build-ml-pipeline

Build ML Pipeline (Declaration)

Declarative shape of a Python ML pipeline from data source to predictor.

Terms used in this skill

Read these once; they're referenced throughout.

• X marker — the .skb.mark_as_X() call that anchors the predict-time slice. Everything upstream runs identically at fit and predict; everything downstream is per-prediction work.
• Predict grid — the rows you want predictions for at predict time. For IID flat tables: the loaded frame itself. For time-series / panels: a (group, time) set.
• Cold-start row — a predict-grid row that has no in-slice history available (typical for lags at the start of the slice).
• Predict-time replay — re-binding the graph to a fresh source identifier at predict (e.g. learner.predict({"data_dir": …})).
• Cross-row step — a feature whose output for a row reads values from other rows (lag, rolling window, group aggregation, side-table join by time/group, drop_nulls on a shifted column).
• Layers 1 / 2 / 3 — source / predict-grid + X-marker / features after the marker. Defined in Rule 2.

Next-step pointers — where you go after this skill

You came here for…	→ next
Declared pipeline → CV strategy	→ evaluate-ml-pipeline (the G-CV-SPLITTER gate, rule 3)
Declared pipeline → smoke test	→ test-ml-pipeline → smoke-test-ml-pipeline
Symbol lookup mid-declaration	→ python-api (Shape 1 / 1b / 3)
Missing skrub/sklearn import	→ python-env-manager § install
Modified pipeline.py / features.py / data.py	→ python-code-style (ruff + NumPyDoc)

Always re-emit the Pre-flight checklist with evidence before declaring the turn done.

Canonical pipeline shape — IID flat-table

The 90% case. Copy + adapt; replace TARGET_COL and the regressor.

import skrub
from sklearn.ensemble import HistGradientBoostingRegressor

from <pkg>.data import TARGET_COL, load_raw


def build_learner(data_dir_preview=None):
    """Return the unfit learner (skrub SkrubLearner)."""
    data_dir = (
        skrub.var("data_dir", value=str(data_dir_preview))
        if data_dir_preview is not None
        else skrub.var("data_dir")
    )

    # Layer 1 + 2: load + mark X / y on the source frame.
    # No cross-row feature steps → marker sits here.
    data = data_dir.skb.apply_func(load_raw)
    X = data.drop(columns=[TARGET_COL]).skb.mark_as_X()
    y = data[TARGET_COL].skb.mark_as_y()

    # Layer 3: estimator at the tail. Feature engineering (if any)
    # chains between mark_as_X and the final .skb.apply.
    predictions = X.skb.apply(
        HistGradientBoostingRegressor(random_state=0), y=y
    )
    return predictions.skb.make_learner()

For history-dependent / panel / cold-start cases (≠ IID): → references/layer_examples.md § history-dependent.

For loader-baked-shift counter-example (what NOT to do): → references/layer_examples.md § counter-example.

Stop conditions — read before anything else

Each Stop condition: rule → symptom → recovery. Scan top to bottom; any match means STOP.

S1. Missing dependency

• Rule: import skrub raising means python-env-manager is next, not a substitute library.
• Symptom: ModuleNotFoundError: No module named 'skrub'.
• Recovery: invoke python-env-manager for the install command. Do NOT substitute with sklearn.Pipeline / make_pipeline / FunctionTransformer — that silently rewrites this skill out of the project.

S2. Symbol from memory is forbidden

• Rule: every skrub / scikit-learn / skore name must come from a python-api lookup this turn.
• Symptom: you type tabular_learner (renamed in 0.7+), mark_as_y(col) (signature dropped the positional in 0.9+), or any name "you remember".
• Recovery: invoke python-api. Recognition is not a lookup; names drift between releases.

S3. Splitter selection is out of scope

• Rule: no KFold / StratifiedKFold / train_test_split / any splitter import in pipeline code.
• Symptom: you're about to type from sklearn.model_selection import KFold in pipeline.py.
• Recovery: that's evaluate-ml-pipeline's territory. This skill only wires split_kwargs AT the X marker (see Rule 2).

