TwoPy 0.3.8__tar.gz → 0.4.0__tar.gz

{twopy-0.3.8 → twopy-0.4.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: twopy
-Version: 0.3.8
+Version: 0.4.0
 Summary: Two-photon imaging analysis tool with a napari interface.
 Author-email: Gustavo Madeira Santana <fromweb1@gumadeiras.com>
 License-Expression: MIT
@@ -31,7 +31,7 @@ Two-photon imaging analysis tool for the Clark Lab output format.
 
 twopy lets you open two-photon recordings, draw ROIs, plot responses in real time, process and analyze them, and save them.
 
-When you first load a recording, twopy converts it to HDF5 files that it owns. Those files include the aligned movie, mean image, stimulus tables, photodiode signals, and recording metadata. Analysis and the GUI both work from the converted files, so the original source files remain separate from twopy's outputs. By default, converted recordings and interactive analysis outputs are cached locally under `~/.cache/twopy/recordings` for speed; saving ROIs and analysis copies the changed output files back to the configured `analysis_output` location in the background.
+When you first load a recording, twopy converts it to HDF5 files that it owns. These files contain the aligned movie, mean image, stimulus tables, photodiode signals, and recording metadata. Analysis and the GUI use only the converted files. Thus, the original source files stay separate from twopy outputs. By default, twopy uses `~/.cache/twopy/recordings` as a local cache. When you save ROIs and analysis, twopy copies changed files to `analysis_output` in the background.
 
 ## Install
 
@@ -55,7 +55,7 @@ Create the config template in your user folder:
 twopy config setup
 ```
 
-twopy prints the config path it wrote. On macOS and Linux the default is `~/.config/twopy/config.yml`; on Windows it is under `%APPDATA%\twopy\config.yml`. Edit that file with your database, data, and output paths before launching twopy. If you launch `twopy` before a config exists, twopy creates the same template, prints the path, and stops so you can edit it.
+twopy prints the config path that it wrote. The default path on macOS and Linux is `~/.config/twopy/config.yml`. On Windows, the path is under `%APPDATA%\twopy\config.yml`. Before you start twopy, add your database, data, and output paths to that file. If the config does not exist, twopy creates the template and prints its path. Then, twopy stops so you can edit it.
 
 Validate the active config and show its path and file contents:
 

{twopy-0.3.8 → twopy-0.4.0}/README.md

@@ -8,7 +8,7 @@ Two-photon imaging analysis tool for the Clark Lab output format.
 
 twopy lets you open two-photon recordings, draw ROIs, plot responses in real time, process and analyze them, and save them.
 
-When you first load a recording, twopy converts it to HDF5 files that it owns. Those files include the aligned movie, mean image, stimulus tables, photodiode signals, and recording metadata. Analysis and the GUI both work from the converted files, so the original source files remain separate from twopy's outputs. By default, converted recordings and interactive analysis outputs are cached locally under `~/.cache/twopy/recordings` for speed; saving ROIs and analysis copies the changed output files back to the configured `analysis_output` location in the background.
+When you first load a recording, twopy converts it to HDF5 files that it owns. These files contain the aligned movie, mean image, stimulus tables, photodiode signals, and recording metadata. Analysis and the GUI use only the converted files. Thus, the original source files stay separate from twopy outputs. By default, twopy uses `~/.cache/twopy/recordings` as a local cache. When you save ROIs and analysis, twopy copies changed files to `analysis_output` in the background.
 
 ## Install
 
@@ -32,7 +32,7 @@ Create the config template in your user folder:
 twopy config setup
 ```
 
-twopy prints the config path it wrote. On macOS and Linux the default is `~/.config/twopy/config.yml`; on Windows it is under `%APPDATA%\twopy\config.yml`. Edit that file with your database, data, and output paths before launching twopy. If you launch `twopy` before a config exists, twopy creates the same template, prints the path, and stops so you can edit it.
+twopy prints the config path that it wrote. The default path on macOS and Linux is `~/.config/twopy/config.yml`. On Windows, the path is under `%APPDATA%\twopy\config.yml`. Before you start twopy, add your database, data, and output paths to that file. If the config does not exist, twopy creates the template and prints its path. Then, twopy stops so you can edit it.
 
