marco-dvcs 0.1.35

A minimal dataset versioning system for text data with a focus on reproducibility.

Marco Dataset Versioning System

A minimal dataset versioning system for text data with a strong focus on reproducibility and transparency. Treat your text datasets like code — immutable, versioned, reproducible, and explainable.

Marco acts as a lightweight Python library, meaning you can initialize it in any machine learning project folder to safely version and preprocess your datasets without altering your original files.

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🚀 Installation (Linux / macOS)

On modern Linux environments (Arch Linux, Ubuntu 23.04+), Python packages must be installed inside a Virtual Environment (PEP 668) to prevent conflicts with system packages.

Follow these steps to safely install Marco into your ML project:

1. Navigate to your ML project folder (e.g. your bag-of-words project):

   cd ~/projects/my-bag-of-words-model
   

2. Create and activate a Python Virtual Environment:

   # Create a virtual environment named 'venv'
   python3 -m venv venv
   
   # Activate it (required every time you open a new terminal in this folder)
   source venv/bin/activate
   

   You should now see (venv) at the start of your terminal prompt.

3. Install Marco:

   pip install marco-dvcs
   

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🛠️ Usage Guide

Once marco is installed in your virtual environment, you have access to the full CLI.

1. Initialize a Repository

Initialize Marco tracking in your current directory. This creates a .marco/ data versioning environment specific to that project.

marco init

2. Create an Immutable Version

Upload a text/CSV/TSV dataset to create an immutable version. Marco computes a cryptographically secure SHA-256 hash from the raw data combined with the preprocessing configuration.

Interactive Mode — if you don't supply a config file, Marco guides you through building the preprocessing pipeline (lowercasing, tokenization, stopword removal, deduplication):

marco upload my_dataset.csv -t v1-raw

Config Mode — supply a JSON config directly:

marco upload my_dataset.csv -c my_config.json -t v1-processed

With Training Results Tracking — attach a training results CSV to track experiment outcomes directly inside the version:

marco upload my_dataset.csv -t v1-trained -r ./training_results.csv

Note: During upload, Marco automatically generates a raw_stats.json artifact inside the version directory. This file captures pristine, pre-pipeline dataset statistics — including vocabulary size, document length distributions (avg, median, std, min, max), and label distributions.

3. List Versions

View all versions you've created, along with their tags and timestamps.

marco list

4. Restore / Checkout Data

Extract the processed dataset from Marco's storage back into your active workspace for model training.

marco restore v1-processed -o ./training_data.tsv

5. Export / Import Versions

Easily share dataset versions with teammates by packing them into .tar.gz archives.

# Export version 'v1-raw' to the 'exports' folder
marco export v1-raw ./exports/

# Import an archive received from a teammate
marco import ./exports/marco_version_e5e0b767.tar.gz

6. Delete Versions

Delete a dataset version to recover disk space. Marco intelligently updates the lineage (parents history) of any descendant versions so that your Git-style history tree remains intact.

marco delete v1-raw
# or by hash
marco rm e5e0b767

7. Diff Versions — Unified ---/+++ Format

marco diff prints a line-by-line unified diff directly to the terminal — no files written, no clutter.

Diff the raw source data (default):

marco diff v1.0 v2.0

Diff the post-pipeline preprocessed output:

marco diff v1.0 v2.0 --target preprocessed

Diff the DAG preprocessing configuration:

marco diff v1.0 v2.0 --target config

Control how many context lines surround each hunk (default: 3):

marco diff v1.0 v2.0 --context 10

Save a full Markdown metrics report to a folder (opt-in):

marco diff v1.0 v2.0 --save ./reports

Example terminal output:

--- v1.0 (abc12345)/raw.txt
+++ v2.0 (def67890)/raw.txt
@@ -1,5 +1,6 @@
 positive  Great product, love it!
-negative  Terrible experience.
+negative  Poor experience, not recommended.
+negative  Worst purchase I ever made.
 positive  Highly recommend to everyone.
 neutral   It was okay, nothing special.

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8. KL Divergence & Token Analytics

Marco goes beyond simple vocabulary size tracking. It uses KL divergence (Kullback-Leibler) to measure exactly how token probability distributions shift between two dataset versions — telling you whether common words disappeared or rare domain terms suddenly dominated.

marco token-analytics v1-raw v2-processed

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🔬 Reproducibility Proof

Marco guarantees that a dataset version is not just stored — it is provably reproducible. The marco/reproducibility_proof/ module lets you mathematically verify that re-running the exact same pipeline on the same raw data produces a byte-identical result.

