aind-log-utils 0.2.3

Add logging to Code Ocean capsules

aind_log_utils

Usage

Typical programmatic usage of this library looks like this:

import logging
from aind_log_utils.log import setup_logging

setup_logging("my_process_name", subject_id="subject1", 
                        asset_name="asset1")

logging.info("my log message")

asset_name should be in the form "<mouse_id>". for example: behavior_746346_2024-12-18_12-48-05

Installation

To use the software, in the root directory, run

pip install -e .

To develop the code, run

pip install -e .[dev]

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: .flake8

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.