 Validate the active config and show its path and file contents:
 

{twopy-0.3.8 → twopy-0.4.0}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "twopy"
-version = "0.3.8"
+version = "0.4.0"
 description = "Two-photon imaging analysis tool with a napari interface."
 readme = "README.md"
 requires-python = ">=3.13,<3.14"

{twopy-0.3.8 → twopy-0.4.0}/src/twopy/analysis/background_subtraction.py

@@ -5,7 +5,7 @@ Outputs: raw ROI traces, estimated background traces, corrected traces, and
 method metadata.
 
 This module owns analysis-time background correction. ROI storage and raw ROI
-trace extraction stay in ``twopy.roi``; dF/F and trial analysis can consume the
+trace extraction stay in ``twopy.roi``. dF/F and trial analysis can use the
 auditable outputs produced here.
 """
 
@@ -243,8 +243,8 @@ def _validate_background_method(method: BackgroundCorrectionMethod) -> None:
     }
     if method not in allowed_methods:
         msg = (
-            f"Unknown background correction method {method!r}; "
-            f"supported methods: {', '.join(sorted(allowed_methods))}"
+            f"Unknown background correction method {method!r}. "
+            f"Supported methods: {', '.join(sorted(allowed_methods))}"
         )
         raise ValueError(msg)
 
@@ -722,7 +722,7 @@ def _crop_roi_masks_for_domain(
     if outside.size:
         msg = (
             "ROI pixels fall outside the selected spatial domain "
-            f"{spatial_crop.source}; affected ROI indices: {outside.tolist()}"
+            f"{spatial_crop.source}. Affected ROI indices: {outside.tolist()}"
         )
         raise ValueError(msg)
     return cropped_masks
@@ -759,7 +759,7 @@ def _validate_percentile(percentile: float) -> None:
     rule at the extremes.
     """
     if not 0.0 < percentile < 100.0:
-        msg = f"Background percentile must be between 0 and 100; got {percentile}"
+        msg = f"Background percentile must be between 0 and 100. Got {percentile}"
         raise ValueError(msg)
 
 
@@ -808,7 +808,7 @@ def _resolve_roi_y_stripe_radius(
     """
     radius = max(1, round(row_count / 20)) if local_y_radius is None else local_y_radius
     if radius < 0:
-        msg = f"local_y_radius must be nonnegative; got {radius}"
+        msg = f"local_y_radius must be nonnegative. Got {radius}"
         raise ValueError(msg)
     return radius
 
@@ -831,7 +831,7 @@ def _resolve_stripe_y_height(
         max(1, round(row_count / 20)) if stripe_y_height is None else stripe_y_height
     )
     if height <= 0:
-        msg = f"stripe_y_height must be positive; got {height}"
+        msg = f"stripe_y_height must be positive. Got {height}"
         raise ValueError(msg)
     return height
 
@@ -912,8 +912,8 @@ def _roi_y_stripe_background_pixel_indices(
         msg = (
             "ROI y-stripe P% background subtraction needs unlabeled background "
             "pixels outside all ROIs in the selected spatial domain. The current "
-            "ROI masks cover every pixel, which is common for dense grid ROIs; "
-            "use shared y-stripe P% or leave unlabeled background pixels."
+            "ROI masks cover every pixel, which is common for dense grid ROIs. "
+            "Use shared y-stripe P% or leave unlabeled background pixels."
         )
         raise ValueError(msg)
 
@@ -930,7 +930,7 @@ def _roi_y_stripe_background_pixel_indices(
             msg = (
                 f"ROI {roi_index} has no local background candidates within "
                 f"{local_y_radius} rows. ROI y-stripe P% only uses unlabeled "
-                "pixels outside all ROIs; increase the local y radius, use "
+                "pixels outside all ROIs. Increase the local y radius, use "
                 "shared y-stripe P%, or leave unlabeled background pixels near "
                 "this ROI."
             )

{twopy-0.3.8 → twopy-0.4.0}/src/twopy/analysis/dff.py

@@ -6,7 +6,7 @@ Outputs: ROI dF/F traces, fitted baselines, shared exponential tau, and
 per-ROI amplitudes.
 
