Added neat log isolation so it didn't keep writing test logs into the repo dir

Author: joshfactorial

tests/conftest.py

@@ -0,0 +1,30 @@
+import logging
+import pytest
+
+
+@pytest.fixture(autouse=True)
+def _isolate_neat_logging():
+    """
+    Close and remove any FileHandlers attached to NEAT loggers before each test.
+    Prevents 'ValueError: I/O operation on closed file' errors when a FileHandler
+    from a previous test is still attached after its underlying file is closed.
+    Propagation is left intact so caplog can capture NEAT log output.
+    """
+    def _close_file_handlers(logger):
+        for h in list(logger.handlers):
+            if isinstance(h, logging.FileHandler):
+                logger.removeHandler(h)
+                try:
+                    h.close()
+                except Exception:
+                    pass
+
+    for name, logger in list(logging.Logger.manager.loggerDict.items()):
+        if (name == "neat" or name.startswith("neat.")) and isinstance(logger, logging.Logger):
+            _close_file_handlers(logger)
+
+    yield
+
+    for name, logger in list(logging.Logger.manager.loggerDict.items()):
+        if (name == "neat" or name.startswith("neat.")) and isinstance(logger, logging.Logger):
+            _close_file_handlers(logger)

tests/test_cli/test_basic_cli.py

@@ -36,6 +36,7 @@ def test_basic_cli():
             stdout=subprocess.PIPE,
             stderr=subprocess.PIPE,
             text=True,
+            cwd=str(td),
         )
         assert proc.returncode == 0, f"STDERR:\n{proc.stderr}"
         assert out.exists()

tests/test_read_simulator/test_options.py

@@ -1,7 +1,6 @@
 from neat.read_simulator.utils.options import Options
 
 from pathlib import Path as _PathAlias
-import logging as _logging
 import numpy as _np
 import textwrap as _textwrap
 import pytest as _pytest
@@ -11,42 +10,6 @@ def _project_root() -> _PathAlias:
     return _PathAlias(__file__).resolve().parents[2]
 
 
-@_pytest.fixture(autouse=True)
-def _isolate_neat_logging():
-    """
-    Prevent flaky 'ValueError: I/O operation on closed file' logging errors under pytest.
-    """
-    # Clear handlers on NEAT and all child loggers
-    for name, logger in list(_logging.Logger.manager.loggerDict.items()):
-        if name == "neat" or name.startswith("neat."):
-            if isinstance(logger, _logging.Logger):
-                for h in list(logger.handlers):
-                    logger.removeHandler(h)
-                    try:
-                        h.close()
-                    except Exception:
-                        pass
-                logger.handlers.clear()
-                logger.propagate = True # child loggers will propagate to 'neat'
-
-    neat_logger = _logging.getLogger("neat")
-    neat_logger.handlers.clear()
-    neat_logger.addHandler(_logging.NullHandler())
-    neat_logger.propagate = False # stop at 'neat' (do not reach root)
-
-    yield
-
-    # Rremove NullHandler
-    for h in list(neat_logger.handlers):
-        neat_logger.removeHandler(h)
-        try:
-            h.close()
-        except Exception:
-            pass
-    neat_logger.handlers.clear()
-    neat_logger.propagate = True
-
-
 def test_basic_options():
     reference = _project_root() / "data" / "H1N1.fa"
     base_options = Options(reference)