TwoPy 0.3.6__tar.gz → 0.3.8__tar.gz

{twopy-0.3.6 → twopy-0.3.8}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: twopy
-Version: 0.3.6
+Version: 0.3.8
 Summary: Two-photon imaging analysis tool with a napari interface.
 Author-email: Gustavo Madeira Santana <fromweb1@gumadeiras.com>
 License-Expression: MIT

{twopy-0.3.6 → twopy-0.3.8}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "twopy"
-version = "0.3.6"
+version = "0.3.8"
 description = "Two-photon imaging analysis tool with a napari interface."
 readme = "README.md"
 requires-python = ">=3.13,<3.14"

{twopy-0.3.6 → twopy-0.3.8}/src/twopy/napari/plotting/docks/response_plot_widget.py

@@ -583,11 +583,12 @@ class _ResponsePlotWidget(QWidget):
         """Show the copyable update command when a newer release is known."""
         if notice is None:
             return
-        self._update_notice_label.setText(notice.command)
+        self._update_notice_label.setText(notice.text)
+        print(notice.text, flush=True)
         if self._viewer is not None:
             refresh_empty_viewer_message(
                 self._viewer,
-                update_command=notice.command,
+                update_command=notice.text,
             )
 
     def _ignore_update_notice_error(self, _error: Exception) -> None:

{twopy-0.3.6 → twopy-0.3.8}/src/twopy/napari/plotting/export.py

@@ -388,7 +388,7 @@ def current_recording_image(
     Returns:
         Two-dimensional display-coordinate image.
     """
-    movie_layer = _layer_by_name(viewer, "aligned movie")
+    movie_layer = _visible_layer_by_name(viewer, "aligned movie")
     if movie_layer is not None:
         data = np.asarray(cast(NapariLayerWithData, movie_layer).data)
         if data.ndim == 3:
@@ -397,6 +397,12 @@ def current_recording_image(
         if data.ndim == 2:
             return cast(npt.NDArray[np.float64], data)
 
+    mean_layer = _visible_layer_by_name(viewer, "mean image")
+    if mean_layer is not None:
+        data = np.asarray(cast(NapariLayerWithData, mean_layer).data)
+        if data.ndim == 2:
+            return cast(npt.NDArray[np.float64], data)
+
     mean_image = recording.alignment_valid_crop.crop_image(recording.mean_image)
     return cast(npt.NDArray[np.float64], mean_image)
 
@@ -948,3 +954,11 @@ def _layer_by_name(viewer: object | None, name: str) -> object | None:
         if getattr(layer, "name", None) == name:
             return layer
     return None
+
+
+def _visible_layer_by_name(viewer: object | None, name: str) -> object | None:
+    """Return a named layer only when napari is currently showing it."""
+    layer = _layer_by_name(viewer, name)
+    if layer is None or not bool(getattr(layer, "visible", True)):
+        return None
+    return layer

{twopy-0.3.6 → twopy-0.3.8}/src/twopy/napari/session.py

@@ -269,6 +269,27 @@ def remove_loaded_recording_layers(
         _remove_layer(viewer, layer)
 
 
+def _clear_all_viewer_layers(viewer: object) -> None:
+    """Clear every viewer layer because twopy owns the layer stack."""
+    layer_collection = getattr(viewer, "layers", None)
+    clear = getattr(layer_collection, "clear", None)
+    if callable(clear):
+        clear()
+        return
+
+    for collection_name in ("images", "labels"):
+        collection = getattr(viewer, collection_name, None)
+        if isinstance(collection, list):
+            collection.clear()
+
+    selection = getattr(layer_collection, "selection", None)
+    if selection is not None and hasattr(selection, "active"):
+        try:
+            cast(_LayerSelection, selection).active = None
+        except (AttributeError, TypeError):
+            return
+
+
 def record_loaded_view(
     state: NapariSessionState,
     *,
@@ -444,7 +465,7 @@ def unload_loaded_recording(state: NapariSessionState, index: int) -> None:
 
 
 def unload_all_loaded_recordings(state: NapariSessionState) -> None:
-    """Unload every recording and remove all owned layers from napari.
+    """Unload every recording and clear all twopy-owned layers from napari.
 
