[tests] Add tests for experiment

tests/test_cli.py

@@ -436,6 +436,70 @@ def test_evaluate_pasa_montgomery(temporary_basedir):
             )
 
 
+@pytest.mark.skip_if_rc_var_not_set("datadir.montgomery")
+def test_experiment(temporary_basedir):
+    from mednet.scripts.experiment import experiment
+
+    runner = CliRunner()
+
+    output_folder = str(temporary_basedir / "experiment")
+    num_epochs = 2
+    result = runner.invoke(
+        experiment,
+        [
+            "-vv",
+            "pasa",
+            "montgomery",
+            f"--epochs={num_epochs}",
+            f"--output-folder={output_folder}",
+        ],
+    )
+    _assert_exit_0(result)
+
+    assert os.path.exists(os.path.join(output_folder, "command.sh"))
+    assert os.path.exists(os.path.join(output_folder, "predictions.json"))
+    assert os.path.exists(os.path.join(output_folder, "model", "command.sh"))
+    assert os.path.exists(os.path.join(output_folder, "model", "constants.csv"))
+    assert os.path.exists(
+        os.path.join(
+            output_folder, "model", f"model-at-epoch={num_epochs-1}.ckpt"
+        )
+    )
+    # Need to glob because we cannot be sure of the checkpoint with lowest validation loss
+    assert (
+        len(
+            glob.glob(
+                os.path.join(
+                    output_folder,
+                    "model",
+                    "model-at-lowest-validation-loss-epoch=*.ckpt",
+                )
+            )
+        )
+        == 1
+    )
+    assert os.path.exists(
+        os.path.join(output_folder, "model", "model-summary.txt")
+    )
+    assert os.path.exists(os.path.join(output_folder, "model", "trainlog.pdf"))
+    assert (
+        len(
+            glob.glob(
+                os.path.join(
+                    output_folder, "model", "logs", "events.out.tfevents.*"
+                )
+            )
+        )
+        == 1
+    )
+    assert os.path.exists(
+        os.path.join(output_folder, "evaluation", "plots.pdf")
+    )
+    assert os.path.exists(
+        os.path.join(output_folder, "evaluation", "summary.rst")
+    )
+
+
 # This script does not work anymore, either fix or remove the script + this test
 # def test_evaluatevis(temporary_basedir):
 #     import pandas as pd