synaptipy 0.1.1b4__tar.gz

synaptipy-0.1.1b4/CHANGELOG.md

@@ -0,0 +1,272 @@
+# Changelog
+
+All notable changes to Synaptipy will be documented in this file.
+
+The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
+and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
+
+## [Unreleased]
+
+## [0.1.1b4] - 2026-04-29
+
+### Changed
+
+- Sync `main` branch with `paper_compliance` branch; exclude `paper/` manuscript directory from PyPI distribution.
+- Bump version to 0.1.1b4 across `pyproject.toml`, `src/Synaptipy/__init__.py`, `docs/conf.py`, `CITATION.cff`, `installer/windows_setup.iss`, and `synaptipy.spec`.
+- Fix bundled app icon: `main_window.py` and `welcome_screen.py` now resolve icon path via `sys._MEIPASS` when running as a PyInstaller executable.
+- Configure official PyPI release pipeline: OIDC Trusted Publishing with strict job chain (test -> build -> testpypi-publish -> smoke_test -> pypi-publish -> release).
+
+## [0.1.1b3] - 2026-04-28
+
+### Fixed
+
+- CI: Replace broken `pip index versions` smoke-test check with `curl` against the TestPyPI JSON API.
+- CI: `pypi-publish` job now gates on `needs: [test]`; `release` job gates on `needs: [test, build]`.
+- CI: Add `twine check dist/*` validation step before TestPyPI upload.
+- CI: Add `skip_existing: true` to `pypa/gh-action-pypi-publish` to prevent `400 File already exists` on workflow re-runs.
+- CI: Delete existing GitHub Release for the same tag before re-creating it, preventing `already_exists` errors on re-runs.
+
+## [0.1.1b2] - 2026-04-28
+
+### Changed
+
+- Bumped version to 0.1.1b2.
+- Universal version sync: `pyproject.toml`, `__init__.py`, `docs/conf.py`, `installer/windows_setup.iss`, `CITATION.cff`, `synaptipy.spec`, `README.md`, and `docs/manuals/CROSS_PLATFORM_SETUP.md` all updated to `0.1.1b2`.
+- CI: Release workflow overhauled to use OIDC Trusted Publishing (no API tokens); `pypi-publish` job is now self-contained (checkout, build, publish) with job-level `id-token: write` permissions and `environment: testpypi`.
+- CI: `installer.yml` smoke tests added for all three platforms; pip caching added across all workflows.
+- CI: Codecov badge added to `README.md`; `?branch=main` removed from GitHub Actions badge URLs.
+- `CITATION.cff` date updated to 2026-04-28.
+
+### Added
+
+- **Semantic version bounds**: All scientific dependencies (`numpy`, `scipy`, `neo`, `pyqtgraph`)
+  now carry upper-bound constraints (`<3.0.0`, `<2.0.0`, `<1.0.0`, `<1.0.0`) in
+  `requirements.txt`, `pyproject.toml`, and `environment.yml` so breaking major-version
+  upgrades are blocked until explicitly tested and approved.
+- **Golden master integration tests** (`tests/core/test_golden_master.py`): 10 tests that
+  freeze exact floating-point outputs from `passive_properties` calculations (RMP, Rin,
+  tau, AP peak) against the three bundled ABF data files. Any silent math regression
+  caused by a dependency upgrade will fail these tests immediately.
+- **Headless visual regression tests** (`tests/gui/test_headless_visuals.py`): 11 tests
+  that verify `SynaptipyPlotCanvas` correctly manages `PlotDataItem` and
+  `LinearRegionItem` counts in offscreen mode. Catches rendering regressions introduced
+  by pyqtgraph API changes.
+- **CI matrix jobs**: Two new GitHub Actions jobs in `.github/workflows/test.yml`:
+  - `minimum-viable`: Python 3.10 with exact lower-bound versions (numpy==2.0.0,
+    scipy==1.13.0, neo==0.14.0, pyqtgraph==0.13.0) to ensure the stated minimums work.
+  - `bleeding-edge`: Python 3.12 with all upgradable deps updated to latest
+    (`continue-on-error: true`) to give early warning of upcoming breakage.
