ezmsg-simbiophys 1.0.0__tar.gz

ezmsg_simbiophys-1.0.0/.github/workflows/docs.yml

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+name: Documentation
+
+on:
+  push:
+    branches:
+      - main
+  pull_request:
+    branches:
+      - main
+      - dev
+  release:
+    types: [published]
+  workflow_dispatch:
+
+permissions:
+  contents: read
+  pages: write
+  id-token: write
+
+# Allow only one concurrent deployment
+concurrency:
+  group: "pages"
+  cancel-in-progress: false
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0  # Needed for hatch-vcs to determine version
+
+      - name: Install uv
+        uses: astral-sh/setup-uv@v6
+        with:
+          enable-cache: true
+          python-version: "3.12"
+
+      - name: Install the project
+        run: uv sync --only-group docs
+
+      - name: Build documentation
+        run: |
+          cd docs
+          uv run make html
+
+      - name: Add .nojekyll file
+        run: touch docs/build/html/.nojekyll
+
+      - name: Upload artifact
+        uses: actions/upload-pages-artifact@v3
+        with:
+          path: 'docs/build/html'
+
+  deploy:
+    # Only deploy when a release is published
+    if: github.event_name == 'release'
+    environment:
+      name: github-pages
+      url: ${{ steps.deployment.outputs.page_url }}
+    runs-on: ubuntu-latest
+    needs: build
+    steps:
+      - name: Deploy to GitHub Pages
+        id: deployment
+        uses: actions/deploy-pages@v4

ezmsg_simbiophys-1.0.0/.github/workflows/python-publish.yml

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+# This workflow will upload a Python Package using Twine when a release is created
+
+name: Upload Python Package
+
+on:
+  release:
+    types: [published]
+  workflow_dispatch:
+
+jobs:
+  build:
+    name: build and upload release to PyPI
+    runs-on: ubuntu-latest
+    environment: "release"
+    permissions:
+      id-token: write  # IMPORTANT: this permission is mandatory for trusted publishing
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Install uv
+        uses: astral-sh/setup-uv@v6
+
+      - name: Build Package
+        run: uv build
+
+      - name: Publish package distributions to PyPI
+        run: uv publish

ezmsg_simbiophys-1.0.0/.github/workflows/python-tests.yml

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+name: Test package
+
+on:
+  push:
+    branches: [main]
+  pull_request:
+    branches:
+      - main
+      - dev
+  workflow_dispatch:
+
+jobs:
+  build:
+    strategy:
+      matrix:
+        python-version: ["3.10.15", "3.11", "3.12", "3.13"]
+        os:
+          - "ubuntu-latest"
+          - "windows-latest"
+          - "macos-latest"
+    runs-on: ${{matrix.os}}
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Install the latest version of uv
+        uses: astral-sh/setup-uv@v6
+
+      - name: Install the project
+        run: uv sync --python ${{ matrix.python-version }}
+
+      - name: Lint
+        run: uv tool run ruff check --output-format=github src
+
+      - name: Run tests
+        run: uv run pytest tests

ezmsg_simbiophys-1.0.0/.gitignore

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+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+*.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/
+cover/
+
+# Translations
+*.mo
+*.pot
+
+# Sphinx documentation
+docs/_build/
+docs/build/
+docs/source/_build
+docs/source/generated
+docs/source/api/generated
+
+# PyBuilder
+.pybuilder/
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+# .python-version
+
+# PEP 582
+__pypackages__/
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/
+
+# pytype static type analyzer
+.pytype/
+
+# Cython debug symbols
+cython_debug/
+
+# JetBrains IDE
+.idea/
+
+# VS Code
+.vscode/
+
+# Ruff cache
+.ruff_cache/
+
+# hatch-vcs generated version file
+src/ezmsg/simbiophys/__version__.py
+
+# uv lockfile (optional - comment if you want to track it)
+uv.lock
+
+# Claude
+settings.local.json

ezmsg_simbiophys-1.0.0/.pre-commit-config.yaml

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+repos:
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.8.3
+    hooks:
+      # Run the linter.
+      - id: ruff
+        args: [ --fix ]
+      # Run the formatter.
+      - id: ruff-format

ezmsg_simbiophys-1.0.0/LICENSE

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+MIT License
+
+Copyright (c) 2025 ezmsg-org
+
+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.

