parametrise integration tests

tests/test_integration/brainglobe_workflows/test_cellfinder.py

@@ -1,92 +1,161 @@
 import subprocess
 import sys
 from pathlib import Path
+from typing import Optional
 
 import pytest
 
 from brainglobe_workflows.cellfinder import main
 
 
-# TODO: test main with default and custom json (local and GIN)?
-def test_main(monkeypatch: pytest.MonkeyPatch, tmp_path: Path):
+@pytest.mark.parametrize(
+    "input_config",
+    [
+        None,
+        "input_config_fetch_GIN",
+        "input_config_fetch_local",
+    ],
+)
+def test_main(
+    input_config: Optional[str],
+    monkeypatch: pytest.MonkeyPatch,
+    tmp_path: Path,
+    request: pytest.FixtureRequest,
+):
     """Test main function for setting up and running cellfinder workflow
 
     Parameters
     ----------
+    input_config : Optional[str]
+        Path to input config json file
     monkeypatch : pytest.MonkeyPatch
         Pytest fixture to use monkeypatching utils
     tmp_path : Path
         Pytest fixture providing a temporary path for each test
+    request : pytest.FixtureRequest
+        Pytest fixture to enable requesting fixtures by name
     """
     # monkeypatch to change current directory to
     # pytest temporary directory
     # (cellfinder cache directory is created in cwd)
     monkeypatch.chdir(tmp_path)
 
     # run main
-    cfg = main()
+    if not input_config:
+        cfg = main()  # use default config
+    else:
+        cfg = main(str(request.getfixturevalue(input_config)))
 
-    # check output files are those expected?
+    # check output files exist
     assert (cfg.detected_cells_path).is_file()
 
 
-# TODO: test main CLI with default and specific json?
-def test_app_wrapper(monkeypatch: pytest.MonkeyPatch, tmp_path: Path):
+@pytest.mark.parametrize(
+    "input_config",
+    [
+        None,
+        "input_config_fetch_GIN",
+        "input_config_fetch_local",
+    ],
+)
+def test_app_wrapper(
+    input_config: Optional[str],
+    monkeypatch: pytest.MonkeyPatch,
+    tmp_path: Path,
+    request: pytest.FixtureRequest,
+):
     """Test running the cellfinder worklfow from the command line
 
     Parameters
     ----------
+    input_config : Optional[str]
+        Path to input config json file
     monkeypatch : pytest.MonkeyPatch
         Pytest fixture to use monkeypatching utils
     tmp_path : Path
         Pytest fixture providing a temporary path for each test
+    request : pytest.FixtureRequest
+        Pytest fixture to enable requesting fixtures by name
     """
     # monkeypatch to change current directory to
     # pytest temporary directory
     # (cellfinder cache directory is created in cwd)
     monkeypatch.chdir(tmp_path)
 
-    # run workflow script with no CLI arguments,
+    # define CLI input
+    script_path = (
+        Path(__file__).resolve().parents[3]
+        / "brainglobe_workflows"
+        / "cellfinder.py"
+    )
+    subprocess_input = [
+        sys.executable,
+        str(script_path),
+    ]
+    # append config if required
+    if input_config:
+        subprocess_input.append("--config")
+        subprocess_input.append(str(request.getfixturevalue(input_config)))
+
+    # run workflow script from the CLI
     subprocess_output = subprocess.run(
-        [
-            sys.executable,
-            Path(__file__).resolve().parents[3]
-            / "brainglobe_workflows"
-            / "cellfinder.py",
-        ],
-        stdout=subprocess.PIPE,
-        stderr=subprocess.STDOUT,
-        text=True,
-        encoding="utf-8",
+        subprocess_input,
+        # stdout=subprocess.PIPE,
+        # stderr=subprocess.STDOUT,
+        # text=True,
+        # encoding="utf-8",
     )
 
     # check returncode
     assert subprocess_output.returncode == 0
 
 
-# TODO: test main CLI with default and specific json?
-def test_main_entry_point(monkeypatch: pytest.MonkeyPatch, tmp_path: Path):
+@pytest.mark.parametrize(
+    "input_config",
+    [
+        None,
+        "input_config_fetch_GIN",
+        "input_config_fetch_local",
+    ],
+)
+def test_main_entry_point(
+    input_config: Optional[str],
+    monkeypatch: pytest.MonkeyPatch,
+    tmp_path: Path,
+    request: pytest.FixtureRequest,
+):
     """Test running the cellfinder workflow via the predefined entry point
 
     Parameters
     ----------
+    input_config : Optional[str]
+        Path to input config json file
     monkeypatch : pytest.MonkeyPatch
         Pytest fixture to use monkeypatching utils
     tmp_path : Path
         Pytest fixture providing a temporary path for each test
+    request : pytest.FixtureRequest
+        Pytest fixture to enable requesting fixtures by name
     """
-    #  monkeypatch to change current directory to
+    # monkeypatch to change current directory to
     # pytest temporary directory
     # (cellfinder cache directory is created in cwd)
     monkeypatch.chdir(tmp_path)
 
+    # define CLI input
+    subprocess_input = ["cellfinder-workflow"]
+    # append config if required
+    if input_config:
+        subprocess_input.append("--config")
+        subprocess_input.append(str(request.getfixturevalue(input_config)))
+
     # run workflow with no CLI arguments,
     subprocess_output = subprocess.run(
-        ["cellfinder-workflow"],
-        stdout=subprocess.PIPE,
-        stderr=subprocess.STDOUT,
-        text=True,
-        encoding="utf-8",
+        subprocess_input,
+        # stdout=subprocess.PIPE,
+        # stderr=subprocess.STDOUT,
+        # text=True,
+        # encoding="utf-8",
     )
 
     # check returncode