py-neuromodulation 0.0.5__tar.gz → 0.0.6__tar.gz

py_neuromodulation-0.0.6/.github/workflows/docs_pages.yml

@@ -0,0 +1,57 @@
+name: docs_pages_workflow
+ 
+on:
+  push:
+    branches: [ main ]
+ 
+jobs:
+ 
+  build_docs_job:
+    runs-on: ubuntu-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+ 
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v2.3.4
+      
+      - name: Install and cache Linux packages
+        if: ${{ runner.os == 'Linux' }}
+        uses: tecolicom/actions-use-apt-tools@v1
+        with:
+          tools: binutils qtbase5-dev qt5-qmake libpugixml1v5
+
+      - name: Set up Python with uv
+        uses: drivendataorg/setup-python-uv-action@v1
+        with:
+          python-version: '3.10'
+          cache: packages
+          cache-dependency-path: pyproject.toml
+ 
+      - name: Install dependencies
+        run: |
+          uv pip install .[docs]
+
+      - name: make the sphinx docs
+        run: |
+          make -C docs clean 
+          make -C docs html
+
+      - name: Init new repo in dist folder and commit generated files
+        run: |
+          cd docs/build/html/
+          git init
+          touch .nojekyll
+          git add -A
+          git config --local user.email "github-actions[bot]@users.noreply.github.com"
+          git config --local user.name "github-actions[bot]"
+          git commit -m 'deploy'
+          git config --global --add safe.directory /github/workspace/docs/build/html
+
+      - name: Force push to destination branch
+        uses: ad-m/github-push-action@master
+        with:
+          github_token: ${{ secrets.GITHUB_TOKEN }}
+          branch: gh-pages
+          force: true
+          directory: ./docs/build/html

py_neuromodulation-0.0.6/.github/workflows/python-publish.yml

@@ -0,0 +1,39 @@
+name: Publish Python Package
+
+on:
+  push:
+    tags:
+      - 'v*'  # Only trigger on tag pushes like v1.0.0
+
+jobs:
+  publish:
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v3
+
+      - name: Set up Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: '3.11'  # Specify your Python version
+
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install build
+
+      - name: Build package
+        run: python -m build
+
+      - name: Publish to PyPI
+        uses: pypa/gh-action-pypi-publish@v1.10.0
+        with:
+          password: ${{ secrets.PYPI_API_TOKEN }}
+
+      - name: Create GitHub release
+        uses: softprops/action-gh-release@v1
+        with:
+          files: dist/*
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}

py_neuromodulation-0.0.6/.github/workflows/tests.yml

@@ -0,0 +1,59 @@
+name: Tests
+on:
+  push:
+    branches:
+      - main
+      - "**"
+    paths-ignore:
+      - "docs/**"
+      - "*.md"
+      - "*.rst"
+      - "*.txt"
+  pull_request:
+    branches:
+      - main
+      - "*.x"
+    paths-ignore:
+      - "docs/**"
+      - "*.md"
+      - "*.rst"
+      - "*.txt"
+jobs:
+  tests:
+    name: ${{ matrix.platform.name }} Python ${{ matrix.python }}
+    runs-on: ${{ matrix.platform.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        platform:
+          - os: ubuntu-latest
+            name: Linux
+          - os: macos-latest
+            name: MacOS
+          - os: windows-latest
+            name: Windows
+        python:
+          - "3.11"
+          - "3.12"
+    steps:
+      - uses: actions/checkout@v4
+      - name: Install and cache Linux packages
+        if: ${{ runner.os == 'Linux' }}
+        uses: awalsh128/cache-apt-pkgs-action@latest
+        with:
+          packages: binutils qtbase5-dev qt5-qmake libpugixml1v5
+      - name: Install uv
+        uses: astral-sh/setup-uv@v3
+        with:
+          version: "0.4.12"
+          enable-cache: true
+          cache-dependency-glob: "**/pyproject.toml"
+      - name: Install Python and dependencies
+        run: |
+          uv python install ${{ matrix.python }}
+          uv venv
+          uv pip install .[test]
+      - name: Run tests
+        run: |
+          ${{ (runner.os == 'Windows' && '.venv\Scripts\activate') || 'source .venv/bin/activate' }}
+          pytest -n auto tests/

