eegprep 0.2.22__tar.gz → 0.3.0__tar.gz

eegprep-0.3.0/MANIFEST.in

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+prune src/eegprep/bin
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eegprep-0.3.0/PKG-INFO

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+Metadata-Version: 2.4
+Name: eegprep
+Version: 0.3.0
+Summary: EEG preprocessing pipeline on Python
+Author-email: Arnaud Delorme <adelorme@gmail.com>, Young Truong <dt.young112@gmail.com>
+License: BSD 2-Clause License
+        
+        Copyright (c) 2025, Swartz Center for Computational Neuroscience
+        
+        Redistribution and use in source and binary forms, with or without
+        modification, are permitted provided that the following conditions are met:
+        
+        1. Redistributions of source code must retain the above copyright notice,
+        this list of conditions and the following disclaimer.
+        
+        2. Redistributions in binary form must reproduce the above copyright notice,
+        this list of conditions and the following disclaimer in the documentation
+        and/or other materials provided with the distribution.
+        
+        THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+        AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+        IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+        ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE
+        LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
+        CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
+        SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
+        INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
+        CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
+        ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF
+        THE POSSIBILITY OF SUCH DAMAGE.
+        
+Project-URL: Homepage, https://github.com/sccn/eegprep
+Project-URL: Issues, https://github.com/sccn/eegprep/issues
+Keywords: eeg,preprocessing,EEGLAB
+Classifier: Development Status :: 3 - Alpha
+Classifier: Intended Audience :: Science/Research
+Classifier: Topic :: Scientific/Engineering :: Medical Science Apps.
+Classifier: Programming Language :: Python :: 3
+Classifier: License :: OSI Approved :: BSD License
+Classifier: Operating System :: OS Independent
+Requires-Python: >=3.10
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: colorama>=0.4.6
+Requires-Dist: eeglabio>=0.1.2
+Requires-Dist: h5py>=3.3.0
+Requires-Dist: matplotlib>=3.4.0
+Requires-Dist: mne>=1.10.0
+Requires-Dist: neo>=0.14.2
+Requires-Dist: numpy>=1.20
+Requires-Dist: oct2py>=5.5.0
+Requires-Dist: packaging>=23.0
+Requires-Dist: psutil>=7.0.0
+Requires-Dist: pybids>=0.4
+Requires-Dist: pyedflib>=0.1.42
+Requires-Dist: pyyaml>=6.0
+Requires-Dist: python-picard<0.9,>=0.8
+Requires-Dist: scipy>=1.7.0
+Requires-Dist: sympy>=1.14.0
+Requires-Dist: threadpoolctl>=3.6.0
+Provides-Extra: torch
+Requires-Dist: torch>=2.0; extra == "torch"
+Provides-Extra: gui
+Requires-Dist: pyqtgraph>=0.13.7; extra == "gui"
+Requires-Dist: PySide6>=6.6; extra == "gui"
+Provides-Extra: console
+Requires-Dist: eegprep[gui]; extra == "console"
+Requires-Dist: ipython>=8.0; extra == "console"
+Provides-Extra: docs
+Requires-Dist: sphinx>=7.0; extra == "docs"
+Requires-Dist: pydata-sphinx-theme>=0.14.0; extra == "docs"
+Requires-Dist: sphinx-gallery>=0.14.0; extra == "docs"
+Requires-Dist: numpydoc>=1.6.0; extra == "docs"
+Requires-Dist: sphinx-design>=0.5.0; extra == "docs"
+Requires-Dist: myst-parser>=1.0.0; extra == "docs"
+Requires-Dist: sphinx-copybutton>=0.5.0; extra == "docs"
+Requires-Dist: sphinx-togglebutton>=0.3.0; extra == "docs"
+Requires-Dist: sphinxcontrib-spelling>=7.1.0; extra == "docs"
+Provides-Extra: all
+Requires-Dist: eegprep[torch]; extra == "all"
+Requires-Dist: eegprep[gui]; extra == "all"
+Requires-Dist: eegprep[console]; extra == "all"
+Requires-Dist: eegprep[docs]; extra == "all"
+Dynamic: license-file
+
+<p align="center">
+  <img src="https://github.com/user-attachments/assets/d7230b12-7fb8-4abb-94a0-33c47286b019" width="300" alt="EEGPrep logo">
+</p>
+
+# EEGPrep
+
+[![Tests](https://github.com/sccn/eegprep/actions/workflows/test.yml/badge.svg)](https://github.com/sccn/eegprep/actions/workflows/test.yml)
+[![Documentation Status](https://github.com/sccn/eegprep/actions/workflows/docs.yml/badge.svg)](https://github.com/sccn/eegprep/actions/workflows/docs.yml)
+[![Python](https://img.shields.io/badge/python-3.10%2B-blue)](https://www.python.org/)
+[![License](https://img.shields.io/badge/license-BSD--3--Clause-blue)](LICENSE)
+
+EEGPrep is an EEGLAB-compatible, Python-native toolkit for loading, cleaning,
+visualizing, scripting, and validating EEG preprocessing workflows. It keeps the
+EEGLAB concepts researchers already know, including `EEG`, `ALLEEG`,
+`CURRENTSET`, `pop_*` functions, command history, ICA fields, channel locations,
+events, epochs, STUDY workflows, and EEGBrowser-style review, while providing a
+standalone Python package with GUI, interactive console, CLI, tests, and Sphinx
+documentation.