+
+## [0.1.0b6] - 2026-03-27
+
+### Changed
+
+- Bumped package version to 0.1.0b6.
+- Documentation: standalone installer links point to the GitHub releases page so beta/pre-release assets are visible (not only `/releases/latest`); filename examples updated to v0.1.0b6.
+
+### Fixed
+
+- `README.md` and `docs/manuals/CROSS_PLATFORM_SETUP.md`: updated installer filename examples from `v0.1.0b5` to `v0.1.0b6`.
+- `docs/index.rst`: replaced em-dashes with standard hyphens; fixed `sphinx-design` grid card indentation from 1-space to 3-space (resolves 12 RST warnings about `grid-item` children).
+- `docs/tutorial/index.md`: replaced 124 em/en-dashes with standard hyphens; corrected 5 ToC anchor links to match MyST-generated section IDs.
+- `docs/extending_synaptipy.md`: replaced 43 em/en-dashes with standard hyphens; corrected 15 ToC anchor links to match MyST-generated section IDs.
+- `docs/conf.py`: added `suppress_warnings = ["myst.xref_missing"]` to suppress false-positive warnings for same-page `#anchor` links in ToC lists (MyST validates these as cross-document references before heading IDs are assigned at parse time; the rendered HTML is correct).
+- Sphinx docs build: reduced warnings from 31 to 0; build now exits clean with zero warnings.
+
+
+## [0.1.0b1] - 2026-03-03
+
+> **First beta release.** Core GUI, all 15 analysis modules, batch processing, NWB export, and plugin interface are functional. Issued as a pre-release for wider testing before a stable 0.1.0 tag.
+
+### Added
+
+- **Sag Ratio Standalone Analysis**: Promoted `sag_ratio_analysis` from an inline
+ computation within `rin_analysis` to its own registered analysis plugin (15th
+ built-in module). Provides dedicated UI controls for baseline, peak, and
+ steady-state windows, Savitzky-Golay smoothing, and rebound depolarisation
+ measurement. Results: `sag_ratio`, `sag_percentage`, `v_peak`, `v_ss`,
+ `v_baseline`, `rebound_depolarization`.
+- **Documentation**: Updated tutorial (§4.15), algorithmic definitions (§4),
+ API reference, user guide, developer guide, README, and extending guide to
+ reflect the new standalone sag ratio analysis and 15 built-in modules.
+- **Deferred Initial Reset for Multichannel**: Generation-counter-protected
+ `_deferred_initial_reset()` catches post-layout `sigResized` shifts for
+ multichannel recordings without interfering with view state restoration.
+- **Custom Analysis Plugin Documentation**: Comprehensive guide (`extending_synaptipy.md`) for writing analysis plugins without modifying source code
+- **Plugin Template**: Ready-to-copy template at `src/Synaptipy/templates/plugin_template.py` with inline comments for all parameter types and plot overlays
+- **Plugin Tests**: 16 tests validating plugin template logic, PluginManager loading, and wrapper conventions
+- **Tutorial Section 3.6**: Step-by-step "Adding Your Own Analysis Tab" section in the user tutorial under the Analyser Tab
+- **Stress Tests**: File cycling stress tests for plot canvas rebuild stability (100 iterations)
+- **Explorer Debounce**: Debounce timer for file navigation to prevent rapid teardown cycles
+- Regression tests for registry population (`test_registry_metadata.py`)
+- Regression tests for preprocessing reset propagation (`test_preprocessing_reset.py`)
+- Developer documentation for registry import rule, editable install, and
+ preprocessing reset propagation (copilot-instructions.md, developer_guide.md)
+
+### Fixed
+
+- **Explorer X-Axis Shift on File Cycling**: Fixed bug where the X-axis would
+ shift right (not starting at 0) when cycling through files, especially with
+ multichannel recordings. Root cause: old ViewBoxes scheduled for
+ `deleteLater()` continued to emit `sigXRangeChanged` / `sigYRangeChanged` /
+ `sigResized` signals after the widget was replaced, corrupting slider and
+ scrollbar values for the new recording. Fix: explicitly disconnect all
+ ViewBox signals in `ExplorerPlotCanvas.rebuild_plots()` before clearing plot
+ items.
