Merge pull request #4 from ezmsg-org/dev

dev -> main for release

Author: cboulay

.github/workflows/python-tests.yml

@@ -13,7 +13,7 @@ jobs:
   build:
     strategy:
       matrix:
-        python-version: ["3.10.15", "3.11", "3.12", "3.13"]
+        python-version: ["3.11", "3.12", "3.13"]
         os:
           - "ubuntu-latest"
           - "windows-latest"

README.md

@@ -2,7 +2,13 @@
 
 A namespace package for [ezmsg](https://github.com/iscoe/ezmsg) to visualize running graphs and data.
 
-The data visualization is highly fragile. Expect bugs.
+Key features:
+
+* **Graph visualization** - Visualize ezmsg graph topologies
+* **Data visualization** - Real-time data plotting and monitoring
+* **Debug tools** - Tools for debugging ezmsg pipelines
+
+> The data visualization is highly fragile. Expect bugs.
 
 ## Installation
 
@@ -16,6 +22,18 @@ On Mac, you should use brew:
 * `export CFLAGS="-I $(brew --prefix graphviz)/include"`
 * `export LDFLAGS="-L $(brew --prefix graphviz)/lib"`
 
+On Windows, follow the instructions [here](https://pygraphviz.github.io/documentation/stable/install.html#windows). Short version:
+
+* Download and install [Visual C/C++](https://visualstudio.microsoft.com/visual-cpp-build-tools/)
+* Download and install [graphviz](https://gitlab.com/graphviz/graphviz/-/releases). Get the most recent Windows x64 CMake releases.
+* Install pygraphviz in your environment:
+```
+python -m pip install --config-settings="--global-option=build_ext"
+    --config-settings="--global-option=-IC:\Program Files\Graphviz\include"
+    --config-settings="--global-option=-LC:\Program Files\Graphviz\lib"
+    pygraphviz
+```
+
 ### Release
 
 Install the latest release from pypi with: `pip install ezmsg-tools` (or `uv add ...` or `poetry add ...`).
@@ -24,26 +42,36 @@ More than likely, you will want to include at least one of the extras when insta
 
 `pip install "ezmsg-tools[all]"`
 
-### Development Version
+Or install the latest development version:
 
-If you intend to edit `ezmsg-tools` then please refer to the [Developers](#developers) section below.
+`pip install "ezmsg-tools[all] @ git+https://github.com/ezmsg-org/ezmsg-tools.git@dev"`
 
-You can add the development version of ezmsg-tools directly from GitHub:
+## Getting Started
 
-* Using `pip`: `pip install git+https://github.com/ezmsg-org/ezmsg-tools.git@dev`
-* Using `poetry`: `poetry add "git+https://github.com/ezmsg-org/ezmsg-tools.git@dev"`
-* Using `uv`: `uv add git+https://github.com/ezmsg-org/ezmsg-tools --branch dev`
+This package includes some entrypoints with useful tools.
 
-You probably want to include the extras when installing the development version:
+### ezmsg-signal-monitor
 
-* `pip install "ezmsg-tools[all] @ git+https://github.com/ezmsg-org/ezmsg-tools.git@dev"`
+The pipeline must be running on a graph service exposed on the network. For example, first, run the GraphService on an open port:
 
-## Getting Started
+`ezmsg --address 127.0.0.1:25978 start`
 
-This package includes some entrypoints with useful tools.
+Then run your usual pipeline but make sure it attaches to the graph address by passing `graph_address=("127.0.0.1", 25978)` as a kwarg to `ez.run`.
+
+While the pipeline is running, you can run the signal-monitor tool with (`uv run`) `ezmsg-signal-monitor --graph-addr 127.0.0.1:25978`.
+
+This launches a window with graph visualized on the left. Click on a node's output box to get a live visualization on the right side of the screen plotting the data as it leaves that node. Use `a` to toggle auto-scaling. With auto-scaling off, use `-`, and `=` to zoom out and in, respectively. See the [phosphor docs](https://www.ezmsg.org/phosphor/) for the full list of keyboard shortcuts.
+
+> Currently only 2-D outputs are supported!
+
+Don't forget to shutdown your graph service when you are done, e.g.: `ezmsg --address 127.0.0.1:25978 shutdown` 
 
 ### ezmsg-performance-monitor
 
+**DEPRECATED**
+
+> ezmsg will soon includes a built-in performance monitor that can be used instead of this tool.
+
 This tool operates on logfiles created by ezmsg. Logfiles will automatically be created when running a pipeline containing nodes decorated with `ezmsg.sigproc.util.profile.profile_subpub`,
 and if the `EZMSG_LOGLEVEL` environment variable is set to DEBUG. The logfiles will be created in `~/.ezmsg/profile/ezprofiler.log` by default but this can be changed with the `EZMSG_PROFILE` environment variable.
 