{py_neuromodulation-0.0.5 → py_neuromodulation-0.0.6}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: py_neuromodulation
-Version: 0.0.5
+Version: 0.0.6
 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
@@ -33,11 +33,8 @@ Classifier: Development Status :: 2 - Pre-Alpha
 Classifier: License :: OSI Approved :: MIT License
 Classifier: Programming Language :: Python
 Classifier: Topic :: Software Development :: Libraries :: Python Modules
-Requires-Python: >=3.10
-Requires-Dist: filterpy>=1.4.5
+Requires-Python: >=3.11
 Requires-Dist: fooof
-Requires-Dist: hatch>=1.9.4
-Requires-Dist: imbalanced-learn
 Requires-Dist: joblib>=1.3.2
 Requires-Dist: matplotlib>=3.9.0
 Requires-Dist: mne
@@ -45,23 +42,18 @@ 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: numpy>=1.21.2
 Requires-Dist: pandas>=2.0.0
-Requires-Dist: pip>=24.2
 Requires-Dist: pyarrow>=14.0.2
-Requires-Dist: pybispectra>=1.0.0
+Requires-Dist: pybispectra>=1.2.0
 Requires-Dist: pydantic>=2.7.3
-Requires-Dist: pynput
 Requires-Dist: pyparrm
 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: statsmodels
 Provides-Extra: dev
 Requires-Dist: notebook; extra == 'dev'
 Requires-Dist: pytest-cov; extra == 'dev'

py_neuromodulation-0.0.6/docs/Makefile

@@ -0,0 +1,20 @@
+# Minimal makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line, and also
+# from the environment for the first two.
+SPHINXOPTS    ?=
+SPHINXBUILD   ?= sphinx-build
+SOURCEDIR     = source
+BUILDDIR      = build
+
+# Put it first so that "make" without argument is like "make help".
+help:
+	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+.PHONY: help Makefile
+
+# Catch-all target: route all unknown targets to Sphinx using the new
+# "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
+%: Makefile
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)

py_neuromodulation-0.0.6/docs/make.bat

@@ -0,0 +1,35 @@
+@ECHO OFF
+
+pushd %~dp0
+
+REM Command file for Sphinx documentation
+
+if "%SPHINXBUILD%" == "" (
+	set SPHINXBUILD=sphinx-build
+)
+set SOURCEDIR=source
+set BUILDDIR=build
+
+if "%1" == "" goto help
+
+%SPHINXBUILD% >NUL 2>NUL
+if errorlevel 9009 (
+	echo.
+	echo.The 'sphinx-build' command was not found. Make sure you have Sphinx
+	echo.installed, then set the SPHINXBUILD environment variable to point
+	echo.to the full path of the 'sphinx-build' executable. Alternatively you
+	echo.may add the Sphinx directory to PATH.
+	echo.
+	echo.If you don't have Sphinx installed, grab it from
+	echo.http://sphinx-doc.org/
+	exit /b 1
+)
+
+%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+goto end
+
+:help
+%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+
+:end
+popd

py_neuromodulation-0.0.6/docs/source/_static/css/project-template.css

@@ -0,0 +1,16 @@
+@import url("theme.css");
+
+.highlight a {
+    text-decoration: underline;
+}
+
+.deprecated p {
+    padding: 10px 7px 10px 10px;
+    color: #b94a48;
+    background-color: #F3E5E5;
+    border: 1px solid #eed3d7;
+}
+
+.deprecated p span.versionmodified {
+    font-weight: bold;
+}

