bfxpm 1.0.0

BfxPM: Bioinformatician’s Project Manager for reproducible workflows.

BfxPM: Bioinformatics Project Manager

BfxPM is a professional-grade CLI ecosystem designed for the high-throughput, data-heavy workflows of modern computational biology. It transforms messy research directories into standardized, FAIR-compliant project structures, while providing an Agentic AI layer to assist with complex bioinformatic tasks.

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🤖 New: Agentic AI Integration

BfxPM now features a built-in BioAssistant powered by SmolAgents and the Gemini 1.5 Pro/Flash SDK.

• bfxpm ai chat: Interactive, project-aware assistant that understands your directory structure and data types.
• Transparent Reasoning: Real-time "Internal Thoughts" display shows the agent's logic before it acts.
• Safety Interceptor: Automatically intercepts destructive commands (like rm), creates timestamped backups in .bfxpm/backups/, and requires manual confirmation.
• Local & Cloud Flexibility: Configure via bfxpm ai setup to use either local (Ollama) or cloud models.

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🚀 Key Features

📂 Professional Scaffolding

• FAIR Compliance: Instantly scaffold projects with CONTRIBUTING.md, CITATION.cff, LICENSE, and standard GitHub Action workflows.
• MkDocs Ready: One-command generation of a complete documentation suite (docs/, mkdocs.yml).
• Scientific Attribution: Auto-populates metadata with your ORCID ID and project specifics.

🔄 Intelligent Organization & Mapping

• bfxpm organize: A specialized detection engine that routes sequences, alignments, and reports (PDF/HTML) into dedicated subfolders (results/reports vs results/figures).
• Outside-In Vacuum: Run organization from a parent folder to "vacuum" messy files into your project structure.
• bfxpm map --rollback: Take immutable snapshots of your project state and revert instantly.

🧬 Bioinformatics Toolset

• bfxpm env: Standardized environment management for common bioinformatic stacks.
• bfxpm pipeline: Scaffold analysis pipelines specifically for Nextflow and Snakemake.
• bfxpm fetch: Intelligent data retrieval and routing from external biological repositories.
• bfxpm tree: A high-performance scientific tree viewer with pager support and hidden file toggles.

🛡️ Data Integrity & Publication

• bfxpm checksum: Full manifest management to detect bit-rot in massive datasets.
• bfxpm flow: Record interactive terminal sessions into reproducible shell scripts.
• bfxpm deposit: One-command preparation for deposition to Zenodo, FigShare, and Dryad.

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🛠️ Installation

Prerequisites

• Python 3.13+ (Recommended)
• Conda (Optional, for bfxpm env features)

via Pip

pip install bfxpm-bio

via Conda

conda install -c bioconda bfxpm

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📖 Quick Start

1. Initialize a "Gold Standard" project:

bfxpm init

2. Interact with your BioAssistant:

bfxpm ai setup  # Configure your API keys
bfxpm ai chat   # "How should I structure my differential expression analysis?"

3. Clean up the "Mess":

bfxpm organize  # Automatically routes files and asks about unknown folders

4. Visualize & Document:

bfxpm tree --all  # View all files including hidden .git/
bfxpm report      # Generate a comprehensive project status report
bfxpm exit        # Safely exit the BfxPM session

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🏢 Architecture & Development

Project Structure

BfxPM follows a modular, production-grade architecture:

• src/bfxpm/agents/: AI agent logic and safety interceptors.
• src/bfxpm/commands/: Individual CLI command modules.
• scripts/publish.py: One-touch interactive publishing to PyPI and Anaconda.

Developer Environment

To set up for contributions:

git clone https://github.com/jyoda68/bioinformatics_project_manager.git
cd bioinformatics_project_manager
python -m venv .venv
source .venv/bin/activate
pip install -e ".[dev]"

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📄 License & Attribution

Licensed under the MIT License. See LICENSE for details. Developed and maintained by Jyotirmoy Das.

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Developer's Notes

• Python 3.13 Upgrade: Migrated to Python 3.13 to leverage the latest performance improvements and resolver features.
• SDK Transition: Switched to the google-genai unified SDK for more robust Gemini integrations.
• Safety First: Destructive command interception is now a core part of the codebase to prevent accidental data loss in large-scale bioinformatic projects.

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Developed with ❤️ for Bioinformaticians by a Bioinformatician