@@ -52,25 +80,11 @@ You can decorate other nodes with `ezmsg.sigproc.util.profile.profile_subpub` to
 
 During a run with profiling enabled, the logfiles will be created in the specified location. You may wish to additionally create a graph file: (`uv run`) `EZMSG_LOGLEVEL=WARN ezmsg mermaid > ~/.ezmsg/profile/ezprofiler.mermaid`
 
-During or after a pipeline run with profiling enabled, you can run (`uv run `) `performance-monitor` to visualize the performance of the nodes in the pipeline.
+During or after a pipeline run with profiling enabled, you can run (`uv run `) `ezmsg-performance-monitor` to visualize the performance of the nodes in the pipeline.
 
 > Unlike `signal-monitor`, this tool does not require the pipeline to attach to an existing graph service because it relies exclusively on the logfile.
 
-### ezmsg-signal-monitor
-
-The pipeline must be running on a graph service exposed on the network. For example, first, run the GraphService on an open port:
-
-`ezmsg --address 127.0.0.1:25978 start`
-
-Then run your usual pipeline but make sure it attaches to the graph address by passing `graph_address=("127.0.0.1", 25978)` as a kwarg to `ez.run`.
-
-While the pipeline is running, you can run the signal-monitor tool with (`uv run`) `signal-monitor --graph-addr 127.0.0.1:25978`.
-
-This launches a window with graph visualized on the left. Click on a node's output box to get a live visualization on the right side of the screen plotting the data as it leaves that node. Use `a` to toggle auto-scaling. With auto-scaling off, use `-`, and `=` to zoom out and in, respectively.
-
-> Currently only 2-D outputs are supported!
-
-Don't forget to shutdown your graph service when you are done, e.g.: `ezmsg --address 127.0.0.1:25978 shutdown` 
+> This performance monitor is soon to be deprecated in favor of monitoring tools built-in to ezmsg. 
 
 ## Developers
 
@@ -80,9 +94,9 @@ We use [`uv`](https://docs.astral.sh/uv/getting-started/installation/) for devel
 2. Fork ezmsg-tools and clone your fork to your local computer.
 3. Open a terminal and `cd` to the cloned folder.
 4. Make sure `pygraphviz` [pre-requisites](#pre-requisites) are installed.
-    * On mac: `export CFLAGS="-I $(brew --prefix graphviz)/include"` and `export LDFLAGS="-L $(brew --prefix graphviz)/lib"`
-5. `uv sync --all-extras --python 3.10` to create a .venv and install ezmsg-tools including dev and test dependencies.
-6. After editing code and making commits, Run the test suite before making a PR: `uv run pytest`
+5. `uv sync --all-extras` to create a .venv and install ezmsg-tools including dev and test dependencies. 
+6. (Optional) Install pre-commit hooks: `uv run pre-commit install`
+7. After editing code and making commits, Run the test suite before making a PR: `uv run pytest`
 
 ## Troubleshooting
 

docs/source/index.md

@@ -0,0 +1,16 @@
+```{include} ../../README.md
+```
+
+## Documentation
+
+```{toctree}
+:maxdepth: 2
+:caption: Contents:
+
+api/index
+```
+
+## Indices and tables
+
+- {ref}`genindex`
+- {ref}`modindex`

docs/source/index.rst

@@ -6,27 +6,29 @@ authors = [
 ]
 license = "MIT"
 readme = "README.md"
-requires-python = ">=3.10.15"
+requires-python = ">=3.11"
 dynamic = ["version"]
 dependencies = [
-  "ezmsg>=3.6.1",
+  "ezmsg>=3.6.2",
   "numpy>=1.26.0",
+  "typer>=0.24.1",
 ]
 
