From c423a4dece1c0a5dbf6b92eee1294030a39d1df7 Mon Sep 17 00:00:00 2001
From: Leonardo Schwarz <leonardo.schwarz@fgcz.ethz.ch>
Date: Wed, 6 Nov 2024 12:58:33 +0100
Subject: [PATCH] migrate test

---
 .../invoke/test_invoke_subprocess.py          | 38 ++++++++++++++++++
 tests/unit/workflow/__init__.py               |  0
 tests/unit/workflow/test_snakemake_invoke.py  | 39 -------------------
 3 files changed, 38 insertions(+), 39 deletions(-)
 delete mode 100644 tests/unit/workflow/__init__.py
 delete mode 100644 tests/unit/workflow/test_snakemake_invoke.py

diff --git a/tests/unit/snakemake_invoke/invoke/test_invoke_subprocess.py b/tests/unit/snakemake_invoke/invoke/test_invoke_subprocess.py
index c230ef2..709b620 100644
--- a/tests/unit/snakemake_invoke/invoke/test_invoke_subprocess.py
+++ b/tests/unit/snakemake_invoke/invoke/test_invoke_subprocess.py
@@ -1,7 +1,25 @@
 import pytest
+import sys
+from pathlib import Path
+from snakemake_invoke.config import SnakemakeInvokeConfig
 from snakemake_invoke.invoke.invoke_subprocess import InvokeSubprocess
 
 
+@pytest.fixture()
+def config_snakefile_path() -> Path:
+    return Path("/tmp/workflow/Snakefile")
+
+
+@pytest.fixture
+def config(config_snakefile_path):
+    return SnakemakeInvokeConfig(snakefile_path=config_snakefile_path)
+
+
+@pytest.fixture
+def invoke(config):
+    return InvokeSubprocess(config=config)
+
+
 @pytest.mark.parametrize(
     "input_args,expected",
     [
@@ -16,3 +34,23 @@
 def test_args_to_shell_command(input_args, expected):
     result = InvokeSubprocess._args_to_shell_command(input_args)
     assert result == expected
+
+
+def test_get_base_command(invoke) -> None:
+    base_command = invoke.get_base_command(
+        extra_args=["--keep-going"],
+        work_dir=Path("/tmp/work"),
+    )
+    assert base_command == [
+        sys.executable,
+        "-m",
+        "snakemake",
+        "-d",
+        "/tmp/work",
+        "--cores",
+        "1",
+        "--snakefile",
+        "/tmp/workflow/Snakefile",
+        "--rerun-incomplete",
+        "--keep-going",
+    ]
diff --git a/tests/unit/workflow/__init__.py b/tests/unit/workflow/__init__.py
deleted file mode 100644
index e69de29..0000000
diff --git a/tests/unit/workflow/test_snakemake_invoke.py b/tests/unit/workflow/test_snakemake_invoke.py
deleted file mode 100644
index f4ed6d4..0000000
--- a/tests/unit/workflow/test_snakemake_invoke.py
+++ /dev/null
@@ -1,39 +0,0 @@
-from __future__ import annotations
-
-from pathlib import Path
-
-import pytest
-import sys
-from pytest_mock import MockerFixture
-
-from snakemake_invoke.snakemake_invoke import SnakemakeInvoke
-
-
-@pytest.fixture
-def default_invoke() -> SnakemakeInvoke:
-    return SnakemakeInvoke()
-
-
-def test_get_base_command(mocker: MockerFixture, default_invoke: SnakemakeInvoke) -> None:
-    mocker.patch.object(SnakemakeInvoke, "snakefile_path", "/tmp/workflow/Snakefile")
-    base_command = default_invoke.get_base_command(
-        extra_args=["--keep-going"],
-        work_dir=Path("/tmp/work"),
-    )
-    assert base_command == [
-        sys.executable,
-        "-m",
-        "snakemake",
-        "-d",
-        "/tmp/work",
-        "--cores",
-        "1",
-        "--snakefile",
-        "/tmp/workflow/Snakefile",
-        "--rerun-incomplete",
-        "--keep-going",
-    ]
-
-
-if __name__ == "__main__":
-    pytest.main()