ezmsg 3.4.0__tar.gz → 3.5.0__tar.gz

ezmsg-3.5.0/.envrc

@@ -0,0 +1,2 @@
+export VIRTUAL_ENV=.venv
+layout python

ezmsg-3.5.0/.flake8

@@ -0,0 +1,7 @@
+[flake8]
+exclude =
+    migrations,
+    __pycache__,
+    env,
+max_line_length = 120
+max_complexity = 10

ezmsg-3.5.0/.git-blame-ignore-revs

@@ -0,0 +1,4 @@
+# chore: format files with ruff. Add pre-commit-config.
+5b4c220154d33cac15a75d3d7d978a75e67f2b8a
+# Ran `black` formatter on entire codebase and fixed non-standard line-endings with `dos2unix`.
+4e4f20be40a73f2162a565732bae76ea0c812739

ezmsg-3.5.0/.github/workflows/ci.yml

@@ -0,0 +1,37 @@
+name: Test package
+
+on:
+  push:
+    branches: [main]
+  pull_request:
+    branches: [main]
+  workflow_dispatch:
+
+jobs:
+  build:
+    strategy:
+      matrix:
+        python-version: ["3.8", "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: Run tests
+        run: uv run pytest tests

ezmsg-3.5.0/.github/workflows/publish.yml

@@ -0,0 +1,28 @@
+name: Upload Python Package
+
+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_TOKEN }}
+        run: uvx twine upload dist/*

ezmsg-3.5.0/.gitignore

@@ -0,0 +1,143 @@
+# 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/

ezmsg-3.5.0/.pre-commit-config.yaml

@@ -0,0 +1,10 @@
+repos:
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    # Ruff version.
+    rev: v0.5.0
+    hooks:
+      # Run the linter.
+      - id: ruff
+        args: [--fix]
+      # Run the formatter.
+      - id: ruff-format

ezmsg-3.5.0/.python-version

@@ -0,0 +1 @@
+3.11

ezmsg-3.5.0/.readthedocs.yaml

@@ -0,0 +1,13 @@
+version: 2
+
+build:
+  os: ubuntu-22.04
+  tools:
+    python: "3.12"
+
+python:
+  install:
+    - requirements: docs/requirements.txt
+
+sphinx:
+  configuration: docs/source/conf.py

{ezmsg-3.4.0 → ezmsg-3.5.0}/PKG-INFO

@@ -1,29 +1,24 @@
-Metadata-Version: 2.1
+Metadata-Version: 2.3
 Name: ezmsg
-Version: 3.4.0
+Version: 3.5.0
 Summary: A simple DAG-based computation model
-License: MIT
-Author: Milsap, Griffin
-Author-email: griffin.milsap@gmail.com
-Requires-Python: >=3.8,<4.0
-Classifier: License :: OSI Approved :: MIT License
+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
 Classifier: Operating System :: OS Independent
 Classifier: Programming Language :: Python :: 3
-Classifier: Programming Language :: Python :: 3.8
-Classifier: Programming Language :: Python :: 3.9
-Classifier: Programming Language :: Python :: 3.10
-Classifier: Programming Language :: Python :: 3.11
-Classifier: Programming Language :: Python :: 3.12
-Provides-Extra: all-ext
-Provides-Extra: sigproc
-Provides-Extra: vispy
-Provides-Extra: websocket
-Provides-Extra: zmq
-Requires-Dist: ezmsg-sigproc ; extra == "sigproc" or extra == "all-ext"
-Requires-Dist: ezmsg-vispy ; extra == "vispy" or extra == "all-ext"
-Requires-Dist: ezmsg-websocket ; extra == "websocket" or extra == "all-ext"
-Requires-Dist: ezmsg-zmq ; extra == "zmq" or extra == "all-ext"
-Requires-Dist: typing-extensions (>=4.9.0,<5.0.0)
+Requires-Python: >=3.8
+Requires-Dist: typing-extensions>=4.9.0
+Provides-Extra: docs
+Requires-Dist: ezmsg-sigproc>=1.2.3; extra == 'docs'
+Requires-Dist: sphinx-rtd-theme==2.0.0; extra == 'docs'
+Requires-Dist: sphinx<=7.2; extra == 'docs'
+Provides-Extra: test
+Requires-Dist: flake8>=5.0.4; extra == 'test'
+Requires-Dist: numpy>=1.24.2; extra == 'test'
+Requires-Dist: pytest-asyncio>=0.23.8; extra == 'test'
+Requires-Dist: pytest-cov>=5.0.0; extra == 'test'
+Requires-Dist: pytest>=7.0.0; extra == 'test'
 Description-Content-Type: text/markdown
 
