update viash version

.github/workflows/build.yaml

@@ -16,6 +16,6 @@ on:
 
 jobs:
   build:
-    uses: openproblems-bio/actions/.github/workflows/build.yml@main
+    uses: viash-io/viash-actions/.github/workflows/build.yaml@v6
     with:
-      version: ${{ github.event.inputs.version }}
+      version: ${{ github.event.inputs.version }}

.github/workflows/test.yaml

@@ -8,4 +8,4 @@ on:
 
 jobs:
   build:
-    uses: openproblems-bio/actions/.github/workflows/test.yml@main
+    uses: viash-io/viash-actions/.github/workflows/test.yaml@v6

CHANGELOG.md

@@ -16,6 +16,8 @@
 
 * Updated `api` files (PR #5).
 
+* Updated configs, components and CI to the latest Viash version (PR #8).
+
 ## MINOR CHANGES
 
 * Updated `README.md` (PR #5).

_viash.yaml

@@ -1,37 +1,53 @@
-viash_version: 0.9.0-RC6
+viash_version: 0.9.0-RC7
 
 # Step 1: Change the name of the task.
 # example: task_name_of_this_task
 name: task_template
 organization: openproblems-bio
 version: dev
-# Step 2: Update the description to a short description of the task.
-description: |
-  An OpenProblems benchmark task.
+
 license: MIT
-# Step 3: Add keywords to describe the task.
+# Step 2: Add keywords to describe the task.
 keywords: [single-cell, openproblems, benchmark]
-# Step 4: Update the `task_template` to the name of the task from step 1.
+# Step 3: Update the `task_template` to the name of the task from step 1.
 links:
   issue_tracker: https://github.com/openproblems-bio/task_template/issues
   repository: https://github.com/openproblems-bio/task_template
   docker_registry: ghcr.io
-# Step 5: Update the info fields to the text from the task issue. 
+
+
+# Step 4: Update the label, summary and description.
+# A unique, human-readable, short label. Used for creating summary tables and visualisations.
+label: Template
+summary: A one sentence summary of purpose and methodology. Used for creating an overview tables.
+description: |
+  Provide a clear and concise description of your task, detailing the specific problem it aims
+  to solve. Outline the input data types, the expected output, and any assumptions or constraints.
+  Be sure to explain any terminology or concepts that are essential for understanding the task.
+
+  Explain the motivation behind your proposed task. Describe the biological or computational 
+  problem you aim to address and why it's important. Discuss the current state of research in
+  this area and any gaps or challenges that your task could help address. This section 
+  should convince readers of the significance and relevance of your task.
+
+# A list of references to relevant literature. Each reference should be a DOI or a bibtex entry
+references:
+  doi:
+    - 10.21203/rs.3.rs-4181617/v1
+  # bibtex:
+  #   - |
+  #     @article{doe_2021_template,
+  #       doi = {10.21203/rs.3.rs-4181617/v1},
+  #       url = {https://doi.org/10.21203/rs.3.rs-4181617/v1},
+  #       author = {Doe, John},
+  #       title = {A template for creating new tasks},
+  #       publisher = {Research Square},
+  #       year = {2021},
+  #     }
+
 info:
-  # A unique, human-readable, short label. Used for creating summary tables and visualisations.
-  label: Template
-  description: |
-    Provide a clear and concise description of your task, detailing the specific problem it aims
-    to solve. Outline the input data types, the expected output, and any assumptions or constraints.
-    Be sure to explain any terminology or concepts that are essential for understanding the task.
-  summary: A one sentence summary of purpose and methodology. Used for creating an overview tables.
-  motivation: |
-    Explain the motivation behind your proposed task. Describe the biological or computational 
-    problem you aim to address and why it’s important. Discuss the current state of research in
-    this area and any gaps or challenges that your task could help address. This section 
-    should convince readers of the significance and relevance of your task.
   image: The name of the image file to use for the component on the website.
-  # Step 6: Replace the task_template to the name of the task in `info.name`.
+  # Step 5: Replace the task_template to the name of the task.
   test_resources:
     - type: s3
       path: s3://openproblems-data/resources_test/task_template/
@@ -40,10 +56,10 @@ info:
       path: s3://openproblems-data/resources_test/common/
       dest: resources_test/common
 
