@zigrivers/scaffold 3.21.0 → 3.23.0

package/content/knowledge/data-science/data-science-testing.md

@@ -0,0 +1,183 @@
+---
+name: data-science-testing
+description: Testing strategy for solo DS code — pytest for pure functions, pandera for DataFrame schemas at test time and at ingest boundaries, and committed CSV fixtures for deterministic tests
+topics: [data-science, testing, pytest, pandera]
+---
+
+Data-science code rots quietly. A notebook cell that worked on Tuesday's snapshot silently breaks on Friday's because an upstream column was renamed, a dtype shifted from `int64` to `float64`, or a categorical grew a new level nobody tested for. Refactors that move feature logic out of a notebook into `src/` routinely regress because there was no test pinning the old behavior. Tests catch these failures at the line that introduced them instead of at the end of a three-hour pipeline run.
+
+## Summary
+
+Treat DS testing as three separate layers with distinct tools. Use `pytest` for pure-function unit tests — feature engineering, metric calculations, preprocessing helpers in `src/`. Use `pandera` for DataFrame-level contracts: schemas assert column names, dtypes, value ranges, and non-null expectations, and those same schemas run both in tests and at runtime at ingest boundaries. Use committed CSV fixtures in `tests/fixtures/` loaded through pytest fixtures for deterministic, reviewable test data. Keep this doc's scope to CODE correctness; model quality (AUC, calibration, drift) belongs in `data-science-model-evaluation.md`.
+
+## Deep Guidance
+
+### Unit tests with pytest
+
+Every helper in `src/` that transforms data is a pure function candidate for `pytest`. Arrange small inputs, act by calling the function, assert on the output. If a helper reaches for a database or filesystem, push that I/O out to the caller so the core logic stays testable without mocks.
+
+```python
+# tests/test_features.py
+import numpy as np
+import pandas as pd
+import pytest
+from src.features import impute_missing_ages
+
+class TestImputeMissingAges:
+    def test_fills_nan_with_median(self):
+        df = pd.DataFrame({"age": [10.0, 20.0, 30.0, np.nan]})
+        result = impute_missing_ages(df)
+        assert result["age"].isna().sum() == 0
+        assert result.loc[3, "age"] == 20.0  # median of [10, 20, 30]
+
+    def test_preserves_non_null_values(self):
+        df = pd.DataFrame({"age": [10.0, 20.0, 30.0, np.nan]})
+        result = impute_missing_ages(df)
+        pd.testing.assert_series_equal(
+            result.loc[:2, "age"], df.loc[:2, "age"], check_names=False
+        )
+
+    def test_all_nan_raises(self):
+        df = pd.DataFrame({"age": [np.nan, np.nan]})
+        with pytest.raises(ValueError, match="all-null"):
+            impute_missing_ages(df)
+```
+
+Run with `pytest -q`. Add `--cov=src` via `pytest-cov` once the project has more than a handful of helpers; aim for coverage on feature-engineering and metrics modules, not notebooks.
+
+Four rules keep this layer productive:
+
+- **Name tests after the behavior, not the function**: `test_fills_nan_with_median` beats `test_impute_missing_ages_1`. The name is the failure message when CI turns red.
+- **One assertion family per test**: a test checks either output values, or output shape, or error behavior — not all three. Split into three tests. Failures point at the broken property immediately.
+- **Use `pd.testing.assert_frame_equal` and `np.testing.assert_allclose`**: never compare DataFrames with `==` or floats with exact equality. Pass `rtol`/`atol` explicitly so the tolerance is visible in the test.
+- **Mark slow tests**: decorate any test that loads a non-trivial dataset with `@pytest.mark.slow` and run the default suite with `-m "not slow"` so `pytest` stays under ~5 seconds on save.
+
+### Data-frame validation with pandera
+
+Column drift is the single most common source of silent DS bugs. `pandera` encodes a DataFrame contract once and reuses it as a test assertion and a runtime guard at ingest boundaries — the moment a CSV, parquet file, or API response becomes a DataFrame.
+
+```python
+# src/schemas.py
+import pandera.pandas as pa
+from pandera.typing import Series
+
+class CustomersSchema(pa.DataFrameModel):
+    customer_id: Series[int] = pa.Field(unique=True, ge=0)
+    age: Series[float] = pa.Field(ge=0, le=120, nullable=True)
+    signup_date: Series[pa.DateTime]
+    segment: Series[str] = pa.Field(isin=["free", "pro", "enterprise"])
+
+    class Config:
+        strict = True  # reject unexpected columns
+
+# src/ingest.py — runtime validation at the boundary
+from src.schemas import CustomersSchema
+
+def load_customers(path: str) -> pd.DataFrame:
+    df = pd.read_csv(path, parse_dates=["signup_date"])
+    return CustomersSchema.validate(df)  # raises SchemaError on violation
+```
+
+The same schema doubles as a test fixture contract:
