ezmsg-sigproc 1.2.3__tar.gz → 1.3.1__tar.gz

ezmsg_sigproc-1.3.1/.github/workflows/python-publish-ezmsg-sigproc.yml

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+# This workflow will upload a Python Package using Twine when a release is created
+
+name: Upload Python Package - ezmsg-sigproc
+
+on:
+  release:
+    types: [published]
+  workflow_dispatch:
+
+permissions:
+  contents: read
+
+jobs:
+  deploy:
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Install uv
+        uses: astral-sh/setup-uv@v2
+
+      - name: Build Package
+        run: uv build
+
+      - name: Publish Package
+        env:
+          TWINE_USERNAME: __token__
+          TWINE_PASSWORD: ${{ secrets.PYPI_API_TOKEN }}
+        run: uvx twine upload dist/*

ezmsg_sigproc-1.3.1/.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: [3.9, "3.10", "3.11", "3.12"]
+        os:
+          - "ubuntu-latest"
+          - "windows-latest"
+          - "macos-latest"
+    runs-on: ${{matrix.os}}
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Install uv
+        uses: astral-sh/setup-uv@v2
+        with:
+          enable-cache: true
+          cache-dependency-glob: "uv.lock"
+
+      - name: Set up Python ${{ matrix.python-version }}
+        run: uv python install ${{ matrix.python-version }}
+
+      - name: Install the project
+        run: uv sync --all-extras --dev
+
+      - name: Lint
+        run:
+          uv tool run ruff check --output-format=github src
+
+      - name: Run tests
+        run: uv run pytest tests

ezmsg_sigproc-1.3.1/.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
+#  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/
+cover/
+
+# 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/
+docs/source/_build
+docs/source/generated
+
+# PyBuilder
+.pybuilder/
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+#   For a library or package, you might want to ignore these files since the code is
+#   intended to run in multiple environments; otherwise, check them in:
+# .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/
+
+# 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
+.idea/
+
+src/ezmsg/sigproc/__version__.py

ezmsg_sigproc-1.3.1/.pre-commit-config.yaml

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+repos:
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    # Ruff version.
+    rev: v0.6.7
+    hooks:
+      # Run the linter.
+      - id: ruff
+        args: [ --fix ]
+      # Run the formatter.
+      - id: ruff-format

ezmsg_sigproc-1.3.1/PKG-INFO

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+Metadata-Version: 2.3
+Name: ezmsg-sigproc
+Version: 1.3.1
+Summary: Timeseries signal processing implementations in ezmsg
+Author-email: Griffin Milsap <griffin.milsap@gmail.com>, Preston Peranich <pperanich@gmail.com>, Chadwick Boulay <chadwick.boulay@gmail.com>
+License-Expression: MIT
+License-File: LICENSE.txt
+Requires-Python: >=3.9
+Requires-Dist: ezmsg>=3.5.0
+Requires-Dist: numpy>=2.0.2
+Requires-Dist: pywavelets>=1.6.0
+Requires-Dist: scipy>=1.13.1
+Provides-Extra: test
+Requires-Dist: flake8>=7.1.1; extra == 'test'
+Requires-Dist: frozendict>=2.4.4; extra == 'test'
+Requires-Dist: pytest-asyncio>=0.24.0; extra == 'test'
+Requires-Dist: pytest-cov>=5.0.0; extra == 'test'
+Requires-Dist: pytest>=8.3.3; extra == 'test'
+Description-Content-Type: text/markdown
+
+# ezmsg.sigproc
+
+Timeseries signal processing implementations for ezmsg
+
+## Dependencies
+
+* `ezmsg`
+* `numpy`
+* `scipy`
+* `pywavelets`
+
+## Installation
+
+### Release
+
+Install the latest release from pypi with: `pip install ezmsg-sigproc` (or `uv add ...` or `poetry add ...`).
+
+### Development Version
+
+You can add the development version of `ezmsg-sigproc` to your project's dependencies in one of several ways.
+
+You can clone it and add its path to your project dependencies. You may wish to do this if you intend to edit `ezmsg-sigproc`. If so, please refer to the [Developers](#developers) section below.
+
+You can also add it directly from GitHub:
+
+* Using `pip`: `pip install git+https://github.com/ezmsg-org/ezmsg-sigproc.git@dev`
+* Using `poetry`: `poetry add "git+https://github.com/ezmsg-org/ezmsg-sigproc.git@dev"`
+* Using `uv`: `uv add git+https://github.com/ezmsg-org/ezmsg-sigproc --branch dev`
+
+## Developers
+
+We use [`uv`](https://docs.astral.sh/uv/getting-started/installation/) for development. It is not strictly required, but if you intend to contribute to ezmsg-sigproc then using `uv` will lead to the smoothest collaboration.
+
+1. Install [`uv`](https://docs.astral.sh/uv/getting-started/installation/) if not already installed.
+2. Fork ezmsg-sigproc and clone your fork to your local computer.
+3. Open a terminal and `cd` to the cloned folder.
+4. `uv sync` to create a .venv and install dependencies.
+5. `uv run pre-commit install` to install pre-commit hooks to do linting and formatting.
+6. After editing code and making commits, Run the test suite before making a PR: `uv run pytest tests`