-# Step 7: Update the authors of the task.
+# Step 6: Update the authors of the task.
 authors: 
   # Full name of the author, usually in the name of FirstName MiddleName LastName.
-  - name: Kai Waldrant 
+  - name: John Doe
     # Role of the author. Possible values:
     # 
     # * `"author"`: Authors who have made substantial contributions to the component.
@@ -52,13 +68,20 @@ authors:
     roles: [ "author", "maintainer" ]
     # Additional information on the author
     info: 
-      github: KaiWaldrant
-      orcid: 0009-0003-8555-1361
-      email: ...
-      twitter: ...
-      linkedin: ...
-# Step 8: Remove all of the comments of the steps you completed
-# Step 9: High five yourself!
+      github: johndoe
+      orcid: 0000-0000-0000-0000
+      email: [email protected]
+      twitter: johndoe
+      linkedin: johndoe
+
+# Step 7: Remove all of the comments of the steps you completed
+# Step 8: High five yourself!
 
 config_mods: |
   .runners[.type == "nextflow"].config.labels := { lowmem : "memory = 20.Gb", midmem : "memory = 50.Gb", highmem : "memory = 100.Gb", lowcpu : "cpus = 5", midcpu : "cpus = 15", highcpu : "cpus = 30", lowtime : "time = 1.h", midtime : "time = 4.h", hightime : "time = 8.h", veryhightime : "time = 24.h" }
+
+repositories:
+  - name: openproblems-v2
+    type: github
+    repo: openproblems-bio/openproblems-v2
+    tag: main_build

src/api/comp_control_method.yaml

@@ -32,7 +32,6 @@ test_resources:
   - type: python_script
     path: /common/component_tests/run_and_check_output.py
   - type: python_script
-    path: /common/component_tests/check_method_config.py
-  - path: /common/library.bib
+    path: /common/component_tests/check_config.py
   - path: /resources_test/task_template/pancreas
     dest: resources_test/task_template/pancreas

src/api/comp_method.yaml

@@ -23,7 +23,6 @@ test_resources:
   - type: python_script
     path: /common/component_tests/run_and_check_output.py
   - type: python_script
-    path: /common/component_tests/check_method_config.py
-  - path: /common/library.bib
+    path: /common/component_tests/check_config.py
   - path: /resources_test/task_template/pancreas
     dest: resources_test/task_template/pancreas

src/api/comp_metric.yaml

@@ -20,10 +20,9 @@ arguments:
     direction: output
     required: true
 test_resources:
-  - type: python_script
-    path: /common/component_tests/check_metric_config.py
   - type: python_script
     path: /common/component_tests/run_and_check_output.py
-  - path: /common/library.bib
+  - type: python_script
+    path: /common/component_tests/check_config.py
   - path: /resources_test/task_template/pancreas
     dest: resources_test/task_template/pancreas

src/api/file_common_dataset.yaml

@@ -1,9 +1,10 @@
 type: file
 example: "resources_test/common/pancreas/dataset.h5ad"
+label: "Common Dataset"
+summary: A subset of the common dataset.
 info:
-  label: "Common Dataset"
-  summary: A subset of the common dataset.
-  slots:
+  format:
+    type: h5ad
     layers:
       - type: integer
         name: counts

src/api/file_prediction.yaml

@@ -1,10 +1,11 @@
 #TODO: Change to the required and/or optional fields of the anndata
 type: file
 example: "resources_test/task_template/pancreas/prediction.h5ad"
+label: "Predicted data"
+summary: A predicted dataset as output by a method.
 info:
-  label: "Predicted data"
-  summary: A predicted dataset as output by a method.
-  slots:
+  format:
+    type: h5ad
     obs:
       - type: string
         name: label_pred

src/api/file_score.yaml

@@ -1,10 +1,11 @@
+#TODO: Change to the required and/or optional fields of the anndata
 type: file
 example: resources/score.h5ad
+label: Score
+summary: "File indicating the score of a metric."
 info:
-  label: Score
-  summary: "File indicating the score of a metric."
-  file_type: h5ad
-  slots:
+  format:
+    type: h5ad
     uns:
       - type: string
         name: dataset_id

