Revert "Add support for Pip packages (experimental)"

This reverts commit 3bced2f.

README.md

@@ -11,15 +11,15 @@ that it can be used in your Docker (replace-with-your-own-fav-container-engine)
 
 * Build container images on-demand for a given container file (aka Dockerfile);
 * Build container images on-demand based on one or more [Conda](https://conda.io/) packages;
-* Build container images on-demand based on one or more [Spack](https://spack.io/) packages (experimental);
-* Build container images on-demand based on one or more Pip packages (experimental);
+* Build container images on-demand based on one or more [Spack](https://spack.io/)  packages;
 * Build container images for a specified target platform (currently linux/amd64 and linux/arm64);
 * Push and cache built containers to a user-provided container repository;
 * Build Singularity native containers both using a Singularity spec file, Conda package(s) and Spack package(s);
 * Push Singularity native container images to OCI-compliant registries;
 
 ### Installation 
 
+
 #### Binary download 
 
 Download the Wave pre-compiled binary for your operating system from the 

app/build.gradle

@@ -22,7 +22,7 @@ repositories {
 
 dependencies {
     implementation 'io.seqera:wave-api:0.6.0'
-    implementation 'io.seqera:wave-utils:0.10.0'
+    implementation 'io.seqera:wave-utils:0.9.0'
     implementation 'info.picocli:picocli:4.6.1'
     implementation 'com.squareup.moshi:moshi:1.15.0'
     implementation 'com.squareup.moshi:moshi-adapters:1.14.0'

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

@@ -62,7 +62,6 @@
 import static io.seqera.wave.util.DockerHelper.addPackagesToSpackFile;
 import static io.seqera.wave.util.DockerHelper.condaFileFromPackages;
 import static io.seqera.wave.util.DockerHelper.condaFileFromPath;
-import static io.seqera.wave.util.DockerHelper.condaFileFromPipPackages;
 import static io.seqera.wave.util.DockerHelper.condaFileToDockerFile;
 import static io.seqera.wave.util.DockerHelper.condaFileToSingularityFile;
 import static io.seqera.wave.util.DockerHelper.condaPackagesToDockerFile;
@@ -149,12 +148,9 @@ public class App implements Runnable {
     @Option(names = {"--conda-file"}, paramLabel = "''", description = "A Conda file used to build the container e.g. /some/path/conda.yaml.")
     private String condaFile;
 
-    @Option(names = {"--conda-package", "--conda"}, paramLabel = "''", description = "One or more Conda packages used to build the container e.g. bioconda::samtools=1.17.")
+    @Option(names = {"--conda-package"}, paramLabel = "''", description = "One or more Conda packages used to build the container e.g. bioconda::samtools=1.17.")
     private List<String> condaPackages;
 
-    @Option(names = {"--pip-package", "--pip"}, paramLabel = "''", description = "One or more Pip packages used to build the container e.g. numpy.")
-    private List<String> pipPackages;
-
     @Option(names = {"--conda-base-image"}, paramLabel = "''", description = "Conda base image used to to build the container (default: ${DEFAULT-VALUE}).")
     private String condaBaseImage = CondaOpts.DEFAULT_MAMBA_IMAGE;
 
@@ -167,7 +163,7 @@ public class App implements Runnable {
     @Option(names = {"--spack-file"}, paramLabel = "''",  description = "A Spack file used to build the container e.g. /some/path/spack.yaml.")
     private String spackFile;
 
-    @Option(names = {"--spack-package", "--spack"}, paramLabel = "''", description = "One or more Spack packages used to build the container e.g. cowsay.")
+    @Option(names = {"--spack-package"}, paramLabel = "''", description = "One or more Spack packages used to build the container e.g. cowsay.")
     private List<String> spackPackages;
 
     @Option(names = {"--spack-run-command"}, paramLabel = "''",  description = "Dockerfile RUN commands used to build the container.")
@@ -284,7 +280,7 @@ protected void validateArgs() {
         if( !isEmpty(image) && !isEmpty(containerFile) )
             throw new IllegalCliArgumentException("Argument --image and --containerfile conflict each other - Specify an image name or a container file for the container to be provisioned");
 
-        if( isEmpty(image) && isEmpty(containerFile) && isEmpty(condaFile) && isEmpty(condaPackages) && isEmpty(spackFile) && isEmpty(spackPackages) && isEmpty(pipPackages) )
+        if( isEmpty(image) && isEmpty(containerFile) && isEmpty(condaFile) && condaPackages==null  && isEmpty(spackFile) && spackPackages ==null  )
             throw new IllegalCliArgumentException("Provide either a image name or a container file for the Wave container to be provisioned");
 
         if( freeze && isEmpty(buildRepository) )
@@ -309,25 +305,6 @@ protected void validateArgs() {
         if( condaPackages!=null && !isEmpty(containerFile) )
             throw new IllegalCliArgumentException("Option --conda-package and --containerfile conflict each other");
 
-        // -- check pip options
-        if( pipPackages!=null && !isEmpty(image) )
-            throw new IllegalCliArgumentException("Option --pip-package and --image conflict each other");
-
-        if( pipPackages!=null && !isEmpty(containerFile) )
-            throw new IllegalCliArgumentException("Option --pip-package and --containerfile conflict each other");
-
-        if( pipPackages!=null && condaPackages!=null )
-            throw new IllegalCliArgumentException("Option --pip-package and --conda-package conflict each other");
-
-        if( pipPackages!=null && spackPackages!=null )
-            throw new IllegalCliArgumentException("Option --pip-package and --spack-package conflict each other");
-
-        if( pipPackages!=null && !isEmpty(condaFile) )
-            throw new IllegalCliArgumentException("Option --pip-package and --conda-file conflict each other");
-
-        if( pipPackages!=null && !isEmpty(spackFile) )
-            throw new IllegalCliArgumentException("Option --pip-package and --spack-file conflict each other");
-
         // -- check spack options
         if( !isEmpty(spackFile) && spackPackages!=null )
             throw new IllegalCliArgumentException("Option --spack-file and --spack-package conflict each other");
@@ -571,7 +548,7 @@ protected String containerFileBase64() {
             return encodePathBase64(containerFile);
         }
 
-        if (!isEmpty(condaFile) || !isEmpty(condaPackages) || !isEmpty(pipPackages) ) {
+        if (!isEmpty(condaFile) || !isEmpty(condaPackages)) {
             String result;
             final String lock = condaLock();
             if (!isEmpty(lock)) {
@@ -610,11 +587,6 @@ else if (!isEmpty(condaPackages) && isEmpty(condaLock())) {
             final Path path = condaFileFromPackages(packages, condaChannels());
             return path != null ? encodePathBase64(path.toString()) : null;
         }
-        else if( !isEmpty(pipPackages) ) {
-            final String packages = pipPackages.stream().collect(Collectors.joining(" "));
-            final Path path = condaFileFromPipPackages(packages);
-            return path != null ? encodePathBase64(path.toString()) : null;
-        }
         else
             return null;
     }

app/src/main/resources/io/seqera/wave/cli/usage-examples.txt

@@ -15,9 +15,6 @@ Examples:
   # Build a container based on Conda lock file served via prefix.dev service
   wave --conda-package https://prefix.dev/envs/pditommaso/wave/conda-lock.yml
 
-  # Build a container based on Conda packages
-  wave --pip-package numpy --pip-package pandas
-
   # Build a container based on Spack packages
   wave --spack-package cowsay