pEEGy 1.6.4__tar.gz

peegy-1.6.4/.gitignore

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+/build
+*.pyc
+/dist
+*-info
+.idea
+/venv

peegy-1.6.4/.gitlab-ci.yml

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+image: python:3.12
+variables:
+    QT_QPA_PLATFORM: 'offscreen'
+    XDG_RUNTIME_DIR: '/tmp/runtime-root'
+    TWINE_USERNAME: '__token__'
+    TWINE_PYPI_TEST: $PYPI_TEST_TOKEN
+    TWINE_PYPI: $PYPI_TOKEN
+
+make_doc:
+  stage: test
+  script:
+    - echo "$XDG_RUNTIME_DIR"
+    - apt-get update
+    - apt-get -y install graphviz
+    - apt-get -y install libgl1 libglx-mesa0
+    - pip install -U sphinx sphinx-gallery memory_profiler sphinx-multiversion twine build wheel setuptools
+    - pip install -r requirements.txt
+    - cd doc
+    - sphinx-build . ../public
+  artifacts:
+    paths:
+      - public
+  only:
+    - branches
+  except:
+    - master
+    - stable
+
+check_pip8:
+  stage: test
+  script:
+    - pip install -U flake8
+    - flake8 --max-line-length 120 peegy
+  only:
+    - branches
+  except:
+    - master
+    - stable
+
+code_speller_check:
+  stage: test
+  script:
+    - pip install codespell
+    - codespell peegy
+  only:
+    - branches
+  except:
+    - master
+    - stable
+
+make_wheel:
+  stage: test
+  script:
+    - echo "$XDG_RUNTIME_DIR"
+    - apt-get update
+    - apt-get -y install graphviz
+    - apt-get -y install libgl1 libglx-mesa0
+    - pip install -U sphinx sphinx-gallery memory_profiler sphinx-multiversion twine build wheel setuptools
+    - pip install -r requirements.txt
+    - python3 -m build
+  only:
+    - branches
+  except:
+    - master
+    - stable
+
+pages:
+  stage: deploy
+  script:
+    - echo "$XDG_RUNTIME_DIR"
+    - apt-get update
+    - apt-get -y install graphviz
+    - apt-get -y install libgl1 libglx-mesa0
+    - pip install -U sphinx sphinx-gallery memory_profiler sphinx-multiversion twine build wheel setuptools
+    - pip install -r requirements.txt
+    - cd doc
+    - sphinx-build . ../public
+    - cd ..
+    - python3 -m build
+  artifacts:
+    paths:
+      - public
+  only:
+    - master
+
+stable:
+  stage: deploy
+  script:
+    - echo "$XDG_RUNTIME_DIR"
+    - apt-get update
+    - apt-get -y install graphviz
+    - apt-get -y install libgl1 libglx-mesa0
+    - pip install -U sphinx sphinx-gallery memory_profiler sphinx-multiversion twine build wheel setuptools
+    - pip install -r requirements.txt
+    - cd doc
+    - sphinx-build . ../public
+    - cd ..
+    - python3 -m build
+    - python3 -m twine upload --repository testpypi dist/* -u $TWINE_USERNAME -p $TWINE_PYPI_TEST
+    - pip install -i https://test.pypi.org/simple/ peegy
+    - python3 -m twine upload dist/* -u $TWINE_USERNAME -p $TWINE_PYPI
+  artifacts:
+    paths:
+      - dist
+  only:
+    - stable
+
+
+publish_zenodo:
+  stage: deploy
+  rules:
+    - if: '$CI_COMMIT_TAG'
+  before_script:
+    - pip install gitlab2zenodo
+  script:
+    - ARCHIVE="${CI_PROJECT_NAME}-${CI_COMMIT_TAG}.zip"
+    - git archive --format=zip --output="$ARCHIVE" "$CI_COMMIT_TAG"
+    - python scripts/zenodo_from_toml.py
+    - g2z-send --publish --metadata zenodo.json "$ARCHIVE"