ezmsg_sigproc-1.3.1/README.md

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+# ezmsg.sigproc
+
+Timeseries signal processing implementations for ezmsg
+
+## Dependencies
+
+* `ezmsg`
+* `numpy`
+* `scipy`
+* `pywavelets`
+
+## Installation
+
+### Release
+
+Install the latest release from pypi with: `pip install ezmsg-sigproc` (or `uv add ...` or `poetry add ...`).
+
+### Development Version
+
+You can add the development version of `ezmsg-sigproc` to your project's dependencies in one of several ways.
+
+You can clone it and add its path to your project dependencies. You may wish to do this if you intend to edit `ezmsg-sigproc`. If so, please refer to the [Developers](#developers) section below.
+
+You can also add it directly from GitHub:
+
+* Using `pip`: `pip install git+https://github.com/ezmsg-org/ezmsg-sigproc.git@dev`
+* Using `poetry`: `poetry add "git+https://github.com/ezmsg-org/ezmsg-sigproc.git@dev"`
+* Using `uv`: `uv add git+https://github.com/ezmsg-org/ezmsg-sigproc --branch dev`
+
+## Developers
+
+We use [`uv`](https://docs.astral.sh/uv/getting-started/installation/) for development. It is not strictly required, but if you intend to contribute to ezmsg-sigproc then using `uv` will lead to the smoothest collaboration.
+
+1. Install [`uv`](https://docs.astral.sh/uv/getting-started/installation/) if not already installed.
+2. Fork ezmsg-sigproc and clone your fork to your local computer.
+3. Open a terminal and `cd` to the cloned folder.
+4. `uv sync` to create a .venv and install dependencies.
+5. `uv run pre-commit install` to install pre-commit hooks to do linting and formatting.
+6. After editing code and making commits, Run the test suite before making a PR: `uv run pytest tests`

ezmsg_sigproc-1.3.1/pyproject.toml

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+[project]
+name = "ezmsg-sigproc"
+description = "Timeseries signal processing implementations in ezmsg"
+authors = [
+  { name = "Griffin Milsap", email = "griffin.milsap@gmail.com" },
+  { name = "Preston Peranich", email = "pperanich@gmail.com" },
+  { name = "Chadwick Boulay", email = "chadwick.boulay@gmail.com" }
+]
+license = "MIT"
+readme = "README.md"
+requires-python = ">=3.9"
+dynamic = ["version"]
+dependencies = [
+    "ezmsg>=3.5.0",
+    "numpy>=2.0.2",
+    "pywavelets>=1.6.0",
+    "scipy>=1.13.1",
+]
+
+[project.optional-dependencies]
+test = [
+    "flake8>=7.1.1",
+    "frozendict>=2.4.4",
+    "pytest-asyncio>=0.24.0",
+    "pytest-cov>=5.0.0",
+    "pytest>=8.3.3",
+]
+
+[build-system]
+requires = ["hatchling", "hatch-vcs"]
+build-backend = "hatchling.build"
+
+[tool.hatch.version]
+source = "vcs"
+
+[tool.hatch.build.hooks.vcs]
+version-file = "src/ezmsg/sigproc/__version__.py"
+
+[tool.hatch.build.targets.wheel]
+packages = ["src/ezmsg"]
+
+[tool.uv]
+dev-dependencies = [
+    "pre-commit>=3.8.0",
+    "ruff>=0.6.7",
+]
+
+[tool.pytest.ini_options]
+norecursedirs = "tests/helpers"
+addopts = "-p no:warnings"

