freshdata-cleaner 1.0.0

Fast, safe, automatic data cleaning for real-world tabular data.

freshdata

Automated DataFrame cleaning for pandas — explainable, safe, and production-ready.

One call turns a messy CSV, Excel, or SQL export into analysis- and ML-ready data — and tells you exactly what it changed and why.

Documentation · Quickstart · API Reference · Examples · Changelog

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freshdata is an automated data-cleaning library for Python that does real, intelligent preprocessing of real-world tabular data. It is not a fillna wrapper: a rule-based decision engine profiles every column (missing ratio, dtype, skewness, cardinality, inferred role) and chooses the right action per column — then logs a rationale, a risk level, and a confidence score for each decision so nothing happens silently.

import pandas as pd
import freshdata as fd

df = pd.read_csv("export.csv")

cleaned = fd.clean(df)                              # one line
cleaned, report = fd.clean(df, return_report=True)  # ... with a full audit trail
print(report.summary())

freshdata clean report
  rows:    525 -> 500 (-25)
  columns: 7 -> 6 (-1)
  missing: 421 -> 0 cell(s)
  memory:  100.8 KB -> 89.2 KB
  time:    0.017s
  engine:  25 duplicate row(s) removed; 20 outlier(s) flagged; imputed: age, segment
  actions (7):
    - [fix_dtypes] 'mostly_gone': converted to Int64
    - [drop_duplicates] dropped 25 duplicate row(s) (4.8% of rows, keep='first')
    - [missing] 'age': filled 12 missing value(s) with median (39.6846)
    - [missing] 'segment': filled 90 missing value(s) with sentinel "Missing" ('Missing')
    - [missing] 'mostly_gone': preserved 300 missing value(s)
    - [outliers] 'amount': flagged 15 outlier(s), 3.0% of values (method=iqr, factor=1.5) in new column 'amount_outlier'
    - [outliers] 'age': flagged 5 outlier(s), 1.0% of values (method=iqr, factor=1.5) in new column 'age_outlier'
  review (1):
    ? column 'mostly_gone' preserved at 60.0% missing in balanced mode

✨ Key features

• Automated DataFrame cleaning in one call — fd.clean(df) handles missing values, outliers, duplicates, dtype repair, and messy column names.
• Per-column decision engine — infers each column's role (id, target, datetime, free text, categorical, numeric) and applies explicit, documented threshold rules instead of one blunt global strategy.
• Explainable by design — every decision carries a rationale, risk level, and confidence score. If a NaN survives, the report says exactly why.
• Safe defaults — never imputes an identifier, never modifies a target/label column, never force-fills free text, never removes outliers blindly.
• AI-ready preprocessing — produces clean, typed, leakage-aware frames ready for scikit-learn, XGBoost, or any ML pipeline.
• Data profiling — fd.profile(df) gives read-only data-quality insight using the same inference code as clean, so previews are faithful.
• pandas-first, Polars-optional — pandas + NumPy core; pass a Polars frame and get a Polars frame back when the optional adapter is installed.
• Enterprise layer — opt-in fuzzy clustering, PII masking, semantic validation, a 0–100 Data Trust Score, OpenLineage metadata, and a batch CLI.
• Typed, tested, fast — fully type-hinted (py.typed), 800+ tests, 95%+ coverage, vectorized pandas/NumPy throughout.

🤔 Why FreshData exists

Most data-cleaning code is hand-written, one-off, and silent. People reach for df.dropna() or df.fillna(0) and quietly corrupt their analysis — imputing an ID, leaking a target, or deleting the very outliers that were the signal. General-purpose tools don't fix this:

• pandas gives you primitives, not decisions — you still write every rule.
• profiling tools (sweetviz, ydata-profiling) describe data but don't clean it.
• validation tools (Great Expectations) check data but don't repair it.

freshdata fills the gap: an opinionated engine that makes the right cleaning decision per column and explains it, so you get reproducible, auditable, ML-ready data without writing — or trusting — yet another bespoke script.

📦 Installation

pip install freshdata-cleaner                 # pandas + numpy only
pip install "freshdata-cleaner[ml]"           # + scikit-learn (KNN imputation, IsolationForest)
pip install "freshdata-cleaner[enterprise]"   # + polars, pyarrow, requests, pyyaml (enterprise layer + CLI)
pip install "freshdata-cleaner[all]"          # everything, including cleanlab

Requires Python ≥ 3.9 and pandas ≥ 1.5. Verify the install:

python -c "import freshdata as fd; print(fd.__version__)"

🚀 Quickstart

import pandas as pd
import freshdata as fd

df = pd.read_csv("messy_export.csv")