peegy-1.6.4/CODE_OF_CONDUCT.md

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+# Contributor Covenant Code of Conduct
+
+## Our Pledge
+
+We as members, contributors, and leaders pledge to make participation in our
+community a harassment-free experience for everyone, regardless of age, body
+size, visible or invisible disability, ethnicity, sex characteristics, gender
+identity and expression, level of experience, education, socio-economic status,
+nationality, personal appearance, race, caste, color, religion, or sexual
+identity and orientation.
+
+We pledge to act and interact in ways that contribute to an open, welcoming,
+diverse, inclusive, and healthy community.
+
+## Our Standards
+
+Examples of behavior that contributes to a positive environment for our
+community include:
+
+* Demonstrating empathy and kindness toward other people
+* Being respectful of differing opinions, viewpoints, and experiences
+* Giving and gracefully accepting constructive feedback
+* Accepting responsibility and apologizing to those affected by our mistakes,
+  and learning from the experience
+* Focusing on what is best not just for us as individuals, but for the overall
+  community
+
+Examples of unacceptable behavior include:
+
+* The use of sexualized language or imagery, and sexual attention or advances of
+  any kind
+* Trolling, insulting or derogatory comments, and personal or political attacks
+* Public or private harassment
+* Publishing others' private information, such as a physical or email address,
+  without their explicit permission
+* Other conduct which could reasonably be considered inappropriate in a
+  professional setting
+
+## Enforcement Responsibilities
+
+Community leaders are responsible for clarifying and enforcing our standards of
+acceptable behavior and will take appropriate and fair corrective action in
+response to any behavior that they deem inappropriate, threatening, offensive,
+or harmful.
+
+Community leaders have the right and responsibility to remove, edit, or reject
+comments, commits, code, wiki edits, issues, and other contributions that are
+not aligned to this Code of Conduct, and will communicate reasons for moderation
+decisions when appropriate.
+
+## Scope
+
+This Code of Conduct applies within all community spaces, and also applies when
+an individual is officially representing the community in public spaces.
+Examples of representing our community include using an official e-mail address,
+posting via an official social media account, or acting as an appointed
+representative at an online or offline event.
+
+## Enforcement
+
+Instances of abusive, harassing, or otherwise unacceptable behavior may be
+reported to the community leaders responsible for enforcement at
+[jaime.undurraga@gmail.com](mailto:jaime.undurraga@gmail.com).
+All complaints will be reviewed and investigated promptly and fairly.
+
+All community leaders are obligated to respect the privacy and security of the
+reporter of any incident.
+
+## Enforcement Guidelines
+
+Community leaders will follow these Community Impact Guidelines in determining
+the consequences for any action they deem in violation of this Code of Conduct:
+
+### 1. Correction
+
+**Community Impact**: Use of inappropriate language or other behavior deemed
+unprofessional or unwelcome in the community.
+
+**Consequence**: A private, written warning from community leaders, providing
+clarity around the nature of the violation and an explanation of why the
+behavior was inappropriate. A public apology may be requested.
+
+### 2. Warning
+
+**Community Impact**: A violation through a single incident or series of
+actions.
+
+**Consequence**: A warning with consequences for continued behavior. No
+interaction with the people involved, including unsolicited interaction with
+those enforcing the Code of Conduct, for a specified period of time. This
+includes avoiding interactions in community spaces as well as external channels
+like social media. Violating these terms may lead to a temporary or permanent
+ban.
+
+### 3. Temporary Ban
+
+**Community Impact**: A serious violation of community standards, including
+sustained inappropriate behavior.
+
+**Consequence**: A temporary ban from any sort of interaction or public
+communication with the community for a specified period of time. No public or
+private interaction with the people involved, including unsolicited interaction
+with those enforcing the Code of Conduct, is allowed during this period.
+Violating these terms may lead to a permanent ban.
+
+### 4. Permanent Ban
+
+**Community Impact**: Demonstrating a pattern of violation of community
+standards, including sustained inappropriate behavior, harassment of an
+individual, or aggression toward or disparagement of classes of individuals.
+
+**Consequence**: A permanent ban from any sort of public interaction within the
+community.
+
+## Attribution
+
+This Code of Conduct is adapted from the [Contributor Covenant][homepage],
+version 2.1, available at
+[https://www.contributor-covenant.org/version/2/1/code_of_conduct.html][v2.1].
+
+Community Impact Guidelines were inspired by
+[Mozilla's code of conduct enforcement ladder][Mozilla CoC].
+
+For answers to common questions about this code of conduct, see the FAQ at
+[https://www.contributor-covenant.org/faq][FAQ]. Translations are available at
+[https://www.contributor-covenant.org/translations][translations].
+
+[homepage]: https://www.contributor-covenant.org
+[v2.1]: https://www.contributor-covenant.org/version/2/1/code_of_conduct.html
+[Mozilla CoC]: https://github.com/mozilla/diversity
+[FAQ]: https://www.contributor-covenant.org/faq
+[translations]: https://www.contributor-covenant.org/translations