1. Verify a Single Version

Re-runs the full preprocessing pipeline from scratch and compares the freshly computed output hash against the stored hash in the manifest.

marco verify v1-raw
# or with a full hash
marco verify fe44032c

Example output:

🔬 Verifying version: fe44032c70164a71...

  Pipeline Step Verification:
    ✅  step_1 normalize_newlines
    ✅  step_2 lowercase

  Stored  output_hash: ed610672ea28e065...
  Recomputed   hash:   ed610672ea28e065...

  ✅ VERIFIED — output hash matches. Version is reproducible.

• On PASS: the manifest is updated with "verified": true, a timestamp, the current environment snapshot, and per-step hashes.
• On FAIL: a verification_report.json is written inside the version folder with a row-level delta showing exactly which rows differ. Exit code is 1.

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2. Verify All Versions at Once

Audit every version in the repository and get a clean summary table.

marco verify-all

Example output:

──────────────────────────────────────────────────────────────────────
  Marco Reproducibility Audit — 3 version(s) found
──────────────────────────────────────────────────────────────────────
🔬 Verifying version: a3f9c1d2...  ✅ VERIFIED
🔬 Verifying version: fe44032c...  ✅ VERIFIED
🔬 Verifying version: 83f77823...  ❌ FAIL
──────────────────────────────────────────────────────────────────────
  Summary: 2/3 versions passed.
──────────────────────────────────────────────────────────────────────

Returns exit code 1 if any version fails — making it CI/CD friendly.

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How the 7-Layer Reproducibility Engine Works

#	Guarantee	How It Works
1	Step-by-step hash verification	Hashes the output after every individual DAG step. Pinpoints exactly which step introduced non-determinism (✅ step_1, ❌ step_2).
2	Byte-exact canonical enforcer	Before hashing, data is serialized into a strictly defined canonical TSV format: Unix line endings only, fixed column order (label, text, n_tokens), UTF-8 encoding. Prevents false FAIL results from OS differences (Windows CRLF vs Linux LF).
3	Row-level delta on FAIL	When a hash mismatch occurs, computes exactly which rows were added or removed between the stored output and the fresh recompute, saved in verification_report.json.
4	Permanent audit trail	Every verification run (PASS or FAIL) is appended to .marco/verification_log.jsonl with a timestamp, result, and full environment snapshot — a tamper-evident history.
5	Environment fingerprinting	Stores Python version, NumPy/Pandas versions, and platform info in the manifest at verification time. Warns on re-verification if the environment changed: "Python 3.10 → 3.14 (may explain hash mismatch)".
6	Stochastic operation detector	Scans the pipeline DAG config for non-deterministic functions (e.g. shuffle, random_sample) that lack a seed parameter. Warns before verifying so expectations are set correctly.
7	Manifest integrity update	On PASS: sets "verified": true in manifest.json and persists per-step hashes. On FAIL: sets "verified": false and keeps verification_report.json alongside the version data.

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Verification Report (verification_report.json)

When a version fails, Marco writes a full diagnostic file at .marco/versions/<version_id>/verification_report.json:

{
  "version_id": "fe44032c...",
  "verified_at": "2026-03-18T14:01:00Z",
  "result": "FAIL",
  "stored_hash": "ed610672...",
  "computed_hash": "a3f9c1d2...",
  "step_hashes": {
    "step_1": "aabbcc...",
    "step_2": "ddeeff..."
  },
  "stochastic_warnings": [],
  "environment_warnings": ["python_version changed: '3.10' → '3.14'"],
  "row_delta": {
    "count_stored": 1000,
    "count_computed": 998,
    "removed": [["pos", "hello world"], ["neg", "bad product"]],
    "added": []
  }
}

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🧠 Architecture Overview

Marco decouples logic from the file system. All core engine operations live inside marco/core/:

• locker.py — File-based concurrency control using .lock files.
• repository.py — CRUD operations for dataset versions and refs.json tagging. Enforces file immutability by setting read-only permissions (0o444) on all version files immediately after creation.
• preprocessor.py — A robust Directed Acyclic Graph (DAG) preprocessing engine with deterministic topological execution.
• comparator.py — Version comparison via Markdown metric reports (compare_versions) and classic ---/+++ unified diffs (diff_versions_text) using Python's stdlib difflib.

Reproducibility Proof Engine (marco/reproducibility_proof/)

• canonicalizer.py — Enforces byte-exact canonical serialization (Unix line endings, fixed column order). Also detects stochastic/non-deterministic pipeline operations.
• audit_log.py — Appends every verification run (PASS or FAIL) to .marco/verification_log.jsonl with a full environment snapshot.
• verify.py — End-to-end reproducibility verification with step-by-step hashing, row-level delta reports, environment fingerprinting, and a verify_all() batch audit command.

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Have fun building safer machine learning pipelines!