Test/add xfel calibrate cli tests

Description

This MR adds in some basic tests for the CLI in xfel_calibrate. Done since I want to edit the CLI a bit for SQS Moonshot but the CLI is kinda spaghetti so I'm worried about breaking things and not realising it.

How Has This Been Tested?

Locally, tested by breaking code and checking that the tests fail.

Relevant Documents (optional)

Part of SQS Moonshot, see:

• https://git.xfel.eu/gitlab/moonshot/sqs/issues/13
• https://git.xfel.eu/gitlab/moonshot/sqs/issues/19

Types of changes

• Test (additional or refactored tests)

Checklist:

• My code follows the code style of this project.

Reviewers

@calibration

tests/test_xfel_calibrate_cli.py

+import ast
 import sys
+from pathlib import Path
+from typing import Generator, List, NamedTuple
 from unittest import mock
-import pytest
+from datetime import date
 
+import nbformat
+import pytest
 import xfel_calibrate.calibrate as calibrate
 import xfel_calibrate.settings as commands
+from nbparameterise import extract_parameters
 
 
 @mock.patch.object(sys, "argv", ["xfel-calibrate", "--help"])
@@ -38,7 +44,17 @@ def test_help_nb(capsys):
     assert err == ""
 
 
-def test_execute_nb(fake_process, capsys, tmpdir):
+class CallResult(NamedTuple):
+    argv: List[str]
+    out: str
+    err: str
+    tmp_path: Path
+
+
+@pytest.fixture
+def call_result(
+    fake_process, capsys, tmp_path: Path
+) -> Generator[CallResult, None, None]:
     #  Fake calls to slurm
     fake_process.register_subprocess(commands.free_nodes_cmd, stdout=["1"])
     fake_process.register_subprocess(commands.preempt_nodes_cmd, stdout=["1"])
@@ -51,18 +67,105 @@ def test_execute_nb(fake_process, capsys, tmpdir):
         ["git", fake_process.any(), "describe", "--tag"], stdout=["0.0.0"]
     )
 
-    argv = ["xfel-calibrate", "Tutorial", "TEST", "--out-folder", str(tmpdir)]
+    argv = [
+        "xfel-calibrate",
+        "Tutorial",
+        "TEST",
+        "--runs",
+        "1000",
+        "--out-folder",
+        str(tmp_path),
+    ]
     with mock.patch.object(sys, "argv", argv):
-        with mock.patch.object(calibrate, "temp_path", str(tmpdir)):
+        with mock.patch.object(calibrate, "temp_path", str(tmp_path)):
             calibrate.run()
 
-    out, err = capsys.readouterr()
+            out, err = capsys.readouterr()
+
+            yield CallResult(argv, out, err, tmp_path)
+
+
+def test_call(call_result: CallResult):
+    argv, out, err, tmp_path = call_result
 
     assert "sbatch" in out
     assert "--job-name xfel_calibrate" in out
-    assert str(tmpdir) in out
+    assert str(tmp_path) in out
     assert "Submitted job: " in out
 
     assert err == ""
 
-    print(out)
+
+@pytest.mark.skip(reason="not implemented")
+def test_output_metadata_yml(call_result: CallResult):
+    # TODO: Finish this test later, not a priority
+    argv, out, err, tmp_path = call_result
+
+    metadata_yml_path = list(tmp_path.glob("**/calibration_metadata.yml"))  # noqa
+
+
+def test_output_ipynb(call_result: CallResult):
+    argv, out, err, tmp_path = call_result
+
+    nb_path = list(tmp_path.glob("**/*/*.ipynb"))
+
+    assert len(nb_path) == 1
+
+    with nb_path[0].open() as f:
+        nb = nbformat.read(f, as_version=4)
+
+    parameters = {p.name: p.value for p in extract_parameters(nb)}
+
+    assert parameters["out_folder"] == str(tmp_path)
+    assert parameters["sensor_size"] == [10, 30]
+    assert parameters["random_seed"] == [2345]
+    assert parameters["runs"] == 1000
+
+
+def test_output_finalize(call_result: CallResult):
+    argv, out, err, tmp_path = call_result
+
+    finalize_path = list(tmp_path.glob("**/*/finalize.py"))[0]
+    finalize_ast = ast.parse(finalize_path.read_text())
+
+    finalize_kwargs = {
+        k.arg: ast.literal_eval(k.value)
+        for k in ast.walk(finalize_ast)
+        if type(k) is ast.keyword and k.arg != "finaljob"
+    }
+
+    today = date.today()
+
+    assert finalize_kwargs["joblist"] == []
+    assert str(tmp_path) in finalize_kwargs["run_path"]
+    assert str(tmp_path) in finalize_kwargs["out_path"]
+    assert finalize_kwargs["project"] == "Tutorial Calculation"
+    assert finalize_kwargs["calibration"] == "Tutorial Calculation"
+    assert finalize_kwargs["author"] == "Astrid Muennich"
+    assert finalize_kwargs["version"] == "0.0.0"
+    assert str(tmp_path) in finalize_kwargs["report_to"]
+    assert finalize_kwargs["data_path"] == ""
+    assert str(today) in finalize_kwargs["request_time"]
+    assert str(today) in finalize_kwargs["submission_time"]
+
+
+@pytest.mark.skip(reason="not implemented")
+def test_output_rst(call_result: CallResult):
+    # TODO: Finish this test later, not a priority
+    argv, out, err, tmp_path = call_result
+
+    rst_path = list(tmp_path.glob("**/*/InputParameters.rst"))[0]  # noqa
+
+
+def test_output_sh(call_result: CallResult):
+    argv, out, err, tmp_path = call_result
+
+    sh_path = list(tmp_path.glob("**/*/run_calibrate.sh"))[0]
+
+    sh_target = (
+        "# pycalibration version: 0.0.0\nxfel-calibrate Tutorial TEST "
+        + "--runs 1000 --out-folder "
+        + str(tmp_path)
+    )
+
+    assert sh_path.read_text() == sh_target