 # <img src="https://raw.githubusercontent.com/iscoe/ezmsg/main/docs/source/logo.png" width="50"/> ezmsg
@@ -111,4 +106,3 @@ These publications provide insights into the practical applications and impact o
 ## Financial Support
 
 `ezmsg` is supported by Johns Hopkins University (JHU), the JHU Applied Physics Laboratory (APL), and by the Wyss Center for Bio and Neuro Engineering.
-

ezmsg-3.5.0/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)

ezmsg-3.5.0/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
+
+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

ezmsg-3.5.0/docs/requirements.txt

@@ -0,0 +1,2 @@
+sphinx-rtd-theme
+ezmsg-sigproc @ git+https://github.com/ezmsg-org/ezmsg-sigproc@dev

ezmsg-3.5.0/docs/source/about.rst

@@ -0,0 +1,4 @@
+How ``ezmsg`` works
+===================
+
+When an ``ezmsg`` pipeline is started, ``ezmsg`` initializes two additional processes to manage execution. The first is the SharedMemoryServer, which allocates blocks of memory to nodes. The second is the GraphServer, which keeps track of the graph state during execution. One GraphServer should be initialized per ezmsg pipeline, and one SharedMemoryServer should be initialized per machine which the pipeline is running on. Check out the Other page for more information on managing the SharedMemoryServer and GraphServer during pipeline execution.

ezmsg-3.5.0/docs/source/api.rst

@@ -0,0 +1,84 @@
+API
+===
+
+An ``ezmsg`` pipeline is created from a few basic components.
+``ezmsg`` provides a framework for you to define your own graphs using its building blocks.
+Inherit from its base components to define a pipeline that works for your project.
+
+.. automodule:: ezmsg.core
+
+Most ``ezmsg`` classes intended for use in building pipelines are available in ``ezmsg.core``.
+It is convention to ``import ezmsg.core as ez`` and then use this shorthand in your code. e.g.,
+
+.. code-block:: python
+
+   class MyUnit(ez.Unit):
+       ...
+
+Components
+----------
+
+.. autoclass:: Component
+
+.. autoclass:: Collection
+   :show-inheritance:
+   :members:
+
+.. autoclass:: NetworkDefinition
+
+.. autoclass:: Unit
+   :show-inheritance:
+   :members:
+   :inherited-members:
+
+
+Unit Function Decorators
+^^^^^^^^^^^^^^^^^^^^^^^^
+
+These function decorators can be added to member functions.
+
+.. automethod:: ezmsg.core.subscriber
+
+.. automethod:: ezmsg.core.publisher
+
+.. automethod:: ezmsg.core.main
+
+.. automethod:: unit.thread
+
+.. automethod:: ezmsg.core.task
+
+.. automethod:: ezmsg.core.process
+
+.. automethod:: ezmsg.core.timeit
+
+
+Component Interaction
+---------------------
+
+.. autoclass:: Settings
+
+.. autoclass:: State
+
+
+Stream
+------
+
+Facilitates a flow of ``Messages`` into or out of a ``Component``.
+
+.. autoclass:: InputStream
+
+.. autoclass:: OutputStream
+
+
+Custom Exceptions
+-----------------
+
+.. autoclass:: Complete
+
+.. autoclass:: NormalTermination
+
+
+Entry Point
+-----------
+
+.. automethod:: ezmsg.core.run

ezmsg-3.5.0/docs/source/conf.py

@@ -0,0 +1,59 @@
+# Configuration file for the Sphinx documentation builder.
+
+# -- Project information
+
+project = "ezmsg"
+copyright = "2022, JHU/APL"
+author = "JHU/APL"
+
+release = "3.3.4"
+version = "3.3.4"
+
+# -- General configuration
+
+extensions = [
+    "sphinx.ext.duration",
+    "sphinx.ext.doctest",
+    "sphinx.ext.autodoc",
+    "sphinx.ext.autosummary",
+    "sphinx.ext.intersphinx",
+    "sphinx.ext.linkcode",
+    "sphinx.ext.napoleon",
+]
+
+intersphinx_mapping = {
+    "python": ("https://docs.python.org/3/", None),
+    "sphinx": ("https://www.sphinx-doc.org/en/master/", None),
+    "numpy": ("https://docs.scipy.org/doc/numpy", None),
+    "scipy": ("https://docs.scipy.org/doc/scipy/reference", None),
+}
+intersphinx_disabled_domains = ["std"]
+
+templates_path = ["_templates"]
+
+# -- Options for HTML output
+
+html_theme = "sphinx_rtd_theme"
+
+# -- Options for EPUB output
+epub_show_urls = "footnote"
+
+add_module_names = False
+
+branch = "dev"
+code_url = f"https://github.com/iscoe/ezmsg/blob/{branch}/"
+sigproc_code_url = f"https://github.com/ezmsg-org/ezmsg-sigproc/blob/{branch}/"
+
+
+def linkcode_resolve(domain, info):
+    if domain != "py":
+        return None
+    if not info["module"]:
+        return None
+    filename = info["module"].replace(".", "/")
+    if "sigproc" in filename:
+        return f"{sigproc_code_url}src/{filename}.py"
+    elif "core" in filename:
+        return f"{code_url}src/ezmsg/core/__init__.py"
+    else:
+        return f"{code_url}src/{filename}.py"