+
+EEGPrep is built for EEG researchers who want EEGLAB-style workflows, Python
+reproducibility, and agent-friendly automation without requiring MATLAB or an
+EEGLAB checkout at runtime.
+
+**Documentation:** [sccn.github.io/eegprep](https://sccn.github.io/eegprep/) |
+**Issue tracker:** [github.com/sccn/eegprep/issues](https://github.com/sccn/eegprep/issues)
+
+## Why EEGPrep?
+
+- **Familiar to EEGLAB users.** Function names, data structures, menus, history
+  commands, and GUI workflows follow EEGLAB where that helps users move between
+  tools.
+- **Python-native and standalone.** Runtime code lives in the `eegprep` package
+  and works without calling MATLAB or reading the vendored EEGLAB reference tree.
+- **GUI and console share one workspace.** Launch `eegprep-console` and switch
+  between the Qt GUI and Python commands while `EEG`, `ALLEEG`, `CURRENTSET`,
+  `LASTCOM`, `ALLCOM`, `STUDY`, and `CURRENTSTUDY` stay synchronized.
+- **Scriptable from day one.** The same `pop_*` workflows can be used from the
+  GUI, Python scripts, and the command-line interface.
+- **Designed for reproducible research.** CLI commands support structured JSON,
+  manifests, pipeline validation, stable error codes, and bundled agent guidance.
+- **Validated against EEGLAB.** Numerical parity tests and visual parity checks
+  compare EEGPrep behavior with EEGLAB for deterministic workflows.
+
+## Install
+
+EEGPrep uses `uv` for development and CI. For a published release, install the
+lean package with:
+
+```bash
+uv add eegprep
+```
+
+To install all optional extras, including GUI, console, docs, and classifier
+dependencies, use:
+
+```bash
+uv add "eegprep[all]"
+```
+
+If you are installing into a non-`uv` environment, `pip install eegprep` remains
+supported for published releases:
+
+```bash
+pip install eegprep
+```
+
+For a source checkout:
+
+```bash
+git clone https://github.com/sccn/eegprep.git
+cd eegprep
+uv sync --group dev
+```
+
+The complete install can pull in large optional binaries on some platforms,
+especially for ICLabel/PyTorch support. You can install a lightweight CPU-only
+PyTorch build manually if that better matches your system.
+
+## Quick Start
+
+The repository includes tutorial data in `sample_data/`, named after EEGLAB's
+sample-data convention.
+
+### Shared GUI and Python Console
+
+Launch EEGPrep with the main GUI and a synchronized IPython workspace:
+
+```bash
+uv run eegprep-console --full
+```
+
+Then use the GUI to load `sample_data/eeglab_data.set`, run preprocessing
+actions from the menus, and inspect the same state from the console:
+
+```python
+EEG["setname"], EEG["srate"], EEG["nbchan"], EEG["pnts"]
+CURRENTSET
+LASTCOM
+eegh()
+```
+
+You can also run `pop_*` commands directly:
+
+```python
+pop_resample(EEG, 64)
+pop_reref(EEG, [])
+```
+
+GUI actions and console commands append to the same history, so workflows can be
+replayed or moved into scripts.
+
+### GUI Only
+
+```bash
+uv run eegprep-gui --full
+```
+
+Use this when you want the EEGLAB-style menu workflow without an attached
+console.
+
+### Agent-Friendly CLI
+
+The `eegprep` command is intended for headless pipelines, batch processing, and
+AI agents that need machine-readable output.
