Merge pull request #107 from viash-io/develop

Viash 0.5.10

.gitignore

@@ -1,21 +1,29 @@
+# build related
+bin/
+Makefile
+
+# sbt-related
 target/
-.bloop*
-.metals*
-projects/metals.sbt
-/bin/
-.cache-main
-.classpath
-.project
-.settings
+
+# Temporary files / folders
 output
-.cache-tests
-project/metals.sbt
 out/*
-Makefile
 
+# Rstudio-related
 .Rproj.user
 .Rhistory
 *.Rproj
+
+# Idea-related
 .idea
-project/metals.sbt
+.cache-main
+.cache-tests
+.classpath
+.project
+.settings
+
+# VS Code related
 .vscode/settings.json
+**/metals.sbt
+.bloop*
+.metals*

CHANGELOG.md

@@ -1,3 +1,40 @@
+# Viash 0.5.10
+
+## MAJOR CHANGES
+
+* `viash_install`:
+  - Added `--log_prefix`: This prefix is used to determine the path of the log files for `viash_build`, `viash_test` and `viash_push`.
+  - Added `--organization`: Id of the organisation to be used in the Docker image name, i.e. `<registry>/<organization>/<namespace><namespace_sep><name>`.
+  - Added `--target_image_source`: Url to the Git repo in which this project resides.
+  - Removed `--log`.
+
+* `viash_build`:
+  - Reduce code duplication by contructing the command with Bash Arrays.
+  - Renamed `--platforms` to `--platform`.
+  - Added `--organization`: Id of the organisation to be used in the Docker image name, i.e. `<registry>/<organization>/<namespace><namespace_sep><name>`.
+  - Added `--target_image_source`: Url to the Git repo in which this project resides.
+  - Changed default of `--log` from `log.txt` to `.viash_build_log.txt`.
+  - Added `--verbose`: Print out the underlying `viash ns build` command before running it.
+
+* `viash_test`:
+  - Reduce code duplication by contructing the command with Bash Arrays.
+  - Renamed `--platforms` to `--platform`.
+  - Added `--organization`: Id of the organisation to be used in the Docker image name, i.e. `<registry>/<organization>/<namespace><namespace_sep><name>`.
+  - Added `--target_image_source`: Url to the Git repo in which this project resides.
+  - Changed default of `--log` from `log.txt` to `.viash_test_log.txt`.
+  - Changed default of `--tsv` from `log.tsv` to `.viash_test_log.tsv`.
+  - Added `--verbose`: Print out the underlying `viash ns test` command before running it.
+
+* `viash_push`:
+  - Reduce code duplication by contructing the command with Bash Arrays.
+  - Added `--organization`: Id of the organisation to be used in the Docker image name, i.e. `<registry>/<organization>/<namespace><namespace_sep><name>`.
+  - Changed default of `--log` from `log.txt` to `.viash_push_log.txt`.
+  - Added `--verbose`: Print out the underlying `viash ns build` command before running it.
+
+## MINOR CHANGES
+
+* `NextflowPlatform`: Added the `organization` field to the nextflow platform as well.
+
 # Viash 0.5.9
 
 ## NEW FEATURES

build.sbt

@@ -1,6 +1,6 @@
 name := "viash"
 
-version := "0.5.9"
+version := "0.5.10"
 
 scalaVersion := "2.12.10"
 

src/main/scala/com/dataintuitive/viash/platforms/NextFlowPlatform.scala

@@ -33,6 +33,7 @@ case class NextFlowPlatform(
   tag: Option[Version] = None,
   version: Option[Version] = None,
   registry: Option[String] = None,
+  organization: Option[String] = None,
   namespace_separator: String = "_",
   executor: Option[String] = None,
   publish: Option[Boolean] = None,
@@ -63,6 +64,7 @@ case class NextFlowPlatform(
     val imageInfo = Docker.getImageInfo(
       functionality = Some(functionality),
       registry = registry,
+      organization = organization,
       name = image,
       tag = tag.map(_.toString),
       namespaceSeparator = namespace_separator

src/viash/viash_build/config.vsh.yaml

@@ -1,7 +1,6 @@
 functionality:
   name: viash_build
   namespace: viash
-  version: 0.1
   description: |
     Build a project, usually in the context of a pipeline.
   arguments:
@@ -15,39 +14,53 @@ functionality:
     type: string
     description: "The mode to run in. Possible values are: 'development', 'integration', 'release'."
     default: development
-  - name: "--platforms"
+  - name: "--platform"
     alternatives: [ "-p" ]
     type: string
-    description: "Which platforms to test, default is 'docker|nextflow'."
-    default: "docker|nextflow"
+    description: "Which platforms to process."
+    example: "docker|nextflow"
   - name: "--query"
     alternatives: [ "-q" ]
     type: string
-    description: "Filter which components get selected by name and namespace. Can be a regex. Example: '^mynamespace/component1$'."
+    description: "Filter which components get selected by name and namespace. Can be a regex."
+    example: "^mynamespace/component1$"
   - name: "--query_namespace"
     alternatives: [ "-n" ]
     type: string
-    description: "Filter which namespaces get selected by namespace. Can be a regex. Example: '^mynamespace$'."
+    description: "Filter which namespaces get selected by namespace. Can be a regex."
+    example: "^mynamespace$"
   - name: "--query_name"
     type: string
-    description: "Filter which components get selected by name. Can be a regex. Example: '^component1'."
+    description: "Filter which components get selected by name. Can be a regex."
+    example: "^component1$"
   - name: "--tag"
     alternatives: [ "-t" ]
     type: string
     description: The tag/version to be used.
-    default: "dev"
+    example: "0.1.0"
   - name: "--registry"
     alternatives: [ "-r" ]
-    default: ""
+    example: ghcr.io
     type: string
-    description: Docker registry to use, only used when using a registry.
+    description: Which Docker registry to use in the Docker image name.
+  - name: "--organization"
+    alternatives: [ "-o", "--organisation" ]
+    example: myorganisation
+    type: string
+    description: Which organisation name to use in the Docker image name.
+  - name: "--target_image_source"
+    alternatives: [ "-tis" ]
+    type: string
+    description: Which image source to specify in the component builds.
+    example: https://github.com/myorganisation/myrepository
   - name: "--namespace_separator"
-    default: "_"
+    example: "_"
     type: string
     description: The separator to use between the component name and namespace as the image name of a Docker container.
   - name: "--max_threads"
     type: integer
-    description: The maximum number of threads viash will use when `--parallell` during parallel tasks.
+    description: The maximum number of threads viash will use when `--parallel` during parallel tasks.
+    example: 8
   - name: "--config_mod"
     alternatives: [ "-c" ]
     type: string
@@ -62,11 +75,14 @@ functionality:
     alternatives: [ "-l" ]
     type: file
     description: Log file
-    default: log.txt
+    example: .viash_build_log.txt
     direction: output
   - name: "--viash"
     type: file
     description: A path to the viash executable. If not specified, this component will look for 'viash' on the $PATH.
+  - name: "--verbose"
+    type: boolean_true
+    description: "Increase verbosity."
   resources:
     - type: bash_script
       path: script.sh