 This module owns ROI-level dF/F calculation from twopy Python objects. It does
-not decide which stimulus events are baseline epochs; callers pass explicit
+not decide which stimulus events are baseline epochs. Callers pass explicit
 baseline windows derived from converted data and photodiode alignment.
 """
 
@@ -200,8 +200,8 @@ def _validate_dff_inputs(
         raise ValueError(msg)
     if traces.corrected_values.shape[1] != len(traces.labels):
         msg = (
-            "ROI labels must match corrected_values width; "
-            f"got {len(traces.labels)} labels for "
+            "ROI labels must match corrected_values width. "
+            f"Got {len(traces.labels)} labels for "
             f"{traces.corrected_values.shape[1]} ROIs"
         )
         raise ValueError(msg)
@@ -209,12 +209,12 @@ def _validate_dff_inputs(
         msg = "At least one baseline window is required for dF/F"
         raise ValueError(msg)
     if data_rate_hz <= 0:
-        msg = f"data_rate_hz must be positive; got {data_rate_hz}"
+        msg = f"data_rate_hz must be positive. Got {data_rate_hz}"
         raise ValueError(msg)
     if baseline_sample_seconds is not None and baseline_sample_seconds <= 0:
         msg = (
-            "baseline_sample_seconds must be positive or None; "
-            f"got {baseline_sample_seconds}"
+            "baseline_sample_seconds must be positive or None. "
+            f"Got {baseline_sample_seconds}"
         )
         raise ValueError(msg)
     if fit_mode not in _FIT_MODES:
@@ -267,7 +267,7 @@ def _baseline_samples(
         duration = sample_stop - sample_start
         absolute_sample_start = trace_start_frame + sample_start
         # The fit uses one-based movie frame numbers centered on the averaged
-        # half-open sample range. Local indices slice the trace array; absolute
+        # half-open sample range. Local indices slice the trace array. Absolute
         # frame numbers preserve the recording-wide time coordinate.
         frame_numbers.append(float(absolute_sample_start + 1) + (duration / 2.0))
         values.append(fluorescence[sample_start:sample_stop, :].mean(axis=0))
@@ -298,7 +298,7 @@ def _validate_baseline_samples_for_background_method(
     minimum = float(np.nanmin(baseline_samples.values[:, roi_indices]))
     msg = (
         "ROI y-stripe P% background subtraction over-subtracted baseline "
-        f"fluorescence for {labels}; minimum corrected baseline sample is "
+        f"fluorescence for {labels}. Minimum corrected baseline sample is "
         f"{minimum:.6g}. dF/F needs positive baseline fluorescence, so the "
         "local y-stripe pixels are not a valid additive background for those "
         "ROIs. Use shared y-stripe P%, global percentile, or revise the ROIs "
@@ -383,10 +383,10 @@ def _fit_shared_tau(
         Shared exponential ``tau``.
 
     The fit model is ``exp(tau * t + b)`` on the ROI-averaged baseline trace.
-    Only ``tau`` is shared; per-ROI amplitudes are computed in a separate
+    Only ``tau`` is shared. Per-ROI amplitudes are computed in a separate
     transparent step. ``direct_bounded_tau`` handles nonpositive outliers
-    defensively; ``direct_bounded_tau_and_log_amplitude`` preserves a bounded
-    log-amplitude contract; and ``log_linear`` fits in log space.
+    defensively. ``direct_bounded_tau_and_log_amplitude`` preserves a bounded
+    log-amplitude contract. The ``log_linear`` method fits in log space.
     """
     if fit_mode == "log_linear":
         return _fit_shared_tau_log_linear(
@@ -532,8 +532,8 @@ def _fit_shared_tau_with_bounded_log_amplitude(
         msg = (
             "direct_bounded_tau_and_log_amplitude dF/F fit requires first "
             "baseline fluorescence greater than 1.0 to define an ordered "
-            "log-amplitude bound; "
-            f"got {first_value}"
+            "log-amplitude bound. "
+            f"Got {first_value}"
         )
         raise ValueError(msg)
     if np.any(mean_fluorescence <= 0):

