Metadata-Version: 2.4
Name: bionexus
Version: 0.1.0
Summary: BioNexus facilitates cross-modal retrieval between natural products and biosynthetic gene clusters
Project-URL: Homepage, https://github.com/moltools/bionexus
Project-URL: Repository, https://github.com/moltools/bionexus
Project-URL: Issues, https://github.com/moltools/bionexus/issues
Project-URL: Documentation, https://github.com/moltools/bionexus#readme
Author-email: David Meijer <david.meijer@wur.nl>
License-Expression: MIT
License-File: LICENSE
Keywords: biosynthetic-gene-clusters,cross-modal,natural-products,retrieval
Classifier: Development Status :: 5 - Production/Stable
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: MIT License
Classifier: Programming Language :: Python
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.10
Classifier: Programming Language :: Python :: 3.11
Classifier: Programming Language :: Python :: 3.12
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Requires-Python: >=3.10
Requires-Dist: aiohttp
Requires-Dist: alembic
Requires-Dist: biocracker
Requires-Dist: biopython
Requires-Dist: ijson
Requires-Dist: pandas
Requires-Dist: pgvector
Requires-Dist: psycopg[binary]<4.0,>=3.2
Requires-Dist: python-dotenv
Requires-Dist: rdkit
Requires-Dist: requests
Requires-Dist: retromol
Requires-Dist: rich
Requires-Dist: sqlalchemy
Requires-Dist: tqdm
Provides-Extra: dev
Requires-Dist: pytest; extra == 'dev'
Description-Content-Type: text/markdown

# BioNexus

## Setting up database

1) Copy `.env.example` -> `.env` and adjust

2) Start Postgres + Adminer:

    ```bash
    docker-compose up -d db adminer
    ```

    Adminer available at http://localhost:8080 (server: db, user: bionexus, db: bionexus)

3) (Optional) Create local env using `conda`:

    ```bash
    conda create -n bionexus python=3.10
    conda activate bionexus
    pip install -e .[dev]
    ```

4) Create/upgrade schema:

    ```bash
    bionexus upgrade head
    ```

5) Load data:
    
    RetroMol and BioCracker results can be loaded with the load command. For more information, run:

    ```bash 
    bionexus load --help
    ```

    Examples of scripts that extract annotations and references from RetroMol and BioCracker can be found in the `scripts/` folder.

6) Dump for deployoment:

    Make sure the database is running in Docker, then:

    ```bash
    bionexus dump --out ~/Downloads/dumps/bionexus_$(date +%Y%m%d).dump
    ```