+
+```python
+# tests/test_ingest.py
+import pandas as pd
+import pytest
+from pandera.errors import SchemaError
+from src.ingest import load_customers
+
+def test_rejects_invalid_segment(tmp_path):
+    bad = tmp_path / "bad.csv"
+    bad.write_text("customer_id,age,signup_date,segment\n1,30,2024-01-01,vip\n")
+    with pytest.raises(SchemaError, match="segment"):
+        load_customers(str(bad))
+```
+
+Prefer `schema.validate(df)` calls over the `@pa.check_input` decorator — explicit validation is easier to trace in stack traces and does not hide behind import-time decoration.
+
+Three patterns make pandera pay off:
+
+- **Validate once at the boundary, trust downstream**: call `Schema.validate(df)` inside `load_customers`, `load_orders`, or whatever function first produces a DataFrame. Downstream code can then assume columns, dtypes, and ranges without re-checking.
+- **Use `lazy=True` during development**: `Schema.validate(df, lazy=True)` collects every violation instead of failing on the first, which is dramatically faster when fixing a bad CSV.
+- **Version schemas alongside migrations**: when a column renames or a new category lands, update the schema in the same PR as the code change. Schema drift caught in code review is cheaper than schema drift caught in production.
+
+### Fixtures: deterministic test data
+
+Random DataFrames in tests produce flaky failures that are painful to debug. Commit small, hand-curated CSVs to `tests/fixtures/` and load them through pytest `fixture` functions. The CSVs are reviewable in PRs, the fixtures are reusable across test modules.
+
+```python
+# tests/conftest.py
+from pathlib import Path
+import pandas as pd
+import pytest
+
+FIXTURES = Path(__file__).parent / "fixtures"
+
+@pytest.fixture
+def customers_df() -> pd.DataFrame:
+    return pd.read_csv(FIXTURES / "customers_small.csv", parse_dates=["signup_date"])
+
+@pytest.fixture(params=["customers_empty.csv", "customers_one_row.csv", "customers_small.csv"])
+def customers_edge_cases(request) -> pd.DataFrame:
+    return pd.read_csv(FIXTURES / request.param, parse_dates=["signup_date"])
+```
+
+Use `@pytest.mark.parametrize` to cover multiple scenarios without duplicating test bodies:
+
+```python
+@pytest.mark.parametrize(
+    "segment,expected_discount",
+    [("free", 0.0), ("pro", 0.1), ("enterprise", 0.2)],
+)
+def test_discount_by_segment(segment, expected_discount):
+    assert compute_discount(segment) == expected_discount
+```
+
+Keep fixture CSVs under ~50 rows. Anything larger belongs in a `data/` directory and should be generated or downloaded, not committed.
+
+When a test genuinely needs a larger or procedurally generated DataFrame, build it deterministically with a seeded RNG inside a fixture — never inline, and never with the global `np.random` state:
+
+```python
+@pytest.fixture
+def synthetic_transactions() -> pd.DataFrame:
+    rng = np.random.default_rng(seed=42)
+    n = 1000
+    return pd.DataFrame({
+        "user_id": rng.integers(0, 100, size=n),
+        "amount": rng.lognormal(mean=3.0, sigma=1.0, size=n),
+        "ts": pd.date_range("2024-01-01", periods=n, freq="1h"),
+    })
+```
+
+A fixed seed means the same test always sees the same data, so flaky-failure postmortems are possible instead of "must have been a weird random sample."
+
+### Running the suite
+
+Layout and commands stay boring on purpose:
+
+```
+tests/
+  conftest.py          # shared fixtures
+  fixtures/            # small committed CSVs
+    customers_small.csv
+    customers_empty.csv
+  test_features.py     # pytest for src/features.py
+  test_ingest.py       # pandera + ingest tests
+  test_metrics.py      # pytest for src/metrics.py
+```
+
+Wire `pytest` into `pyproject.toml` so `pytest` alone runs the right suite:
+
+```toml
+[tool.pytest.ini_options]
+testpaths = ["tests"]
+addopts = "-q --strict-markers -m 'not slow'"
+markers = ["slow: tests that load non-trivial data"]
+```
+
+Run the fast suite on every save (a file-watcher like `pytest-watch` helps), and run `pytest -m slow` or `pytest` with no marker filter before each commit. In CI, run the full suite unconditionally.
+
+### What NOT to test
+
+Don't unit-test `pandas`, `numpy`, or `pandera` themselves — assume upstream libraries work and pin versions in `pyproject.toml` to catch surprises via dependency bumps, not your own test suite. Don't assert on model quality metrics here (AUC, precision, calibration); those live in `data-science-model-evaluation.md` and run on held-out data, not fixtures. Don't write tests that require a live database, S3 bucket, or trained model file — those belong in integration tests run out-of-band, not the fast `pytest` suite a developer runs on save. And don't test notebooks directly; if a notebook cell has logic worth testing, extract it to `src/` first, then test the function.

