🧪 [Add tests for bionetgen.modelapi.runner.run]

.gitignore

@@ -10,3 +10,5 @@ temp_testing/*
 build
 dist
 Issues/rule_keywords/test_DeleteMolecules_changed.bngl
+.jules/
+__pycache__/

bionetgen/core/utils/utils.py

@@ -1,6 +1,6 @@
 import os, subprocess
 from bionetgen.core.exc import BNGPerlError
-from distutils import spawn
+import shutil as spawn
 
 from bionetgen.core.utils.logging import BNGLogger
 
@@ -589,7 +589,7 @@ def _try_path(candidate_path):
             return hit
 
     # 3) On PATH
-    bng_on_path = spawn.find_executable("BNG2.pl")
+    bng_on_path = spawn.which("BNG2.pl")
     if bng_on_path:
         tried.append(bng_on_path)
         hit = _try_path(bng_on_path)
@@ -616,7 +616,7 @@ def test_perl(app=None, perl_path=None):
     logger.debug("Checking if perl is installed.", loc=f"{__file__} : test_perl()")
     # find path to perl binary
     if perl_path is None:
-        perl_path = spawn.find_executable("perl")
+        perl_path = spawn.which("perl")
     if perl_path is None:
         raise BNGPerlError
     # check if perl is actually working

bionetgen/simulator/csimulator.py

@@ -1,7 +1,10 @@
 import ctypes, os, tempfile, bionetgen
 import numpy as np
 
-from distutils import ccompiler
+try:
+    from distutils import ccompiler
+except ImportError:
+    pass
 from .bngsimulator import BNGSimulator
 from bionetgen.main import BioNetGen
 from bionetgen.core.exc import BNGCompileError

tests/test_runner.py

@@ -0,0 +1,59 @@
+import os
+import pytest
+from unittest.mock import patch, MagicMock, ANY
+from bionetgen.modelapi.runner import run
+
+
+@patch("bionetgen.modelapi.runner.BNGCLI")
+def test_runner_with_out(mock_bngcli):
+    mock_cli_instance = MagicMock()
+    mock_bngcli.return_value = mock_cli_instance
+    mock_cli_instance.result = "mock_result"
+
+    inp = "test.bngl"
+    out = "test_out"
+
+    result = run(inp, out=out, suppress=True, timeout=10)
+
+    mock_bngcli.assert_called_once_with(inp, out, ANY, suppress=True, timeout=10)
+    mock_cli_instance.run.assert_called_once()
+    assert result == "mock_result"
+
+
+@patch("bionetgen.modelapi.runner.BNGCLI")
+@patch("bionetgen.modelapi.runner.TemporaryDirectory")
+def test_runner_without_out(mock_tempdir, mock_bngcli):
+    mock_cli_instance = MagicMock()
+    mock_bngcli.return_value = mock_cli_instance
+    mock_cli_instance.result = "mock_result"
+
+    mock_tempdir_instance = MagicMock()
+    mock_tempdir.return_value.__enter__.return_value = "temp_out"
+
+    inp = "test.bngl"
+
+    result = run(inp, suppress=False, timeout=None)
+
+    mock_tempdir.assert_called_once()
+    mock_bngcli.assert_called_once_with(
+        inp, "temp_out", ANY, suppress=False, timeout=None
+    )
+    mock_cli_instance.run.assert_called_once()
+    assert result == "mock_result"
+
+
+@patch("bionetgen.modelapi.runner.BNGCLI")
+def test_runner_exception(mock_bngcli):
+    mock_cli_instance = MagicMock()
+    mock_bngcli.return_value = mock_cli_instance
+    mock_cli_instance.run.side_effect = Exception("Test Exception")
+
+    inp = "test.bngl"
+    out = "test_out"
+
+    cur_dir = os.getcwd()
+
+    with pytest.raises(Exception, match="Test Exception"):
+        run(inp, out=out)
+
+    assert os.getcwd() == cur_dir