{twopy-0.3.8 → twopy-0.4.0}/src/twopy/analysis/epoch_mapping.py

@@ -118,7 +118,7 @@ def _interpolate_epoch_numbers(
         Integer epoch number per imaging frame.
     """
     if frame_count < 1:
-        msg = f"frame_count must be positive; got {frame_count}"
+        msg = f"frame_count must be positive. Got {frame_count}"
         raise ValueError(msg)
 
     positive = epoch_values != 0

{twopy-0.3.8 → twopy-0.4.0}/src/twopy/analysis/group_matching.py

@@ -588,7 +588,7 @@ def _validate_status(status: ManualRoiMatchStatus) -> ManualRoiMatchStatus:
 def _validate_group_cell_id(group_cell_id: int) -> int:
     """Return a positive group-cell id."""
     if group_cell_id < 1:
-        msg = f"Manual ROI group_cell_id must be positive; got {group_cell_id}."
+        msg = f"Manual ROI group_cell_id must be positive. Got {group_cell_id}."
         raise ValueError(msg)
     return group_cell_id
 

{twopy-0.3.8 → twopy-0.4.0}/src/twopy/analysis/kernels/__init__.py

@@ -2,7 +2,7 @@
 
 Inputs: converted stimulus tables plus ROI response traces computed by twopy.
 Outputs: per-ROI temporal kernels on the stimulus sample clock. Olfactory
-recordings expose left/right and ipsi/contra kernels; visual recordings expose
+recordings expose left/right and ipsi/contra kernels. Visual recordings expose
 one contrast kernel.
 
 This package keeps reverse-correlation analysis native to twopy data. It does
@@ -65,7 +65,7 @@ class StimulusKernelOptions:
             epochs and applies ``discard_first_stimulus_epoch``.
         num_stim_past: Number of stimulus samples before a response sample.
         num_stim_future: Number of stimulus samples after a response sample.
-        method: Fitting method. ``"ols"`` solves a least-squares design matrix;
+        method: Fitting method. ``"ols"`` solves a least-squares design matrix.
             ``"xcorr"`` computes reverse correlation.
         hemisphere: Recording hemisphere used to map raw left/right streams to
             ipsi/contra. ``None`` reads the value from converted recording
@@ -93,7 +93,7 @@ class RecordingKernelFit:
     Args:
         roi_labels: Labels for the fitted ROI rows.
         time_seconds: Kernel sample times. Negative times are future stimulus
-            samples; positive times are stimulus samples before the response.
+            samples. Positive times are stimulus samples before the response.
         stimulus_modality: Sensory modality used to interpret the stimulus.
         stimulus_column: Converted stimulus column used for fitting.
         epoch_names: Unique readable epoch names fitted independently.
@@ -347,6 +347,6 @@ def _validate_options(options: StimulusKernelOptions) -> None:
         raise ValueError(msg)
     if options.hemisphere is not None and options.hemisphere not in {"left", "right"}:
         msg = (
-            f"hemisphere must be 'left', 'right', or None; got {options.hemisphere!r}."
+            f"hemisphere must be 'left', 'right', or None. Got {options.hemisphere!r}."
         )
         raise ValueError(msg)

{twopy-0.3.8 → twopy-0.4.0}/src/twopy/analysis/persistence.py

@@ -164,7 +164,7 @@ def save_analysis_outputs(
     The HDF5 file is the complete audit trail. CSV files are derived exports for
     quick spreadsheet plotting and checks, and are written after the HDF5 file.
     Each output file is written through a temporary sibling path so a failed
-    write leaves the previous complete file in place; the HDF5 and CSV files are
+    write leaves the previous complete file in place. The HDF5 and CSV files are
     not replaced as one multi-file transaction.
     """
     summary_outputs = (

{twopy-0.3.8 → twopy-0.4.0}/src/twopy/analysis/response_maps.py

@@ -86,7 +86,7 @@ class ResponseMapOptions:
     finite response across all epochs has magnitude 1. The original dF/F divisor
     is stored on ``ResponseMapData``.
 
