Save integration logs in standard location (#27)

* Save integration logs during CI tests

---------

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

Author: irm-codebase

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

@@ -14,9 +14,24 @@ jobs:
         python-version: ["3.12"]
     steps:
       - uses: actions/checkout@v4
-      - name: setup-pixi
+      - name: Setup pixi
         uses: prefix-dev/[email protected]
-      - name: Run tests
-        run: pixi run pytest tests/clio_test.py
-      - name: Run linting
+      - name: Run integration tests
+        id: tests
+        run: pixi run test-integration
+        continue-on-error: true
+      - name: Run snakemake linting
+        id: linting
         run: pixi run snakemake --lint
+        continue-on-error: true
+      - name: Save integration logs
+        if: ${{ always() }}
+        uses: actions/upload-artifact@v4
+        with:
+          name: integration-test-logs-${{ matrix.os }}
+          path: tests/integration/results/integration_test/logs
+          if-no-files-found: ignore
+          retention-days: 30
+      - name: Fail if integration or linting failed
+        if: ${{ steps.tests.outcome == 'failure' || steps.linting.outcome == 'failure' }}
+        run: exit 1

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 --cores 2  # run the workflow!
 ```

template/pixi.toml.jinja

@@ -21,7 +21,7 @@ snakefmt = ">=0.10.2"
 snakemake-minimal = ">=8.29.0"
 
 [tasks]
-test = {cmd = "pytest tests/"}
+test-integration = {cmd = "pytest tests/clio_test.py"}
 
 [feature.docs.dependencies]
 mkdocs-material = ">=9.6.7"

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

@@ -5,7 +5,7 @@ configfile: workflow.source_path("./test_config.yaml")
 rule create_external_input:
     message: "Example of a rule external to your module."
     output:
-        text_file = "results/{{module_short_name}}/resources/user/user_message.md"
+        text_file = "results/integration_test/resources/user/user_message.md"
     run:
         from pathlib import Path
         from textwrap import dedent
@@ -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"

tests/template_test.py

@@ -42,7 +42,9 @@ def test_mkdocs_build(pixi_built):
 
 def test_pytest(pixi_built):
     """The template's tests should pass by default."""
-    assert subprocess.run("pixi run test", shell=True, check=True, cwd=pixi_built)
+    assert subprocess.run(
+        "pixi run test-integration", shell=True, check=True, cwd=pixi_built
+    )
 
 
 def test_linting(pixi_built):