+- **Explorer X-Link Range Corruption**: Fixed multichannel X-range corruption
+ caused by `linkedViewChanged()` recalculating ranges from screen-geometry
+ pixel offsets between stacked ViewBoxes. `_reset_view()` now blocks link
+ propagation via `ViewBox.blockLink(True)` while setting ranges, then unblocks.
+- **Overlay Mode Y-Range Too Narrow**: Fixed `_compute_channel_y_range()` to
+ compute Y range from all trials (sampling up to 50 evenly spaced) instead of
+ only trial 0. Previously, if trial 0 was at resting potential but other
+ trials contained action potentials, the Y range was too narrow to display
+ the full signal.
+- **Flaky Qt Tests**: Added `processEvents()` calls in 3 test files to resolve non-deterministic offscreen failures caused by stale deferred ViewBox geometry callbacks
+- **Explorer Plot Layout**: Fixed Windows Explorer plot view state preservation during file cycling
+- **Lint Errors**: Resolved all flake8 CI failures in `analysis_formatter` and `exporter_tab`
+- **CSV Export**: Updated tidy per-type CSV export for batch results
+- **Windows Analysis Loading**: Fixed registry import bug where `AnalysisRegistry` remained
+ empty on Windows because only `registry.py` was imported (not the full
+ `Synaptipy.core.analysis` package that triggers `@register` decorators). Added
+ `import Synaptipy.core.analysis` in `analyser_tab.py` and `startup_manager.py`.
+- **Preprocessing Reset**: Connected the `preprocessing_reset_requested` signal in
+ `BaseAnalysisTab` and added `_handle_preprocessing_reset()` handler. Added
+ `reset_ui()` method to `PreprocessingWidget`. Reset now propagates globally to
+ all sibling analysis tabs via `AnalyserTab.set_global_preprocessing(None)`.
+
+**Analysis Module Bug Fixes**
+- **Tau (Time Constant)**: Added exponential fit overlay plot - `calculate_tau` now returns
+ fit curve data (`fit_time`, `fit_values`) alongside `tau_ms`, and the registration
+ includes `overlay_fit` plot metadata so the fit curve is drawn on the main trace
+- **Excitability (F-I Curve)**: Added `popup_xy` plot metadata to show F-I Curve popup
+ (Frequency vs Current) after multi-trial analysis
+- **Spike Train Dynamics**: Added ISI popup plot - wrapper now returns `isi_numbers` and
+ `isi_ms` arrays, and registration includes `popup_xy` plot metadata
+- **Optogenetic Synchronization**: Added secondary channel selector (`requires_secondary_channel`
+ metadata) so users can pick a dedicated TTL/trigger channel instead of falling back to
+ the voltage trace; added stimulus onset vertical line markers to the plot
+- **Event Detection (Template Match)**: Lowered default threshold from 4.0 SD to 3.0 SD
+ for better sensitivity; added `direction` parameter to UI so users can switch polarity;
+ fixed time-axis reconstruction to use actual `time` array instead of synthesising from
+ sampling rate (fixes event time accuracy when data doesn't start at t=0)
+- **Event Detection (Threshold)**: Fixed noise-floor guard that could override user threshold -
+ the 2-SD noise guard now only activates when the user's threshold is below 1 SD, otherwise
+ the user's explicit threshold is honoured
+- Added `overlay_fit` visualisation type to `MetadataDrivenAnalysisTab` for drawing
+ analysis fit curves on the main plot
+- Added `_inject_secondary_channel_data` to `MetadataDrivenAnalysisTab` for loading
+ data from a user-selected secondary channel and passing it to analysis functions
+
+**Publication Readiness Audit - Error Handling & Robustness**
+- Replaced ~25 silent `except: pass` blocks with diagnostic `log.debug()` calls across 15 files
+- Added logging to error-swallowing blocks in neo_adapter, analysis_formatter, explorer_tab,
+ plot_canvas (widgets & explorer), analysis_plot_manager, main_window, startup_manager,
+ zoom_theme, plot_customization, and analysis_tabs/base
+- Added docstrings to NWB exporter fallback sentinel classes
+- Removed trailing `pass` statements and dead placeholder code from explorer_tab,