package/content/knowledge/ml/README.md

@@ -0,0 +1,10 @@
+# `ml/` knowledge
+
+Production machine-learning domain knowledge injected into universal pipeline
+steps by `content/methodology/ml-overlay.yml`.
+
+## Lockstep pairs with `data-science/`
+
+Five documents here mirror documents in `content/knowledge/data-science/`. See
+`content/knowledge/data-science/README.md` for the full pair table. Edits to
+one side should trigger review of the other to prevent recommendation drift.

package/content/methodology/data-science-overlay.yml

@@ -0,0 +1,39 @@
+# methodology/data-science-overlay.yml
+name: data-science
+description: >
+  Data science overlay — injects solo / small-team data science domain
+  knowledge into existing pipeline steps for local-first, reproducibility-first
+  analytical work and model prototyping.
+project-type: data-science
+
+knowledge-overrides:
+  # Foundational
+  create-prd:            { append: [data-science-requirements] }
+  user-stories:          { append: [data-science-requirements] }
+  coding-standards:      { append: [data-science-conventions, data-science-notebook-discipline] }
+  project-structure:     { append: [data-science-project-structure] }
+  dev-env-setup:         { append: [data-science-dev-environment] }
+  git-workflow:          { append: [data-science-reproducibility] }
+
+  # Architecture & Design
+  system-architecture:   { append: [data-science-architecture] }
+  tech-stack:            { append: [data-science-architecture, data-science-dev-environment] }
+  adrs:                  { append: [data-science-architecture] }
+  domain-modeling:       { append: [data-science-data-versioning] }
+  database-schema:       { append: [data-science-data-versioning] }
+  security:              { append: [data-science-security] }
+  operations:            { append: [data-science-experiment-tracking, data-science-observability, data-science-reproducibility] }
+
+  # Testing
+  tdd:                   { append: [data-science-testing] }
+  create-evals:          { append: [data-science-testing, data-science-model-evaluation] }
+
+  # Reviews
+  review-architecture:   { append: [data-science-architecture] }
+  review-database:       { append: [data-science-data-versioning] }
+  review-security:       { append: [data-science-security] }
+  review-operations:     { append: [data-science-experiment-tracking, data-science-observability] }
+  review-testing:        { append: [data-science-testing, data-science-model-evaluation] }
+
+  # Planning
+  implementation-plan:   { append: [data-science-architecture] }

package/dist/cli/commands/dashboard.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"dashboard.d.ts","sourceRoot":"","sources":["../../../src/cli/commands/dashboard.ts"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,aAAa,EAAE,MAAM,OAAO,CAAA;AA4B1C,UAAU,aAAa;IACrB,MAAM,CAAC,EAAE,MAAM,CAAA;IACf,IAAI,CAAC,EAAE,OAAO,CAAA;IACd,OAAO,CAAC,EAAE,OAAO,CAAA;IACjB,IAAI,CAAC,EAAE,MAAM,CAAA;IACb,KAAK,CAAC,EAAE,OAAO,CAAA;IACf,MAAM,CAAC,EAAE,MAAM,CAAA;IACf,SAAS,CAAC,EAAE,OAAO,CAAA;IACnB,WAAW,CAAC,EAAE,OAAO,CAAA;IACrB,OAAO,CAAC,EAAE,MAAM,CAAA;CACjB;AAkCD,QAAA,MAAM,gBAAgB,EAAE,aAAa,CAAC,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,EAAE,aAAa,CAyL3E,CAAA;AAED,eAAe,gBAAgB,CAAA"}
+{"version":3,"file":"dashboard.d.ts","sourceRoot":"","sources":["../../../src/cli/commands/dashboard.ts"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,aAAa,EAAE,MAAM,OAAO,CAAA;AAgC1C,UAAU,aAAa;IACrB,MAAM,CAAC,EAAE,MAAM,CAAA;IACf,IAAI,CAAC,EAAE,OAAO,CAAA;IACd,OAAO,CAAC,EAAE,OAAO,CAAA;IACjB,IAAI,CAAC,EAAE,MAAM,CAAA;IACb,KAAK,CAAC,EAAE,OAAO,CAAA;IACf,MAAM,CAAC,EAAE,MAAM,CAAA;IACf,SAAS,CAAC,EAAE,OAAO,CAAA;IACnB,WAAW,CAAC,EAAE,OAAO,CAAA;IACrB,OAAO,CAAC,EAAE,MAAM,CAAA;CACjB;AAkCD,QAAA,MAAM,gBAAgB,EAAE,aAAa,CAAC,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,EAAE,aAAa,CAkO3E,CAAA;AAED,eAAe,gBAAgB,CAAA"}

