aind-data-schema-models
Installation
To install from pypi, run
pip install aind-data-schema-models
To install from source, in the root directory, run
pip install -e .
To develop the code, run
pip install -e .[dev]
Contributing
How to add a new model class
The model class files, brain_atlas.py etc, are auto-generated. You should never need to modify the class files directly.
Instead, take a look at the jinja2 templates in the folder _generators/templates. The filename of the template is used to pull the corresponding .csv file and populate the data DataFrame. In the template you can pull data from the various columns and use them to populate each of the fields in your class.
To re-build all the models, run the run_all.sh bash script in the root folder, which loops through the template files and runs them through the generate_code function.
There are a few special cases, e.g. if data are missing in columns they will show up as float: nan. See the organizations.txt template for examples of how to handle this.
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 |
|
feat(pencil): add 'graphiteWidth' option |
|
perf(pencil): remove graphiteWidth optionBREAKING CHANGE: The graphiteWidth option has been removed.The default graphite width of 10mm is always used for performance reasons. |
(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 doc_template/source/ src
Then to create the documentation HTML files, run
sphinx-build -b html doc_template/source/ doc_template/build/html
More info on sphinx installation can be found here.
1 maintainer
Metadata
1 maintainer
Release files for aind-data-schema-models 0.8.0
For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.
Source distribution (sdist)
| File | Size | Uploaded | |
|---|---|---|---|
| aind_data_schema_models-0.8.0.tar.gz | 555.6 kB | Details |
Built distribution (wheel)
| File | Interpreter | ABI | Platform | Reset |
|---|---|---|---|---|
| aind_data_schema_models-0.8.0-py3-none-any.whl | Python 3 | none | any | Details |
Total release size: 1.1 MB
Release files / aind_data_schema_models-0.8.0.tar.gz
| Download URL | aind_data_schema_models-0.8.0.tar.gz |
|---|---|
| Size | 555.6 kB |
| Tags | Source |
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SHA-256 checksum How to use checksums |
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Release files / aind_data_schema_models-0.8.0-py3-none-any.whl
| Download URL | aind_data_schema_models-0.8.0-py3-none-any.whl |
|---|---|
| Size | 533.8 kB |
| Tags | Python 3 |
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SHA-256 checksum How to use checksums |
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