 [dependency-groups]
 dev = [
     "pre-commit>=4.0.0",
     "scipy>=1.14.1",
-    "ezmsg-sigproc>=2.0.0",
+    "ezmsg-sigproc>=2.18.0",
+    "ezmsg-simbiophys>=1.4.1",
     {include-group = "lint"},
     {include-group = "test"},
 ]
 lint = [
     "ruff>=0.12.9",
 ]
 test = [
-    "ezmsg-sigproc>=1.6.0",
     "pytest>=8.3.3",
+    "ezmsg-simbiophys>=1.4.1",
 ]
 docs = [
   "sphinx>=7.0",
@@ -45,17 +47,20 @@ perfmon = [
     "typer>=0.15.1",
     "pygtail>=0.14.0",
     "dash-bootstrap-components>=1.6.0",
-    "ezmsg-baseproc",
+    "ezmsg-baseproc>=1.1.0",
 ]
 sigmon = [
-    "pygame>=2.6.1",
+    "PySide6>=6.7",
     "pygraphviz>=1.14",
     "typer>=0.15.1",
+    "phosphor>=0.2",
+    "pandas",
+    "ezmsg-qt",
 ]
 
 [project.scripts]
-ezmsg-performance-monitor = "ezmsg.tools.perfmon.main:main"
-ezmsg-signal-monitor = "ezmsg.tools.sigmon.main:main"
+ezmsg-performance-monitor = "ezmsg.tools.perfmon.cli:main"
+ezmsg-signal-monitor = "ezmsg.tools.sigmon.cli:main"
 
 [build-system]
 requires = ["hatchling", "hatch-vcs"]
@@ -89,4 +94,5 @@ known-third-party = ["ezmsg"]
 
 [tool.uv.sources]
 # Uncomment to use development version of ezmsg from git
-ezmsg = { git = "https://github.com/ezmsg-org/ezmsg.git", branch = "feature/profiling" }
+#ezmsg = { git = "https://github.com/ezmsg-org/ezmsg.git", branch = "dev" }
+ezmsg-qt = { git = "https://github.com/ezmsg-org/ezmsg-qt.git", branch = "dynamic_subscriber" }

pyproject.toml

@@ -0,0 +1,74 @@
+"""Test graph for sigmon development.
+
+Generates synthetic EEG (time-domain) and routes a copy through
+Window + Spectrum to produce frequency-domain data. Both branches
+terminate at a no-op Sink so the topics exist in the graph for
+sigmon to subscribe to.
+
+Usage:
+    uv run python scripts/eeg_generator_graph.py
+"""
+
+import ezmsg.core as ez
+from ezmsg.sigproc.spectrum import Spectrum, SpectrumSettings
+from ezmsg.sigproc.window import Window, WindowSettings
+from ezmsg.simbiophys import EEGSynth, EEGSynthSettings
+from ezmsg.util.messages.axisarray import AxisArray
+
+
+class Sink(ez.Unit):
+    """Consumes messages and does nothing."""
+
+    INPUT_SIGNAL = ez.InputStream(AxisArray)
+
+    @ez.subscriber(INPUT_SIGNAL)
+    async def on_message(self, msg: AxisArray) -> None:
+        pass
+
+
+def main() -> None:
+    eeg = EEGSynth(
+        EEGSynthSettings(
+            fs=2000.0,
+            n_time=100,
+            n_ch=16,
+            alpha_freq=10.5,
+        )
+    )
+
+    win = Window(
+        WindowSettings(
+            axis="time",
+            window_dur=0.5,
+            window_shift=0.2,
+        )
+    )
+
+    spec = Spectrum(
+        SpectrumSettings(
+            axis="time",
+        )
+    )
+
+    time_sink = Sink()
+    freq_sink = Sink()
+
+    ez.run(
+        components={
+            "EEG": eeg,
+            "WIN": win,
+            "SPEC": spec,
+            "TIME_SINK": time_sink,
+            "FREQ_SINK": freq_sink,
+        },
+        connections=(
+            (eeg.OUTPUT_SIGNAL, time_sink.INPUT_SIGNAL),
+            (eeg.OUTPUT_SIGNAL, win.INPUT_SIGNAL),
+            (win.OUTPUT_SIGNAL, spec.INPUT_SIGNAL),
+            (spec.OUTPUT_SIGNAL, freq_sink.INPUT_SIGNAL),
+        ),
+    )
+
+
+if __name__ == "__main__":
+    main()

scripts_nbs/generator/eeg_generator_graph.py

@@ -7,9 +7,9 @@
 from ezmsg.sigproc.downsample import Downsample
 from ezmsg.sigproc.scaler import AdaptiveStandardScaler
 from ezmsg.sigproc.slicer import Slicer
-from ezmsg.sigproc.synth import EEGSynth
 from ezmsg.sigproc.wavelets import CWT, MinPhaseMode
 from ezmsg.sigproc.window import Anchor
+from ezmsg.simbiophys.eeg import EEGSynth
 from ezmsg.util.terminate import TerminateOnTotal