spike sorting

Author: magland

CHANGELOG.md

@@ -1,6 +1,7 @@
 # Changes
 
 ## August 13, 2025
+- Added job cancellation functionality to JobStatusHandler component with red "Cancel Job" button for running jobs
 - Added continuous integration workflow to test neurosift Python package installation, NWB file creation with pynwb, and CLI functionality
 
 ## August 11, 2025

job_runners/neurosift_job_runner/pyproject.toml

@@ -17,7 +17,6 @@ dependencies = [
     "numpy",
     "scipy",
     "lindi",
-    "dendro>=0.6.22",
     "rastermap",
     "click",
 ]

job_runners/neurosift_job_runner_2/pyproject.toml

@@ -17,7 +17,6 @@ dependencies = [
     "numpy",
     "scipy",
     "lindi",
-    "dendro>=0.6.22",
     "click",
 ]
 

job_runners/neurosift_job_runner_3/.gitignore

@@ -0,0 +1,138 @@
+# 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
+
+# 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
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+.python-version
+
+# celery beat schedule file
+celerybeat-schedule
+celerybeat.pid
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyderworkspace
+
+# 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/
+
+# Docker
+.dockerignore
+
+# VS Code
+.vscode/
+
+# PyCharm
+.idea/
+
+# Local environment variables
+.env.local
+.env.development.local
+.env.test.local
+.env.production.local

job_runners/neurosift_job_runner_3/Dockerfile

@@ -0,0 +1,22 @@
+FROM python:3.10-slim
+
+WORKDIR /app
+
+# Install build dependencies
+RUN apt-get update && \
+    apt-get install -y --no-install-recommends \
+    build-essential \
+    && rm -rf /var/lib/apt/lists/*
+
+# Copy the package files
+COPY pyproject.toml /app/
+COPY src /app/src/
+
+# Install the package and its dependencies
+RUN pip install --no-cache-dir -e .
+
+# Set environment variables
+ENV PYTHONUNBUFFERED=1
+
+# Set the entry point to the CLI command
+ENTRYPOINT ["neurosift-job-runner-3"]

job_runners/neurosift_job_runner_3/pyproject.toml

@@ -0,0 +1,28 @@
+[build-system]
+requires = ["hatchling"]
+build-backend = "hatchling.build"
+
+[project]
+name = "neurosift_job_runner_3"
+version = "0.1.0"
+description = "Command line tool for running Neurosift jobs"
+authors = [
+    { name = "Jeremy Magland" },
+]
+# readme = "README.md"
+requires-python = ">=3.8"
+dependencies = [
+    "requests",
+    "pydantic",
+    "numpy",
+    "scipy",
+    "spikeinterface",
+    "mountainsort5",
+    "click",
+]
+
+[project.scripts]
+neurosift-job-runner-3 = "neurosift_job_runner_3.cli:main"
+
+[tool.hatch.build.targets.wheel]
+packages = ["src/neurosift_job_runner_3"]

job_runners/neurosift_job_runner_3/src/neurosift_job_runner_3/__init__.py

@@ -0,0 +1,9 @@
+"""Neurosift Job Runner package.
+
+A job runner for executing Neurosift jobs from the command line.
+"""
+
+from .core import process_job
+from .cli import cli
+
+__all__ = ["process_job", "cli"]

job_runners/neurosift_job_runner_3/src/neurosift_job_runner_3/cli.py

@@ -0,0 +1,70 @@
+#!/usr/bin/env python3
+
+import sys
+import logging
+from typing import Optional
+
+import click
+
+from .job_utils import get_job, update_job_status
+from .processors import (
+    process_mountainsort5_job,
+)
+
+
+@click.group()
+@click.version_option()
+def cli() -> None:
+    """Neurosift Job Runner - Command line tool for running Neurosift jobs."""
+    pass
+
+
+@cli.command()
+@click.argument("job_id")
+@click.option("--api-base-url", help="Base URL for the API", envvar="NEUROSIFT_API_URL")
+def run_job(job_id: str, api_base_url: Optional[str] = None) -> None:
+    """Run a specific job by ID.
+
+    JOB_ID is the ID of the job to run.
+    """
+    try:
+        # Get job information
+        job = get_job(job_id, api_base_url=api_base_url)
+
+        if job["status"] not in ["pending"]:
+            click.echo(
+                f"Error: Job {job_id} is not pending (status: {job['status']})",
+                err=True,
+            )
+            sys.exit(1)
+
+        click.echo(f"Processing job {job_id} of type {job['type']}")
+
+        # Process job based on type
+        handler_map = {"mountainsort5": process_mountainsort5_job}
+
+        handler = handler_map.get(job["type"])
+        if handler:
+            handler(job, api_base_url=api_base_url)
+        else:
+            error_msg = f"Unknown job type: {job['type']}"
+            click.echo(f"Error: {error_msg}", err=True)
+            update_job_status(
+                job_id,
+                {"status": "failed", "error": error_msg},
+                api_base_url=api_base_url,
+            )
+            sys.exit(1)
+
+    except Exception as e:
+        click.echo(f"Error processing job: {e}", err=True)
+        sys.exit(1)
+
+
+def main() -> None:
+    """Entry point for the neurosift-job-runner-2 command-line tool."""
+    cli(auto_envvar_prefix="NEUROSIFT")
+
+
+if __name__ == "__main__":
+    main()

job_runners/neurosift_job_runner_3/src/neurosift_job_runner_3/core.py

@@ -0,0 +1,63 @@
+from typing import Optional
+import logging
+import sys
+
+from .job_utils import get_job, update_job_status
+
+
+# Lazy imports for job processors to avoid loading all dependencies upfront
+def get_job_processor(job_type: str):
+    """Dynamically import and return the appropriate job processor."""
+    if job_type == "image_series_to_mp4":
+        from .processors.image_series_to_mp4 import process_image_series_to_mp4_job
+
+        return process_image_series_to_mp4_job
+    else:
+        raise ValueError(f"Unknown job type: {job_type}")
+
+
+def process_job(job_id: str, api_base_url: Optional[str] = None) -> None:
+    """Process a job by its ID.
+
+    Args:
+        job_id: The ID of the job to process
+        api_base_url: Optional base URL for the API
+
+    Raises:
+        SystemExit: If job processing fails
+    """
+    try:
+        # Get job information
+        kwargs = {}
+        if api_base_url:
+            kwargs["api_base_url"] = api_base_url
+        job = get_job(job_id, **kwargs)
+
+        if job["status"] not in ["pending"]:
+            error_msg = f"Job {job_id} is not pending (status: {job['status']})"
+            logging.error(error_msg)
+            sys.exit(1)
+
+        logging.info(f"Processing job {job_id} of type {job['type']}")
+
+        try:
+            # Get the appropriate processor for this job type
+            process_func = get_job_processor(job["type"])
+            # Process the job
+            process_func(job, **kwargs)
+        except ImportError as e:
+            error_msg = f"Failed to import processor for job type {job['type']}: {e}"
+            logging.error(error_msg)
+            update_job_status(
+                job_id, {"status": "failed", "error": error_msg}, **kwargs
+            )
+            sys.exit(1)
+        except Exception as e:
+            error_msg = f"Error processing job: {e}"
+            logging.error(error_msg)
+            update_job_status(job_id, {"status": "failed", "error": str(e)}, **kwargs)
+            sys.exit(1)
+
+    except Exception as e:
+        logging.error(f"Error processing job: {e}")
+        sys.exit(1)