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LevyDecisionNeuroLab / pipeline

A repository for pipeline scripts - including organizing files, prepossessing and analyses
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Add requirements.txt file #1

Open orduek opened 2 years ago

orduek commented 2 years ago

Add requierments.txt file, so people will have an easy time installing a conda environment.

cherruc commented 2 years ago

Done!

cherruc commented 2 years ago

https://github.com/LevyDecisionNeuroLab/pipeline/blob/6bb3780751dfc19d3c82fa23f3ad4863a92fbe78/requirements.txt

orduek commented 2 years ago

Great! Thanks, Chelsea. How did you generated the file?

cherruc commented 2 years ago

I accessed the Farnam shell and generated the file with the following commands:

module load miniconda
source info --env
source activate py_37
conda list
conda list -e > requirements.txt

Apparently Google says the requirements.txt file can be installed into a new project environment with: conda install -n <env_name> requirements.txt

orduek commented 2 years ago

Yes. Indeed this is the advantage of using a requierements.txt file. I think we can maybe make it a bit shorter, as many things are dependencies installed by the computer.

orduek commented 2 years ago

could you please remove the current req.txt file and generate a new one (maybe with fewer packages)? Currently, it generates a lot of vulnerabilities. Thanks!

cherruc commented 2 years ago

Hi Or, I generated this from the one-time environment setup we did with:

module load miniconda
conda create -n py37_dev python=3.7 numpy scipy pandas matplotlib ipython jupyter
source activate env_name
conda install -c brainiak -c defaults -c conda-forge brainiak
conda install -c conda-forge nipype

Which packages would not be necessary? Thanks!

orduek commented 2 years ago

have you tried using pip3 freeze instead of conda? Take a look here https://stackoverflow.com/questions/31684375/automatically-create-requirements-txt