peegy-1.6.4/CONTRIBUTING.md

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+# Contributing to pEEGy
+
+Thanks for taking the time to contribute to pEEGy!
+
+The following document is a set of guidelines for contributing to pEEGy hosted in [Gitlab](https://gitlab.com/jundurraga/peegy).
+These are mostly guidelines, not rules. Use your best judgment, and feel free to propose changes to this document in a pull request.
+
+## Code of Conduct
+
+This project and everyone participating in it is governed by the [pEEGy Code of Conduct](CODE_OF_CONDUCT.md). By participating, you are expected to uphold this code. Please report unacceptable behavior to [jaime.undurraga@gmail.com](mailto:jaime.undurraga@gmail.com).
+
+## How Can I Contribute?
+
+### Reporting Bugs
+
+This section provides a guideline for submitting a bug report. Following these guidelines helps maintainers and the community understand your report, reproduce the behavior, and find related reports.
+
+At the moment of creating a bug report, please include as many details as possible.
+
+#### Before Submitting A Bug Report
+
+* Check if you can find the cause of the problem and fix things yourself. Next, generate a pull request with the solution.
+* Check if you can reproduce the problem.
+
+#### How Do I Submit A Bug Report?
+
+Bugs are tracked as [pEEGy issues](https://gitlab.com/jundurraga/peegy/-/issues). Create an issue and provide the following information.
+
+Explain the problem and include additional details to help maintainers reproduce the problem:
+
+* **Use a clear and descriptive title** for the issue to identify the problem.
+* **Describe the exact steps which reproduce the problem** in as many details as possible. When listing steps, **don't just say what you did, but explain how you did it**.
+* **Provide specific examples to demonstrate the steps**.
+* **Describe the behavior you observed after following the steps** and point out what exactly is the problem with that behavior.
+* **Explain which behavior you expected to see instead and why.**
+
+### Suggesting Enhancements
+
+When providing an enhancement suggestion for pEEGy (new features or minor improvements to existing functionality), please include as many details as possible.
+This will help maintainers and the community understand your suggestion and find related suggestions.
+
+
+### Pull Requests
+
+1. Please create your own branch and develop your contributions there.
+2. Once you have performed your modifications (a new feature or a fix), ensure to include a test script using your contribution.
+This will allow to validate and ensure the quality of the code.
+3. Describe the parameters of your modifications/contributions in a meaningful way so others can understand what it is, what it does, what it is needed, and how to use it.
+
+### Git Commit Messages
+
+* Use the present tense ("Add feature" not "Added feature")
+* Use the imperative mood ("Plot waveform ..." not "Plots waveform...")
+* Consider starting the commit message with an applicable text:
+    * feat: when adding a new feature
+    * fix: when fixing a bug
+    * doc: When changing documentation

peegy-1.6.4/LICENSE.txt

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+Copyright 2022
+
+Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated
+documentation files (the "Software"), to deal in the Software without restriction, including without limitation
+the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to
+permit persons to whom the Software is furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all copies or substantial portions of the
+Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE
+WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS
+OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR
+OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+

peegy-1.6.4/MANIFEST.in

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+include peegy/layouts/*.lay