ezmsg_simbiophys-1.0.0/PKG-INFO

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+Metadata-Version: 2.4
+Name: ezmsg-simbiophys
+Version: 1.0.0
+Summary: Signal simulation and synthesis for ezmsg
+Author-email: Chadwick Boulay <chadwick.boulay@gmail.com>
+License-Expression: MIT
+License-File: LICENSE
+Requires-Python: >=3.10.15
+Requires-Dist: ezmsg-baseproc>=1.0.3
+Requires-Dist: ezmsg-sigproc>=2.6.0
+Requires-Dist: ezmsg>=3.6.0
+Requires-Dist: numpy>=1.26.0
+Description-Content-Type: text/markdown
+
+# ezmsg-simbiophys
+
+ezmsg namespace package for simulating biophysical signals such as ECG, EEG, and intracranial recordings.
+
+## Installation
+
+```bash
+pip install ezmsg-simbiophys
+```
+
+## Dependencies
+
+- `ezmsg`
+- `ezmsg-baseproc`
+- `ezmsg-sigproc`
+- `numpy`
+
+
+## Development
+
+We use [`uv`](https://docs.astral.sh/uv/getting-started/installation/) for development.
+
+1. Install [`uv`](https://docs.astral.sh/uv/getting-started/installation/) if not already installed.
+2. Fork this repository and clone your fork locally.
+3. Open a terminal and `cd` to the cloned folder.
+4. Run `uv sync` to create a `.venv` and install dependencies.
+5. (Optional) Install pre-commit hooks: `uv run pre-commit install`
+6. After making changes, run the test suite: `uv run pytest tests`
+
+## License
+
+MIT License - see [LICENSE](LICENSE) for details.

ezmsg_simbiophys-1.0.0/README.md

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+# ezmsg-simbiophys
+
+ezmsg namespace package for simulating biophysical signals such as ECG, EEG, and intracranial recordings.
+
+## Installation
+
+```bash
+pip install ezmsg-simbiophys
+```
+
+## Dependencies
+
+- `ezmsg`
+- `ezmsg-baseproc`
+- `ezmsg-sigproc`
+- `numpy`
+
+
+## Development
+
+We use [`uv`](https://docs.astral.sh/uv/getting-started/installation/) for development.
+
+1. Install [`uv`](https://docs.astral.sh/uv/getting-started/installation/) if not already installed.
+2. Fork this repository and clone your fork locally.
+3. Open a terminal and `cd` to the cloned folder.
+4. Run `uv sync` to create a `.venv` and install dependencies.
+5. (Optional) Install pre-commit hooks: `uv run pre-commit install`
+6. After making changes, run the test suite: `uv run pytest tests`
+
+## License
+
+MIT License - see [LICENSE](LICENSE) for details.

ezmsg_simbiophys-1.0.0/docs/Makefile

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+# 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)

ezmsg_simbiophys-1.0.0/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
+
+%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.https://www.sphinx-doc.org/
+	exit /b 1
+)
+
+if "%1" == "" goto help
+
+%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+goto end
+
+:help
+%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+
+:end
+popd

ezmsg_simbiophys-1.0.0/docs/source/api/index.rst

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+API Reference
+=============
+
+.. autosummary::
+   :toctree: generated
+   :recursive:
+
+   ezmsg.simbiophys

ezmsg_simbiophys-1.0.0/docs/source/conf.py

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+# Configuration file for the Sphinx documentation builder.
+
+import os
+import sys
+
+# Add the source directory to the path
+sys.path.insert(0, os.path.abspath("../../src"))
+
+# -- Project information --------------------------
+
+project = "ezmsg.simbiophys"
+copyright = "2025, ezmsg Contributors"
+author = "ezmsg Contributors"
+
+# The version is managed by hatch-vcs and stored in __version__.py
+try:
+    from ezmsg.simbiophys.__version__ import version as release
+except ImportError:
+    release = "unknown"
+
+# For display purposes, extract the base version without git commit info
+version = release.split("+")[0] if release != "unknown" else release
+
+# -- General configuration --------------------------
+
+extensions = [
+    "sphinx.ext.autodoc",
+    "sphinx.ext.autosummary",
+    "sphinx.ext.napoleon",
+    "sphinx.ext.intersphinx",
+    "sphinx.ext.viewcode",
+    "sphinx.ext.duration",
+    "sphinx_autodoc_typehints",
+    "sphinx_copybutton",
+    "myst_parser",  # For markdown files
+]
+
+templates_path = ["_templates"]
+source_suffix = {
+    ".rst": "restructuredtext",
+    ".md": "markdown",
+}
+exclude_patterns = ["_build", "Thumbs.db", ".DS_Store"]
+
+# The toctree master document
+master_doc = "index"
+
+# -- Autodoc configuration ------------------------------
+
+# Auto-generate API docs
+autosummary_generate = True
+autosummary_imported_members = False
+autodoc_typehints = "description"
+autodoc_member_order = "bysource"
+autodoc_typehints_format = "short"
+python_use_unqualified_type_names = True
+autodoc_default_options = {
+    "members": True,
+    "member-order": "bysource",
+    "special-members": "__init__",
+    "undoc-members": True,
+    "show-inheritance": True,
+}
+
+# Don't show the full module path in the docs
+add_module_names = False
+
+# -- Intersphinx configuration --------------------------
+
+intersphinx_mapping = {
+    "python": ("https://docs.python.org/3/", None),
+    "numpy": ("https://numpy.org/doc/stable/", None),
+    "ezmsg": ("https://www.ezmsg.org/ezmsg/", None),
+}
+intersphinx_disabled_domains = ["std"]
+
+# -- Options for HTML output -----------------------------
+
+html_theme = "pydata_sphinx_theme"
+html_static_path = ["_static"]
+
+# Set the base URL for the documentation
+html_baseurl = "https://www.ezmsg.org/ezmsg-simbiophys/"
+
+html_theme_options = {
+    "logo": {
+        "text": f"ezmsg.simbiophys {version}",
+        "link": "https://ezmsg.org",
+    },
+    "header_links_before_dropdown": 4,
+    "navbar_start": ["navbar-logo"],
+    "navbar_end": ["theme-switcher", "navbar-icon-links"],
+    "icon_links": [
+        {
+            "name": "GitHub",
+            "url": "https://github.com/ezmsg-org/ezmsg-simbiophys",
+            "icon": "fa-brands fa-github",
+        },
+        {
+            "name": "ezmsg.org",
+            "url": "https://www.ezmsg.org",
+            "icon": "fa-solid fa-house",
+        },
+    ],
+}
+
+# Timestamp is inserted at every page bottom in this strftime format.
+html_last_updated_fmt = "%Y-%m-%d"
+
+# -- Options for linkcode -----------------------------
+
+branch = "main"
+code_url = f"https://github.com/ezmsg-org/ezmsg-simbiophys/blob/{branch}/"
+
+
+def linkcode_resolve(domain, info):
+    if domain != "py":
+        return None
+    if not info["module"]:
+        return None
+    filename = info["module"].replace(".", "/")
+    return f"{code_url}src/{filename}.py"

