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

.github/workflows/ci.yml

@@ -0,0 +1,31 @@
+name: CI
+
+on:
+  pull_request:
+  push:
+    branches:
+      - main
+      - full_build
+
+jobs:
+  core:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ["3.10", "3.11"]
+    steps:
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+      - name: Install package
+        run: |
+          python -m pip install -U pip
+          python -m pip install -e ".[test]"
+          python -m pip install ruff
+      - name: Ruff check
+        run: ruff check .
+      - name: Ruff format check
+        run: ruff format --check .
+      - name: Core tests
+        run: pytest tests/unit tests/stages tests/integration

RELEASE_CHECKLIST.md

@@ -0,0 +1,11 @@
+# Release checklist
+
+- [ ] Core CI (`pytest tests/unit tests/stages tests/integration`) is green.
+- [ ] `ruff check .` is green.
+- [ ] `ruff format --check .` is green.
+- [ ] Happy-path integration fixture passes (or has explicit xfail with blocking issue).
+- [ ] Missing-lvl1-then-domestication integration fixture passes (or has explicit xfail with blocking issue).
+- [ ] Optional automation tests are documented and kept manual.
+- [ ] Core tests do not import optional automation dependencies.
+- [ ] README testing commands remain accurate.
+- [ ] Known upstream blockers are documented with issue references.

pyproject.toml

@@ -31,7 +31,7 @@ dependencies = [
 
 [project.optional-dependencies]
 test = [
-  "pytest < 5.0.0",
+  "pytest>=7,<9",
   "pytest-cov[all]"
 ]
 automation = [
@@ -48,3 +48,9 @@ automation = [
 dev = [
     "ruff>=0.14.0",
 ]
+
+
+[tool.pytest.ini_options]
+markers = [
+  "automation: optional/manual automation tests",
+]

tests/README.md

@@ -0,0 +1,33 @@
+# Testing guide
+
+## Core (required) checks
+
+Core CI is compiler-only and offline (except fixture-local SBOL files).
+
+```bash
+ruff check .
+ruff format --check .
+pytest tests/unit tests/stages tests/integration
+```
+
+Core tests must not require SynBioHub, PUDU, Opentrons, or SBOLInventory.
+
+## Optional automation checks
+
+```bash
+python -m pip install -e '.[automation,test]'
+pytest tests/automation
+```
+
+Automation tests are marked with `@pytest.mark.automation` and are manual/optional.
+
+## Skip vs xfail guidance
+
+- Use `skip` for intentionally manual checks (e.g., hardware simulation).
+- Use `xfail` only for known core blockers and include explicit issue references.
+
+## Fixtures
+
+- `tests/fixtures/sbol/`: fixture-local SBOL files.
+- `tests/fixtures/data/`: small deterministic JSON/data fixtures.
+- Shared fixture helpers are in `tests/conftest.py`.

tests/automation/README.md

@@ -0,0 +1,10 @@
+# Automation test suite (optional/manual)
+
+These tests are intentionally separated from core CI.
+
+Run only when optional dependencies are installed:
+
+```bash
+python -m pip install -e '.[automation,test]'
+pytest tests/automation
+```

tests/automation/test_opentrons_simulation_optional.py

@@ -0,0 +1,7 @@
+import pytest
+
+pytestmark = pytest.mark.automation
+
+
+def test_opentrons_simulation_manual_only():
+    pytest.skip("Manual/optional automation validation only. TODO(#67): wire real simulation checks in automation environment.")

tests/conftest.py

@@ -0,0 +1,30 @@
+from __future__ import annotations
+
+import sbol2
+import pytest
+
+from buildcompiler.api import BuildOptions
+from buildcompiler.domain import BuildRequest, BuildStage, DesignKind
+
+
+@pytest.fixture
+def default_build_options() -> BuildOptions:
+    options = BuildOptions()
+    options.execution.max_iterations = 5
+    return options
+
+
+@pytest.fixture
+def minimal_sbol_document() -> sbol2.Document:
+    return sbol2.Document()
+
+
+@pytest.fixture
+def minimal_lvl2_request() -> BuildRequest:
+    return BuildRequest(
+        id="req-lvl2-1",
+        stage=BuildStage.ASSEMBLY_LVL2,
+        source_identity="https://example.org/module/main",
+        source_display_id="main",
+        source_kind=DesignKind.MODULE_DEFINITION,
+    )