py_neuromodulation-0.0.6/docs/source/_templates/custom-class-template.rst

@@ -0,0 +1,7 @@
+{{ fullname | escape | underline}}
+
+.. currentmodule:: {{ module }}
+
+.. autoclass:: {{ objname }}
+    :members:
+    :inherited-members:

py_neuromodulation-0.0.6/docs/source/_templates/custom-module-template.rst

@@ -0,0 +1,67 @@
+{{ fullname | escape | underline}}
+
+.. automodule:: {{ fullname }}
+  
+    {% block attributes %}
+    {% if attributes %}
+    .. rubric:: Module Attributes
+
+    .. autosummary::
+        :toctree:
+    {% for item in attributes %}
+        {{ item }}
+    {%- endfor %}
+    {% endif %}
+    {% endblock %}
+
+    {% block functions %}
+    {% if functions %}
+    .. rubric:: {{ _('Functions') }}
+
+    .. autosummary::
+        :toctree:
+        :nosignatures:
+    {% for item in functions %}
+        {{ item }}
+    {%- endfor %}
+    {% endif %}
+    {% endblock %}
+
+    {% block classes %}
+    {% if classes %}
+    .. rubric:: {{ _('Classes') }}
+
+    .. autosummary::
+        :toctree:
+        :template: custom-class-template.rst
+    {% for item in classes %}
+        {{ item }}
+    {%- endfor %}
+    {% endif %}
+    {% endblock %}
+
+    {% block exceptions %}
+    {% if exceptions %}
+    .. rubric:: {{ _('Exceptions') }}
+
+    .. autosummary::
+        :toctree:
+    {% for item in exceptions %}
+        {{ item }}
+    {%- endfor %}
+    {% endif %}
+    {% endblock %}
+
+{% block modules %}
+{% if modules %}
+.. rubric:: Modules
+
+.. autosummary::
+    :toctree:
+    :template: custom-module-template.rst
+    :recursive:
+{% for item in modules %}
+    {{ item }}
+{%- endfor %}
+{% endif %}
+{% endblock %}

py_neuromodulation-0.0.6/docs/source/api_documentation.rst

@@ -0,0 +1,51 @@
+API Documentation
+=================
+
+Parametrization
+---------------
+
+.. toctree::
+   :maxdepth: 4
+
+   nm_stream_abc
+   nm_stream
+   nm_settings
+   nm_define_nmchannels
+   nm_generator
+   nm_run_analysis
+   nm_resample
+   nm_normalization
+   nm_rereference
+   nm_projection
+   nm_IO
+
+Feature Estimation
+------------------
+
+.. toctree::
+   :maxdepth: 4
+
+   nm_features
+   nm_filter
+   nm_oscillatory
+   nm_fooof
+   nm_kalmanfilter 
+   nm_hjorth
+   nm_sharpwaves
+   nm_bursts
+   nm_coherence
+   nm_nolds
+   nm_mne_connectivity
+   nm_linelength
+
+Analysis
+--------
+
+.. toctree::
+   :maxdepth: 4
+
+   nm_analysis
+   nm_decode
+   nm_plots
+   nm_RMAP
+   nm_stats

