Add test infrastructure for model results

Fixes #5
Fixes timtroendle#28
Fixes timtroendle#31

Author: timtroendle

default/{{cookiecutter.project_short_name}}/Snakefile

@@ -23,7 +23,7 @@ rule all:
     message: "Run entire analysis and compile report."
     input:
         "build/report.html",
-        "build/test-report.html"
+        "build/test.success"
 
 
 rule run:
@@ -102,7 +102,16 @@ rule clean: # removes all generated results
 
 
 rule test:
-    conda: "envs/test.yaml"
-    output: "build/test-report.html"
-    shell:
-        "py.test --html={output} --self-contained-html"
+    # To add more tests, do
+    # (1) Add to-be-tested workflow outputs as inputs to this rule.
+    # (2) Turn them into pytest fixtures in tests/test_runner.py.
+    # (3) Create or reuse a test file in tests/my-test.py and use fixtures in tests.
+    message: "Run tests"
+    input:
+        test_dir = "tests",
+        tests = map(str, Path("tests").glob("**/test_*.py")),
+        model_results = rules.run.output[0],
+    log: "build/test-report.html"
+    output: "build/test.success"
+    conda: "./envs/test.yaml"
+    script: "./tests/test_runner.py"

default/{{cookiecutter.project_short_name}}/envs/test.yaml

@@ -7,6 +7,3 @@ dependencies:
     - pandas=2.0.1
     - pytest=7.3.1
     - pytest-html=4.1.1
-    - pip=23.1.2
-    - pip:
-        - pytest-pythonpath # adds the root path "./" to PYTHONPATH

default/{{cookiecutter.project_short_name}}/tests/test_model.py

@@ -1,6 +1,12 @@
-"""Test case for the model."""
-import scripts.model
+"""Test case for the model results.
 
+Pytest fixtures are provided from within the test runner.
+"""
 
-def test_model():
-    assert scripts.model.linear_model(slope=1, x0=4, x=0) == 4
+
+def test_model_results_at_0(model_results):
+    assert model_results[0] == 5
+
+
+def test_model_results_at_1(model_results):
+    assert model_results[1] == 9

default/{{cookiecutter.project_short_name}}/tests/test_runner.py

@@ -0,0 +1,38 @@
+import sys
+from pathlib import Path
+
+import pandas as pd
+import pytest
+
+
+def run_test(snakemake):
+    exit_code = pytest.main(
+        [
+            snakemake.input.test_dir,
+            f"--html={snakemake.log[0]}",
+            "--self-contained-html",
+            "--verbose"
+        ],
+        plugins=[
+            _create_config_plugin(snakemake=snakemake)
+        ]
+    )
+    if exit_code == 0:
+        Path(snakemake.output[0]).touch()
+    sys.exit(exit_code)
+
+
+def _create_config_plugin(snakemake):
+    """Creates fixtures from Snakemake configuration."""
+
+    class SnakemakeConfigPlugin():
+
+        @pytest.fixture()
+        def model_results(self):
+            return pd.read_pickle(snakemake.input.model_results)
+
+    return SnakemakeConfigPlugin()
+
+
+if __name__ == "__main__":
+    run_test(snakemake)