S4. skrub.X(...) / skrub.y(...) are not acceptable graph roots

• Rule: root on skrub.var("<source>", value=preview) instead.
• Symptom: code starts with skrub.X(df) / skrub.y(s).
• Recovery: rewrite to skrub.var("data_dir", value=...) → .skb.apply_func(load_fn) → .skb.mark_as_X(). The shortcuts (1) bake the marker at the source — defeating Layer 1; (2) force a pre-loaded binding, breaking predict-time replay; (3) silently re-enable the late-mark_as_X bug for cross-row features.

S5. Late mark_as_X is forbidden when any feature step is cross-row

• Rule: for any cross-row step (lag, rolling, group-agg, target shift, side-join, drop_nulls on shifted col), the X marker goes UPSTREAM of that step. The step references the cross-row source as an additional apply_func argument (Layer 1 source → Layer 3 feature, via the marker bypass).
• Symptom: the smoke test fails on len(predictions) != n_predict_grid_rows; OR a feature_steps=[] toggle appears in build_learner "to make predict work for cold-start"; OR a temp-dir gymnastic at predict time to fake history; OR a wrapper estimator whose only job is to filter NaN rows the pipeline itself produced. (Don't be misled by syntax — pl.col("x").shift(k) IS cross-row.)
• Recovery: fix the graph topology via Rule 2's three-layer model. Don't loosen the smoke-test assertion. Don't wrap the predictor. Don't feature_steps=[].
• Proof: smoke test (smoke-test-ml-pipeline) — pipeline with marker in the right place passes by construction.

S6. Layer 1 doesn't know the question

• Rule: Layer 1 (sources + loaders) describes what data exists. Anything that requires knowing which rows we want predictions for — any horizon / lag / window / shift — belongs to Layer 2 or downstream, never Layer 1.
• Symptom: the loader's body contains a target.shift(-HORIZON), a drop_nulls("y"), or any task-specific filter.
• Recovery: push the task-specific operation past the marker into Layer 2 (target derivation via a stateful estimator) or Layer 3 (history-dependent feature). The smoke test passes trivially when the bug is fused into Layer 1 — CV looks fine, and the structural debt only surfaces when the next experiment composes against the raw source.
• Constructive test: would an external consumer — a SQL view, a feature store, a second model — derive this same output without knowing your task? No → push it past the marker.

S7. All Python execution goes to scratch/

• Rule: every Python command (version check, signature lookup, data inspection, loader sanity-check, anything) lands in scratch/<YYYY-MM-DD>_<HHMMSS>_<short>.py and runs via pixi run python scratch/<ts>_<short>.py.
• Symptom: you catch yourself typing pixi run python -c or python -c.
• Recovery: write the file first, then execute. Inline is forbidden regardless of length (see python-api § Stop conditions). No 2-line carve-out.

S8. Don't filter warnings

• Rule: no warnings.filterwarnings(...) in pipeline.py or scratch probes unless the user explicitly asks. See python-code-style § Stop conditions.

Forbidden shortcuts

Shortcut	Why it's wrong
tabular_learner from memory	Renamed to tabular_pipeline in skrub 0.7+. Memory typed → ImportError on modern installs
mark_as_y(target_column) positional arg	Dropped in 0.9+. Use .skb.select("...") BEFORE the mark
skrub.X(df) / skrub.y(s) as roots	Forbidden (S4). Use skrub.var("<source>", value=...)
value="data/train.parquet" literal in pipeline.py	Resolves against CWD; breaks runs from non-root dirs. Expose data_dir_preview as kwarg; caller passes PROJECT_ROOT / "data"
feature_steps=[] toggle "to make predict work"	S5 symptom. Fix the graph, not the predict-time bypass
skore.evaluate(learner, X, y, ...)	SkrubLearner takes an env-dict. Use data={"data_dir": ..., ...}
bare sklearn.Pipeline as top-level	Rewrite as skrub DataOps graph (Rule 1)
Inline pixi run python -c "..."	S7. Write to scratch/<ts>_*.py instead

Pre-flight — emit before any code

Each ticked box requires an actual tool call this turn. Empty Evidence = unchecked.

