py-neuromodulation 0.0.4__tar.gz → 0.0.5__tar.gz

{py_neuromodulation-0.0.4 → py_neuromodulation-0.0.5}/.gitignore

@@ -1,175 +1,196 @@
-# Byte-compiled / optimized / DLL files
-__pycache__/
-*.py[cod]
-*$py.class
-
-# C extensions
-*.so
-
-# Distribution / packaging
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-.Python
-build/
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-.eggs/
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-pip-wheel-metadata/
-share/python-wheels/
-*.egg-info/
-.installed.cfg
-*.egg
-MANIFEST
-
-# PyInstaller
-#  Usually these files are written by a python script from a template
-#  before PyInstaller builds the exe, so as to inject date/other infos into it.
-*.manifest
-*.spec
-
-# Installer logs
-pip-log.txt
-pip-delete-this-directory.txt
-
-# Unit test / coverage reports
-htmlcov/
-.tox/
-.nox/
-.coverage
-.coverage.*
-.cache
-nosetests.xml
-coverage.xml
-*.cover
-*.py,cover
-.hypothesis/
-.pytest_cache/
-
-# Translations
-*.mo
-*.pot
-
-# Django stuff:
-*.log
-local_settings.py
-db.sqlite3
-db.sqlite3-journal
-
-# Flask stuff:
-instance/
-.webassets-cache
-
-# Scrapy stuff:
-.scrapy
-
-# Sphinx documentation
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-
-# PyBuilder
-target/
-
-# Jupyter Notebook
-.ipynb_checkpoints
-
-# IPython
-profile_default/
-ipython_config.py
-
-# pyenv
-.python-version
-
-# pipenv
-#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
-#   However, in case of collaboration, if having platform-specific dependencies or dependencies
-#   having no cross-platform support, pipenv may install dependencies that don't work, or not
-#   install all needed dependencies.
-#Pipfile.lock
-
-# PEP 582; used by e.g. github.com/David-OConnor/pyflow
-__pypackages__/
-
-# Celery stuff
-celerybeat-schedule
-celerybeat.pid
-
-# SageMath parsed files
-*.sage.py
-
-# Environments
-.env
-.venv
-env/
-venv/
-ENV/
-env.bak/
-venv.bak/
-
-# Visual Studio Code
-.vscode
-
-# PyCharm
-.idea
-
-# Spyder project settings
-.spyderproject
-.spyproject
-
-# Rope project settings
-.ropeproject
-
-# mkdocs documentation
-/site
-
-# mypy
-.mypy_cache/
-.dmypy.json
-dmypy.json
-
-# Pyre type checker
-.pyre/
-
-# Ignore pickles
-*.pkl
-**/*.pkl
-*.p
-
-.pdf
-
-sphinx/sub/*
-
-docs/build/*
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-
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-py_neuromodulation/data/derivatives/*
-
-requirements.lock
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-
-.python-version
-
-py_neuromodulation/ConnectivityDecoding/connectome_folder/*
-
-plot_0_first_demo.py
-
-requirements.lock
-requirements-dev.lock
-
-plot_1_example_BIDS.py
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# Distribution / packaging
+.pypirc/
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+pip-wheel-metadata/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py,cover
+.hypothesis/
+.pytest_cache/
+/test_data
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+.python-version
+
+# pipenv
+#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
+#   However, in case of collaboration, if having platform-specific dependencies or dependencies
+#   having no cross-platform support, pipenv may install dependencies that don't work, or not
+#   install all needed dependencies.
+#Pipfile.lock
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Visual Studio Code
+.vscode
+
+# PyCharm
+.idea
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/
+
+# Ignore pickles
+*.pkl
+**/*.pkl
+*.p
+
+.pdf
+
+sphinx/sub/*
+
+docs/build/*
+docs/source/_build/*
+docs/previous/*
+docs/source/auto_examples/*
+docs/source/data/*
+
+examples/data/derivatives/*
+examples/other_examples/*
+examples/plot_7_lsl_example.ipynb
+examples/lange_n8.ipynb
+
+examples/sub/*
+examples/utils/*
+examples/temp_raw.fif
+
+sub/
+
+py_neuromodulation/data/derivatives/*
+
+.python-version
+
+py_neuromodulation/ConnectivityDecoding/connectome_folder/*
+
+plot_0_first_demo.py
+plot_1_example_BIDS.py
+temp_raw.fif
+
+requirements.lock
+requirements-dev.lock
+
+docs/source/bin/pandoc
+
+docs/source/sg_execution_times.rst
+
+figures_ucsf/*
+catboost_info/*
+out_per
+.DS_Store
+
+# Temp dev files
+# Testing scripts
+/*.py 
+# Stream output
+/*.csv
+/*.db
+/*.sqlite
+# Profiler files
+/*.prof
+/profiling/*
+
+gui_dev/node_modules/*
+test/data/*

{py_neuromodulation-0.0.4 → py_neuromodulation-0.0.5}/LICENSE

@@ -1,21 +1,21 @@
-MIT License
-
-Copyright (c) 2021 Interventional Cognitive Neuromodulation - Neumann Lab Berlin
-
-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.
+MIT License
+
+Copyright (c) 2021 Interventional Cognitive Neuromodulation - Neumann Lab Berlin
+
+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.