+
+```bash
+uv run eegprep inspect sample_data/eeglab_data.set --json
+uv run eegprep validate sample_data/eeglab_data.set --json
+uv run eegprep capabilities --json
+uv run eegprep skills get eegprep-cli
+```
+
+Transform commands use the same EEGPrep processing functions as the Python API
+and write manifests for reproducibility:
+
+```bash
+uv run eegprep resample sample_data/eeglab_data.set \
+  --freq 64 \
+  --output sample_data/eeglab_data_64hz.set \
+  --manifest sample_data/eeglab_data_64hz_manifest.json \
+  --json
+```
+
+### Python API
+
+```python
+from pathlib import Path
+
+from eegprep import pop_eegfiltnew, pop_loadset, pop_resample, pop_saveset
+
+input_file = Path("sample_data") / "eeglab_data.set"
+output_file = Path("sample_data") / "eeglab_data_quickstart.set"
+
+EEG = pop_loadset(input_file)
+EEG, filter_com = pop_eegfiltnew(
+    EEG,
+    locutoff=1.0,
+    hicutoff=40.0,
+    plotfreqz=False,
+    return_com=True,
+)
+EEG, resample_com = pop_resample(EEG, 64, return_com=True)
+pop_saveset(EEG, output_file)
+
+print(filter_com)
+print(resample_com)
+```
+
+`return_com=True` returns the updated dataset and the replayable command string
+that EEGPrep records in GUI and console history.
+
+## For EEGLAB Users
+
+| EEGLAB concept | EEGPrep equivalent |
+| --- | --- |
+| `eeglab` GUI | `uv run eegprep-gui --full` or `uv run eegprep-console --full` |
+| `EEG`, `ALLEEG`, `CURRENTSET` | Shared `EEGPrepSession` state in the GUI and console |
+| MATLAB command history | `LASTCOM`, `ALLCOM`, and `eegh()` in `eegprep-console` |
+| `pop_*` wrappers | Python `eegprep.pop_*` functions with `return_com=True` |
+| EEGBrowser / scrolling review | EEGPrep EEGBrowser and `pop_eegplot` workflows |
+| clean_rawdata, ICLabel, FIRFilt, DIPFIT, EEG-BIDS | Bundled EEGPrep plugin ports and menu integrations |
+| STUDY workflows | Python STUDY structures, GUI paths, and `std_*` helpers |
+| MATLAB scripts | Python scripts, CLI pipelines, and history-derived commands |
+
+EEGPrep follows EEGLAB's one-based user-facing indices where researchers expect
+them, while using zero-based Python indices internally. Continuous data is
+channel-major, usually `(nbchan, pnts)`, and epoched data is usually
+`(nbchan, pnts, trials)`.
+
+## What Is Included
+
+- EEGLAB `.set` loading/saving, BIDS import/export, and common EEG file I/O.
+- BIDS derivative workflows intended to interoperate with EEGPrep, EEGLAB,
+  FieldTrip, Brainstorm, MNE, and other EEG analysis tools.
+- Dataset, event, channel-location, epoch, and history workflows.
+- Filtering, resampling, rereferencing, cleaning, rejection, interpolation, ICA,
+  component review, ICLabel, DIPFIT, topographies, spectra, time-frequency, and
+  statistics workflows.
+- EEGBrowser-style scrolling inspection, marking, and rejection.
+- STUDY and group-level workflow support.
+- Extension SDK, plugin discovery, extension validation, and agent-facing
+  extension authoring guidance.
+- Sphinx documentation, API reference, examples, and a structured CLI.
+
+## Documentation
+
+Start with the [online documentation](https://sccn.github.io/eegprep/):
+
+- [Quick Start](https://sccn.github.io/eegprep/user_guide/quickstart.html)
+- [GUI and Console Session](https://sccn.github.io/eegprep/user_guide/gui_console_session.html)
+- [Scripting Workflows](https://sccn.github.io/eegprep/user_guide/scripting_workflows.html)
+- [EEGBrowser](https://sccn.github.io/eegprep/user_guide/eegbrowser.html)
+- [Extensions](https://sccn.github.io/eegprep/user_guide/extensions.html)
+- [API Reference](https://sccn.github.io/eegprep/api/index.html)
+
+Repository documentation helpers are kept in [`docs/`](docs/). The docs
+workflow publishes the Sphinx site to GitHub Pages.
+
+## Project Status
+
+EEGPrep is in active pre-release development. It is intended to become a
+standalone Python counterpart for core EEGLAB preprocessing workflows. Current
+development emphasizes EEGLAB parity, GUI and console usability, BIDS support,
+extension support, and reproducible headless workflows.
+
+Use EEGPrep with the same care you would apply to any research preprocessing
+software: validate pipelines on representative data, inspect intermediate
+outputs, and record the exact version and command history used for analysis.