-    Pixel mode is the default because it preserves spatial detail; its default
+    Pixel mode is the default because it preserves spatial detail. Its default
     two-pixel Gaussian smoothing reduces isolated noisy pixels without changing
     the saved analysis contract. Window mode is useful when users want explicit
     block averaging before dF/F. Window size and stride are constrained by the
@@ -110,7 +110,7 @@ class EpochResponseMap:
         epoch_number: One-based stimulus epoch number.
         response_values: Movie-coordinate signed response map for the displayed
             crop. Values are normalized by ``ResponseMapData.response_scale``
-            after epoch averaging; multiply by that scale to recover the
+            after epoch averaging. Multiply by that scale to recover the
             original dF/F magnitude.
         trial_count: Number of trials averaged into the map.
     """
@@ -165,7 +165,7 @@ def compute_recording_response_maps(
 
     This reads the converted aligned movie for the valid crop, not microscope
     source MAT/TIFF files. Callers can pass explicit epoch windows for tests or
-    audits; normal workflows let twopy derive photodiode-aligned windows from
+    audits. Normal workflows let twopy derive photodiode-aligned windows from
     converted synchronization metadata.
     """
     resolved_options = options or ResponseMapOptions()
@@ -398,20 +398,20 @@ def _require_response_map_shapes(map_data: ResponseMapData) -> None:
     """Require heatmap spatial arrays to match their recorded crop."""
     if map_data.mean_image.ndim != 2:
         msg = (
-            f"response heatmap mean_image must be 2-D; got {map_data.mean_image.shape}"
+            f"response heatmap mean_image must be 2-D. Got {map_data.mean_image.shape}"
         )
         raise ValueError(msg)
     if map_data.mean_image.shape != map_data.spatial_crop.shape:
         msg = (
-            "response heatmap mean_image shape must match spatial_crop shape; "
-            f"got {map_data.mean_image.shape} and {map_data.spatial_crop.shape}"
+            "response heatmap mean_image shape must match spatial_crop shape. "
+            f"Got {map_data.mean_image.shape} and {map_data.spatial_crop.shape}"
         )
         raise ValueError(msg)
     for epoch in map_data.epochs:
         if epoch.response_values.shape != map_data.mean_image.shape:
             msg = (
                 "response heatmap response_values shape must match mean_image "
-                f"shape; got {epoch.response_values.shape} for "
+                f"shape. Got {epoch.response_values.shape} for "
                 f"{epoch.epoch_name!r} and {map_data.mean_image.shape}"
             )
             raise ValueError(msg)
@@ -454,22 +454,22 @@ def _validate_options(options: ResponseMapOptions, shape: tuple[int, int]) -> No
         or options.pixel_smoothing_sigma < 0
     ):
         msg = (
-            "pixel_smoothing_sigma must be finite and nonnegative; "
-            f"got {options.pixel_smoothing_sigma}"
+            "pixel_smoothing_sigma must be finite and nonnegative. "
+            f"Got {options.pixel_smoothing_sigma}"
         )
         raise ValueError(msg)
     if options.window_size_pixels < 1:
-        msg = f"window_size_pixels must be positive; got {options.window_size_pixels}"
+        msg = f"window_size_pixels must be positive. Got {options.window_size_pixels}"
         raise ValueError(msg)
     if options.window_stride_pixels < 1:
         msg = (
-            f"window_stride_pixels must be positive; got {options.window_stride_pixels}"
+            f"window_stride_pixels must be positive. Got {options.window_stride_pixels}"
         )
         raise ValueError(msg)
     if options.window_stride_pixels > options.window_size_pixels:
         msg = (
-            "window_stride_pixels cannot exceed window_size_pixels; "
-            f"got {options.window_stride_pixels} > {options.window_size_pixels}"
+            "window_stride_pixels cannot exceed window_size_pixels. "
+            f"Got {options.window_stride_pixels} > {options.window_size_pixels}"
         )
         raise ValueError(msg)
     if options.window_size_pixels > min(shape):
@@ -482,14 +482,14 @@ def _validate_options(options: ResponseMapOptions, shape: tuple[int, int]) -> No
         options.baseline_sample_seconds <= 0
     ):
         msg = (
-            "baseline_sample_seconds must be finite and positive; "
-            f"got {options.baseline_sample_seconds}"
+            "baseline_sample_seconds must be finite and positive. "
+            f"Got {options.baseline_sample_seconds}"
         )
         raise ValueError(msg)
     if not 0.0 <= options.foreground_percentile <= 100.0:
         msg = (
-            "foreground_percentile must be between 0 and 100; "
-            f"got {options.foreground_percentile}"
+            "foreground_percentile must be between 0 and 100. "
+            f"Got {options.foreground_percentile}"
         )
         raise ValueError(msg)
 

{twopy-0.3.8 → twopy-0.4.0}/src/twopy/analysis/response_processing/__init__.py

@@ -6,7 +6,7 @@ Outputs: processed response objects plus optional quality-control scores.
 