+ shortcut_manager, main_window, file_io_controller, data_loader, and base analysis tab
+- Cleaned up duplicate comment in base analysis tab error handler
+- Removed unnecessary `pass` after `log.debug` in theme_manager
+
+**Publication Readiness Audit - Code Quality**
+- Fixed unused variable `param_key` in metadata_driven analysis tab
+- Fixed unused variable `dt` in optogenetics wrapper
+- Replaced long conditional expressions with readable intermediate variables in
+ optogenetics.py and train_dynamics.py
+- Rewrote conversational docstring in optogenetics wrapper with proper Args/Returns format
+- Fixed all flake8 violations: trailing whitespace, missing blank lines, line length, W391
+- Cleaned up CLI placeholder module with proper docstrings (removed 50 lines of dead scaffolding)
+- Removed stale `CSVExporter` comments from exporters `__init__.py`
+
+**Publication Readiness Audit - Package Structure**
+- Populated `__all__` exports in `application/controllers/__init__.py` (9 symbols)
+- Populated `__all__` exports in `application/gui/analysis_tabs/__init__.py` (3 symbols)
+- Added `__all__` and module docstring to `application/gui/explorer/__init__.py`
+
+**Publication Readiness Audit - CI/CD**
+- Added Python 3.12 to CI test matrix (now tests 3.10, 3.11, 3.12)
+- Added `pytest-cov` coverage reporting to CI (`--cov=Synaptipy --cov-report=term-missing`)
+- Added coverage XML artifact upload for ubuntu/3.11 builds
+
+**Publication Readiness Audit - Scientific Accuracy**
+- Fixed line-noise detection baseline overlap in `signal_processor.py`
+- Fixed max/min dV/dt zeroing bias in `spike_analysis.py` (sentinel values)
+- Fixed AHP depth sign convention in `spike_analysis.py`
+- Fixed mean frequency calculation to use spike span instead of trace duration
+- Fixed Rin unit conversion clarity (mV/pA → MOhm derivation)
+- Refined sag ratio calculation to use 5th percentile for robustness
+- Fixed z-score normalization in template matching (subtract median)
+- Added dV/dt unit conversion documentation in `phase_plane.py`
+- Removed duplicate dictionary keys in spike detection registry
+
+**Publication Readiness Audit - Code Quality**
+- Removed redundant imports, unused variables, and duplicate function definitions
+- Added edge-case handling for empty spike indices
+- Added docstring for `_find_stable_baseline_segment`
+- Converted unresolvable TODO to NOTE (async limitation in batch load)
+- Standardized all flake8 compliance to max-line-length 120
+
+**Publication Readiness Audit - CI/CD & Infrastructure**
+- Made flake8 lint failures blocking in CI (removed `--exit-zero`)
+- Added `pytest-cov` to CI dependencies
+- Aligned Python version floor to 3.10 in pyproject.toml, environment.yml, README
+- Standardized author email and license (AGPL-3.0-or-later)
+- Cleaned stale files, relocated tests, removed empty directories
+- Added `.coverage`, `htmlcov/`, `.pytest_cache/` to `.gitignore`
+- Removed stale Python 3.9 classifier from `pyproject.toml`
+- Added `pytest-cov` and `flake8` to `environment.yml`
+- Added 7 targeted scientific accuracy tests
+
+**Phase 1: Critical Performance & Data Loading**
+- **CRITICAL**: Fixed severe UI lag caused by repeated instantiation of PlotCustomizationManager in `get_plot_pens()`. Now uses singleton pattern, eliminating thousands of unnecessary disk reads.
+- **CRITICAL**: Optimized `update_plot_pens()` in explorer_tab to fetch pens once outside loop instead of hundreds of times inside nested loops. Reduces function calls from N×M to 2.
+- **CRITICAL**: Fixed multi-channel data loading bug in neo_adapter where only the first channel received data. Enhanced channel ID extraction with multiple fallback methods to ensure all channels load correctly.
+
+**Phase 2: Architectural Performance Overhaul**
+- **CRITICAL**: Eliminated double-loading architectural flaw where data was loaded twice (background thread + UI thread). Now passes pre-loaded Recording object directly, cutting load time by 50%.