py_neuromodulation-0.0.6/docs/source/conf.py

@@ -0,0 +1,95 @@
+# Configuration file for the Sphinx documentation builder.
+#
+# This file only contains a selection of the most common options. For a full
+# list see the documentation:
+# https://www.sphinx-doc.org/en/master/usage/configuration.html
+
+# -- Path setup --------------------------------------------------------------
+import sys
+from pathlib import Path
+from sphinx_gallery.sorting import FileNameSortKey
+
+print("CURRENT WORKING DIRECTORY")
+print(Path.cwd())
+
+SCRIPT_DIR = Path(__file__).absolute().parent
+
+if SCRIPT_DIR.name == "source":
+    # this check is necessary, so we can also run the script from the root directory
+    SCRIPT_DIR = SCRIPT_DIR.parent.parent / "py_neuromodulation"
+    
+print(f"Script Directory to add: {SCRIPT_DIR}")
+sys.path.append(str(SCRIPT_DIR))
+
+print(sys.path)
+
+exclude_patterns = ["_build", "_templates"]
+
+
+# -- Project information -----------------------------------------------------
+project = "py_neuromodulation"
+copyright = "2021, Timon Merk"
+author = "Timon Merk"
+
+source_parsers = {
+    ".md": "recommonmark.parser.CommonMarkParser",
+}
+
+extensions = [
+    "sphinx.ext.autodoc",
+    "sphinx.ext.autosummary",
+    "sphinx.ext.doctest",
+    "sphinx.ext.intersphinx",
+    "sphinx.ext.viewcode",
+    "sphinx.ext.mathjax",
+    "sphinx.ext.napoleon",
+    "sphinx.ext.autosectionlabel",
+    "sphinx_gallery.gen_gallery",
+    "sphinx_togglebutton",
+    # "nbsphinx",
+]
+
+source_suffix = [
+    ".rst",
+    ".md",
+]
+
+autosummary_generate = True
+
+PYDEVD_DISABLE_FILE_VALIDATION = 1
+
+sphinx_gallery_conf = {
+    "examples_dirs": "../../examples",
+    "gallery_dirs": "auto_examples",
+    "within_subsection_order": FileNameSortKey,
+}
+
+templates_path = ["_templates"]
+exclude_patterns = []
+
+
+html_theme = "pydata_sphinx_theme"
+html_static_path = ["_static"]
+
+html_theme_options = {
+    "show_nav_level": 4,
+    "icon_links": [
+        dict(
+            name="GitHub",
+            url="https://github.com/neuromodulation/py_neuromodulation",
+            icon="fa-brands fa-square-github",
+        )
+    ],
+}
+
+# -- Intersphinx configuration -----------------------------------------------
+
+intersphinx_mapping = {
+    "python": ("https://docs.python.org/3", None),
+    "numpy": ("https://numpy.org/doc/stable", None),
+    "scipy": ("https://docs.scipy.org/doc/scipy", None),
+    "matplotlib": ("https://matplotlib.org/stable", None),
+    "numba": ("https://numba.readthedocs.io/en/latest", None),
+    "mne": ("https://mne.tools/stable", None),
+    "pandas": ("https://pandas.pydata.org/docs", None),
+}

py_neuromodulation-0.0.6/docs/source/contributing.rst

@@ -0,0 +1,36 @@
+Contribution Guide
+==================
+
+Welcome to the contributing guide of py_neuromodulation! We are very happy that you are interested in our project.
+
+In general we recommend placing questions and issues in the `GitHub issue tracker <https://github.com/neuromodulation/py_neuromodulation/issues>`_.
+
+For code formatting we use `ruff <https://docs.astral.sh/ruff/formatter/>`_.
+
+For code development, we recommend using the package manager `rye <https://rye.astral.sh/>`_.
+
+To setup the python environment, type
+
+::
+
+    rye pin 3.12
+
+then sync the environment with
+
+::
+
+    rye sync
+
+Depending on your operating system, activate the rye virtual environment: 
+
+::
+
+    . .venv/bin/activate
+
+To install the documentation dependencies use pip:
+
+::
+
+    python -m pip install .[docs]
+
+

