Package: aind-data-schema
aind-data-schemaA library that definesAINDdata schema and validates JSON files.User documentation available onreadthedocs.OverviewThis repository contains the schemas needed to ingest and validate metadata that are essential to ensuringAINDdata collection is completely reproducible. Our general approach is to semantically version core schema classes and include those version numbers in serialized metadata so that we can flexibly evolve the schemas over time without requiring difficult data migrations. In the future, we will provide a browsable list of these classes rendered toJSONschema, including all historic versions.Be aware that this package is still under heavy preliminary development. Expect breaking changes regularly, although we will communicate these through semantic versioning.A simple example:importdatetimefromaind_data_schema.subjectimportHousing,Subjectt=datetime.datetime(2022,11,22,8,43,00)s=Subject(species="Mus musculus",subject_id="12345",sex="Male",date_of_birth=t.date(),genotype="Emx1-IRES-Cre;Camk2a-tTA;Ai93(TITL-GCaMP6f)",housing=Housing(home_cage_enrichment=["Running wheel"],cage_id="123"),background_strain="C57BL/6J",)s.write_standard_file()# writes subject.json{"describedBy":"https://raw.githubusercontent.com/AllenNeuralDynamics/aind-data-schema/main/src/aind_data_schema/subject.py","schema_version":"0.3.0","species":"Mus musculus","subject_id":"12345","sex":"Male","date_of_birth":"2022-11-22","genotype":"Emx1-IRES-Cre;Camk2a-tTA;Ai93(TITL-GCaMP6f)","mgi_allele_ids":null,"background_strain":"C57BL/6J","source":null,"rrid":null,"restrictions":null,"breeding_group":null,"maternal_id":null,"maternal_genotype":null,"paternal_id":null,"paternal_genotype":null,"wellness_reports":null,"housing":{"cage_id":"123","room_id":null,"light_cycle":null,"home_cage_enrichment":["Running wheel"],"cohoused_subjects":null},"notes":null}Installing and UpgradingTo install the latest version:pip install aind-data-schemaEvery merge to themainbranch is automatically tagged with a new major/minor/patch version and uploaded to PyPI. To upgrade to the latest version:pip install aind-data-schema --upgradeTo develop the code, check out this repo and run the following in the cloned directory:pip install -e .[dev]ContributingIf you've found a bug in the schemas or would like to make a minor change, open anIssueon this repository. If you'd like to propose a large change or addition, or generally have a question about how things work, head start a newDiscussion!Linters and testingThere are several libraries used to run linters, check documentation, and run tests.To run tests locally, navigate to AIND-DATA-SCHEMA directory in terminal and run (this will not run any on-line only tests):python -m unittestPlease test your changes using thecoveragelibrary, which will run the tests and log a coverage report:coverage run -m unittest discover && coverage reportTo test any of the following modules, conda/pip install the relevant package (interrogate, flake8, black, isort), navigate to relevant directory, and run any of the following commands in place of [command]:[command] -v .Useinterrogateto check that modules, methods, etc. have been documented thoroughly:interrogate .Useflake8to check that code is up to standards (no unused imports, etc.):flake8 .Useblackto automatically format the code into PEP standards:black .Useisortto automatically sort import statements:isort .Pull requestsFor internal members, please create a branch. For external members, please fork the repo and open a pull request from the fork. We'll primarily useAngularstyle 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 the build system 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 changesfeat: A new featurefix: A bug fixperf: A code change that improves performancerefactor: A code change that neither fixes a bug nor adds a featuretest: Adding missing tests or correcting existing testsDocumentationTo generate the rst files source files for documentation, run:sphinx-apidoc -o docs/source/ srcThen to create the documentation html files, run:sphinx-build -b html docs/source/ docs/build/htmlMore info on sphinx installation can be found here:https://www.sphinx-doc.org/en/master/usage/installation.html