py-neuromodulation 0.0.4__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-0.0.4 → py_neuromodulation-0.0.6}/.gitignore

@@ -1,175 +1,196 @@
-# Byte-compiled / optimized / DLL files
-__pycache__/
-*.py[cod]
-*$py.class
-
-# C extensions
-*.so
-
-# 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/
-
-# 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/sub/*
-examples/utils/*
-
-sub/
-
-py_neuromodulation/data/derivatives/*
-
-requirements.lock
-requirements-dev.lock
-
-.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-0.0.6}/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-0.0.6}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: py_neuromodulation
-Version: 0.0.4
+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
@@ -33,40 +33,48 @@ 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: black>=24.2.0
-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: 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: 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: pyarrow>=14.0.2
-Requires-Dist: pybids
-Requires-Dist: pybispectra>=1.0.0
-Requires-Dist: pynput
+Requires-Dist: pybispectra>=1.2.0
+Requires-Dist: pydantic>=2.7.3
 Requires-Dist: pyparrm
-Requires-Dist: pytest>=8.0.2
-Requires-Dist: scikit-image
+Requires-Dist: pyqt5
 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
 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 +119,10 @@ 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