 This package is GUI-independent. It owns the math and validates option values
 for response smoothing, low-pass filtering, and correlation-based response
-quality control. Workflow code decides when to call it; persistence code decides
+quality control. Workflow code decides when to call it. Persistence code decides
 how to save the resulting audit trail.
 """
 

{twopy-0.3.8 → twopy-0.4.0}/src/twopy/analysis/response_processing/apply.py

@@ -367,8 +367,8 @@ def _normalization_factors(
     if len(bad_indices) > 0:
         bad_labels = ", ".join(grouped.roi_labels[index] for index in bad_indices)
         msg = (
-            "Normalization epoch must have a nonzero response for every ROI; "
-            f"invalid ROI labels: {bad_labels}"
+            "Normalization epoch must have a nonzero response for every ROI. "
+            f"Invalid ROI labels: {bad_labels}"
         )
         raise ValueError(msg)
     return RoiNormalizationFactors(
@@ -387,8 +387,8 @@ def _mask_excluded_rois(
     """Return grouped responses with excluded ROI columns set to NaN."""
     if included_mask.shape != (len(grouped.roi_labels),):
         msg = (
-            "included_mask must match ROI label count; "
-            f"got {included_mask.shape} for {len(grouped.roi_labels)} labels"
+            "included_mask must match ROI label count. "
+            f"Got {included_mask.shape} for {len(grouped.roi_labels)} labels"
         )
         raise ValueError(msg)
     trials: list[RoiResponseTrial] = []
@@ -427,7 +427,7 @@ def _copy_trial_with_values(
 def _validate_dff_for_processing(dff: RoiDeltaFOverF) -> None:
     """Validate a dF/F object before value-only processing."""
     if dff.values.ndim != 2:
-        msg = f"dF/F values must have shape (frames, rois); got {dff.values.shape}"
+        msg = f"dF/F values must have shape (frames, rois). Got {dff.values.shape}"
         raise ValueError(msg)
     if dff.values.shape[1] != len(dff.labels):
         msg = (

{twopy-0.3.8 → twopy-0.4.0}/src/twopy/analysis/response_processing/options.py

@@ -156,25 +156,25 @@ def _validate_smoothing_options(options: SmoothingOptions) -> None:
         msg = f"Unknown smoothing method {options.method!r}"
         raise ValueError(msg)
     if options.window_frames < 1:
-        msg = f"smoothing window_frames must be at least 1; got {options.window_frames}"
+        msg = f"smoothing window_frames must be at least 1. Got {options.window_frames}"
         raise ValueError(msg)
     if options.polynomial_order < 0:
         msg = (
-            "smoothing polynomial_order must be non-negative; "
-            f"got {options.polynomial_order}"
+            "smoothing polynomial_order must be non-negative. "
+            f"Got {options.polynomial_order}"
         )
         raise ValueError(msg)
     if options.method == "savgol":
         if options.window_frames % 2 == 0:
             msg = (
-                "Savitzky-Golay smoothing window_frames must be odd; "
-                f"got {options.window_frames}"
+                "Savitzky-Golay smoothing window_frames must be odd. "
+                f"Got {options.window_frames}"
             )
             raise ValueError(msg)
         if options.polynomial_order >= options.window_frames:
             msg = (
-                "Savitzky-Golay polynomial_order must be below window_frames; "
-                f"got order {options.polynomial_order} and window "
+                "Savitzky-Golay polynomial_order must be below window_frames. "
+                f"Got order {options.polynomial_order} and window "
                 f"{options.window_frames}"
             )
             raise ValueError(msg)
@@ -190,7 +190,7 @@ def _validate_low_pass_options(
         msg = f"Unknown low-pass method {options.method!r}"
         raise ValueError(msg)
     if options.order < 1:
-        msg = f"low-pass order must be at least 1; got {options.order}"
+        msg = f"low-pass order must be at least 1. Got {options.order}"
         raise ValueError(msg)
     if options.method == "none":
         return
@@ -199,13 +199,13 @@ def _validate_low_pass_options(
         raise ValueError(msg)
     if data_rate_hz is not None:
         if data_rate_hz <= 0:
-            msg = f"data_rate_hz must be positive; got {data_rate_hz}"
+            msg = f"data_rate_hz must be positive. Got {data_rate_hz}"
             raise ValueError(msg)
         nyquist_hz = data_rate_hz / 2.0
         if options.cutoff_hz >= nyquist_hz:
             msg = (
-                "low-pass cutoff_hz must be below Nyquist; "
-                f"got {options.cutoff_hz} Hz for {data_rate_hz} Hz data"
+                "low-pass cutoff_hz must be below Nyquist. "
+                f"Got {options.cutoff_hz} Hz for {data_rate_hz} Hz data"
             )
             raise ValueError(msg)
 
