Silence the three autonerves-rooted CLI-noise sources

Fixes the three root causes identified by the 2026-08-06 /cli_noise_clean
audit (PyAutoMind draft/maintenance/pyautonerves/cli_noise_autonerves_batch.md):

1. fits leak — fitsable.ndarray_via_fits_from and header_obj_from called
   fits.open without closing, emitting 'ResourceWarning: unclosed file' in
   every downstream repo that loads FITS. Both now use 'with fits.open(...)'.
2. pytest collection — test_test_mode.py imported the real API functions
   test_mode_level/test_mode_samples by bare name, so pytest collected them
   as tests (PytestReturnNotNoneWarning, an ERROR in future pytest). The
   unused test_mode_level import is dropped and test_mode_samples is
   aliased to _test_mode_samples.
3. check_version false positive — with workspace_root defaulting to cwd,
   every library import from inside a library's own source repo warned
   'Cannot verify the workspace ... is compatible'. check_version now skips
   silently when the root is a package source checkout (setup.py or
   pyproject.toml at its top level) and no version floor is recorded; a
   recorded floor is still enforced, and a genuine workspace missing its
   version keys still warns.

Regression tests added for all three.

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_015NrwGppUCg8r4Foed6bgSf

Author: claude

autonerves/fitsable.py

@@ -207,8 +207,10 @@ def ndarray_via_fits_from(
     --------
     array_2d = ndarray_via_fits_from(file_path='/path/to/file/filename.fits', hdu=0)
     """
-    hdu_list = fits.open(file_path, do_not_scale_image_data=do_not_scale_image_data)
-    return ndarray_via_hdu_from(hdu_list[hdu])
+    with fits.open(
+        file_path, do_not_scale_image_data=do_not_scale_image_data
+    ) as hdu_list:
+        return ndarray_via_hdu_from(hdu_list[hdu])
 
 
 def header_obj_from(file_path: Union[Path, str], hdu: int) -> Dict:
@@ -233,8 +235,8 @@ def header_obj_from(file_path: Union[Path, str], hdu: int) -> Dict:
     --------
     array_2d = ndarray_via_fits_from(file_path='/path/to/file/filename.fits', hdu=0)
     """
-    hdu_list = fits.open(file_path)
-    return hdu_list[hdu].header
+    with fits.open(file_path) as hdu_list:
+        return hdu_list[hdu].header
 
 
 

autonerves/workspace.py

@@ -82,6 +82,22 @@ def _version_date(parsed_version):
         return None
 
 
+def _is_source_checkout(root):
+    """
+    True when ``root`` is a Python package source checkout (a ``setup.py`` or
+    ``pyproject.toml`` at its top level) rather than a workspace clone.
+
+    ``check_version`` is called unconditionally on library import with
+    ``workspace_root`` defaulting to the current working directory, so any
+    pytest run or script executed from inside a library's own repo would
+    otherwise warn "Cannot verify the workspace ..." on every import — a
+    false positive, since a source checkout is not a workspace and records
+    no version floor to verify. Workspace clones ship neither file, so a
+    genuine workspace missing its version keys still warns.
+    """
+    return (root / "setup.py").exists() or (root / "pyproject.toml").exists()
+
+
 def _library_name_from_workspace(workspace_root):
     name = workspace_root.name
     suffix = "_workspace"
@@ -168,7 +184,10 @@ def check_version(library_version, workspace_root=None):
     installs) warn on inequality rather than raising.
 
     If no floor source is found, a warning is emitted and the check is
-    skipped.
+    skipped — unless ``workspace_root`` is a package source checkout
+    (``setup.py``/``pyproject.toml`` at its top level), in which case the
+    check is skipped silently: running from inside a library's own repo is
+    not a workspace-compatibility question at all.
 
