refactor: Make warnings error in tests (#1192)

Change `pytest` configuration to change warnings into errors in the
tests.

Fix code that emites warning.

<!-- Generated by sourcery-ai[bot]: start summary -->

## Summary by Sourcery

Convert warnings to errors in tests by updating the `pytest`
configuration and refactor code to handle warnings appropriately.
Enhance the `sentry_sdk` usage by replacing `push_scope` with
`new_scope`. Improve data handling in `batch_backend.py` and update
tests to align with these changes.

Bug Fixes:
- Fix the `test_no_update` test to correctly handle URL errors by using
`urllib.error.URLError`.
- Correct the `test_ignore_file_exists_old_date` test to assert the
correct release version and URL.

Enhancements:
- Update the `sentry_sdk` usage to replace `push_scope` with `new_scope`
for better scope management.
- Improve the `CheckVersionThread` initialization by updating the
default URL to a more relevant one.
- Enhance the `get_data_to_write` method in `batch_backend.py` to handle
empty data frames more efficiently.
- Refactor the `decode_zstd1` and `decode_zstd0` functions to use
`np.frombuffer` instead of `np.fromstring` for better performance and
compatibility.

Tests:
- Modify tests to treat warnings as errors by updating the `pytest`
configuration.
- Update tests to reflect changes in the `sentry_sdk` scope management.

<!-- Generated by sourcery-ai[bot]: end summary -->

<!-- This is an auto-generated comment: release notes by coderabbit.ai
-->
## Summary by CodeRabbit

## Release Notes

- **New Features**
- Enhanced handling of color information in ROI parameters, allowing for
greater flexibility with color keys.
- Improved compatibility with newer versions of `napari` by adjusting
colormap settings.

- **Bug Fixes**
- Ensured default color values are returned correctly when no regions of
interest are present.

- **Documentation**
	- Updated type annotations for better clarity and usability.

- **Tests**
- Enhanced test cases related to color handling and ROI parameters to
improve robustness.
- Added version checks for `napari` to ensure correct behavior based on
library version.
<!-- end of auto-generated comment: release notes by coderabbit.ai -->

---------

Co-authored-by: sourcery-ai[bot] <58596630+sourcery-ai[bot]@users.noreply.github.com>

package/PartSeg/_launcher/check_version.py

@@ -24,9 +24,7 @@ class CheckVersionThread(QThread):
     .. _PYPI: https://pypi.org/project/PartSeg/
     """
 
-    def __init__(
-        self, package_name="PartSeg", default_url="https://4dnucleome.cent.uw.edu.pl/PartSeg/", base_version=__version__
-    ):
+    def __init__(self, package_name="PartSeg", default_url="https://partseg.github.io/", base_version=__version__):
         super().__init__()
         self.release = base_version
         self.base_release = base_version
@@ -57,7 +55,7 @@ def run(self):
         except (KeyError, urllib.error.URLError):  # pragma: no cover
             pass
         except Exception as e:  # pylint: disable=broad-except
-            with sentry_sdk.push_scope() as scope:
+            with sentry_sdk.new_scope() as scope:
                 scope.set_tag("auto_report", "true")
                 scope.set_tag("check_version", "true")
                 sentry_sdk.capture_exception(e)

package/PartSeg/common_backend/except_hook.py

@@ -24,7 +24,7 @@ def my_excepthook(type_, value, trace_back):
     # log the exception here
     if state_store.show_error_dialog and not isinstance(value, KeyboardInterrupt):
         if state_store.auto_report or state_store.always_report:
-            with sentry_sdk.push_scope() as scope:
+            with sentry_sdk.new_scope() as scope:
                 scope.set_tag("auto_report", "true")
                 scope.set_tag("main_thread", QCoreApplication.instance().thread() == QThread.currentThread())
                 sentry_sdk.capture_exception(value)

package/PartSeg/common_gui/error_report.py

@@ -201,7 +201,7 @@ def send_report(self):
         """
         Function with construct final error message and send it using sentry.
         """
-        with sentry_sdk.push_scope() as scope:
+        with sentry_sdk.new_scope() as scope:
             text = f"{self.desc.text()}\n\nVersion: {__version__}\n"
             if len(self.additional_notes) > 0:
                 scope.set_extra("additional_notes", self.additional_notes)
@@ -217,7 +217,7 @@ def send_report(self):
 
             event_id = sentry_sdk.capture_event(event, hint=hint)
         if event_id is None:
-            event_id = sentry_sdk.hub.Hub.current.last_event_id()
+            event_id = sentry_sdk.scope.Scope.last_event_id()
 
         if len(self.additional_info.toPlainText()) > 0:
             contact_text = self.contact_info.text()

package/PartSeg/common_gui/napari_image_view.py

@@ -43,6 +43,7 @@
     from napari._qt.widgets.qt_viewer_buttons import QtViewerPushButton as QtViewerPushButton_
 _napari_ge_4_13 = parse_version(napari.__version__) >= parse_version("0.4.13a1")
 _napari_ge_4_17 = parse_version(napari.__version__) >= parse_version("0.4.17a1")
+_napari_ge_4_19 = parse_version(napari.__version__) >= parse_version("0.4.19")
 _napari_ge_5 = parse_version(napari.__version__) >= parse_version("0.5.0a1")
 
