Move integration tests within the template

template/{{ module_short_name }}/pixi.toml.jinja

@@ -20,7 +20,8 @@ snakefmt = ">=0.10.2"
 snakemake-minimal = ">=8.29.0"
 networkx = ">=3.4.2"  # TODO: remove after clio-tools is released
 cffconvert = ">=2.0.0"  # TODO: remove after clio-tools is released
-pydantic = ">=2.10.6"
+pydantic = ">=2.10.6"  # TODO: remove after clio-tools is released
+pyyaml = ">=6.0.2"  # TODO: remove after clio-tools is released
 
 [pypi-dependencies]
 mkdocs-mermaid2-plugin = ">=1.2.1"

template/{{ module_short_name }}/tests/clio_test.py.jinja

@@ -0,0 +1,36 @@
+"""Set of standard clio tests."""
+
+import subprocess
+from pathlib import Path
+
+import pytest
+from clio_tools.data_module import ModuleInterface
+
+
+@pytest.fixture(scope="module")
+def module_path():
+    """Parent directory of the project."""
+    return Path(__file__).parent.parent
+
+
+def test_interface_file(module_path):
+    """The interfacing file should be correct."""
+    assert ModuleInterface.from_yaml(module_path / "INTERFACE.yaml")
+
+
+def test_snakemake_all_failure(module_path):
+    """The snakemake 'all' rule should return an error by default."""
+    process = subprocess.run(
+        "snakemake", shell=True, cwd=module_path, capture_output=True
+    )
+    assert "This workflow must be called as a snakemake module" in str(process.stderr)
+
+
+def test_snakemake_integration_testing(module_path):
+    """Run a light-weight test simulating someone using this module."""
+    assert subprocess.run(
+        "snakemake --use-conda",
+        shell=True,
+        check=True,
+        cwd=module_path / "tests/integration",
+    )

tests/template_test.py

@@ -7,8 +7,8 @@
 from copier import run_copy
 
 
-@pytest.fixture(scope="module", params=["MIT"])
-def simple_template(request, tmp_path_factory, template_path, simple_answers):
+@pytest.fixture(scope="module", params=["Apache-2.0"])
+def template_project(request, tmp_path_factory, template_path, simple_answers):
     """Run the template in a temporary location, for further testing."""
     path = tmp_path_factory.mktemp(request.param)
     modified_answers = deepcopy(simple_answers)
@@ -18,59 +18,25 @@ def simple_template(request, tmp_path_factory, template_path, simple_answers):
 
 
 @pytest.fixture(scope="module")
-def pixi_built(simple_template):
+def pixi_built(template_project):
     """Create a pixi environment for the temporary template project."""
-    pixi_config = simple_template / "pixi.toml"
+    pixi_config = template_project / "pixi.toml"
     subprocess.run(
         f"pixi install --manifest-path {pixi_config}",
         shell=True,
-        cwd=simple_template,
+        cwd=template_project,
         check=True,
     )
-    return simple_template
-
-@pytest.fixture(scope="module")
-def snakemake_built(pixi_built):
-    """Create snakemake environments in the temporary template project."""
-    subprocess.run(
-        "pixi run snakemake --conda-create-envs-only",
-        shell=True,
-        cwd=pixi_built,
-        check=True
-    )
-    return pixi_built
+    return template_project
 
 
-def test_template_license(simple_template):
-    """Generated license files should match the copier request."""
-    assert (simple_template / "LICENSE").exists()
-
-
-def test_citation_file(pixi_built):
-    """The generated citation file should be valid."""
-    citation_file = pixi_built / "CITATION.cff"
+def test_mkdocs_build(pixi_built):
+    """The template's mkdocs should build without issues."""
     assert subprocess.run(
-        f"pixi run cffconvert -i {citation_file.name} --validate",
-        shell=True,
-        check=True,
-        cwd=pixi_built,
+        "pixi run mkdocs build", shell=True, check=True, cwd=pixi_built
     )
 
 
-def test_mkdocs_build(pixi_built):
-    """Mkdocs should build without issues."""
-    assert subprocess.run("pixi run mkdocs build", shell=True, check=True, cwd=pixi_built)
-
-
-def test_snakemake_all_failure(snakemake_built):
-    """The 'all' rule should return an error by default."""
-    process = subprocess.run("pixi run snakemake", shell=True, cwd=snakemake_built, capture_output=True)
-    assert "This workflow must be called as a snakemake module" in str(process.stderr)
-
-
-def test_snakemake_integration_testing(snakemake_built):
-    """The automatic integration test should run by default."""
-    assert subprocess.run("pixi run snakemake --use-conda",
-        check=True,
-        cwd=snakemake_built / "tests/integration",
-    )
+def test_pytest(pixi_built):
+    """The template's tests should pass by default."""
+    assert subprocess.run("pixi run pytest", shell=True, check=True, cwd=pixi_built)