     The check can be disabled in two ways:
 
@@ -203,6 +222,8 @@ def check_version(library_version, workspace_root=None):
             floor_version = version_file.read_text().strip()
 
     if floor_version is None or floor_version == "":
+        if _is_source_checkout(root):
+            return
         warnings.warn(_missing_version_warning(root, library_version))
         return
 

test_autonerves/test_fitsable.py

@@ -70,6 +70,22 @@ def test__output_to_fits__header_dict():
     assert header["A"] == 1
 
 
+def test__fits_readers_close_their_file_handles():
+    """Regression: `fits.open` without close leaked file handles, emitting
+    `ResourceWarning: unclosed file` throughout every downstream repo that
+    loads FITS via these helpers."""
+    import gc
+    import warnings
+
+    with warnings.catch_warnings():
+        warnings.simplefilter("error", ResourceWarning)
+        fitsable.ndarray_via_fits_from(
+            file_path=test_data_path / "3x3_ones.fits", hdu=0
+        )
+        fitsable.header_obj_from(file_path=test_data_path / "3x3_ones.fits", hdu=0)
+        gc.collect()
+
+
 def test__header_obj_from():
     header_obj = fitsable.header_obj_from(
         file_path=test_data_path / "3x3_ones.fits", hdu=0

test_autonerves/test_test_mode.py

@@ -10,11 +10,14 @@
 
 from autonerves.test_mode import (
     is_test_mode,
-    test_mode_level,
-    test_mode_samples,
     with_test_mode_segment,
 )
 
+# ``test_mode_samples`` is real API, but its ``test_`` prefix means a bare-name
+# import here would be collected by pytest as a test function
+# (PytestReturnNotNoneWarning, an ERROR in future pytest) — alias it instead.
+from autonerves.test_mode import test_mode_samples as _test_mode_samples
+
 
 @pytest.fixture(autouse=True)
 def _restore_test_mode_env():
@@ -69,13 +72,13 @@ def _restore_samples_env(self):
 
     def test__env_unset_returns_historical_default_of_four(self):
         os.environ.pop("PYAUTO_TEST_MODE_SAMPLES", None)
-        assert test_mode_samples() == 4
+        assert _test_mode_samples() == 4
 
     def test__env_set_returns_value(self):
         os.environ["PYAUTO_TEST_MODE_SAMPLES"] = "50000"
-        assert test_mode_samples() == 50000
+        assert _test_mode_samples() == 50000
 
     def test__values_below_four_raise(self):
         os.environ["PYAUTO_TEST_MODE_SAMPLES"] = "3"
         with pytest.raises(ValueError):
-            test_mode_samples()
+            _test_mode_samples()

test_autonerves/test_workspace.py

@@ -33,6 +33,26 @@ def test_missing_sources_warns(tmp_path):
         check_version("2026.7.22.1", workspace_root=tmp_path)
 
 
+@pytest.mark.parametrize("marker", ["setup.py", "pyproject.toml"])
+def test_missing_sources_in_source_checkout_skips_silently(tmp_path, marker):
+    """A package source checkout (setup.py/pyproject.toml at the root) is not
+    a workspace — importing a library from inside its own repo must not warn
+    that the "workspace" version cannot be verified."""
+    (tmp_path / marker).write_text("")
+    with warnings.catch_warnings():
+        warnings.simplefilter("error")
+        check_version("2026.7.22.1", workspace_root=tmp_path)
+
+
+def test_source_checkout_with_version_floor_still_checked(tmp_path):
+    """The source-checkout skip only covers the no-floor false positive — a
+    recorded floor is still enforced even with a setup.py present."""
+    (tmp_path / "setup.py").write_text("")
+    (tmp_path / "version.txt").write_text("2026.7.22.1\n")
+    with pytest.raises(WorkspaceVersionMismatchError):
+        check_version("2025.1.1.1", workspace_root=tmp_path)
+
+
 def test_env_override_skips_mismatch(tmp_path, monkeypatch):
     monkeypatch.setenv("PYAUTO_SKIP_WORKSPACE_VERSION_CHECK", "1")
     (tmp_path / "version.txt").write_text("2025.1.1.1\n")