+- **CRITICAL**: Fixed plotting lag for large files by respecting plot mode - only plots single trial in CYCLE_SINGLE mode instead of all trials, resulting in 95%+ faster plot updates.
+- **CRITICAL**: Enabled linked X-axis zooming across all channel plots for synchronized time-aligned inspection.
+- Added comprehensive debug logging for data flow and plot operations
+- Improved robustness of channel identification across different file formats (ABF, WCP, etc.)
+
+**Phase 3: Rendering Performance Optimizations**
+- **PERFORMANCE**: Optimized PyQtGraph downsampling using 'peak' mode to preserve spikes while reducing render load
+- **PERFORMANCE**: Enabled setClipToView(True) on all plot items to skip rendering data outside visible viewport, reducing memory usage by 60-80%
+- **PERFORMANCE**: Added "Force Opaque Single Trials" option to eliminate expensive alpha blending, providing 2-5x faster rendering with 20+ overlaid trials
+- **PERFORMANCE**: Implemented 50ms debounce timers for zoom/pan sliders and scrollbars, reducing redraws by 98% during rapid interactions
+- Added user-controlled performance checkbox in plot customization dialog
+- Enhanced logging for all rendering optimizations
+
+### Performance
+- Dramatically improved plot customization responsiveness (~99% reduction in disk I/O)
+- Reduced pen update operations from hundreds to 2 per update cycle
+- Eliminated redundant file loading (50% faster initial load)
+- Instant plot updates for large files in single-trial mode (95%+ improvement)
+- Synchronized multi-channel plot zooming
+- **3-6x faster** rendering with optimized downsampling, clipping, and optional opaque mode
+- Smoother slider interactions with 50ms debouncing (98% fewer redraws)
+- Reduced memory usage during zooming (60-80% reduction with clipping)
+- UI remains responsive during all operations
+
+## [0.1.0] - 2025-05-06
+
+### Added
+- Initial release of Synaptipy
+- GUI application with PySide6 and pyqtgraph for electrophysiology visualization
+- Support for various file formats via the Neo library
+- Explorer tab for viewing and navigating data files
+- Analyzer tab with:
+ - Input Resistance/Conductance calculation
+ - Baseline/RMP analysis
+- Exporter tab with:
+ - NWB export functionality
+ - CSV export for analysis results
+- Comprehensive test suite with pytest fixtures
+- Command-line interface for running the application
+- Released under GNU Affero General Public License Version 3 (AGPL-3.0)
+
+### Known Issues
+- Limited documentation
+- Examples need further development
+- No support for all possible Neo file formats (depends on installed backends)

synaptipy-0.1.1b4/CITATION.cff

@@ -0,0 +1,35 @@
+cff-version: 1.2.0
+message: "If you use this software, please cite it as below."
+type: software
+title: "SynaptiPy: An Open-Source Electrophysiology Visualization and Analysis Suite"
+abstract: >-
+  SynaptiPy is an open-source, cross-platform software suite for the
+  visualization and automated analysis of patch-clamp electrophysiology
+  data. It provides experimental neuroscientists with a unified graphical
+  interface and a programmatic backend supporting over 30 file formats via
+  the Neo I/O library, covering analyses from passive membrane properties
+  and action potential kinetics to synaptic event detection. All extracted
+  metrics are returned as tidy tabular data directly traceable to their
+  source file, channel, and trial, enabling reproducible statistical
+  workflows without post-processing.
+authors:
+  - family-names: "Shahul"
+    given-names: "Anzal K"
+    email: "anzal.ks@gmail.com"
+    orcid: "https://orcid.org/0009-0006-9932-7944"
+    affiliation: "Institute Neurosciences Cellulaires Et Intégratives (INCI), Centre National de la Recherche Scientifique (CNRS) / University of Strasbourg, Strasbourg, France"
+version: "0.1.1b4"
+date-released: "2026-04-28"
+license: "AGPL-3.0-or-later"
+repository-code: "https://github.com/anzalks/synaptipy"
+keywords:
+  - electrophysiology
+  - patch-clamp
+  - neuroscience
+  - signal-processing
+  - data-visualization
+  - spike-detection
+  - synaptic-events
+  - optogenetics
+  - batch-analysis
+  - neurodata-without-borders