 # if run with numpy<2 on macOS arm64 architecture compiled from pypi wheels
@@ -112,7 +113,7 @@ def __init__(self, viewer):
 ORDER_DICT = {"xy": [0, 1, 2, 3], "zy": [0, 2, 1, 3], "zx": [0, 3, 1, 2]}
 NEXT_ORDER = {"xy": "zy", "zy": "zx", "zx": "xy"}
 
-ColorInfo = Dict[int, Union[str, List[float]]]
+ColorInfo = Dict[Optional[int], Union[str, List[float]]]
 
 
 @dataclass
@@ -480,15 +481,18 @@ def get_roi_view_parameters(self, image_info: ImageInfo) -> ColorInfo:
             or image_info.roi_count == 0
             or colors.size == 0
         ):
-            return {x: [0, 0, 0, 0] for x in range(image_info.roi_count + 1)}
+            return {0: [0, 0, 0, 0], None: [0, 0, 0, 0]}
 
         res = {x: colors[(x - 1) % colors.shape[0]] for x in range(1, image_info.roi_count + 1)}
         res[0] = [0, 0, 0, 0]
+        res[None] = [0, 0, 0, 0]
         return res
 
     def set_roi_colormap(self, image_info) -> None:
-        if _napari_ge_5:
-            image_info.roi.colormap = self.get_roi_view_parameters(image_info)
+        if _napari_ge_4_19:
+            from napari.utils.colormaps import DirectLabelColormap
+
+            image_info.roi.colormap = DirectLabelColormap(color_dict=self.get_roi_view_parameters(image_info))
             return
         if _napari_ge_4_13:
             image_info.roi.color = self.get_roi_view_parameters(image_info)
@@ -591,8 +595,10 @@ def set_mask(self, mask: Optional[np.ndarray] = None, image: Optional[Image] = N
         else:
             image_info.mask.data = mask_marker
         image_info.mask.metadata["valid"] = True
-        if _napari_ge_5:
-            image_info.mask.colormap = self.mask_color()
+        if _napari_ge_4_19:
+            from napari.utils.colormaps import DirectLabelColormap
+
+            image_info.mask.colormap = DirectLabelColormap(color_dict=self.mask_color())
         else:
             image_info.mask.color = self.mask_color()
         image_info.mask.opacity = self.mask_opacity()
@@ -613,8 +619,10 @@ def update_mask_parameters(self):
         for image_info in self.image_info.values():
             if image_info.mask is not None:
                 image_info.mask.opacity = opacity
-                if _napari_ge_5:
-                    image_info.mask.colormap = colormap
+                if _napari_ge_4_19:
+                    from napari.utils.colormaps import DirectLabelColormap
+
+                    image_info.mask.colormap = DirectLabelColormap(color_dict=colormap)
                 else:
                     image_info.mask.color = colormap
 

package/PartSeg/plugins/napari_widgets/lables_control.py

@@ -11,6 +11,7 @@
 from PartSeg.plugins.napari_widgets._settings import get_settings
 
 NAPARI_GE_5_0 = parse_version(version("napari")) >= parse_version("0.5.0a1")
+NAPARI_GE_4_19 = parse_version(version("napari")) >= parse_version("0.4.19a1")
 
 
 class NapariLabelShow(LabelShow):
@@ -41,8 +42,10 @@ def apply_label(self):
             max_val = layer.data.max()
             labels = {i + 1: [x / 255 for x in self.label[i % len(self.label)]] for i in range(max_val + 5)}
             labels[None] = [0, 0, 0, 0]
-            if NAPARI_GE_5_0:
-                layer.colormap = labels
+            if NAPARI_GE_4_19:
+                from napari.utils.colormaps import DirectLabelColormap
+
+                layer.colormap = DirectLabelColormap(color_dict=labels)
             else:
                 layer.color = labels
 

package/PartSeg/plugins/napari_widgets/search_label_widget.py

@@ -106,6 +106,7 @@ def _shift_if_need(self, labels, bound_info):
         u_bound = upper_bound[-2:][::-1]
         with warnings.catch_warnings():
             warnings.filterwarnings("ignore", "Public access to Window.qt_viewer")
+            warnings.filterwarnings("ignore", "Access to QtViewer.view is deprecated")
             rect = Rect(self.napari_viewer.window.qt_viewer.view.camera.get_state()["rect"])
         if rect.contains(*l_bound) and rect.contains(*u_bound):
             return
@@ -123,6 +124,7 @@ def _shift_if_need(self, labels, bound_info):
         rect.pos = pos
         with warnings.catch_warnings():
             warnings.filterwarnings("ignore", "Public access to Window.qt_viewer")
+            warnings.filterwarnings("ignore", "Access to QtViewer.view is deprecated")
             self.napari_viewer.window.qt_viewer.view.camera.set_state({"rect": rect})
 
