update to viash 0.9.0-RC2 (viash-hub#15)

* fix argument issues

* update to viash 0.9.0-RC1

* move links and reference into info for now

* try to use ns-list without platform

* update reference to references

* update pear

* update busco to viash 0.9.0

* update json schema

* remove functionality:

* remove info:

* change platforms into engines and runners

* add dependabot

* fix matrix jq query

* try with patched viash actions

* try to get the ci to work

* fix

* another attempt

* fix

.github/dependabot.yml

@@ -0,0 +1,6 @@
+version: 2
+updates:
+  - package-ecosystem: "github-actions"
+    directory: "/"
+    schedule:
+      interval: "daily"

.github/workflows/test.yaml

@@ -48,34 +48,45 @@ jobs:
       run: |
         LANG=C viash ns list > /dev/null
 
-    - name: Get changed files
-      id: changed-files
-      uses: tj-actions/changed-files@v42
-      with:
-        separator: ";"
-        diff_relative: true
-
-    - id: ns_list
-      uses: viash-io/viash-actions/ns-list@v5
-      with:
-        platform: docker
-        format: json
-        query: ^(?!workflows)
+    # see https://github.com/viash-io/viash/issues/654
+    # and https://github.com/viash-io/viash-actions/pull/27
+    # - name: Get changed files
+    #   id: changed-files
+    #   uses: tj-actions/changed-files@v42
+    #   with:
+    #     separator: ";"
+    #     diff_relative: true
+    # - id: ns_list
+    #   uses: viash-io/viash-actions/ns-list@v5
+    #   with:
+    #     platform: docker
+    #     format: json
+    #     query: ^(?!workflows)
+    # - id: ns_list_filtered
+    #   uses: viash-io/viash-actions/project/detect-changed-components@v5
+    #   with:
+    #     input_file: "${{ steps.ns_list.outputs.output_file }}"
+    # - id: set_matrix
+    #   run: |
+    #     echo "matrix=$(jq -c '[ .[] | 
+    #       { 
+    #         "name": (.functionality.namespace + "/" + .functionality.name),
+    #         "config": .info.config,
+    #         "dir": .info.config | capture("^(?<dir>.*\/)").dir
+    #       }
+    #     ]' ${{ contains(steps.get_head_commit_message.outputs.HEAD_COMMIT_MESSAGE, 'ci force') && steps.ns_list.outputs.output_file || steps.ns_list_filtered.outputs.output_file }} )" >> $GITHUB_OUTPUT
 
-    - id: ns_list_filtered
-      uses: viash-io/viash-actions/project/detect-changed-components@v5
-      with:
-        input_file: "${{ steps.ns_list.outputs.output_file }}"
 
     - id: set_matrix
       run: |
+        viash ns list --format json > ns_list.json
         echo "matrix=$(jq -c '[ .[] | 
           { 
-            "name": (.functionality.namespace + "/" + .functionality.name),
-            "config": .info.config,
-            "dir": .info.config | capture("^(?<dir>.*\/)").dir
+            "name": (.namespace + "/" + .name),
+            "config": .build_info.config,
+            "dir": .build_info.config | capture("^(?<dir>.*\/)").dir
           }
-        ]' ${{ contains(steps.get_head_commit_message.outputs.HEAD_COMMIT_MESSAGE, 'ci force') && steps.ns_list.outputs.output_file || steps.ns_list_filtered.outputs.output_file }} )" >> $GITHUB_OUTPUT
+        ]' ns_list.json )" >> $GITHUB_OUTPUT
 
   # phase 2
   viash_test: