aind-codeocean-pipeline-monitor

Package for starting a pipeline, waiting for it to finish, and optionally capturing the results as a data asset.

Installation

The repo can be install from PyPI. To pip install all of the necessary dependencies to run the pipeline monitor, run:

pip install aind-codeocean-pipeline-monitor[full]

To install only the minimum dependencies required for model validation, run:

pip install aind-codeocean-pipeline-monitor

To install the package for development, clone this repo and run

pip install -e .[dev]

Usage

• Define job using PipelineMonitorJobSettings class.
• Define a CodeOcean client.
• Construct a PipelineMonitorJob with these settings.
• Run the job with the run_job method.

import os

from codeocean import CodeOcean
from codeocean.computation import DataAssetsRunParam, RunParams
from urllib3.util import Retry

from aind_codeocean_pipeline_monitor.job import PipelineMonitorJob
from aind_codeocean_pipeline_monitor.models import (
    CaptureSettings,
    PipelineMonitorSettings,
)

domain = os.getenv("CODEOCEAN_DOMAIN")
token = os.getenv("CODEOCEAN_TOKEN")
# Recommend adding retry strategy to requests session
retry = Retry(
    total=5,
    backoff_factor=1,
    status_forcelist=[429, 500, 502, 503, 504],
    allowed_methods=["GET", "POST"],
)
client = CodeOcean(domain=domain, token=token, retries=retry)

# Please consult Code Ocean docs for info about RunParams and DataAssetParams
settings = PipelineMonitorSettings(
    run_params=RunParams(
        capsule_id="<your capsule id>",
        data_assets=[
            DataAssetsRunParam(
                id="<your input data asset id>",
                mount="<your input data mount>",
            )
        ],
    ),
    capture_settings=CaptureSettings(
        tags=["derived"]
    ),  # 'tags' is the only required field
)

job = PipelineMonitorJob(job_settings=settings, client=client)
job.run_job()

Contributing

Linters and testing

There are several libraries used to run linters, check documentation, and run tests.

• Please test your changes using the coverage library, which will run the tests and log a coverage report:

coverage run -m unittest discover && coverage report

• Use interrogate to check that modules, methods, etc. have been documented thoroughly:

interrogate .

• Use flake8 to check that code is up to standards (no unused imports, etc.):

flake8 .

• Use black to automatically format the code into PEP standards:

black .

• Use isort to automatically sort import statements:

isort .

Pull requests

For internal members, please create a branch. For external members, please fork the repository and open a pull request from the fork. We'll primarily use Angular style for commit messages. Roughly, they should follow the pattern:

<type>(<scope>): <short summary>

where scope (optional) describes the packages affected by the code changes and type (mandatory) is one of:

• build: Changes that affect build tools or external dependencies (example scopes: pyproject.toml, setup.py)
• ci: Changes to our CI configuration files and scripts (examples: .github/workflows/ci.yml)
• docs: Documentation only changes
• feat: A new feature
• fix: A bugfix
• perf: A code change that improves performance
• refactor: A code change that neither fixes a bug nor adds a feature
• test: Adding missing tests or correcting existing tests

Semantic Release

The table below, from semantic release, shows which commit message gets you which release type when semantic-release runs (using the default configuration):

Commit message	Release type
fix(pencil): stop graphite breaking when too much pressure applied	Patch Fix Release, Default release
feat(pencil): add 'graphiteWidth' option	Minor Feature Release
perf(pencil): remove graphiteWidth option BREAKING CHANGE: The graphiteWidth option has been removed. The default graphite width of 10mm is always used for performance reasons.	Major Breaking Release (Note that the BREAKING CHANGE: token must be in the footer of the commit)

Documentation

To generate the rst files source files for documentation, run

sphinx-apidoc -o docs/source/ src

Then to create the documentation HTML files, run

sphinx-build -b html docs/source/ docs/build/html

More info on sphinx installation can be found here.