py_neuromodulation-0.0.6/docs/source/index.rst

@@ -0,0 +1,66 @@
+.. py_neuromodulation documentation master file, created by
+   sphinx-quickstart on Sun Apr 18 11:04:51 2021.
+
+Welcome to py_neuromodulation's documentation!
+==============================================
+
+The *py_neuromodulation* toolbox allows for real time capable feature estimation of invasive electrophysiological data.
+
+.. toctree::
+   :maxdepth: 2
+   :caption: Contents
+
+   installation
+   usage
+   auto_examples/index
+   api_documentation
+   contributing
+
+Why py_neuromodulation?
+-----------------------
+
+Analyzing neural data can be a troublesome, trial and error prone,
+and beginner unfriendly process. *py_neuromodulation* allows using a simple
+interface for extraction of established features and includes commonly applied pre -and postprocessing methods.
+
+Basically only **time series data** with a corresponding **sampling frequency** are required.
+
+The output will be a pandas DataFrame including different time-resolved computed features. Internally a **stream** get's initialized,
+which simulates an *online* data-stream that can also be be used for real-time analysis.
+
+The following features are currently included:
+
+* oscillatory: fft, stft or bandpass filtered band power
+* `temporal waveform shape <https://www.sciencedirect.com/science/article/pii/S1364661316302182>`_
+* `fooof <https://fooof-tools.github.io/fooof/>`_
+* `mne_connectivity estimates <https://mne.tools/mne-connectivity/stable/index.html>`_ 
+* `Hjorth parameter <https://en.wikipedia.org/wiki/Hjorth_parameters>`_
+* `non-linear dynamical estimates <https://nolds.readthedocs.io/en/latest/>`_
+* various burst features
+* line length 
+* and more...
+
+Find here the preprint of **py_neuromodulation** called *"Invasive neurophysiology and whole brain connectomics for neural decoding in patients with brain implants"* [1]_.
+
+
+How can those features be used?
+-------------------------------
+
+The original intention for writing this toolbox was movement decoding from invasive brain signals [2]_.
+The application however could be any neural decoding and analysis problem.
+*py_neuromodulation* offers wrappers around common practice machine learning methods for efficient analysis.
+
+References
+----------
+
+.. [1] Merk, T. et al. *Invasive neurophysiology and whole brain connectomics for neural decoding in patients with brain implants*, `https://doi.org/10.21203/rs.3.rs-3212709/v1` (2023).
+.. [2] Merk, T. et al. *Electrocorticography is superior to subthalamic local field potentials for movement decoding in Parkinson’s disease*. Elife 11, e75126, `https://doi.org/10.7554/eLife.75126` (2022).
+
+
+
+Indices and tables
+------------------
+
+* :ref:`genindex`
+* :ref:`modindex`
+* :ref:`search`

py_neuromodulation-0.0.6/docs/source/installation.rst

@@ -0,0 +1,46 @@
+Installation
+============
+
+py_neuromodulation requires at least python 3.10. For installation you can use pip:
+
+.. code-block::
+
+    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:
+
+.. 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
+
+Then install the packages listed in the `pyproject.toml`:
+
+.. code-block::
+
+    pip install .
+
+
+Optionally the ipython kernel can be specified for the installed pynm-test conda environment:
+
+.. code-block::
+
+    ipython kernel install --user --name=pynm-test
+
+Then *py_neuromodulation* can be imported via:
+
+.. code-block::
+
+    import py_neuromodulation as nm

py_neuromodulation-0.0.6/docs/source/nm_IO.rst

@@ -0,0 +1,5 @@
+nm_IO.py
+========
+
+.. automodule:: nm_IO
+      :members:

py_neuromodulation-0.0.6/docs/source/nm_RMAP.rst

@@ -0,0 +1,5 @@
+nm_RMAP.py
+==========
+
+.. automodule:: nm_RMAP
+      :members:

py_neuromodulation-0.0.6/docs/source/nm_analysis.rst

@@ -0,0 +1,5 @@
+nm_analysis.py
+==============
+
+.. automodule:: nm_analysis
+      :members:

py_neuromodulation-0.0.6/docs/source/nm_bursts.rst

@@ -0,0 +1,5 @@
+nm_bursts.py
+============
+
+.. automodule:: nm_bursts
+      :members:

py_neuromodulation-0.0.6/docs/source/nm_coherence.rst

@@ -0,0 +1,5 @@
+nm_coherence.py
+===============
+
+.. automodule:: nm_coherence
+      :members: