Add clone deep option

Signed-off-by: Paolo Di Tommaso <[email protected]>
nextflow-io · Apr 22, 2023 · b44b645 · b44b645
1 parent a0e501b
commit b44b645
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Showing 5 changed files with 24 additions and 9 deletions.
diff --git a/docs/cli.rst b/docs/cli.rst
@@ -449,6 +449,8 @@ please refer to the ``nextflow pull`` command.
 +---------------------------+------------+--------------------------------------------------------------------------------+
 | Name, shorthand (if any)  | Default    | Description                                                                    |
 +===========================+============+================================================================================+
+| -d, -deep                 |            | Create a shallow clone of the specified depth.                                              |
++---------------------------+------------+--------------------------------------------------------------------------------+
 | -help, -h                 |  false     | Print the command usage.                                                       |
 +---------------------------+------------+--------------------------------------------------------------------------------+
 | -hub                      |  github    | Service hub where the project is hosted. Options: ``gitlab`` or ``bitbucket``  |
@@ -1045,6 +1047,8 @@ and modifies it accordingly. For downloading a pipeline into a local directory,
 | Name, shorthand (if any)  | Default    | Description                                                                    |
 +===========================+============+================================================================================+
 | -all                      |  false     | Update all downloaded projects.                                                |
++---------------------------+-------------+--------------------------------------------------------------------------------+
+| -d, -deep                 |            | Create a shallow clone of the specified depth.                                              |
 +---------------------------+------------+--------------------------------------------------------------------------------+
 | -help, -h                 |  false     | Print the command usage.                                                       |
 +---------------------------+------------+--------------------------------------------------------------------------------+
@@ -1115,6 +1119,8 @@ facilitates rapid iterations, inspections of any pipeline as well as debugging.
 +---------------------------+-------------+--------------------------------------------------------------------------------+
 | -cache                    |             | Enable/disable processes caching.                                              |
 +---------------------------+-------------+--------------------------------------------------------------------------------+
+| -deep                     |             | Create a shallow clone of the specified depth.                                              |
++---------------------------+-------------+--------------------------------------------------------------------------------+
 | -disable-jobs-cancellation|             | Prevent the cancellation of child jobs on execution termination                |
 +---------------------------+-------------+--------------------------------------------------------------------------------+
 | -dsl1                     | false       | Execute the workflow using DSL1 syntax.                                        |

diff --git a/modules/nextflow/src/main/groovy/nextflow/cli/CmdClone.groovy b/modules/nextflow/src/main/groovy/nextflow/cli/CmdClone.groovy
@@ -40,6 +40,9 @@ class CmdClone extends CmdBase implements HubOptions {
     @Parameter(names='-r', description = 'Revision to clone - It can be a git branch, tag or revision number')
     String revision
 
+    @Parameter(names=['-d','-deep'], description = 'Create a shallow clone of the specified depth')
+    Integer deep
+
     @Override
     final String getName() { NAME }
 
@@ -66,7 +69,7 @@ class CmdClone extends CmdBase implements HubOptions {
 
         manager.checkValidRemoteRepo()
         print "Cloning ${manager.project}${revision ? ':'+revision:''} ..."
-        manager.clone(target, revision)
+        manager.clone(target, revision, deep)
         print "\r"
         println "${manager.project} cloned to: $target"
     }

diff --git a/modules/nextflow/src/main/groovy/nextflow/cli/CmdPull.groovy b/modules/nextflow/src/main/groovy/nextflow/cli/CmdPull.groovy
@@ -43,7 +43,8 @@ class CmdPull extends CmdBase implements HubOptions {
     @Parameter(names=['-r','-revision'], description = 'Revision of the project to run (either a git branch, tag or commit SHA number)')
     String revision
 
-
+    @Parameter(names=['-d','-deep'], description = 'Create a shallow clone of the specified depth')
+    Integer deep
 
     @Override
     final String getName() { NAME }
@@ -75,7 +76,7 @@ class CmdPull extends CmdBase implements HubOptions {
             log.info "Checking $it ..."
             def manager = new AssetManager(it, this)
 
-            def result = manager.download(revision)
+            def result = manager.download(revision,deep)
             manager.updateModules()
 
             def scriptFile = manager.getScriptFile()

diff --git a/modules/nextflow/src/main/groovy/nextflow/cli/CmdRun.groovy b/modules/nextflow/src/main/groovy/nextflow/cli/CmdRun.groovy
@@ -137,6 +137,9 @@ class CmdRun extends CmdBase implements HubOptions {
     @Parameter(names=['-r','-revision'], description = 'Revision of the project to run (either a git branch, tag or commit SHA number)')
     String revision
 
+    @Parameter(names=['-d','-deep'], description = 'Create a shallow clone of the specified depth')
+    Integer deep
+
     @Parameter(names=['-latest'], description = 'Pull latest changes before run')
     boolean latest
 
@@ -522,7 +525,7 @@ class CmdRun extends CmdBase implements HubOptions {
             if( offline )
                 throw new AbortOperationException("Unknown project `$repo` -- NOTE: automatic download from remote repositories is disabled")
             log.info "Pulling $repo ..."
-            def result = manager.download(revision)
+            def result = manager.download(revision,deep)
             if( result )
                 log.info " $result"
             checkForUpdate = false

diff --git a/modules/nextflow/src/main/groovy/nextflow/scm/AssetManager.groovy b/modules/nextflow/src/main/groovy/nextflow/scm/AssetManager.groovy
@@ -572,7 +572,7 @@ class AssetManager {
      * @param revision The revision to download
      * @result A message representing the operation result
      */
-    String download(String revision=null) {
+    String download(String revision=null, Integer deep=null) {
         assert project
 
         /*
@@ -594,9 +594,10 @@ class AssetManager {
             clone
                 .setURI(cloneURL)
                 .setDirectory(localPath)
-                .setDepth(1)
                 .setCloneSubmodules(manifest.recurseSubmodules)
-                .call()
+            if( deep )
+                clone.setDepth(deep)
+            clone.call()
 
             if( revision ) {
                 // use an explicit checkout command *after* the clone instead of cloning a specific branch
@@ -664,7 +665,7 @@ class AssetManager {
      * @param directory The folder when the pipeline will be cloned
      * @param revision The revision to be cloned. It can be a branch, tag, or git revision number
      */
-    void clone(File directory, String revision = null) {
+    void clone(File directory, String revision = null, Integer deep=null) {
 
         def clone = Git.cloneRepository()
         def uri = getGitRepositoryUrl()
@@ -682,7 +683,8 @@ class AssetManager {
 
         if( revision )
             clone.setBranch(revision)
-
+        if( deep )
+            clone.setDepth(deep)
         clone.call()
     }