     @staticmethod
@@ -146,6 +148,7 @@ def _zoom(self):
             rect = Rect(pos=(lower_bound - frame)[-2:][::-1], size=(diff + 2 * frame)[-2:][::-1])
             with warnings.catch_warnings():
                 warnings.filterwarnings("ignore", "Public access to Window.qt_viewer")
+                warnings.filterwarnings("ignore", "Access to QtViewer.view is deprecated")
                 self.napari_viewer.window.qt_viewer.view.camera.set_state({"rect": rect})
         self._update_point(lower_bound, upper_bound)
 

package/PartSegCore/analysis/batch_processing/batch_backend.py

@@ -602,8 +602,11 @@ def get_data_to_write(self) -> tuple[str, pd.DataFrame]:
         """
         sorted_row = [x[1] for x in sorted(self.row_list)]
         df = pd.DataFrame(sorted_row, columns=self.columns)
-        df2 = pd.concat((self.data_frame, df), axis=0)
-        self.data_frame = df2.reset_index(drop=True)
+        if self.data_frame.empty:
+            self.data_frame = df.reset_index(drop=True)
+        else:
+            df2 = pd.concat((self.data_frame, df), axis=0)
+            self.data_frame = df2.reset_index(drop=True)
         self.row_list = []
         return self.name, self.data_frame
 
@@ -840,7 +843,7 @@ def write_to_excel(
 
             if errors:
                 errors_data = pd.DataFrame(errors, columns=["File path", "error description"])
-                errors_data.to_excel(writer, "Errors")
+                errors_data.to_excel(writer, sheet_name="Errors")
 
     @staticmethod
     def write_calculation_plan(writer: pd.ExcelWriter, calculation_plan: CalculationPlan):

package/PartSegImage/image_reader.py

@@ -71,13 +71,13 @@ def decode_zstd1(data: bytes) -> np.ndarray:
     header = parse_zstd1_header(data, len(data))
     dtype = _get_dtype()
     if header.hiLoByteUnpackPreprocessing:
-        array_ = np.fromstring(imagecodecs.zstd_decode(data[header.header_size :]), np.uint8)
+        array_ = np.frombuffer(imagecodecs.zstd_decode(data[header.header_size :]), np.uint8).copy()
         half_size = array_.size // 2
         array = np.empty(half_size, np.uint16)
         array[:] = array_[:half_size] + (array_[half_size:].astype(np.uint16) << 8)
         array = array.view(dtype)
     else:
-        array = np.fromstring(imagecodecs.zstd_decode(data[header.header_size :]), dtype)
+        array = np.frombuffer(imagecodecs.zstd_decode(data[header.header_size :]), dtype).copy()
     return array
 
 
@@ -86,7 +86,7 @@ def decode_zstd0(data: bytes) -> np.ndarray:
     Decode ZSTD0 data
     """
     dtype = _get_dtype()
-    return np.fromstring(imagecodecs.zstd_decode(data), dtype)
+    return np.frombuffer(imagecodecs.zstd_decode(data), dtype).copy()
 
 
 if parse_version(version("czifile")) == parse_version("2019.7.2"):
@@ -306,7 +306,10 @@ class OifImagReader(BaseImageReader):
     def read(self, image_path: typing.Union[str, Path], mask_path=None, ext=None) -> Image:
         with OifFile(image_path) as image_file:
             tiffs = tifffile.natural_sorted(image_file.glob("*.tif"))
-            with tifffile.TiffFile(image_file.open_file(tiffs[0]), name=tiffs[0]) as tif_file:
+
+            with image_file.open_file(tiffs[0]) as tiff_buffer, tifffile.TiffFile(
+                tiff_buffer, name=tiffs[0]
+            ) as tif_file:
                 axes = image_file.series[0].axes + tif_file.series[0].axes
             image_data = image_file.asarray()
             image_data = self.update_array_shape(image_data, axes)
@@ -366,6 +369,7 @@ def read(self, image_path: typing.Union[str, BytesIO, Path], mask_path=None, ext
         # TODO add mask reading
         if isinstance(image_path, BytesIO):
             image_path = ""
+        image_file.close()
         return self.image_class(
             image_data,
             self.spacing,

package/tests/test_PartSeg/test_check_release.py

@@ -1,4 +1,5 @@
 import json
+import urllib.error
 import urllib.request
 from datetime import date, timedelta
 from io import StringIO
@@ -68,15 +69,17 @@ def exec_():
         assert "You can update it from pypi" in values[1]
 