# Clean with sensible, explainable defaults
cleaned, report = fd.clean(df, return_report=True)

print(report.summary())        # human-readable audit trail
report.to_frame()              # decisions as a DataFrame
report.to_dict()               # JSON-friendly for logging / dashboards

Preview the engine's choices before touching your data:

print(fd.profile(df))                    # read-only data-quality report
print(fd.suggest_plan(df).summary())     # the exact plan clean() would run
print(fd.compare_plans(df))              # strategies side by side

🔁 Before vs after

Before — raw export	After — fd.clean(df)
First Name AGE Salary($) empty Ann 34 $1,200.50 Bob N/A - Bob N/A - Cara 41 $2,000 whitespace, N/A/- sentinels, currency strings, an all-empty column, a duplicate row, text dtypes	first_name age salary age_was_missing Ann 34 1200.50 False Bob 38 Missing True Cara 41 2000.00 False snake_case names, real Int64/float64 dtypes, sentinels → missing → imputed, duplicate dropped, empty column removed, a missingness indicator added

Every one of those changes appears in report.summary() with a rationale, risk level, and confidence score — no silent mutations.

🧩 Core API

name	purpose
fd.clean(df, *, return_report=False, config=None, **options)	clean, optionally returning a CleanReport
fd.profile(df, *, include_plan=False, **options)	read-only inspection with actionable issues
fd.suggest_plan(df, **options)	dry-run: primary + alternative models per column
fd.compare_plans(df, *, strategies=...)	side-by-side models across strategies
fd.compare_clean(df, *, strategies=...)	side-by-side actual clean outcomes
fd.explain_clean(df, **options)	what clean() did and why, plus inferred roles
fd.Cleaner(config=None, **options)	reusable configured pipeline (.clean(), .report_)
fd.CleanConfig	frozen dataclass holding every option
fd.CleanReport / fd.Action	audit trail with rationale / risk / confidence

# Tune the engine — explicit choices always override the defaults
cleaned = fd.clean(
    df,
    strategy="balanced",          # "aggressive" | "conservative"
    target_column="churn",        # never modified (no leakage)
    id_columns=("customer_id",),  # never imputed
    preserve_columns=("notes",),  # never dropped
    outlier_method="iqr",         # "zscore" | "auto" | "isolation_forest"
    return_report=True,
)

# Reusable pipeline across many files
cleaner = fd.Cleaner(target_column="churn")
for path in paths:
    out = cleaner.clean(pd.read_csv(path))
    log.info(cleaner.report_.summary())

How the cleaning engine works (two layers)

Layer 1 — representation repair (always on):

order	step	what it does
1	column_names	snake_case names, deduplicate collisions ("a", "a" → "a", "a_2")
2	strip_whitespace	trim surrounding whitespace in text cells
3	normalize_sentinels	"N/A", "null", "-", "", "#REF!", … → missing
4	drop_empty_columns / drop_empty_rows	remove all-missing columns and rows
5	fix_dtypes	text → numeric ("$1,234.56" works) / datetime / boolean, validated
6	drop_duplicates	resolve duplicate rows (first/last/drop/aggregate)

Layer 2 — the decision engine (strategy="balanced", the default) infers each column's role and applies explicit threshold rules:

missing ratio	numeric	categorical	datetime
≤ 5%	mean if ~normal & no outliers, else median	mode if clear majority, else "Unknown"	ffill/bfill if time-ordered
5–30%	median (KNN only in aggressive mode)	mode if dominant, else "Missing"	ffill/bfill if time-ordered
> 30%	preserved + warning (balanced)	same	same

Role gates run first: targets are never modified, IDs are never imputed, free text is never force-filled. Outliers in ID/target columns, preserve_columns, and domain-sensitive columns (AQI, pollutants, fraud/risk names) are always preserved — there the extremes usually are the signal.

⚡ Performance highlights

Typical throughput on a modern laptop (vectorized pandas/NumPy, one-pass engine caching — no C extension required):

Dataset size	Balanced	Aggressive
500 rows	< 0.5 s	< 1 s
3,000 rows	< 2.5 s	< 6 s
29k rows (full AQI)	< 5 s	KNN gated

python benchmarks/bench.py --fixtures --compare   # all fixtures, side by side

📊 How FreshData compares

Capability	freshdata	pandas	pyjanitor	Great Expectations	sweetviz	cleanlab
One-call automatic cleaning	✅	❌	➖	❌	❌	❌
Per-column decisions by inferred role	✅	❌	❌	❌	❌	❌
Missing-value imputation (smart)	✅	➖	➖	❌	❌	❌
Outlier detection & handling	✅	❌	❌	➖	➖	✅
Duplicate resolution	✅	➖	✅	❌	❌	❌
Dtype / format repair	✅	➖	✅	❌	❌	❌
Explainable audit trail	✅	❌	❌	➖	❌	➖
Data profiling	✅	➖	❌	➖	✅	❌
Data validation / quality gates	✅¹	❌	❌	✅	❌	❌
PII masking	✅¹	❌	❌	❌	❌	❌
Label-noise (ML) detection	✅¹	❌	❌	❌	❌	✅
Polars support	✅	❌	❌	➖	❌	❌