peegy-1.6.4/PKG-INFO

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+Metadata-Version: 2.4
+Name: pEEGy
+Version: 1.6.4
+Summary: A python software for analysing EEG data and generate pipelines in python.
+Project-URL: Homepage, https://gitlab.com/open-source-brain/peegy/
+Project-URL: Examples, https://open-source-brain.gitlab.io/peegy/
+Project-URL: Issues, https://gitlab.com/open-source-brain/peegy/-/issues
+Author-email: "Undurraga, Jaime" <jaime.undurraga@gmail.com>
+License: MIT
+License-File: LICENSE.txt
+Keywords: EEG,neuroscience,pipelines,signal-processing
+Classifier: Development Status :: 3 - Alpha
+Classifier: Environment :: Console
+Classifier: Intended Audience :: Science/Research
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Operating System :: MacOS :: MacOS X
+Classifier: Operating System :: Microsoft :: Windows :: Windows 10
+Classifier: Operating System :: POSIX :: Linux
+Classifier: Programming Language :: Python :: 3
+Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
+Requires-Python: >=3.9
+Requires-Dist: astropy>=5.2.1
+Requires-Dist: bidshandler>=0.2.1
+Requires-Dist: cython>=0.29.33
+Requires-Dist: dropbox>=12.0.2
+Requires-Dist: fire>=0.5.0
+Requires-Dist: gitpython>=3.1.31
+Requires-Dist: graphviz>=0.20.1
+Requires-Dist: h5py>=3.8.0
+Requires-Dist: joblib>=1.2.0
+Requires-Dist: lxml>=4.9.2
+Requires-Dist: matplotlib<=3.9.0
+Requires-Dist: numba-progress>=0.0.4
+Requires-Dist: numba>=0.56.4
+Requires-Dist: numpy<=2.3.5,>=2.0.0
+Requires-Dist: opencv-python-headless>=4.12.0.88
+Requires-Dist: pandas>=2.3.3
+Requires-Dist: pillow>=9.4.0
+Requires-Dist: prettytable>=3.7.0
+Requires-Dist: psutil>=5.9.5
+Requires-Dist: pydot>=1.4.2
+Requires-Dist: pyedflib>=0.1.32
+Requires-Dist: pyfftw>=0.13.1
+Requires-Dist: pyqt5-stubs>=5.15.6.0
+Requires-Dist: pyqt5>=5.15.9
+Requires-Dist: pyqtgraph>=0.13.3
+Requires-Dist: pywavelets>=1.4.1
+Requires-Dist: qt5-py>=0.1.0
+Requires-Dist: ray>=2.0.1
+Requires-Dist: scikit-learn>=1.2.2
+Requires-Dist: scipy>=1.16.3
+Requires-Dist: seaborn>=0.13.2
+Requires-Dist: soundfile>=0.12.1
+Requires-Dist: sqlalchemy>=2.0.45
+Requires-Dist: ssqueezepy>=0.6.4
+Requires-Dist: tabulate>=0.9.0
+Requires-Dist: toml>=0.10.2
+Requires-Dist: tqdm>=4.64.1

peegy-1.6.4/Readme.md

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+# pEEGy
+![](doc/_static/peegy.png)
+
+A python software for analysing EEG data and generate pipelines in python. 
+At the moment we work with EDF, BDF, and CNT files, but you can also read whatever data you have and plug it into a pipeline.
+
+The pEEGy steps are basically:
+1) Load BDF/EDF files (raw data)
+2) Define your pipeline for EEG-Analysis (Referencing EEG using predefined EEG Cap Layouts,
+ creating Epochs based on trigger events, down-sampling, removing artifacts, defining Regions
+ of Interest, Statistics to run on the epochs, or plot the data)
+3) Define in which database you want to save the results
+4) Run the above steps.
+
+Examples can be found in [pEEGy](https://open-source-brain.gitlab.io/peegy/) website. 
+
+## Installation
+This software requires Python >= 3.9
+
+Standard installation of stable release can be obtained from the official repository 
+```commandline
+pip install peegy
+```
+### Windows enviroment
+The easiest and painless installation is via [Anaconda](https://www.anaconda.com/products/distribution).
+Once you have installed Anaconda, create a new python environment and launch the terminal in this environment.
+In the terminal run: 
+```commandline
+pip install peegy
+```
+pEEGy will be installed in that new environment. 
+
+
+## Pipeline diagrams
+To generate pipeline diagrams, you will need to install [Graphviz](https://graphviz.org/download/)
+
+## Development version
+The development version can be obtained from our official Gitlab repository 
+
+```commandline
+git clone https://gitlab.com/open-source-brain/peegy.git
+```
+
+This will clone into the folder 'pEEGy'.
+
+To be able to look in the (generated) sql-databases, we recommend using DB Browser (https://sqlitebrowser.org/)
+
+### For Windows
+
+Precompiled PyFFTW is easier to install via conda.
+If you are using window, this is the easiest way to have PyFFT running.
+
+```commandline
+conda install -c conda-forge pyfftw
+```
+
+## Examples
+Please have a look at the 'examples' folder for different EEG analysis examples in the time or frequency domain.
+
+## Sidekicks 
+We have also created other tools for EEG experiments. 
+- If you have a [Biosemi](https://www.biosemi.com/) EEG system, you can use [BiosemiRealtime](https://gitlab.com/jundurraga/biosemi_real_time) 
+to allow realtime processing in the time- and frequency-domain.
+- If use are running auditory EEG experiments such as auditory brainstem responses (ABRs), auditory steady-state 
+responses (ASSRs), frequency-following responses (FFRs), auditory change complex (ACC), and other auditory evoked
+responses. We have a matlab toolbox [AEP_GUI](https://gitlab.com/jundurraga/ucl-matlab) to generate and present 
+these stimuli in a reliable way. 

peegy-1.6.4/examples/README.txt

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+.. _general_examples:
+
+Examples
+=========