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CellMaps Annotate Hierarchy

https://readthedocs.org/projects/cellmaps-annotate-hierarchy/badge/?version=latest

Python Boilerplate contains all the boilerplate you need to create a Python package with command line

  • Free software: MIT license

Dependencies

Set up an environment

conda create -n gpt_env python=3.11.5
conda activate gpt_env
pip install -r requirements.txt

Set up an environment variable to store GPT-4 API key

conda activate gpt_env
conda env config vars set OPENAI_API_KEY="<your api key>"
conda deactivate  # reactivate

conda activate gpt_env
echo $OPENAI_API_KEY # make sure the key setup

# in python
%python
import os
import openai

openai.api_key = os.environ["OPENAI_API_KEY"]

From OpenAI website for the best practice for API key safety: https://help.openai.com/en/articles/5112595-best-practices-for-api-key-safety

Compatibility

  • Python 3.11+

Usage

Example usage

Check Notebook GPT4_pipeline_Demo

Command line usage

cd ./cellmaps_annotate_hierarchy
python .query_llm_for_analysis.py --config ./gpt4_config.json \
         --initialize \
         --input ./data/example_NeST_table_sub.tsv \
         --input_sep  ','\
         --set_index 'NEST ID' \
         --gene_column Genes\
         --gene_sep ',' \
         --start 0 \
         --end 27 \
         --output_file 'data/demo_commandline.tsv'

The instruction below is not ready for operation now (Sep 2023)

Installation

git clone https://github.com/idekerlab/cellmaps_annotate_hierarchy
cd cellmaps_annotate_hierarchy
make dist
pip install dist/cellmaps_annotate_hierarchycmd*whl

Run make command with no arguments to see other build/deploy options including creation of Docker image

make

Output:

clean                remove all build, test, coverage and Python artifacts
clean-build          remove build artifacts
clean-pyc            remove Python file artifacts
clean-test           remove test and coverage artifacts
lint                 check style with flake8
test                 run tests quickly with the default Python
test-all             run tests on every Python version with tox
coverage             check code coverage quickly with the default Python
docs                 generate Sphinx HTML documentation, including API docs
servedocs            compile the docs watching for changes
testrelease          package and upload a TEST release
release              package and upload a release
dist                 builds source and wheel package
install              install the package to the active Python's site-packages
dockerbuild          build docker image and store in local repository
dockerpush           push image to dockerhub

For developers

To deploy development versions of this package

Below are steps to make changes to this code base, deploy, and then run against those changes.

  1. Make changes

    Modify code in this repo as desired

  2. Build and deploy

# From base directory of this repo cellmaps_annotate_hierarchy
pip uninstall cellmaps_annotate_hierarchy -y ; make clean dist; pip install dist/cellmaps_annotate_hierarchy*whl

Needed files

TODO: Add description of needed files

Via Docker

Example usage

TODO: Add information about example usage

docker run -v `pwd`:`pwd` -w `pwd` idekerlab/cellmaps_annotate_hierarchy:0.1.0 cellmaps_annotate_hierarchycmd.py # TODO Add other needed arguments here

Credits

This package was created with Cookiecutter and the audreyr/cookiecutter-pypackage project template.