ezmsg-3.5.0/docs/source/developer.rst

@@ -0,0 +1,12 @@
+Developer Info
+==============
+
+ezmsg developers will want to clone this repo locally then create an env with dependencies using `poetry install`.
+
+Documentation
+-------------
+
+Documentation is built using Sphinx.
+
+`poetry install --with docs`
+`poetry run docs/make html`

ezmsg-3.5.0/docs/source/extensions/sigproc.rst

@@ -0,0 +1,148 @@
+ezmsg-sigproc
+=============
+
+Timeseries signal processing implementations in ezmsg, leveraging numpy and scipy.
+Most of the methods and classes in this extension are intended to be used in building signal processing pipelines.
+They use :class:`ezmsg.util.messages.axisarray.AxisArray` as the primary data structure for passing signals between components.
+The message's data are expected to be a numpy array.
+
+Note for offline processing: some generators might yield valid :class:`AxisArray` messages with ``.data`` size of 0.
+This may occur when the generator receives inadequate data to produce a valid output, such as when windowing or buffering.
+
+ezmsg.sigproc.activation
+-----------------------------
+
+.. automodule:: ezmsg.sigproc.activation
+    :members:
+
+
+ezmsg.sigproc.affinetransform
+-----------------------------
+
+.. automodule:: ezmsg.sigproc.affinetransform
+    :members:
+
+
+ezmsg.sigproc.aggregate
+-----------------------
+
+.. automodule:: ezmsg.sigproc.aggregate
+    :members:
+    :undoc-members:
+
+
+ezmsg.sigproc.bandpower
+-----------------------
+
+.. automodule:: ezmsg.sigproc.bandpower
+    :members:
+
+
+ezmsg.sigproc.filter
+--------------------
+
+.. automodule:: ezmsg.sigproc.filter
+    :members:
+
+ezmsg.sigproc.butterworthfilter
+-------------------------------
+
+.. automodule:: ezmsg.sigproc.butterworthfilter
+    :members:
+
+
+ezmsg.sigproc.decimate
+----------------------
+
+.. automodule:: ezmsg.sigproc.decimate
+    :members:
+
+
+ezmsg.sigproc.downsample
+------------------------
+
+.. automodule:: ezmsg.sigproc.downsample
+    :members:
+
+
+ezmsg.sigproc.ewmfilter
+-----------------------
+
+.. automodule:: ezmsg.sigproc.ewmfilter
+    :members:
+
+
+ezmsg.sigproc.math
+-----------------------
+
+.. automodule:: ezmsg.sigproc.math.clip
+    :members:
+
+.. automodule:: ezmsg.sigproc.math.difference
+    :members:
+
+.. automodule:: ezmsg.sigproc.math.invert
+    :members:
+
+.. automodule:: ezmsg.sigproc.math.log
+    :members:
+
+.. automodule:: ezmsg.sigproc.math.scale
+    :members:
+
+
+ezmsg.sigproc.sampler
+---------------------
+
+.. automodule:: ezmsg.sigproc.sampler
+    :members:
+
+
+ezmsg.sigproc.scaler
+--------------------
+
+.. automodule:: ezmsg.sigproc.scaler
+    :members:
+
+
+ezmsg.sigproc.signalinjector
+----------------------------
+
+.. automodule:: ezmsg.sigproc.signalinjector
+    :members:
+
+
+ezmsg.sigproc.slicer
+---------------------
+
+.. automodule:: ezmsg.sigproc.slicer
+    :members:
+
+
+ezmsg.sigproc.spectrum
+----------------------
+
+.. automodule:: ezmsg.sigproc.spectrum
+    :members:
+    :undoc-members:
+
+
+ezmsg.sigproc.spectrogram
+-------------------------
+
+.. automodule:: ezmsg.sigproc.spectrogram
+    :members:
+
+
+ezmsg.sigproc.synth
+-------------------
+
+.. automodule:: ezmsg.sigproc.synth
+    :members:
+
+
+ezmsg.sigproc.window
+--------------------
+
+.. automodule:: ezmsg.sigproc.window
+    :members:

ezmsg-3.5.0/docs/source/extensions.rst

@@ -0,0 +1,7 @@
+Extensions
+==========
+
+.. toctree::
+   :maxdepth: 1
+
+   extensions/sigproc