@@ -216,7 +216,7 @@ def _validate_normalization_options(options: NormalizationOptions) -> None:
         msg = f"Unknown normalization method {options.method!r}"
         raise ValueError(msg)
     if options.epoch_number is not None and options.epoch_number < 1:
-        msg = f"normalization epoch_number must be positive; got {options.epoch_number}"
+        msg = f"normalization epoch_number must be positive. Got {options.epoch_number}"
         raise ValueError(msg)
     if options.method == "epoch_abs_peak" and options.epoch_number is None:
         msg = "response-size normalization requires an epoch_number"
@@ -230,16 +230,16 @@ def _validate_correlation_options(options: CorrelationFilterOptions) -> None:
         raise ValueError(msg)
     if not -1.0 <= options.minimum_correlation <= 1.0:
         msg = (
-            "minimum_correlation must be between -1 and 1; "
-            f"got {options.minimum_correlation}"
+            "minimum_correlation must be between -1 and 1. "
+            f"Got {options.minimum_correlation}"
         )
         raise ValueError(msg)
     start_seconds, stop_seconds = options.window_seconds
     if start_seconds is not None and not np.isfinite(start_seconds):
-        msg = f"correlation window start must be finite or None; got {start_seconds}"
+        msg = f"correlation window start must be finite or None. Got {start_seconds}"
         raise ValueError(msg)
     if stop_seconds is not None and not np.isfinite(stop_seconds):
-        msg = f"correlation window stop must be finite or None; got {stop_seconds}"
+        msg = f"correlation window stop must be finite or None. Got {stop_seconds}"
         raise ValueError(msg)
     if (
         start_seconds is not None
@@ -247,7 +247,7 @@ def _validate_correlation_options(options: CorrelationFilterOptions) -> None:
         and start_seconds >= stop_seconds
     ):
         msg = (
-            "correlation window start must be before stop; "
-            f"got ({start_seconds}, {stop_seconds})"
+            "correlation window start must be before stop. "
+            f"Got ({start_seconds}, {stop_seconds})"
         )
         raise ValueError(msg)

{twopy-0.3.8 → twopy-0.4.0}/src/twopy/analysis/response_processing/qc.py

@@ -3,7 +3,7 @@
 Inputs: grouped trial responses with explicit relative time vectors.
 Outputs: ROI-level correlation scores and inclusion masks.
 
-The functions here score response consistency; they do not delete raw data.
+The functions here score response consistency. They do not delete raw data.
 Callers can use the inclusion mask for plotting or summaries while preserving
 the scores as an audit trail.
 """
@@ -179,7 +179,7 @@ def _validate_correlation_inputs(
 ) -> None:
     """Validate grouped-response correlation inputs."""
     if not -1.0 <= minimum_correlation <= 1.0:
-        msg = f"minimum_correlation must be between -1 and 1; got {minimum_correlation}"
+        msg = f"minimum_correlation must be between -1 and 1. Got {minimum_correlation}"
         raise ValueError(msg)
     if reference not in {"epoch_mean", "epoch_peak"}:
         msg = f"Unknown correlation reference {reference!r}"