+
+## Numerical Parity
+
+EEGPrep is developed against EEGLAB as a parity oracle. The MATLAB and Python
+implementations are tested for close numerical agreement, including default
+preprocessing pipeline comparisons that target accuracy down to `1e-5` uV where
+the algorithms are deterministic. They have also been compared using the first
+two subjects from the BIDS datasets
+[ds003061](https://nemar.org/dataexplorer/detail?dataset_id=ds003061) and
+[ds002680](https://nemar.org/dataexplorer/detail?dataset_id=ds002680) on NEMAR.
+Observed differences were very small, with the largest reported HighpassFilter
+difference below `0.002`, indicating strong numerical consistency for the tested
+workflows.
+
+<img width="1744" height="1049" alt="MATLAB and Python implementation comparison" src="https://github.com/user-attachments/assets/79c17151-e2e3-4acc-b144-accdf34ae4c5" />
+
+## Development
+
+Run tests from the project root with:
+
+```bash
+uv run pytest tests
+```
+
+For quick local iteration:
+
+```bash
+uv run pytest -m "not slow"
+```
+
+The repo uses `ruff`, `ty`, and `pre-commit.py` for linting, formatting, and
+type-checking:
+
+```bash
+./pre-commit.py --changed-from origin/develop
+uv run --no-sync ruff check .
+uv run --no-sync ruff format --check .
+uv run --no-sync ty check
+```
+
+MATLAB parity tests require MATLAB Engine for Python. Install the engine from
+your MATLAB installation, for example on macOS:
+
+```bash
+uv pip install /Applications/MATLAB_R2025a.app/extern/engines/python
+```
+
+Check the installation:
+
+```python
+import matlab.engine
+
+engine = matlab.engine.start_matlab()
+engine.eval("disp('hello world');", nargout=0)
+```
+
+The MATLAB comparison entry point is `tests/matlab/main_compare.m`.
+
+## Cite
+
+If EEGPrep contributes to your research, please cite EEGPrep and the EEGLAB
+methods it ports. For EEGLAB, cite:
+
+Delorme, A., & Makeig, S. (2004). EEGLAB: an open source toolbox for analysis
+of single-trial EEG dynamics including independent component analysis. *Journal
+of Neuroscience Methods*, 134(1), 9-21.
+
+## Core Maintainers
+
+- Arnaud Delorme, UCSD, CA, USA
+- Suraj Ranganath, UCSD, CA, USA
+- Christian Kothe, Intheon, CA, USA
+- Bruno Aristimunha Pinto, Inria, France
+
+<details>
+<summary>Maintainer release notes</summary>
+
+### Release Process
+
+Releases are published by `.github/workflows/release.yml` when a `v*` tag is
+pushed. That is the only path to PyPI. Full instructions, including the dry run,
+are in [docs/source/releasing.rst](docs/source/releasing.rst).
+
+The version lives in `src/eegprep/__init__.py` (`__version__`); `pyproject.toml`
+reads it via `dynamic = ["version"]`, so there is nothing to edit there.
+
+```bash
+# dry run first: everything except publishing
+gh workflow run release.yml --ref master -f dry_run=true
+
+# bump __version__, land it on master, then tag to release
+git commit -am "release: 0.3.0"
+git push origin develop:master
+git tag -a v0.3.0 -m "Release version 0.3.0" && git push origin v0.3.0
+```
+
+The workflow lints, type-checks, runs the test suite, builds, verifies the
+artifacts, publishes to PyPI with Trusted Publishing (no stored token), and
+creates the GitHub release.
+
+CI does not build Docker images. After the tag is published:
+
+```bash
+docker login
+uv run python scripts/build_docker.py
+```
+
+That builds and pushes `arnodelorme/eegprep:<version>` and updates the image pin
+in `tools/hpc/main.pbs`; commit the pin.
+
+Verify the published release:
+
+```bash
+uv pip install eegprep==X.Y.Z
+```
+
+Packaging follows the Python Packaging User Guide:
+<https://packaging.python.org/en/latest/tutorials/packaging-projects/>.
+
+</details>
+
+<details>
+<summary>Docker notes for SCCN power users</summary>
+
+```bash
+docker build -t eegprep:0.2.9 -f DOCKERFILE .
+docker tag eegprep:0.2.9 arnodelorme/eegprep:0.2.9
+docker push arnodelorme/eegprep:0.2.9
+```
+
+Check the project on Docker Hub: <https://hub.docker.com/>.
+
+Mounted folders are available in `/usr/src/project`.
+
+</details>