[ISSUE-15] Add offline e2e fixtures and modernize core CI (pytest + Ruff)

[Gonza10V]

Motivation

• Provide v1 end-to-end, offline, compiler-only pytest fixtures that exercise the full-build orchestration and keep automation/hardware tests optional and manual.
• Modernize core CI to a fast, local, deterministic pipeline based on pytest and ruff that runs only compiler tests (unit, stages, integration).
• Avoid requiring network/SynBioHub/PUDU/Opentrons for core CI and preserve the new clean-architecture package layout for testing.

Description

• Add a GitHub Actions workflow at .github/workflows/ci.yml that installs the package with test extras and runs ruff check ., ruff format --check ., and pytest tests/unit tests/stages tests/integration on Python 3.10/3.11.
• Modernize the test extra in pyproject.toml to pytest>=7,<9 and add a pytest marker configuration for automation tests under [tool.pytest.ini_options].
• Add shared fixtures in tests/conftest.py (in-memory sbol2.Document, default_build_options, minimal_lvl2_request) and add integration tests tests/integration/test_full_build_happy_path.py and tests/integration/test_missing_lvl1_then_domestication.py that run offline using fake stage implementations.
• Add stage smoke tests under tests/stages/, a unit import boundary test tests/unit/test_core_imports.py (ensures optional automation deps are not side-effect imported), optional/manual automation placeholder tests/automation/test_opentrons_simulation_optional.py, and docs tests/README.md and RELEASE_CHECKLIST.md.

Testing

• Ran core import checks with python -c "from buildcompiler.api import BuildCompiler, full_build", python -c "from buildcompiler.execution import BuildContext, FullBuildExecutor", and python -c "from buildcompiler.reporting import BuildSummary, BuildReport, BuildGraph" and the PUDU adapter imports; these succeeded.
• Ran pytest tests/unit tests/stages tests/integration and observed all core tests pass (89 passed in ~0.44s) verifying the new integration and orchestration fixtures succeeded.
• Ran ruff check . as part of validation and it failed due to pre-existing repository lint debt outside this issue scope (legacy files/notebooks); this is noted and left for separate cleanup.
• Attempted uv run ... verification and it failed while installing the optional automation git dependency SBOLInventory due to environment/network restrictions (git fetch HTTP 403), confirming automation extras remain optional and are not required by core CI.

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[chatgpt-codex-connector]

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[chatgpt-codex-connector]

Limit Ruff CI gates to files that are currently clean

This workflow makes the core job fail before tests even run because it lints and formats the entire repository (ruff check . and ruff format --check .), while the repo still has existing violations outside this change set. I verified in this tree that both commands exit non-zero (e.g., lint errors in files/ and notebooks, and 36 files needing reformat), and ruff check --help confirms it exits with status 1 when diagnostics are found unless --exit-zero is used. As written, every push/PR on these branches will report failing CI even when pytest tests/unit tests/stages tests/integration passes.

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[Gonza10V]

@codex good catch please fix it

[chatgpt-codex-connector]

Summary

• Updated the CI workflow to scope Ruff lint gating to the offline core test surface (tests/conftest.py, tests/unit, tests/stages, tests/integration) so unrelated repository lint debt no longer blocks this PR’s core pipeline.
• Removed the ruff format --check gate from this workflow as part of the follow-up fix, while keeping the core pytest gate intact.
• Committed the change on the current branch with commit f328c1f and created a follow-up PR message via make_pr summarizing these updates.

Testing

• ✅ ruff check tests/conftest.py tests/unit tests/stages tests/integration
• ✅ pytest -q tests/unit tests/stages tests/integration
• ✅ git add .github/workflows/ci.yml && git commit -m "ci: scope ruff gate to offline core test paths"

Web check performed

• ✅ Searched Ruff’s official docs to confirm exit-code behavior and gate semantics: https://docs.astral.sh/ruff/linter/ and https://docs.astral.sh/ruff/formatter/

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