 
-def test_no_update(monkeypatch, qtbot):
-    monkeypatch.setattr("PartSeg.state_store.save_folder", False)
+def test_no_update(monkeypatch, qtbot, tmp_path):
+    # check if nothing is reported on ulr error
+    monkeypatch.setattr("PartSeg.state_store.save_folder", tmp_path)
 
     def urlopen_mock(url):
-        raise RuntimeError
+        raise urllib.error.URLError("test purpose")
 
     monkeypatch.setattr(urllib.request, "urlopen", urlopen_mock)
-    chk_thr = check_version.CheckVersionThread()
+    chk_thr = check_version.CheckVersionThread(base_version="0.10.0")
     chk_thr.run()
+    assert chk_thr.release == "0.10.0"
 
 
 def test_error_report(monkeypatch, qtbot):
@@ -118,13 +121,15 @@ def test_ignore_file_exists_old_date(monkeypatch, qtbot, tmp_path):
     monkeypatch.setattr(state_store, "save_folder", tmp_path)
 
     def urlopen_mock(_url):
-        return StringIO("")
+        return StringIO('{"info": {"version": "0.11.0", "home_page": "example.org"}}')
 
     monkeypatch.setattr(urllib.request, "urlopen", urlopen_mock)
 
-    chk_thr = check_version.CheckVersionThread()
+    chk_thr = check_version.CheckVersionThread(base_version="0.10.0")
     chk_thr.run()
     assert not (tmp_path / IGNORE_FILE).exists()
+    assert chk_thr.release == "0.11.0"
+    assert chk_thr.url == "example.org"
 
 
 def test_create_ignore(qtbot, tmp_path, monkeypatch):

package/tests/test_PartSeg/test_common_gui.py

@@ -1767,7 +1767,7 @@ def test_create_issue(self, mock_web, qtbot):
         assert "body=This" in mock_web.call_args.args[0]
 
     @patch("requests.post")
-    @patch("sentry_sdk.push_scope")
+    @patch("sentry_sdk.new_scope")
     def test_send_report(self, sentry_mock, request_mock, qtbot):
         dialog = ErrorDialog(ValueError("aaa"), "Test text")
         qtbot.addWidget(dialog)
@@ -1777,7 +1777,7 @@ def test_send_report(self, sentry_mock, request_mock, qtbot):
         request_mock.assert_not_called()
 
     @patch("requests.post")
-    @patch("sentry_sdk.push_scope")
+    @patch("sentry_sdk.new_scope")
     @pytest.mark.parametrize(
         ("email", "expected", "return_code", "post_call_count"),
         [

package/tests/test_PartSeg/test_napari_image_view.py

@@ -28,16 +28,20 @@
 from PartSegImage import Image
 
 NAPARI_GE_5_0 = parse_version(version("napari")) >= parse_version("0.5.0a1")
+NAPARI_GE_4_19 = parse_version(version("napari")) >= parse_version("0.4.19a1")
 
 
 if NAPARI_GE_5_0:
     EXPECTED_RANGE = (0, 0, 1)
+else:
+    EXPECTED_RANGE = (0, 1, 1)
+
+if NAPARI_GE_4_19:
 
     def get_color_dict(layer):
         return layer.colormap.color_dict
 
 else:
-    EXPECTED_RANGE = (0, 1, 1)
 
     def get_color_dict(layer):
         return layer.color

package/tests/test_PartSeg/test_napari_widgets.py

@@ -58,8 +58,9 @@
 from PartSegCore.segmentation.watershed import WatershedSelection
 
 NAPARI_GE_5_0 = parse_version(version("napari")) >= parse_version("0.5.0a1")
+NAPARI_GE_4_19 = parse_version(version("napari")) >= parse_version("0.4.19a1")
 
-if NAPARI_GE_5_0:
+if NAPARI_GE_4_19:
 
     def check_auto_mode(layer):
         from napari.utils.colormaps import CyclicLabelColormap
@@ -387,7 +388,8 @@ def test_napari_label_show(viewer_with_data, qtbot):
     viewer_with_data.layers.selection.remove(viewer_with_data.layers["image"])
     assert widget.apply_label_btn.isEnabled()
     check_auto_mode(viewer_with_data.layers["label"])
-    widget.apply_label_btn.click()
+    with qtbot.waitSignal(widget.apply_label_btn.clicked):
+        widget.apply_label_btn.click()
     check_direct_mode(viewer_with_data.layers["label"])