Pre-flight (build-ml-pipeline):
- [ ] Tier 1 mandatory libs importable: sklearn, skrub, skore
      Evidence: scratch/<ts>_check_tier1.py + `pixi run python …` output.
                **Inline `python -c` is NOT evidence.**
- [ ] Tabular library identified: pandas | polars
      Evidence: JOURNAL.md Status (Workspace decisions) | user quote
                | "n/a — pandas already in loader signature"
- [ ] python-api consulted for skrub symbols this turn
      Evidence: Read scratch/api/skrub/<v>/<topic>.md (this turn)
                | "n/a — no new skrub symbol this turn"
- [ ] python-api consulted for sklearn symbols this turn
      Evidence: Read scratch/api/sklearn/<v>/<topic>.md (this turn)
                | "n/a — no new sklearn symbol this turn"
- [ ] Source-binding pattern chosen
      Evidence: list each planned `skrub.var("<name>")` and state
                whether it's a source identifier (e.g. `data_dir`)
                or a predict-grid descriptor. IID: one `skrub.var`
                rooted on the loaded frame is enough.
- [ ] X-marker placement decided
      Evidence: name the DataOp node where `.skb.mark_as_X()` lands.
                IID: on the loaded source frame. Panel / cold-start:
                on the predict-grid node, BEFORE any history-dep step.
- [ ] (Cross-row pipelines only) Each cross-row step references the
      upstream history DataOp as an extra `apply_func` arg
      Evidence: name each step + its history-DataOp argument
                | "n/a — no cross-row steps"
- [ ] Layer 1 audit — every `apply_func` upstream of `mark_as_X`
      passes the constructive test (S6)
      Evidence: per-step "external consumer would derive this: yes/no"
- [ ] Preview value handling
      Evidence: `build_learner` exposes `data_dir_preview=None` kwarg;
                no relative-path literal baked into `pipeline.py`
- [ ] split_kwargs at the X marker decided: groups | time | none
      Evidence: name the column(s) wired OR "n/a — i.i.d., no group
                or time structure"
- [ ] Smoke test wired (`tests/smoke/test_NN_<short_name>.py`)
      Evidence: per `smoke-test-ml-pipeline`; trivial assertions if no
                history-dep
- [ ] Pre-flight re-emitted with evidence before final message.
      Evidence: this checklist appears in the end-of-turn summary.

Scope

• In scope: how the pipeline object is composed — source wiring, preprocessing/feature steps, estimator at the tail.
• Out of scope: fitting, splitting, tuning, persisting, evaluating — those have their own skills.

Core rules

Rule 1 — Skrub DataOps is the pipeline entry point

Declare the pipeline as a skrub DataOps graph rooted at one or more skrub.var(...) calls — not as a bare sklearn.Pipeline. The skrub.X(...) / skrub.y(...) shortcuts are not acceptable roots (see S4). Look up the underlying signatures via python-api.

Reference: https://skrub-data.org/stable/data_ops.html

→ next: Rule 2 (where the marker goes).

Rule 2 — Mark X early; featurize after

The marker is the shared-vs-predict-specific boundary.

One question to place the marker: does any feature step look at rows other than the one currently being processed?

Answer	Placement	Pattern
No (per-row math, stateful encoders that learn at fit and apply per-row)	Marker on the loaded source frame	Canonical IID example above
Yes (lag / rolling / cross-row join / target-shift)	Marker UPSTREAM of every cross-row step	Three-layer model below

The three logical layers:

• Layer 1 — Sources. One skrub.var(...) per input identifier: raw history file(s) / URL(s) / table name(s), side tables, and — for time-series / cold-start panels — the predict-time-grid description (start/end range, list of (group_id, time)). The loader for each source is its first .skb.apply_func. Loaders are pure functions of a single source identifier. Do not load + featurize in one apply_func — that fuses Layers 2 + 3 with the loader and breaks predict-time replay.

• Layer 2 — Predict-time grid + X marker. A DataOp whose rows are exactly the predict grid.

  • IID flat tables: this IS the loaded source frame.
  • Time-series / panel: the (group, time) grid derived from Layer 1's predict-time bounds.

  mark_as_X and mark_as_y go here. Target derivation that requires history (and drop_nulls on y) belongs to a small stateful BaseEstimator with fit_transform → {X, y} / transform → {X, y=None}, attached at this layer.

• Layer 3 — Feature engineering. apply_func chained on the X-branch after mark_as_X. History-dependent steps take the X DataOp as their first argument and the relevant Layer-1 source DataOp(s) as additional arguments — history is referenced, not bound to X. The same history node materializes the full available history at fit and at predict, so a backward lag computed for a row in the predict grid sees real values from the train history — no cold-start NaN.

