Fix onboarding: broken links, run scripts, thumbnail

CHANGELOG.md

@@ -33,5 +33,11 @@
 
 * Updated the `common` submodule (PR #19).
 
+* Fixed broken documentation links in `README.md` and `CONTRIBUTING.md`, and added a quickstart to the README (PR #21).
+
+* `run_test_local.sh` now runs as-is on the template's test resources (PR #21).
+
+* Added a placeholder `thumbnail.svg` and scoped the common test resources to `cxg_mouse_pancreas_atlas` (PR #21).
+
 ## BUGFIXES
 

CONTRIBUTING.md

@@ -68,7 +68,7 @@ This will create a new method in `src/methods/my_method`. Next, you should:
 * Implement the method's code
 * Run the unit test
 
-Please review our documentation on [creating a new method](https://openproblems.bio/documentation/create_component/add_a_method) for more information on how to do this.
+Please review our documentation on [creating a new method](https://openproblems.bio/documentation/create_component/add-a-method/) for more information on how to do this.
 
 
 ### Creating a new metric
@@ -96,7 +96,7 @@ This will create a new metric in `src/metrics/my_metric`. Next, you should:
 * Implement the metric's code
 * Run the unit test
 
-Please review our documentation on [creating a new metric](https://openproblems.bio/documentation/create_component/add_a_metric) for more information.
+Please review our documentation on [creating a new metric](https://openproblems.bio/documentation/create_component/add-a-metric/) for more information.
 
 
 ## Frequently used commands
@@ -141,8 +141,8 @@ viash ns test --parallel
 
 ### Running the benchmark
 
-To run the benchmark, you can use the following command:
+To run the benchmark on the test resources, you can use the following command:
 
 ```bash
-scripts/run_benchmark/run.sh
+scripts/run_benchmark/run_test_local.sh
 ```

README.md

@@ -9,7 +9,7 @@ This repo is a template to create a new task for the OpenProblems v2. This repo
 
 > [!IMPORTANT] 
 > Before creating a new repository, make sure you are part of the OpenProblems task team. This will be done when you create an issue for the task and you get the go ahead to create the task.
-> For more information on how to create a new task, check out the [Create a new task](https://openproblems.bio/documentation/create_task/) documentation.
+> For more information on how to create a new task, check out the [Create a new task](https://openproblems.bio/documentation/create_task/getting-started/) documentation.
 
 The instructions below will guide you through creating a new repository from this template ([creating-a-repository-from-a-template](https://docs.github.com/en/repositories/creating-and-managing-repositories/creating-a-repository-from-a-template#creating-a-repository-from-a-template)).
 
@@ -32,6 +32,22 @@ git clone --recursive git@github.com:openproblems-bio/<repo_name>.git
 
 ## What to do next
 
-Check out the [instructions](https://github.com/openproblems-bio/common_resources/blob/main/INSTRUCTIONS.md) for more information on how to update the example files and components. These instructions also contain information on how to build out the task and basic commands.
+Check out the [task instructions](https://github.com/openproblems-bio/common_resources/blob/main/TASK_INSTRUCTIONS.md) for more information on how to update the example files and components. These instructions also contain information on how to build out the task and basic commands.
+
+To verify that everything works as-is before making changes, run:
+
+```bash
+# download the test resources
+scripts/sync_resources.sh
+
+# build the components and docker images
+viash ns build --parallel --setup cachedbuild
+
+# run the unit tests
+viash ns test --parallel
+
+# run the benchmark on the test resources
+scripts/run_benchmark/run_test_local.sh
+```
 
 For more information on the OpenProblems v2, check out the [documentation](https://openproblems.bio/documentation/).

_viash.yaml

@@ -46,17 +46,20 @@ references:
   #     }
 
 info:
-  image: The name of the image file to use for the component on the website.
-  # Step 5: Replace the task_template to the name of the task.
+  # Step 5: Replace the thumbnail with an image of your task. Should be an
+  # *.svg file renderable to 450x150 px.
+  image: thumbnail.svg
+  # Step 6: Replace the task_template to the name of the task, and the common
+  # dataset to the dataset(s) your task uses.
   test_resources:
     - type: s3
-      path: s3://openproblems-data/resources_test/common/
-      dest: resources_test/common
+      path: s3://openproblems-data/resources_test/common/cxg_mouse_pancreas_atlas/
+      dest: resources_test/common/cxg_mouse_pancreas_atlas
     - type: s3
       path: s3://openproblems-data/resources_test/task_template/
       dest: resources_test/task_template
 