tests/integration/test_full_build_happy_path.py

@@ -0,0 +1,73 @@
+from __future__ import annotations
+
+import sys
+
+from buildcompiler.domain import (
+    BuildRequest,
+    BuildStage,
+    BuildStatus,
+    DesignKind,
+    IndexedPlasmid,
+    MaterialState,
+    StageResult,
+    StageStatus,
+)
+from buildcompiler.execution import BuildContext, FullBuildExecutor
+from buildcompiler.planning import BuildPlan
+from buildcompiler.inventory import Inventory
+from buildcompiler.sbol import SbolResolver
+
+
+class FakeStage:
+    def __init__(self, result_factory):
+        self.result_factory = result_factory
+
+    def run(self, request, *, source_document, target_document):
+        return self.result_factory(request)
+
+
+def _product(identity: str) -> IndexedPlasmid:
+    return IndexedPlasmid(
+        identity=identity,
+        display_id=identity.rsplit("/", 1)[-1],
+        state=MaterialState.GENERATED,
+    )
+
+
+def test_full_build_happy_path_offline(default_build_options, minimal_sbol_document):
+    lvl2_request = BuildRequest(
+        id="req-lvl2",
+        stage=BuildStage.ASSEMBLY_LVL2,
+        source_identity="https://example.org/module/target",
+        source_display_id="target",
+        source_kind=DesignKind.MODULE_DEFINITION,
+    )
+    ctx = BuildContext(
+        sbol=SbolResolver(minimal_sbol_document),
+        inventory=Inventory(),
+        build_document=minimal_sbol_document,
+        options=default_build_options,
+    )
+    executor = FullBuildExecutor(
+        context=ctx,
+        lvl2_stage=FakeStage(
+            lambda request: StageResult(
+                id="res-lvl2",
+                stage=BuildStage.ASSEMBLY_LVL2,
+                status=StageStatus.SUCCESS,
+                request_ids=[request.id],
+                products=[_product("https://example.org/plasmid/lvl2_target")],
+            )
+        ),
+        lvl1_stage=FakeStage(lambda request: StageResult(id="unused1", stage=request.stage, status=StageStatus.BLOCKED, request_ids=[request.id])),
+        domestication_stage=FakeStage(lambda request: StageResult(id="unused2", stage=request.stage, status=StageStatus.BLOCKED, request_ids=[request.id])),
+    )
+
+    result = executor.execute(BuildPlan(lvl2_requests=[lvl2_request]))
+
+    assert result.status == BuildStatus.SUCCESS
+    assert result.summary is not None
+    assert result.final_products
+    assert "pudupy" not in sys.modules
+    assert "opentrons" not in sys.modules
+    assert "SBOLInventory" not in sys.modules

