Metadata-Version: 2.3
Name: dayhoff-tools
Version: 1.3.21
Summary: Common tools for all the repos at Dayhoff Labs
Author: Daniel Martin-Alarcon
Author-email: dma@dayhofflabs.com
Requires-Python: >=3.10,<4.0
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.10
Classifier: Programming Language :: Python :: 3.11
Classifier: Programming Language :: Python :: 3.12
Classifier: Programming Language :: Python :: 3.13
Provides-Extra: embedders
Provides-Extra: full
Requires-Dist: biopython (>=1.84) ; extra == "full"
Requires-Dist: biopython (>=1.85) ; extra == "embedders"
Requires-Dist: boto3 (>=1.36.8)
Requires-Dist: docker (>=7.1.0) ; extra == "full"
Requires-Dist: fair-esm (>=2.0.0) ; extra == "embedders"
Requires-Dist: fair-esm (>=2.0.0) ; extra == "full"
Requires-Dist: firebase-admin (>=6.5.0)
Requires-Dist: h5py (>=3.11.0) ; extra == "full"
Requires-Dist: h5py (>=3.13.0) ; extra == "embedders"
Requires-Dist: numpy (>=1.26.4) ; extra == "embedders"
Requires-Dist: pandas (>=2.2.3) ; extra == "embedders"
Requires-Dist: pandas (>=2.2.3) ; extra == "full"
Requires-Dist: pyyaml (>=6.0)
Requires-Dist: questionary (>=2.0.1)
Requires-Dist: rdkit-pypi (>=2022.9.5) ; extra == "full"
Requires-Dist: requests (>=2.31.0)
Requires-Dist: sentencepiece (>=0.2.0) ; extra == "embedders"
Requires-Dist: sentencepiece (>=0.2.0) ; extra == "full"
Requires-Dist: sqlalchemy (>=2.0.40,<3.0.0) ; extra == "full"
Requires-Dist: toml (>=0.10)
Requires-Dist: torch (>=2.4.0) ; extra == "embedders"
Requires-Dist: tqdm (>=4.67.1) ; extra == "embedders"
Requires-Dist: tqdm (>=4.67.1) ; extra == "full"
Requires-Dist: transformers (==4.36.2) ; extra == "full"
Requires-Dist: transformers (>=4.36.2) ; extra == "embedders"
Requires-Dist: typer (>=0.9.0)
Requires-Dist: tzdata (>=2025.2)
Description-Content-Type: text/markdown

# dayhoff-tools

A set of small, sharp tools for everyone at Dayhoff. Hosted on PyPi, so you can Poetry or pip install like everything else.

## Installation

The base package includes minimal dependencies required for core CLI functionality (like job running):

```bash
pip install dayhoff-tools
# or
poetry add dayhoff-tools
```

### Optional Dependencies

You can install extra sets of dependencies using brackets. Available groups are:

* `core`: Includes common data science and bioinformatics tools (`biopython`, `boto3`, `docker`, `fair-esm`, `h5py`, `questionary`).
* `dev`: Includes development and testing tools (`black`, `pytest`, `pandas`, `numpy`, `torch`, etc.).
* `all`: Includes all dependencies from both `core` and `dev`.

**Examples:**

```bash
# Install with core dependencies
pip install 'dayhoff-tools[core]'
poetry add 'dayhoff-tools[core]'

# Install with all dependencies
pip install 'dayhoff-tools[all]'
poetry add 'dayhoff-tools[all]'
```
