adding the API contracts

.gitignore

@@ -172,4 +172,5 @@ cython_debug/
 
 # PyPI configuration file
 .pypirc
+data/*
 testing.ipynb

CONTRIBUTING.md

@@ -51,6 +51,32 @@ You can run pytest on your work using the following example:
 % uv run pytest
 ```
 
+### Linting, testing, coverage, and updating coverage badges
+
+We apply a custom script to update our coverage badge in the README during our CI workflow.
+When running `scripts/update_coverage_badge.py` the script will parse the `coverage.xml` file generated from pytest and update the badge in the README with the new coverage percentage.
+When running `just all` locally, the coverage badge will not be updated since it is intended to be updated as part of the CI workflow.
+
+```sh
+just all
+```
+
+Where `all` is runnins all defined steps in the `justfile` which includes running tests and generating coverage reports.
+To see all of the steps defined in the `justfile`, you can run:
+
+```sh
+just --list
+```
+
+the coverage badge will be automatically updated as part of the workflow.
+If you want to update the coverage, run:
+
+```sh
+just coverage
+```
+
+This will run the tests and update the coverage badge in the README.
+
 ## Making changes to this repository
 
 We welcome anyone to use [GitHub issues](https://docs.github.com/en/issues/tracking-your-work-with-issues/about-issues) (requires a GitHub login) or create [pull requests](https://docs.github.com/en/pull-requests/collaborating-with-pull-requests/proposing-changes-to-your-work-with-pull-requests/about-pull-requests) (to directly make changes within this repository) to modify content found within this repository.

README.md

@@ -1,6 +1,6 @@
 # ZedProfiler
 
-[![Coverage](https://img.shields.io/badge/coverage-89%25-green)](#quality-gates)
+[![Coverage](https://img.shields.io/badge/coverage-96%25-brightgreen)](#quality-gates)
 
 CPU-first 3D image feature extraction toolkit for high-content and high-throughput image-based profiling.
 

ROADMAP.md

@@ -36,13 +36,13 @@ The roadmap is intended to be a living document and may be updated as needed.
 
 1. PR 1: Packaging and environment baseline
 
-- [ ] Python package scaffold, uv dependency management, version metadata 0.0.1, lint/test tooling, CI skeleton.
-- [ ] Linux support and CPU-only scope statements in metadata and docs.
+- [x] Python package scaffold, uv dependency management, version metadata 0.0.1, lint/test tooling, CI skeleton.
+- [x] Linux support and CPU-only scope statements in metadata and docs.
 
 2. PR 2: Core data model and API contracts
 
-- [ ] Canonical input contracts, loader interfaces, common error types.
-- [ ] Return schema contract (required keys, types, deterministic ordering).
+- [x] Canonical input contracts, loader interfaces, common error types.
+- [x] Return schema contract (required keys, types, deterministic ordering).
 
 3. PR 3: RFC2119 naming specification and validators
 

pyproject.toml

@@ -24,8 +24,11 @@ dependencies = [
   "jinja2>=3.1.6",
   "matplotlib>=3.10.8",
   "pandas>=3.0.2",
-  "pyarrow>=24",
+  "pandera>=0.31.1",
+  "pyarrow>=23.0.1",
+  "pydantic>=2.10",
   "scikit-image>=0.26",
+  "tomli>=2.4.1",
 ]
 scripts.ZedProfiler = "ZedProfiler.cli:trigger"