ezmsg_simbiophys-1.0.0/docs/source/index.rst

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+ezmsg.simbiophys
+=============
+
+Short description of your ezmsg package.
+
+Overview
+--------
+
+``ezmsg-simbiophys`` provides ... for the `ezmsg <https://www.ezmsg.org>`_ framework.
+
+Key features:
+
+* **Feature 1** - Description
+* **Feature 2** - Description
+* **Feature 3** - Description
+
+Installation
+------------
+
+Install from PyPI:
+
+.. code-block:: bash
+
+   pip install ezmsg-simbiophys
+
+Or install the latest development version:
+
+.. code-block:: bash
+
+   pip install git+https://github.com/ezmsg-org/ezmsg-simbiophys@main
+
+Dependencies
+^^^^^^^^^^^^
+
+Core dependencies:
+
+* ``ezmsg`` - Core messaging framework
+* ``numpy`` - Numerical computing
+
+Quick Start
+-----------
+
+For general ezmsg tutorials and guides, visit `ezmsg.org <https://www.ezmsg.org>`_.
+
+.. code-block:: python
+
+   import ezmsg.core as ez
+   from ezmsg.simbiophys import MyUnit
+
+   # Your example code here
+
+Documentation
+-------------
+
+.. toctree::
+   :maxdepth: 2
+   :caption: Contents:
+
+   api/index
+
+
+Indices and tables
+------------------
+
+* :ref:`genindex`
+* :ref:`modindex`

ezmsg_simbiophys-1.0.0/examples/example.py

@@ -0,0 +1,49 @@
+"""
+Example usage of ezmsg-simbiophys package.
+This is just a placeholder to test importing. Actual usage example to come.
+"""
+
+import asyncio
+import importlib
+import typing
+
+import ezmsg.core as ez
+
+# Import your units from the package
+# from ezmsg.simbiophys import MyUnit
+
+
+class ExampleSettings(ez.Settings):
+    """Settings for ExampleUnit."""
+
+    message: str = "Hello from ezmsg-simbiophys!"
+
+
+class ExampleUnit(ez.Unit):
+    """Example ezmsg Unit demonstrating basic patterns."""
+
+    SETTINGS = ExampleSettings
+
+    INPUT = ez.InputStream(str)
+    OUTPUT = ez.OutputStream(str)
+
+    @ez.subscriber(INPUT)
+    @ez.publisher(OUTPUT)
+    async def on_message(self, message: str) -> typing.AsyncGenerator:
+        """Process incoming messages."""
+        result = f"{self.SETTINGS.message} Received: {message}"
+        yield self.OUTPUT, result
+
+
+async def main():
+    """Run the example."""
+    print("ezmsg-simbiophys loaded successfully!")
+    print(f"Version: {importlib.import_module('ezmsg.simbiophys').__version__}")
+
+    # Example: Create and run a simple system
+    # system = ExampleSystem()
+    # await ez.run(SYSTEM=system)
+
+
+if __name__ == "__main__":
+    asyncio.run(main())