Worked examples (full code, IID + history-dependent + counter-example): → references/layer_examples.md. Also see python-api/references/pre_mark_alignment.md for the production-style three-layer walkthrough drawn from this workspace's 01_baseline.

Preview value is a caller-supplied parameter, not a literal in pipeline.py. value= controls what learner.skb.preview() sees during interactive iteration — nothing else. A literal like value="data/train.parquet" resolves against CWD and silently breaks runs not started from the project root. Expose the preview as an optional kwarg on build_learner and leave it None for production fit / cross-validate.

Downstream evaluation contract. A SkrubLearner does NOT implement sklearn's fit(X, y) signature — it takes an environment dict. Pair with skore.evaluate(learner, data={"data_dir": ..., ...}, splitter=...), never with skore.evaluate(learner, X, y, ...) (raises). See evaluate-ml-pipeline; confirm signatures via python-api.

Cross-validation metadata at the X marker. If the data has group structure (subjects, sessions, customer IDs, repeated measures) or temporal ordering, attach the relevant column at .skb.mark_as_X(split_kwargs={...}):

X = data.drop(columns=[...]).skb.mark_as_X(
    split_kwargs={"groups": data["customer_id"]},
)

Keys map to the cross-validator's split(X, y, **split_kwargs) (e.g. groups). Ask the user when you can't tell from data alone whether such structure exists — name suspect columns (anything ending in _id, columns called subject / session / region, any date / timestamp for temporal ordering) and ask whether to wire them. Don't silently leave split_kwargs empty when group structure is plausible — that produces optimistic CV downstream. Choosing the splitter itself is evaluate-ml-pipeline's job; this skill only wires the metadata.

When editing an existing pipeline that uses skrub.X / skrub.y or binds materialized data: do not auto-rewrite. Surface the source-bound alternative and ask whether to refactor. Full catalogue: → references/source-binding.md.

→ next: Rule 3 (attach mechanism).

Rule 3 — Attach data modifications via .skb

Two attach points:

• .skb.apply_func(fn) — wraps a callable that transforms data.
• .skb.apply(estimator) — wraps any sklearn-compatible estimator (transformer in the middle, or the final predictor).

When to use skrub.deferred instead of apply_func: rare — only when the callable must combine multiple DataOps at once (e.g. a custom join over two tables). Even then, check whether a skrub joiner (Joiner / AggJoiner / MultiAggJoiner) covers it first. Default: .skb.apply_func. Details: → references/source-binding.md.

→ next: Rule 4 (function vs estimator).

Rule 4 — Stateless → function. Stateful → estimator.

The only decision rule for picking apply_func vs apply:

• Stateless — output for a row depends only on that row (and constants). No info borrowed across rows.
• Stateful — needs statistics / vocabulary / learned parameters fit on training data and re-applied unchanged to test data.

# Stateless — pure function + apply_func
import numpy as np

X = X.skb.apply_func(lambda df: df.assign(log_price=np.log1p(df["price"])))

# Stateful — estimator + apply
from sklearn.preprocessing import StandardScaler

X = X.skb.apply(StandardScaler())

If a step would silently learn from the test set when called as a plain function, it is stateful — promote it.

→ next: Rule 5 (leakage check).

Rule 5 — Leakage rule

Any computation using statistics learned from the data (means, medians, quantiles, vocabularies, target distribution) MUST be stateful. Calling such a computation as a plain function over the whole frame leaks test into training.

# WRONG — pct rank fits on the full frame, leaks test into training
X = X.skb.apply_func(lambda df: df.assign(p=df["x"].rank(pct=True)))

# RIGHT — quantile transformer learns on training fold only
from sklearn.preprocessing import QuantileTransformer

X = X.skb.apply(QuantileTransformer(output_distribution="uniform"))

Classic traps by name:

• target encoding (must fit on training y only),
• target-aware or quantile-based imputation,
• quantile binning / KBinsDiscretizer(strategy="quantile"),
• OrdinalEncoder / LabelEncoder whose categories come from the full dataset rather than fit on training only,
• vocabulary-building text tokenizers, TF-IDF, IDF weights.

Litmus test: would this output change if I called it on the training subset alone vs the whole frame? If yes → stateful → .skb.apply with an estimator, never .skb.apply_func.

→ next: Decision flow.

