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Implementation of multiple revisions without revisions map #6620

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bbffdb7
replace revision map by bare repo, file mutex to prevent concurrent c…
jorgee Dec 1, 2025
0c546f9
reduce complexity in list and drop commands
jorgee Dec 2, 2025
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4 changes: 4 additions & 0 deletions docs/reference/cli.md
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Original file line number Diff line number Diff line change
Expand Up @@ -1174,6 +1174,8 @@ The `pull` command downloads a pipeline from a Git-hosting platform into the glo
: Update all downloaded projects.

`-d, -deep`
: :::{deprecated} 25.11.X-edge
:::
: Create a shallow clone of the specified depth.

`-h, -help`
Expand Down Expand Up @@ -1251,6 +1253,8 @@ The `run` command is used to execute a local pipeline script or remote pipeline
: Enable/disable processes caching.

`-d, -deep`
: :::{deprecated} 25.11.X-edge
:::
: Create a shallow clone of the specified depth.

`-disable-jobs-cancellation`
Expand Down
18 changes: 10 additions & 8 deletions modules/nextflow/src/main/groovy/nextflow/cli/CmdDrop.groovy
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Expand Up @@ -16,8 +16,6 @@

package nextflow.cli

import static nextflow.scm.AssetManager.DEFAULT_REVISION_DIRNAME

import com.beust.jcommander.Parameter
import com.beust.jcommander.Parameters
import groovy.transform.CompileStatic
Expand All @@ -44,7 +42,7 @@ class CmdDrop extends CmdBase {
@Parameter(names=['-r','-revision'], description = 'Revision of the project to drop (either a git branch, tag or commit SHA number)')
String revision

@Parameter(names=['-a','-all-revisions'], description = 'For specified project, drop all revisions')
@Parameter(names=['-a','-all'], description = 'For specified project, drop all pulled commits')
Boolean allRevisions

@Parameter(names='-f', description = 'Delete the repository without taking care of local changes')
Expand All @@ -60,17 +58,21 @@ class CmdDrop extends CmdBase {
List<AssetManager> dropList = []
if ( allRevisions ) {
def revManager = new AssetManager(args[0])
revManager.listRevisions().each { rev ->
if( rev == DEFAULT_REVISION_DIRNAME )
rev = null
if( !revManager.localRootPath.exists() ) {
throw new AbortOperationException("No match found for: ${revManager.getProjectWithRevision()}")
}
revManager.listCommits().each { rev ->
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@pditommaso pditommaso Dec 1, 2025

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Let's try reducing the cyclomatic complexity of this method, splitting in smaller self-describing private methods.

dropList << new AssetManager(args[0]).setRevisionAndLocalPath(args[0], rev)
}
} else {
dropList << new AssetManager(args[0]).setRevisionAndLocalPath(args[0], revision)
}

if ( !dropList ) {
throw new AbortOperationException("No revisions found for specified project: ${args[0]}")
if ( allRevisions && force ) // When removing all revision with 'force' not throw the exception to remove the project folder
log.warn("No revisions found for specified project: ${args[0]}")
else
throw new AbortOperationException("No revisions found for specified project: ${args[0]}")
}

dropList.each { manager ->
Expand All @@ -82,7 +84,6 @@ class CmdDrop extends CmdBase {
manager.close()
if( !manager.localPath.deleteDir() )
throw new AbortOperationException("Unable to delete project `${manager.getProjectWithRevision()}` -- Check access permissions for path: ${manager.localPath}")
manager.pruneRevisionMap(manager.revision)
return
}

Expand All @@ -91,6 +92,7 @@ class CmdDrop extends CmdBase {

if ( allRevisions ) {
def revManager = new AssetManager(args[0])
log.info("Removing directory ${revManager.localRootPath.absolutePath}")
revManager.localRootPath.deleteDir()
}
}
Expand Down
60 changes: 27 additions & 33 deletions modules/nextflow/src/main/groovy/nextflow/cli/CmdList.groovy
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Expand Up @@ -16,8 +16,6 @@

package nextflow.cli

import static nextflow.scm.AssetManager.DEFAULT_REVISION_DIRNAME

import com.beust.jcommander.Parameter
import com.beust.jcommander.Parameters
import groovy.transform.CompileStatic
Expand Down Expand Up @@ -60,39 +58,35 @@ class CmdList extends CmdBase {
return
}

if( moreDetailed )
detailed = true
if( detailed && allRevisions ) {
all.each{
println(" $it")
def revManager = new AssetManager(it)
revManager.listRevisionsAndCommits().each{ k,v ->
if( k == DEFAULT_REVISION_DIRNAME )
k = '(default)'
if( !moreDetailed )
v = v.substring(0,10)
println(" $v $k") }
}
}
else if( allRevisions ) {
all.each{
println(" $it")
def revManager = new AssetManager(it)
revManager.listRevisions().each{
if( it == DEFAULT_REVISION_DIRNAME )
it = '(default)'
println(" $it")
if( moreDetailed )
detailed = true
if( detailed && allRevisions ) {
all.each {
println(" $it")
def revManager = new AssetManager(it)
revManager.listRevisionsAndCommits().each { k, v ->
if( !moreDetailed )
v = v.substring(0, 10)
println(" $v $k")
}
}
} else if( allRevisions ) {
all.each {
println(" $it")
def revManager = new AssetManager(it)
revManager.listRevisions().each {
println(" $it")
}
}
} else if( allCommits ) {
all.each {
println(" $it")
def revManager = new AssetManager(it)
revManager.listCommits().each { println(" $it") }
}
} else {
all.each { println(" $it") }
}
} else if( allCommits ) {
all.each{
println(" $it")
def revManager = new AssetManager(it)
revManager.listCommits().each{ println(" $it") }
}
} else {
all.each{ println(" $it") }
}
}

}
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@pditommaso pditommaso Dec 1, 2025

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As above, try to make this logic more compact following "Reveal intention" pattern. https://claude.ai/share/32835bb7-8395-431e-a73f-53797de9aaf6

7 changes: 0 additions & 7 deletions modules/nextflow/src/main/groovy/nextflow/cli/CmdPull.groovy
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Expand Up @@ -16,8 +16,6 @@

package nextflow.cli

import static nextflow.scm.AssetManager.DEFAULT_REVISION_DIRNAME

import com.beust.jcommander.Parameter
import com.beust.jcommander.Parameters
import groovy.transform.CompileStatic
Expand Down Expand Up @@ -47,9 +45,6 @@ class CmdPull extends CmdBase implements HubOptions {
@Parameter(names=['-r','-revision'], description = 'Revision of the project to pull (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 }

Expand Down Expand Up @@ -81,8 +76,6 @@ class CmdPull extends CmdBase implements HubOptions {
all.each{ proj ->
def revManager = new AssetManager(proj)
revManager.listRevisions().each{ rev ->
if( rev == DEFAULT_REVISION_DIRNAME )
rev = null
list << new AssetManager(proj, this).setRevisionAndLocalPath(proj, rev)
}
}
Expand Down
3 changes: 0 additions & 3 deletions modules/nextflow/src/main/groovy/nextflow/cli/CmdRun.groovy
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Expand Up @@ -150,9 +150,6 @@ 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

Expand Down
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