src/api/file_solution.yaml

@@ -1,9 +1,11 @@
+#TODO: Change to the required and/or optional fields of the anndata
 type: file
 example: "resources_test/task_template/pancreas/solution.h5ad"
+label: "Solution"
+summary: "The solution for the test data"
 info:
-  label: "Solution"
-  summary: "The solution for the test data"
-  slots:
+  format:
+    type: h5ad
     layers: 
       - type: integer
         name: counts

src/api/file_test_h5ad.yaml

@@ -1,10 +1,11 @@
 #TODO: Change to the required and/or optional fields of the anndata
 type: file
 example: "resources_test/task_template/pancreas/test.h5ad"
+label: "Test data"
+summary: The subset of molecules used for the test dataset
 info:
-  label: "Test data"
-  summary: The subset of molecules used for the test dataset
-  slots:
+  format:
+    type: h5ad
     layers: 
       - type: integer
         name: counts

src/api/file_train_h5ad.yaml

@@ -1,10 +1,11 @@
 #TODO: Change to the required and/or optional fields of the anndata
 type: file
 example: "resources_test/task_template/pancreas/train.h5ad"
+label: "Training data"
+summary: "The training data in h5ad format"
 info:
-  label: "Training data"
-  summary: "The training data in h5ad format"
-  slots:
+  format:
+    type: h5ad
     layers: 
       - type: integer
         name: counts

src/control_methods/true_labels/config.vsh.yaml

@@ -5,22 +5,22 @@
 #   - A unit test
 __merge__: ../../api/comp_control_method.yaml
 
-
 # A unique identifier for your component (required).
 # Can contain only lowercase letters or underscores.
 name: true_labels
 
+# A relatively short label, used when rendering visualisations (required)
+label: True Labels
+# A one sentence summary of how this method works (required). Used when 
+# rendering summary tables.
+summary: "a positive control, solution labels are copied 1 to 1 to the predicted data."
+# A multi-line description of how this component works (required). Used
+# when rendering reference documentation.
+description: |
+  A positive control, where the solution labels are copied 1 to 1 to the predicted data.
+
 # Metadata for your component
 info:
-  # A relatively short label, used when rendering visualisations (required)
-  label: True Labels
-  # A one sentence summary of how this method works (required). Used when 
-  # rendering summary tables.
-  summary: "a positive control, solution labels are copied 1 to 1 to the predicted data."
-  # A multi-line description of how this component works (required). Used
-  # when rendering reference documentation.
-  description: |
-    A positive control, where the solution labels are copied 1 to 1 to the predicted data.
   # Which normalisation method this component prefers to use (required).
   preferred_normalization: counts
 
@@ -43,7 +43,7 @@ resources:
 engines:
   # Specifications for the Docker image for this component.
   - type: docker
-    image: ghcr.io/openproblems-bio/base_images/python:1.1.0
+    image: openproblems/base_python:1.0.0
     # Add custom dependencies here (optional). For more information, see
     # https://viash.io/reference/config/engines/docker/#setup .
     # setup:
@@ -56,4 +56,4 @@ runners:
   # Allows turning the component into a Nextflow module / pipeline.
   - type: nextflow
     directives:
-      label: [midtime,lowmem,lowcpu]
+      label: [midtime, lowmem, lowcpu]

src/data_processors/process_dataset/config.vsh.yaml

@@ -21,14 +21,14 @@ arguments:
 resources:
   - type: python_script
     path: script.py
-  - path: /common/helper_functions/subset_anndata.py
+  - path: /common/helper_functions/subset_h5ad_by_format.py
 
 engines:
   - type: docker
-    image: ghcr.io/openproblems-bio/base_images/python:1.1.0
+    image: openproblems/base_python:1.0.0
 
 runners:
   - type: executable
   - type: nextflow
     directives:
-      label: [highmem,midcpu,midtime]
+      label: [highmem, midcpu, midtime]