-# Step 6: Update the authors of the task.
+# Step 7: Update the authors of the task.
 authors: 
   # Full name of the author, usually in the name of FirstName MiddleName LastName.
   - name: John Doe
@@ -74,7 +77,7 @@ authors:
       twitter: johndoe
       linkedin: johndoe
 
-# Step 7: Remove all of the comments of the steps you completed
+# Step 8: Remove all of the comments of the steps you completed
 
 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" }
@@ -83,6 +86,6 @@ repositories:
   - name: openproblems
     type: github
     repo: openproblems-bio/openproblems
-    tag: build/main # Step 8: Set this to the latest release
+    tag: build/main # Step 9: Set this to the latest release
 
-# Step 9: High five yourself!
+# Step 10: High five yourself!

scripts/run_benchmark/run_full_local.sh

@@ -11,12 +11,11 @@ cd "$REPO_ROOT"
 # please refer to the nextflow information for more details:
 # https://www.nextflow.io/docs/latest/
 
-# remove this when you have implemented the script
-echo "TODO: once the 'run_benchmark' workflow has been implemented, update this script to use it."
-echo "  Step 1: replace 'task_template' with the name of the task in the following command."
-echo "  Step 2: replace the rename keys parameters to fit your run_benchmark inputs"
-echo "  Step 3: replace the settings parameter to fit your run_benchmark outputs"
-echo "  Step 4: remove this message"
+# remove this when you have updated the script for your task
+echo "TODO: update this script to fit your task."
+echo "  Step 1: replace 'task_template' with the name of the task in the commands below."
+echo "  Step 2: update the rename keys to match the run_benchmark workflow inputs."
+echo "  Step 3: remove this message."
 exit 1
 
 set -e

scripts/run_benchmark/run_full_seqeracloud.sh

@@ -6,12 +6,11 @@ REPO_ROOT=$(git rev-parse --show-toplevel)
 # ensure that the command below is run from the root of the repository
 cd "$REPO_ROOT"
 
-# remove this when you have implemented the script
-echo "TODO: once the 'run_benchmark' workflow has been implemented, update this script to use it."
-echo "  Step 1: replace 'task_template' with the name of the task in the following command."
-echo "  Step 2: replace the rename keys parameters to fit your run_benchmark inputs"
-echo "  Step 3: replace the settings parameter to fit your run_benchmark outputs"
-echo "  Step 4: remove this message"
+# remove this when you have updated the script for your task
+echo "TODO: update this script to fit your task."
+echo "  Step 1: replace 'task_template' with the name of the task in the commands below."
+echo "  Step 2: update the rename keys to match the run_benchmark workflow inputs."
+echo "  Step 3: remove this message."
 exit 1
 
 set -e

scripts/run_benchmark/run_test_local.sh

@@ -6,13 +6,9 @@ REPO_ROOT=$(git rev-parse --show-toplevel)
 # ensure that the command below is run from the root of the repository
 cd "$REPO_ROOT"
 
-# remove this when you have implemented the script
-echo "TODO: once the 'run_benchmark' workflow has been implemented, update this script to use it."
-echo "  Step 1: replace 'task_template' with the name of the task in the following command."
-echo "  Step 2: replace the rename keys parameters to fit your run_benchmark inputs"
-echo "  Step 3: replace the settings parameter to fit your run_benchmark outputs"
-echo "  Step 4: remove this message"
-exit 1
+# NOTE: this script works as-is on the template's test resources.
+# When adapting the template to a new task, replace 'task_template' in the
+# paths below and update the arguments to match your run_benchmark workflow.
 
 set -e
 

scripts/run_benchmark/run_test_seqeracloud.sh

@@ -6,12 +6,11 @@ REPO_ROOT=$(git rev-parse --show-toplevel)
 # ensure that the command below is run from the root of the repository
 cd "$REPO_ROOT"
 
-# remove this when you have implemented the script
-echo "TODO: once the 'run_benchmark' workflow has been implemented, update this script to use it."
-echo "  Step 1: replace 'task_template' with the name of the task in the following command."
-echo "  Step 2: replace the rename keys parameters to fit your run_benchmark inputs"
-echo "  Step 3: replace the settings parameter to fit your run_benchmark outputs"
-echo "  Step 4: remove this message"
+# remove this when you have updated the script for your task
+echo "TODO: update this script to fit your task."
+echo "  Step 1: replace 'task_template' with the name of the task in the commands below."
+echo "  Step 2: update the parameters to match the run_benchmark workflow inputs."
+echo "  Step 3: remove this message."
 exit 1
 
 set -e