aind-hcr-data-loader 0.7.0

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aind-hcr-data-loader

Change log

See CHANGELOG.md for full details.

Version	Date	Summary
v0.7.0	04/02/2026	New codeocean_utils module for attaching dataset-catalog records to capsules/pipelines
v0.6.0	03/18/2026	New pairwise/cell-typing/spot-filter modules; major HCRDataset and filters.py additions
v0.5.1	02/23/2026	metrics_base_path, spot_filters.py, comprehensive ROI filtering pipeline
v0.4.0	10/16/2025	Tile overlap, ROI filtering, linear unmixing, neuroglancer links, saveable_plot
v0.3.8	08/11/2025	Cell info loading improvements, metrics paths, error handling

Installation

To use the software, in the root directory, run

pip install -e .

To develop the code, run

pip install -e .[dev]

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