Save integration logs in standard location

Author: irm-codebase

.github/workflows/template-pr-ci.yml

@@ -20,3 +20,9 @@ jobs:
         run: pixi run pytest tests/clio_test.py
       - name: Run linting
         run: pixi run snakemake --lint
+      - name: Archive integration test artifacts
+        uses: actions/upload-artifact@v4
+        with:
+          name: integration-test-logs
+          path: tests/integration/results/integration_test/logs
+          retention-days: 30

pixi.toml

@@ -17,4 +17,4 @@ ruff = ">=0.9.9"
 pyyaml = ">=6.0.2"
 
 [tasks]
-test = {cmd = "pytest tests/"}
+test-integration = {cmd = "pytest tests/clio_test.py"}

template/README.md.jinja

@@ -23,7 +23,7 @@ pixi install --all
 For testing, simply run:
 
 ```shell
-pixi run test
+pixi run test-integration
 ```
 
 To view the documentation locally, use:
@@ -37,5 +37,5 @@ To test a minimal example of a workflow using this module:
 ```shell
 pixi shell    # activate this project's environment
 cd tests/integration/  # navigate to the integration example
-snakemake --use-conda  # run the workflow!
+snakemake --use-conda 2  # run the workflow!
 ```

template/tests/integration/{% if true %}Snakefile{% endif %}.jinja

@@ -23,7 +23,7 @@ rule create_external_input:
 module {{module_short_name}}:
     snakefile: "../../workflow/Snakefile"
     config: config["{{module_short_name}}"]
-    prefix: "results/{{module_short_name}}/"
+    prefix: "results/integration_test/"
 
 # rename all module rules with a prefix, to avoid naming conflicts.
 use rule * from {{module_short_name}} as {{module_short_name}}_*
@@ -33,4 +33,4 @@ rule all:
     message: "A generic test case for your module."
     default_target: True
     input:
-        "results/{{module_short_name}}/results/combined_text.md"
+        "results/integration_test/results/combined_text.md"