     Args:
         state: Mutable napari session state.
@@ -454,8 +475,7 @@ def unload_all_loaded_recordings(state: NapariSessionState) -> None:
     """
     if len(state.loaded_recordings) == 0:
         return
-    for loaded_recording in state.loaded_recordings:
-        remove_loaded_recording_layers(state.viewer, loaded_recording)
+    _clear_all_viewer_layers(state.viewer)
     state.loaded_recordings.clear()
     clear_matching_state = getattr(
         state.group_matching_panel,

{twopy-0.3.6 → twopy-0.3.8}/src/twopy/napari/version_check.py

@@ -1,7 +1,7 @@
 """Check whether PyPI has a newer twopy release for the napari app.
 
 Inputs: installed twopy version, PyPI JSON metadata, and local UI cache.
-Outputs: an optional copyable update command for the Metadata tab.
+Outputs: an optional copyable update notice for the Metadata tab.
 
 The app only tells users how to update. It does not choose or run an
 environment manager, because users may launch twopy from pip, conda, or another
@@ -97,14 +97,24 @@ class UpdateNotice:
         latest_version: Newer version available from the package index.
         command: Update command shown to the user.
 
-    The Metadata tab shows only ``command`` so twopy does not assume how the
-    user's Python environment is managed.
+    The Metadata tab shows text the user can copy. The command stays plain so
+    twopy does not assume how the user's Python environment is managed.
     """
 
     current_version: str
     latest_version: str
     command: str = PIP_UPDATE_COMMAND
 
+    @property
+    def text(self) -> str:
+        """Return the copyable user-facing update notice."""
+        return (
+            "Update available!\n"
+            f"Latest version is {self.latest_version}.\n"
+            "To update, run:\n"
+            f"{self.command}"
+        )
+
 
 def check_for_update(
     *,
@@ -131,9 +141,9 @@ def check_for_update(
         Update notice, or ``None`` when twopy is current or the check cannot
         prove that a newer final release exists.
 
-    A fresh cache avoids one network request per launch. If PyPI is unreachable
-    and an older cache already proves a newer version exists, twopy can still
-    show the update command.
+    A fresh cache avoids one network request per launch only after it has
+    already seen a newer version. If PyPI is unreachable and an older cache
+    proves a newer version exists, twopy can still show the update command.
     """
     checked_now = _utc(now)
     cache = read_version_check_cache(state_file=state_file)
@@ -261,7 +271,7 @@ def _cache_is_fresh(
         latest = Version(cache.latest_version)
     except InvalidVersion:
         return False
-    if latest < current:
+    if latest <= current:
         return False
     return now - checked_at <= max_age
 

{twopy-0.3.6 → twopy-0.3.8}/src/twopy.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: twopy
-Version: 0.3.6
+Version: 0.3.8
 Summary: Two-photon imaging analysis tool with a napari interface.
 Author-email: Gustavo Madeira Santana <fromweb1@gumadeiras.com>
 License-Expression: MIT

{twopy-0.3.6 → twopy-0.3.8}/tests/test_napari_export.py

@@ -4,6 +4,8 @@ Inputs: shared fake napari state and tiny converted recordings.
 Outputs: assertions for one napari workflow area.
 """
 
+from types import SimpleNamespace
+
 from qtpy.QtWidgets import QSizePolicy
 
 from tests.napari_support import (
@@ -41,7 +43,9 @@ from tests.napari_support import (
     temporary_directory,
     unittest,
 )
+from twopy.converted import RecordingData
 from twopy.napari.output_routing import NapariOutputRoute
+from twopy.napari.plotting.export import current_recording_image
 from twopy.napari.plotting.panels import SidebarTextLabel
 
 
@@ -202,6 +206,28 @@ class NapariExportTest(NapariAdapterTestCase):
         self.assertEqual(len(fig.axes), 2)
         np.testing.assert_allclose(fig.axes[1].get_yticks(), (-0.2, 0.0, 0.2))
 