{twopy-0.3.8 → twopy-0.4.0}/src/twopy/analysis/response_processing/signals.py

@@ -44,7 +44,7 @@ def nan_aware_moving_average(
     whose whole window is NaN remain NaN.
     """
     if window_frames < 1:
-        msg = f"window_frames must be at least 1; got {window_frames}"
+        msg = f"window_frames must be at least 1. Got {window_frames}"
         raise ValueError(msg)
     matrix, was_1d = _as_frame_channel_matrix(values)
     if window_frames == 1:
@@ -155,7 +155,7 @@ def _as_frame_channel_matrix(
         return array.reshape(-1, 1), True
     if array.ndim == 2:
         return array, False
-    msg = f"response values must be 1D or 2D; got shape {array.shape}"
+    msg = f"response values must be 1D or 2D. Got shape {array.shape}"
     raise ValueError(msg)
 
 
@@ -208,20 +208,20 @@ def _validate_low_pass_parameters(
 ) -> None:
     """Validate Butterworth filter parameters."""
     if sample_rate_hz <= 0:
-        msg = f"sample_rate_hz must be positive; got {sample_rate_hz}"
+        msg = f"sample_rate_hz must be positive. Got {sample_rate_hz}"
         raise ValueError(msg)
     if cutoff_hz <= 0:
-        msg = f"cutoff_hz must be positive; got {cutoff_hz}"
+        msg = f"cutoff_hz must be positive. Got {cutoff_hz}"
         raise ValueError(msg)
     nyquist_hz = sample_rate_hz / 2.0
     if cutoff_hz >= nyquist_hz:
         msg = (
-            "cutoff_hz must be below Nyquist; "
-            f"got {cutoff_hz} Hz for {sample_rate_hz} Hz data"
+            "cutoff_hz must be below Nyquist. "
+            f"Got {cutoff_hz} Hz for {sample_rate_hz} Hz data"
         )
         raise ValueError(msg)
     if order < 1:
-        msg = f"order must be at least 1; got {order}"
+        msg = f"order must be at least 1. Got {order}"
         raise ValueError(msg)
 
 
@@ -232,18 +232,18 @@ def _validate_savgol_parameters(
 ) -> None:
     """Validate Savitzky-Golay smoothing parameters."""
     if window_frames < 1:
-        msg = f"window_frames must be at least 1; got {window_frames}"
+        msg = f"window_frames must be at least 1. Got {window_frames}"
         raise ValueError(msg)
     if window_frames % 2 == 0:
-        msg = f"window_frames must be odd for Savitzky-Golay; got {window_frames}"
+        msg = f"window_frames must be odd for Savitzky-Golay. Got {window_frames}"
         raise ValueError(msg)
     if polynomial_order < 0:
-        msg = f"polynomial_order must be non-negative; got {polynomial_order}"
+        msg = f"polynomial_order must be non-negative. Got {polynomial_order}"
         raise ValueError(msg)
     if polynomial_order >= window_frames:
         msg = (
-            "polynomial_order must be below window_frames; "
-            f"got {polynomial_order} and {window_frames}"
+            "polynomial_order must be below window_frames. "
+            f"Got {polynomial_order} and {window_frames}"
         )
         raise ValueError(msg)
 

{twopy-0.3.8 → twopy-0.4.0}/src/twopy/analysis/response_window_options.py

@@ -65,7 +65,7 @@ def resolve_response_window_seconds(
         ValueError: If any supplied window duration is negative.
     """
     if max_window_seconds is not None and max_window_seconds < 0.0:
-        msg = f"max_window_seconds must be non-negative; got {max_window_seconds}"
+        msg = f"max_window_seconds must be non-negative. Got {max_window_seconds}"
         raise ValueError(msg)
     if options.auto:
         pre = _validate_non_negative(
@@ -94,6 +94,6 @@ def _validate_non_negative(value: float, *, name: str) -> float:
     """Return ``value`` as a float after enforcing the response-window domain."""
     resolved = float(value)
     if resolved < 0.0:
-        msg = f"{name} must be non-negative; got {resolved}"
+        msg = f"{name} must be non-negative. Got {resolved}"
         raise ValueError(msg)
     return resolved