{py_neuromodulation-0.0.4 → py_neuromodulation-0.0.5}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: py_neuromodulation
-Version: 0.0.4
+Version: 0.0.5
 Summary: Real-time analysis of intracranial neurophysiology recordings.
 Project-URL: bugtracker, https://github.com/neuromodulation/py_neuromodulation/issues
 Project-URL: repository, https://github.com/neuromodulation/py_neuromodulation
@@ -34,39 +34,55 @@ Classifier: License :: OSI Approved :: MIT License
 Classifier: Programming Language :: Python
 Classifier: Topic :: Software Development :: Libraries :: Python Modules
 Requires-Python: >=3.10
-Requires-Dist: black>=24.2.0
 Requires-Dist: filterpy>=1.4.5
 Requires-Dist: fooof
 Requires-Dist: hatch>=1.9.4
 Requires-Dist: imbalanced-learn
-Requires-Dist: ipython
 Requires-Dist: joblib>=1.3.2
-Requires-Dist: matplotlib>=3.3.4
+Requires-Dist: matplotlib>=3.9.0
 Requires-Dist: mne
 Requires-Dist: mne-bids>=0.8
 Requires-Dist: mne-connectivity
+Requires-Dist: mne-lsl>=1.2.0
 Requires-Dist: mrmr-selection
+Requires-Dist: nibabel>=5.2.1
 Requires-Dist: nolds
-Requires-Dist: notebook
 Requires-Dist: numpy>=1.21.2
-Requires-Dist: pandas>=1.2.2
-Requires-Dist: pip
+Requires-Dist: pandas>=2.0.0
+Requires-Dist: pip>=24.2
 Requires-Dist: pyarrow>=14.0.2
-Requires-Dist: pybids
 Requires-Dist: pybispectra>=1.0.0
+Requires-Dist: pydantic>=2.7.3
 Requires-Dist: pynput
 Requires-Dist: pyparrm
-Requires-Dist: pytest>=8.0.2
+Requires-Dist: pyqt5
 Requires-Dist: scikit-image
 Requires-Dist: scikit-learn>=0.24.2
 Requires-Dist: scikit-optimize
 Requires-Dist: scipy>=1.7.1
 Requires-Dist: seaborn>=0.11
-Requires-Dist: wget
+Requires-Dist: statsmodels
 Provides-Extra: dev
-Requires-Dist: black; extra == 'dev'
-Requires-Dist: pytest; extra == 'dev'
+Requires-Dist: notebook; extra == 'dev'
 Requires-Dist: pytest-cov; extra == 'dev'
+Requires-Dist: pytest-sugar; extra == 'dev'
+Requires-Dist: pytest>=8.0.2; extra == 'dev'
+Requires-Dist: ruff; extra == 'dev'
+Provides-Extra: docs
+Requires-Dist: notebook; extra == 'docs'
+Requires-Dist: numpydoc; extra == 'docs'
+Requires-Dist: pydata-sphinx-theme; extra == 'docs'
+Requires-Dist: pytest-cov; extra == 'docs'
+Requires-Dist: pytest-sugar; extra == 'docs'
+Requires-Dist: pytest>=8.0.2; extra == 'docs'
+Requires-Dist: recommonmark; extra == 'docs'
+Requires-Dist: ruff; extra == 'docs'
+Requires-Dist: sphinx; extra == 'docs'
+Requires-Dist: sphinx-gallery; extra == 'docs'
+Requires-Dist: sphinx-togglebutton; extra == 'docs'
+Provides-Extra: test
+Requires-Dist: pytest-xdist; extra == 'test'
+Requires-Dist: pytest>=8.0.2; extra == 'test'
 Description-Content-Type: text/x-rst
 
 py_neuromodulation
@@ -111,23 +127,10 @@ py_neuromodulation requires at least python 3.10. For installation you can use p
 
     pip install py-neuromodulation
 
-
-We recommend however installing the package using `rye <https://rye-up.com/guide/installation/>`_:
-
-.. code-block::
-
-    git clone https://github.com/neuromodulation/py_neuromodulation.git
-    rye pin 3.11
-    rye sync
-
-And then activating the virtual environment e.g. in Windows using:
+Alternatively you can also install the package in a conda environment:
 
 .. code-block::
 
-    .\.venv\Scripts\activate
-
-Alternatively you can also install the package in a conda environment:
-
     conda create -n pynm-test python=3.11
     conda activate pynm-test