Decision flow for a new step

1. Does the operation only need the current row (and constants)? → stateless → pure Python function + .skb.apply_func.
2. Otherwise it must learn from training data and reapply on test. → stateful → sklearn-compatible estimator + .skb.apply.

→ next: Reproducibility (when touching shared modules).

Reproducibility — extending without breaking prior experiments

iterate-ml-experiment enforces a hard rule: every done row in JOURNAL.md History must stay runnable on main and produce the same result. When touching a shared module under src/<pkg>/, default behavior must preserve prior experiments' shape.

Three options, picked by judgment (full procedures + worked examples: → references/reproducibility_mechanics.md):

• Option 1 — parametrize the existing function (with a default-preserving flag). Pick when the change is small and scoped: a step appended at the end, a single conditional, a stateless transform that adds columns without reshaping existing ones. The flag's default mirrors prior behavior.
• Option 2 — add a new function called only from the new experiment. Pick when the change doesn't fit cleanly behind a flag: new estimator at the tail, a step that reshapes the graph, or Option 1 would grow ugly internal branching.
• Option 3 — branch the module. Last resort. Only when the change touches enough internal structure that Options 1 and 2 would obscure the diff. Usually a signal of a deeper layering issue worth surfacing to the user.

Tripwires (load-bearing)

• 3+ flags in one function → parametrization is leaking; reach for Option 2 next.
• Visible branching in the function body that makes it hard to read → reach for Option 2.
• A flag changes default behavior of an existing caller → STOP. Rule broken. Either keep the default preserving, or use Option 2.

Cheap executable check

iterate-ml-experiment § 3's smoke-test gate runs all of tests/smoke/, not just the new one. A prior smoke test going red after a change = default behavior not preserved. Fix before declaring the new experiment ready.

→ next: Common patterns (for recurring shapes).

Common patterns

Short catalogue. Look up exact symbols in python-api. Full catalogue with code: → references/common_patterns.md.

1. Heterogeneous columns — skrub column selectors with cols= on .skb.apply (one apply per group), not ColumnTransformer.
2. Default starting point for tabular data — reach for skrub.tabular_pipeline(...) or TableVectorizer + estimator first; specialize column-by-column only when default is insufficient.
3. Multi-table inputs — one skrub.var(...) per table; join with skrub Joiner / AggJoiner / MultiAggJoiner via .skb.apply(...).
4. Meta-estimator at the tail — StackingClassifier, CalibratedClassifierCV, TransformedTargetRegressor. Wrap the predictor first, then attach via .skb.apply as the final step.
5. Mark hyperparameter knobs in place — wrap with skrub.choose_from / choose_int / choose_float / optional inside the declaration. Don't import GridSearchCV here; the tuning skill owns search.
6. Custom sklearn transformer — author only when (a) no built-in fits and (b) the operation is stateful. Subclass BaseEstimator + TransformerMixin. For a stateless op, write a function and use .skb.apply_func.

Companion skills

Skill	Relationship
python-api	Authoritative lookup of sklearn / skrub / skore. Invoke whenever picking a symbol; cache hits first (Shape 0)
evaluate-ml-pipeline	Owns skore.evaluate, CV selection, metric defaults. Consumes the split_kwargs wired at the X marker
smoke-test-ml-pipeline	Executable proof of Rule 2's early-mark. Smoke failure → route back here; fix the topology, don't loosen the assertion
test-ml-pipeline	Router for tests/. Smoke test pairs 1:1 with the experiment script
python-env-manager	Detection + install commands. Invoke when import skrub raises
python-code-style	Must be invoked after writing or editing pipeline.py / features.py / data.py. Direct pixi run ruff check drops the NumPyDoc convention

References (load on demand)

• references/source-binding.md — full catalogue of source-binding patterns (encouraged / discouraged / OK-but-offer-upgrade) + the apply_func vs deferred decision.
• references/layer_examples.md — worked code for the IID flat-table case, the loader-baked-shift counter-example, and the history-dependent three-layer pattern.
• references/reproducibility_mechanics.md — full Option 1 / 2 / 3 procedures with code, plus the tripwire criterion.
• references/common_patterns.md — full catalogue of recurring pipeline shapes with code snippets.

Companion skill (planned): review-ml-pipeline — methodological review of an existing declaration (leakage audit, statelessness check, step ordering, scope creep). When it flags a problem, return here to fix.