package/dist/cli/commands/dashboard.js

@@ -17,6 +17,9 @@ import { ensureV3Migration } from '../../state/ensure-v3-migration.js';
 import { generateDashboardData, generateHtml, generateMultiServiceDashboardData, generateMultiServiceHtml, } from '../../dashboard/generator.js';
 import { discoverMetaPrompts } from '../../core/assembly/meta-prompt-loader.js';
 import { getPackagePipelineDir, atomicWriteFile } from '../../utils/fs.js';
+import { loadPipelineContext } from '../../core/pipeline/context.js';
+import { resolvePipeline } from '../../core/pipeline/resolver.js';
+import { buildDependencyGraph } from '../../dashboard/dependency-graph.js';
 /**
  * Write HTML to the requested path (or a tmpfile), then optionally open it in
  * the system browser. Shared between single-service and multi-service modes.
@@ -92,12 +95,40 @@ const dashboardCommand = {
         if (isMultiServiceMode) {
             // Load meta-prompts ONCE and share across all services.
             const metaPrompts = discoverMetaPrompts(getPackagePipelineDir(projectRoot));
+            // NEW: load pipeline context once (shared across all services). Default
+            // includeTools: false — tool meta-prompts aren't pipeline participants;
+            // their crossReads would leak into overlay.crossReads and into the graph.
+            const pipelineContext = loadPipelineContext(projectRoot);
+            // NEW: per-service overlay map populated alongside loadedServices below.
+            const perServiceOverlay = new Map();
+            let capturedGlobalSteps;
             // Methodology resolution: prefer config.methodology.preset; else fall back to
             // the first loaded service state's config_methodology; else 'unknown'.
             const configMethodology = config?.methodology?.preset;
             const loadedServices = [];
             let fallbackStateMethodology;
             for (const svc of configuredServices) {
+                // NEW: resolve pipeline per service to capture overlay + globalSteps.
+                // Wrap in try/catch mirroring loadState's STATE_MISSING fallback — a
+                // malformed overlay for one service must not crash the multi-service
+                // dashboard. On failure, warn + skip this service's outgoing graph
+                // contribution; the service's card still renders because the
+                // loadState block below has its own fallback. Incoming edges FROM
+                // other services INTO this service are still rendered — only this
+                // service's OWN outgoing declarations are lost.
+                try {
+                    const svcPipeline = resolvePipeline(pipelineContext, { output, serviceId: svc.name });
+                    perServiceOverlay.set(svc.name, svcPipeline.overlay);
+                    if (!capturedGlobalSteps)
+                        capturedGlobalSteps = svcPipeline.globalSteps;
+                }
+                catch (err) {
+                    output.warn(`Could not resolve pipeline for service '${svc.name}' — `
+                        + 'outgoing graph edges from this service omitted '
+                        + '(incoming edges from other services are still rendered) '
+                        + `(${err.message})`);
+                }
+                // Existing state-loading block (unchanged from HEAD):
                 const svcResolver = new StatePathResolver(projectRoot, svc.name);
                 const svcStateManager = new StateManager(projectRoot, () => [], () => config ?? undefined, svcResolver, new Set(), undefined);
                 let svcState;
@@ -138,9 +169,18 @@ const dashboardCommand = {
                 });
             }
             const methodology = configMethodology ?? fallbackStateMethodology ?? 'unknown';
+            // NEW: build the dependency graph (returns null if no edges after filtering).
+            const dependencyGraph = buildDependencyGraph({
+                config: config,
+                projectRoot,
+                services: configuredServices.map(s => ({ name: s.name, projectType: s.projectType })),
+                perServiceOverlay,
+                globalSteps: capturedGlobalSteps,
+            });
             const dashboardData = generateMultiServiceDashboardData({
                 services: loadedServices,
                 methodology,
+                dependencyGraph, // NEW — threaded into generator
             });
             if (argv['json-only']) {
                 output.result(dashboardData);

package/dist/cli/commands/dashboard.js.map

@@ -1 +1 @@
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