From 335701e3ee256b678e8949987ce2ea7335b50623 Mon Sep 17 00:00:00 2001 From: Jorge Ejarque Date: Mon, 9 Dec 2024 21:02:33 +0100 Subject: [PATCH 1/3] Fixing getRepositoryUrl when project name is not provided (#5560) Signed-off-by: jorgee Signed-off-by: Paolo Di Tommaso Co-authored-by: Paolo Di Tommaso --- .../main/groovy/nextflow/scm/AzureRepositoryProvider.groovy | 4 +++- .../groovy/nextflow/scm/AzureRepositoryProviderTest.groovy | 2 +- 2 files changed, 4 insertions(+), 2 deletions(-) diff --git a/modules/nextflow/src/main/groovy/nextflow/scm/AzureRepositoryProvider.groovy b/modules/nextflow/src/main/groovy/nextflow/scm/AzureRepositoryProvider.groovy index a8cb617bf9..8435099ebf 100644 --- a/modules/nextflow/src/main/groovy/nextflow/scm/AzureRepositoryProvider.groovy +++ b/modules/nextflow/src/main/groovy/nextflow/scm/AzureRepositoryProvider.groovy @@ -35,6 +35,7 @@ final class AzureRepositoryProvider extends RepositoryProvider { private String user private String repo + private String urlPath; private String continuationToken AzureRepositoryProvider(String project, ProviderConfig config=null) { @@ -42,6 +43,7 @@ final class AzureRepositoryProvider extends RepositoryProvider { Azure repo format follows Organization/Project/Repository where Project can be optional If Project is not present then Repository is used as Project (and also as Repository) */ + this.urlPath = project def tokens = project.tokenize('/') this.repo = tokens.removeLast() if( tokens.size() == 1){ @@ -164,7 +166,7 @@ final class AzureRepositoryProvider extends RepositoryProvider { /** {@inheritDoc} */ @Override String getRepositoryUrl() { - "${config.server}/$project" + "${config.server}/${urlPath}" } /** {@inheritDoc} */ diff --git a/modules/nextflow/src/test/groovy/nextflow/scm/AzureRepositoryProviderTest.groovy b/modules/nextflow/src/test/groovy/nextflow/scm/AzureRepositoryProviderTest.groovy index 00e7cc74f0..decec42c1d 100644 --- a/modules/nextflow/src/test/groovy/nextflow/scm/AzureRepositoryProviderTest.groovy +++ b/modules/nextflow/src/test/groovy/nextflow/scm/AzureRepositoryProviderTest.groovy @@ -80,7 +80,7 @@ class AzureRepositoryProviderTest extends Specification { def obj = new ProviderConfig('azurerepos', config.providers.azurerepos as ConfigObject) expect: - new AzureRepositoryProvider('ORGANIZATION/PROJECT/hello', obj).getRepositoryUrl() == 'https://dev.azure.com/ORGANIZATION/PROJECT' + new AzureRepositoryProvider('ORGANIZATION/PROJECT/hello', obj).getRepositoryUrl() == 'https://dev.azure.com/ORGANIZATION/PROJECT/hello' } From b23e42cd6dea0e4ce6bba19c13968546807be5f1 Mon Sep 17 00:00:00 2001 From: Ben Sherman Date: Tue, 10 Dec 2024 04:40:27 -0600 Subject: [PATCH 2/3] Fix docs for `csi` option in `pod` directive (#5585) [ci skip] Signed-off-by: Ben Sherman --- docs/reference/process.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/docs/reference/process.md b/docs/reference/process.md index 95a9456ef8..7383c8d5eb 100644 --- a/docs/reference/process.md +++ b/docs/reference/process.md @@ -1078,11 +1078,11 @@ The following options are available: : *Can be specified multiple times* : Mounts a [ConfigMap](https://kubernetes.io/docs/tasks/configure-pod-container/configure-pod-configmap/) with name and optional key to the given path. If the key is omitted, the path is interpreted as a directory and all entries in the `ConfigMap` are exposed in that path. -`csi: '', mountPath: ''` +`csi: '', mountPath: ''` : :::{versionadded} 22.11.0-edge ::: : *Can be specified multiple times* -: Mounts a [CSI ephemeral volume](https://kubernetes.io/docs/concepts/storage/ephemeral-volumes/#csi-ephemeral-volumes) by name to the given path. +: Mounts a [CSI ephemeral volume](https://kubernetes.io/docs/concepts/storage/ephemeral-volumes/#csi-ephemeral-volumes) with the given configuration to the given path. `emptyDir: , mountPath: ''` : :::{versionadded} 22.11.0-edge From b325378f4b4bb4dc0eaae41888c846dce819f811 Mon Sep 17 00:00:00 2001 From: Christopher Hakkaart Date: Wed, 11 Dec 2024 13:38:12 +0100 Subject: [PATCH 3/3] Update broken link in docs (#5598) Signed-off-by: Christopher Hakkaart Co-authored-by: Ben Sherman --- docs/sharing.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/sharing.md b/docs/sharing.md index 61a840e9f8..6d49b4b159 100644 --- a/docs/sharing.md +++ b/docs/sharing.md @@ -14,7 +14,7 @@ You can configure your credentials for various Git providers in the Git configur ## Using a local repository -Nextflow can work with repositories stored in a local or shared file system. The repository must be created as a [bare repository](https://mijingo.com/blog/what-is-a-bare-git-repository). +Nextflow can work with repositories stored in a local or shared file system. The repository must be created as a [bare repository](https://craftquest.io/articles/what-is-a-bare-git-repository). For example, given a bare repository at `/shared/projects/foo.git`, Nextflow is able to run it using the following syntax: