 'bioconda', 'defaults']
+        req.packages.channels == ['conda-forge', 'bioconda']
         and:
         !req.packages.environment
         and:
@@ -187,7 +187,7 @@ class AppCondaOptsTest extends Specification {
         req.packages.entries == ['https://host.com/file-lock.yml']
         and:
         req.packages.condaOpts == new CondaOpts(mambaImage: CondaOpts.DEFAULT_MAMBA_IMAGE, basePackages: CondaOpts.DEFAULT_PACKAGES)
-        req.packages.channels == ['seqera', 'conda-forge', 'bioconda', 'defaults']
+        req.packages.channels == ['conda-forge', 'bioconda']
         and:
         !req.packages.environment
         and:

app/src/test/groovy/io/seqera/wave/cli/util/GptHelperTest.groovy

@@ -45,6 +45,6 @@ class GptHelperTest extends Specification {
         when:
         def spec = GptHelper.grabPackages("Give me a container image for multiqc 1.15")
         then:
-        spec == new PackagesSpec(type: PackagesSpec.Type.CONDA, entries: ['multiqc=1.15'], channels: ['bioconda','conda-forge','defaults'])
+        spec == new PackagesSpec(type: PackagesSpec.Type.CONDA, entries: ['multiqc=1.15'], channels: ['bioconda','conda-forge'])
     }
 }