ezmsg_sigproc-1.3.1/src/ezmsg/sigproc/__init__.py

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+from .__version__ import __version__ as __version__

ezmsg_sigproc-1.3.1/src/ezmsg/sigproc/__version__.py

@@ -0,0 +1,16 @@
+# file generated by setuptools_scm
+# don't change, don't track in version control
+TYPE_CHECKING = False
+if TYPE_CHECKING:
+    from typing import Tuple, Union
+    VERSION_TUPLE = Tuple[Union[int, str], ...]
+else:
+    VERSION_TUPLE = object
+
+version: str
+__version__: str
+__version_tuple__: VERSION_TUPLE
+version_tuple: VERSION_TUPLE
+
+__version__ = version = '1.3.1'
+__version_tuple__ = version_tuple = (1, 3, 1)

ezmsg_sigproc-1.3.1/src/ezmsg/sigproc/activation.py

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+from dataclasses import replace
+import typing
+
+import numpy as np
+import scipy.special
+import ezmsg.core as ez
+from ezmsg.util.messages.axisarray import AxisArray
+from ezmsg.util.generator import consumer
+
+from .spectral import OptionsEnum
+from .base import GenAxisArray
+
+
+class ActivationFunction(OptionsEnum):
+    """Activation (transformation) function."""
+
+    NONE = "none"
+    """None."""
+
+    SIGMOID = "sigmoid"
+    """:obj:`scipy.special.expit`"""
+
+    EXPIT = "expit"
+    """:obj:`scipy.special.expit`"""
+
+    LOGIT = "logit"
+    """:obj:`scipy.special.logit`"""
+
+    LOGEXPIT = "log_expit"
+    """:obj:`scipy.special.log_expit`"""
+
+
+ACTIVATIONS = {
+    ActivationFunction.NONE: lambda x: x,
+    ActivationFunction.SIGMOID: scipy.special.expit,
+    ActivationFunction.EXPIT: scipy.special.expit,
+    ActivationFunction.LOGIT: scipy.special.logit,
+    ActivationFunction.LOGEXPIT: scipy.special.log_expit,
+}
+
+
+@consumer
+def activation(
+    function: typing.Union[str, ActivationFunction],
+) -> typing.Generator[AxisArray, AxisArray, None]:
+    if type(function) is ActivationFunction:
+        func = ACTIVATIONS[function]
+    else:
+        # str type. There's probably an easier way to support either enum or str argument. Oh well this works.
+        function: str = function.lower()
+        if function not in ActivationFunction.options():
+            raise ValueError(
+                f"Unrecognized activation function {function}. Must be one of {ACTIVATIONS.keys()}"
+            )
+        function = list(ACTIVATIONS.keys())[
+            ActivationFunction.options().index(function)
+        ]
+        func = ACTIVATIONS[function]
+
+    msg_out = AxisArray(np.array([]), dims=[""])
+
+    while True:
+        msg_in: AxisArray = yield msg_out
+        msg_out = replace(msg_in, data=func(msg_in.data))
+
+
+class ActivationSettings(ez.Settings):
+    function: str = ActivationFunction.NONE
+
+
+class Activation(GenAxisArray):
+    SETTINGS = ActivationSettings
+
+    def construct_generator(self):
+        self.STATE.gen = activation(function=self.SETTINGS.function)