Merge pull request #148 from ezmsg-org/dev

Dev

.envrc

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

.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

.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

.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/*

.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

.python-version

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

docs/source/conf.py

@@ -18,7 +18,7 @@
     "sphinx.ext.autosummary",
     "sphinx.ext.intersphinx",
     "sphinx.ext.linkcode",
-    "sphinx.ext.napoleon"
+    "sphinx.ext.napoleon",
 ]
 
 intersphinx_mapping = {
@@ -46,15 +46,14 @@
 
 
 def linkcode_resolve(domain, info):
-    if domain != 'py':
+    if domain != "py":
         return None
-    if not info['module']:
+    if not info["module"]:
         return None
-    filename = info['module'].replace('.', '/')
+    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"
-

docs/source/extensions/sigproc.rst

@@ -1,6 +1,21 @@
 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
 -----------------------------
 
@@ -57,6 +72,25 @@ 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
 ---------------------
 

examples/ezmsg_configs.py

@@ -14,7 +14,7 @@ class TerminatorSettings(ez.Settings):
 
 
 class Terminator(ez.Unit):
-    SETTINGS: TerminatorSettings
+    SETTINGS = TerminatorSettings
 
     @ez.task
     async def terminate(self) -> None:
@@ -31,7 +31,7 @@ class GeneratorSettings(ez.Settings):
 
 
 class Generator(ez.Unit):
-    SETTINGS: GeneratorSettings
+    SETTINGS = GeneratorSettings
 
     OUTPUT = ez.OutputStream(int)
 
@@ -51,7 +51,7 @@ class ModulusSettings(ez.Settings):
 
 
 class Modulus(ez.Unit):
-    SETTINGS: ModulusSettings
+    SETTINGS = ModulusSettings
 
     INPUT = ez.InputStream(int)
     OUTPUT = ez.OutputStream(int)
@@ -70,7 +70,7 @@ class ListenerState(ez.State):
 
 
 class Listener(ez.Unit):
-    STATE: ListenerState
+    STATE = ListenerState
 
     INPUT = ez.InputStream(int)
 
@@ -93,8 +93,7 @@ def network(self) -> ez.NetworkDefinition:
 # CORNER CASES
 
 
-class EmptySystem(ez.Collection):
-    ...
+class EmptySystem(ez.Collection): ...
 
 
 class EmptyTerminateSystem(ez.Collection):

examples/ezmsg_count.py

@@ -1,4 +1,5 @@
 import asyncio
+import time
 import array
 from dataclasses import dataclass
 import ezmsg.core as ez
@@ -20,7 +21,7 @@ class CountSettings(ez.Settings):
 
 
 class Count(ez.Unit):
-    SETTINGS: CountSettings
+    SETTINGS = CountSettings
 
     OUTPUT = ez.OutputStream(int)
 
@@ -29,14 +30,23 @@ async def count(self) -> AsyncGenerator:
         count = 0
         while True:
             await asyncio.sleep(0.1)
-            yield self.OUTPUT, CountMessage(
-                value=count, arr=array.array("b", [0x00] * (2**count))
+            yield (
+                self.OUTPUT,
+                CountMessage(value=count, arr=array.array("b", [0x00] * (2**count))),
             )
             count = count + 1
 
             if count >= self.SETTINGS.num_msgs:
                 raise ez.Complete
 
+    @ez.thread
+    def hello_world(self):
+        i = 0
+        while True:
+            print(f"Hello world {i}")
+            i += 1
+            time.sleep(1)
+
 
 class CountSystem(ez.Collection):
     COUNT = Count()
@@ -61,4 +71,4 @@ def process_components(self):
     # multiprocessing.set_start_method('spawn', force=True)
 
     system = CountSystem()
-    ez.run(SYSTEM = system)
+    ez.run(SYSTEM=system)

examples/ezmsg_generator.py

@@ -46,7 +46,7 @@ class PowSettings(ez.Settings):
 
 
 class Pow(Gen):
-    SETTINGS: PowSettings
+    SETTINGS = PowSettings
 
     def construct_generator(self):
         self.STATE.gen = pow(self.SETTINGS.n)
@@ -66,7 +66,7 @@ class AddSettings(ez.Settings):
 
 
 class Add(Gen):
-    SETTINGS: AddSettings
+    SETTINGS = AddSettings
 
     def construct_generator(self):
         self.STATE.gen = add(self.SETTINGS.n)
@@ -123,10 +123,7 @@ def network(self):
                 (self.POW_0_5.OUTPUT, self.LOG_OUT.INPUT),
             )
 
-    ez.run(
-        SYSTEM=GenOneExample()
-    )
-
+    ez.run(SYSTEM=GenOneExample())
 
     # This example will show the type-hint based introspection to construct ezmsg Units
     # at runtime, which simplifies the integration of generators into Units, reducing
@@ -158,6 +155,4 @@ def network(self):
                 (self.POW_0_5.OUTPUT, self.LOG_OUT.INPUT),
             )
 
-    ez.run(
-        SYSTEM=GenTwoExample()
-    )
+    ez.run(SYSTEM=GenTwoExample())