✅ built-in · ➖ partial / manual · ❌ not a goal · ¹ via the optional enterprise layer

🌍 Real-world use cases

• ML preprocessing — turn raw CSVs into leakage-aware, typed feature matrices before scikit-learn / XGBoost, without imputing IDs or touching the label.
• Analytics & BI ingestion — clean CRM, finance, and survey exports (currency strings, N/A sentinels, duplicate rows) on the way into a warehouse.
• Data-quality gates in ETL — run the enterprise CLI in Airflow/Prefect/cron; fail the job when the Data Trust Score drops below a threshold.
• Exploratory data analysis (EDA) — fd.profile(df) surfaces missingness, dtype issues, and duplicates before you commit to a modeling approach.
• Notebook hygiene — replace ad-hoc dropna/fillna cells with one auditable, reproducible call.

🛠️ Example pipeline

import pandas as pd
import freshdata as fd
from sklearn.ensemble import RandomForestClassifier
from sklearn.model_selection import train_test_split

raw = pd.read_csv("customers.csv")

# 1. Clean with the target protected from leakage
clean_df, report = fd.clean(raw, target_column="churn", return_report=True)
assert not report.warnings, report.warnings        # gate on data quality

# 2. Split & model on AI-ready data
X = pd.get_dummies(clean_df.drop(columns="churn"))
y = clean_df["churn"]
X_tr, X_te, y_tr, y_te = train_test_split(X, y, random_state=0)

model = RandomForestClassifier(random_state=0).fit(X_tr, y_tr)
print("accuracy:", model.score(X_te, y_te))

See examples/ for 8 runnable scripts and notebooks/ for narrated walkthroughs.

Enterprise layer — clustering, PII masking, trust scores, lineage, CLI

from freshdata.enterprise import (
    clean_enterprise, EnterpriseConfig, ClusterConfig, MaskingRule, SemanticValidatorConfig,
)

ec = EnterpriseConfig(
    enable_clustering=True,
    clustering=ClusterConfig(columns=("vendor",)),       # merge "Acme Inc" / "ACME  inc"
    masking=(MaskingRule(name="pii", columns=("email",), strategy="hash", salt="…"),),
    semantic=(SemanticValidatorConfig(name="iso", kind="reference",
              columns=("country",), reference=("US", "CA", "GB")),),
    fail_under_trust=80,                                  # quality gate
)
result = clean_enterprise(df, enterprise=ec)             # df may be pandas OR polars
print(result.quality.to_markdown())                      # before/after trust report
result.lineage.emit("lineage.json")                      # OpenLineage RunEvents
assert result.passed_gate

Batch CLI (exits non-zero when the trust gate fails):

freshdata clean in.csv -o out.parquet --mask email:hash --cluster vendor \
    --report quality.json --lineage lineage.json --fail-under-trust 80
freshdata trust in.csv --fail-under 90
freshdata profile in.csv --json

📚 Documentation

Full documentation lives at https://freshcode-org.github.io/freshdata/:

• Installation
• Quickstart
• Cleaning engine
• Data profiling
• API reference
• Examples
• Benchmarks
• FAQ

🤝 Contributing

Contributions are welcome! Please read CONTRIBUTING.md and our Code of Conduct. Quick start:

git clone https://github.com/FreshCode-Org/freshdata
cd freshdata
pip install -e ".[dev,ml,polars]"
pre-commit install
pytest && ruff check src tests && mypy src/freshdata

Security issues: see SECURITY.md for private disclosure.

🗺️ Roadmap

• Per-column decision engine with explainable reports (0.3)
• Enterprise layer: clustering, masking, trust score, lineage, CLI (0.4)
• Documentation site + examples + packaging governance (0.5)
• Pluggable custom cleaning rules / strategy registry
• Native Polars cleaning engine (beyond the adapter)
• HTML/interactive profiling report
• Config-as-YAML for the core cleaner (not just the CLI)
• 1.0 — stable public API

Have an idea? Open a discussion or issue.

📄 License

MIT — see LICENSE.

👤 Maintainer

Built and maintained by Johnny Wilson Dougherty (@JohnnyWilson-Portfolio).

If freshdata saves you time, please ⭐ the repository — it genuinely helps others discover the project.