tests/integration/test_missing_lvl1_then_domestication.py

@@ -0,0 +1,115 @@
+from __future__ import annotations
+
+from buildcompiler.domain import (
+    BuildRequest,
+    BuildStage,
+    BuildStatus,
+    DesignKind,
+    IndexedPlasmid,
+    MaterialState,
+    MissingBuildInput,
+    StageResult,
+    StageStatus,
+)
+from buildcompiler.execution import BuildContext, FullBuildExecutor
+from buildcompiler.planning import BuildPlan
+from buildcompiler.inventory import Inventory
+from buildcompiler.sbol import SbolResolver
+
+
+class FakeStage:
+    def __init__(self, fn):
+        self.fn = fn
+
+    def run(self, request, *, source_document, target_document):
+        return self.fn(request)
+
+
+def plasmid(identity: str) -> IndexedPlasmid:
+    return IndexedPlasmid(
+        identity=identity,
+        display_id=identity.rsplit("/", 1)[-1],
+        state=MaterialState.GENERATED,
+    )
+
+
+def test_missing_lvl1_promotes_domestication_and_retries(
+    default_build_options, minimal_sbol_document
+):
+    lvl1_attempts = {"n": 0}
+
+    def lvl1_fn(request):
+        lvl1_attempts["n"] += 1
+        if lvl1_attempts["n"] == 1:
+            return StageResult(
+                id="lvl1-blocked",
+                stage=BuildStage.ASSEMBLY_LVL1,
+                status=StageStatus.BLOCKED,
+                request_ids=[request.id],
+                missing_inputs=[
+                    MissingBuildInput(
+                        source_stage=BuildStage.ASSEMBLY_LVL1,
+                        source_design_identity=request.source_identity,
+                        missing_identity="https://example.org/part/promoterA",
+                        missing_display_id="promoterA",
+                        missing_kind="promoter",
+                        required_stage=BuildStage.DOMESTICATION,
+                        reason="missing part",
+                    )
+                ],
+            )
+        return StageResult(
+            id="lvl1-success",
+            stage=BuildStage.ASSEMBLY_LVL1,
+            status=StageStatus.SUCCESS,
+            request_ids=[request.id],
+            products=[plasmid("https://example.org/plasmid/lvl1_after_dom")],
+        )
+
+    def domestication_fn(request):
+        return StageResult(
+            id="dom-success",
+            stage=BuildStage.DOMESTICATION,
+            status=StageStatus.SUCCESS,
+            request_ids=[request.id],
+            products=[plasmid("https://example.org/plasmid/dom_promoterA")],
+        )
+
+    context = BuildContext(
+        sbol=SbolResolver(minimal_sbol_document),
+        inventory=Inventory(),
+        build_document=minimal_sbol_document,
+        options=default_build_options,
+    )
+    executor = FullBuildExecutor(
+        context=context,
+        lvl2_stage=FakeStage(
+            lambda request: StageResult(
+                id="unused-lvl2",
+                stage=request.stage,
+                status=StageStatus.BLOCKED,
+                request_ids=[request.id],
+            )
+        ),
+        lvl1_stage=FakeStage(lvl1_fn),
+        domestication_stage=FakeStage(domestication_fn),
+    )
+
+    plan = BuildPlan(
+        lvl1_requests=[
+            BuildRequest(
+                id="req-lvl1",
+                stage=BuildStage.ASSEMBLY_LVL1,
+                source_identity="https://example.org/engineered/region1",
+                source_display_id="region1",
+                source_kind=DesignKind.COMPONENT_DEFINITION,
+            )
+        ]
+    )
+
+    result = executor.execute(plan)
+
+    assert lvl1_attempts["n"] >= 2
+    assert any(sr.stage == BuildStage.DOMESTICATION for sr in result.stage_results)
+    assert any(p.display_id == "dom_promoterA" for p in result.final_products)
+    assert result.status in {BuildStatus.SUCCESS, BuildStatus.PARTIAL_SUCCESS}

tests/stages/test_domestication.py

@@ -0,0 +1,5 @@
+from buildcompiler.stages import DomesticationStage
+
+
+def test_domestication_stage_importable():
+    assert DomesticationStage

tests/stages/test_stage_assembly_lvl1.py

@@ -0,0 +1,5 @@
+from buildcompiler.stages import AssemblyLvl1Stage
+
+
+def test_assembly_lvl1_stage_importable():
+    assert AssemblyLvl1Stage

tests/stages/test_stage_assembly_lvl2.py

@@ -0,0 +1,5 @@
+from buildcompiler.stages import AssemblyLvl2Stage
+
+
+def test_assembly_lvl2_stage_importable():
+    assert AssemblyLvl2Stage

tests/unit/test_core_imports.py

@@ -3,16 +3,23 @@
 
 def test_core_imports_do_not_load_optional_automation_dependencies():
     import buildcompiler
-    from buildcompiler.adapters.opentrons import OpentronsSimulationAdapter
     from buildcompiler.adapters.pudu import (
+        assembly_route_to_pudu_json,
         plating_to_pudu_json,
         transformation_to_pudu_json,
     )
-    from buildcompiler.api import BuildOptions
+    from buildcompiler.api import BuildCompiler, BuildOptions
+    from buildcompiler.execution import FullBuildExecutor
+    from buildcompiler.reporting import BuildGraph, BuildReport, BuildSummary
 
     assert buildcompiler
+    assert BuildCompiler
     assert BuildOptions
-    assert OpentronsSimulationAdapter
+    assert FullBuildExecutor
+    assert BuildSummary
+    assert BuildReport
+    assert BuildGraph
+    assert assembly_route_to_pudu_json
     assert transformation_to_pudu_json
     assert plating_to_pudu_json