+    def test_recording_export_uses_visible_mean_image_when_movie_hidden(self) -> None:
+        """Confirm recording exports match the visible image layer.
+
+        Inputs: one hidden aligned-movie layer and one visible mean-image layer.
+        Outputs: exported image data comes from the visible mean image.
+        """
+        mean_image = np.array([[1.0, 2.0], [3.0, 4.0]], dtype=np.float64)
+        movie_frame = np.array([[9.0, 9.0], [9.0, 9.0]], dtype=np.float64)
+        viewer = SimpleNamespace(
+            layers={
+                "mean image": SimpleNamespace(data=mean_image, visible=True),
+                "aligned movie": SimpleNamespace(data=movie_frame, visible=False),
+            }
+        )
+
+        image = current_recording_image(
+            viewer=viewer,
+            recording=cast(RecordingData, object()),
+        )
+
+        np.testing.assert_array_equal(image, mean_image)
+
     def test_response_plot_export_draws_epoch_marker(self) -> None:
         """Confirm exported response plots show the coarse epoch top rail.
 

{twopy-0.3.6 → twopy-0.3.8}/tests/test_napari_loaded_recordings.py

@@ -850,6 +850,7 @@ class NapariLoadedRecordingsTest(NapariAdapterTestCase):
 
             unload_buttons["Unload all"].click()
 
+            self.assertEqual(viewer.layer_clear_calls, 1)
             self.assertEqual(loaded_list.count(), 0)
             self.assertFalse(sidebar_buttons["Open Group Matching"].isEnabled())
             self.assertFalse(sidebar_buttons["Reconvert selected"].isEnabled())

{twopy-0.3.6 → twopy-0.3.8}/tests/test_napari_plot_controls.py

@@ -57,7 +57,12 @@ class NapariPlotControlsTest(NapariAdapterTestCase):
             SidebarTextLabel(analysis_text),
             SidebarTextLabel("ROI output: /very/long/path/to/rois.h5"),
             SidebarTextLabel("Saved analysis."),
-            SidebarTextLabel("python -m pip install -U twopy"),
+            SidebarTextLabel(
+                "Update available!\n"
+                "Latest version is 0.3.6.\n"
+                "To update, run:\n"
+                "python -m pip install -U twopy",
+            ),
         )
 
         tab = response_metadata_tab(

{twopy-0.3.6 → twopy-0.3.8}/tests/test_version_check.py

@@ -32,6 +32,15 @@ class VersionCheckTest(unittest.TestCase):
         self.assertIsNotNone(notice)
         assert notice is not None
         self.assertEqual(notice.command, PIP_UPDATE_COMMAND)
+        self.assertEqual(
+            notice.text,
+            (
+                "Update available!\n"
+                "Latest version is 0.3.3.\n"
+                "To update, run:\n"
+                "python -m pip install -U twopy"
+            ),
+        )
 
     def test_same_or_older_release_returns_no_notice(self) -> None:
         """Confirm current installs do not show an update command."""
@@ -84,6 +93,24 @@ class VersionCheckTest(unittest.TestCase):
             assert notice is not None
             self.assertEqual(notice.command, PIP_UPDATE_COMMAND)
 
+    def test_fresh_current_cache_still_checks_for_new_release(self) -> None:
+        """Confirm a same-version cache does not hide a same-day release."""
+        with temporary_directory() as temp_dir:
+            state_file = Path(temp_dir) / "state.json"
+            now = datetime(2026, 6, 18, 12, tzinfo=UTC)
+            _write_cache(state_file, checked_at=now, latest_version="0.3.5")
+
+            notice = check_for_update(
+                current_version="0.3.5",
+                now=now + timedelta(hours=1),
+                state_file=state_file,
+                fetch_latest=lambda: PublishedVersion(version="0.3.6"),
+            )
+
+            self.assertIsNotNone(notice)
+            assert notice is not None
+            self.assertEqual(notice.latest_version, "0.3.6")
+
     def test_stale_cache_is_used_when_network_fails(self) -> None:
         """Confirm old cache still helps when PyPI is unreachable."""
         with temporary_directory() as temp_dir: