Installation

Installation via pip

To install refineGEMs as Python package from PyPI, simply install it via pip:

pip install refineGEMs

The corresponding project site can be found here.

Installation via github

refineGEMs is distributed via the GitHub repository.

The package and all its dependencies can be installed within virtual environments.

Condaenv

Hint

Installing refineGEMs in a conda environment on a MacOS can cause the following issue:
-> After a restart of the device the whole conda set-up may have the wrong python version.
If that is the case:

  1. Deactivate all environments including the base environment

  2. Activate base

  3. Activate the refineGEMs environment

Setup a conda virtual environment and use its pip to install refineGEMs into that environment:

# clone or pull the latest source code
git clone https://github.com/draeger-lab/refinegems.git
cd refinegems

conda create -n <EnvName> python=3.9

conda activate <EnvName>

# check that pip comes from <EnvName>
which pip

pip install .

This will install all packags denoted in setup.py.

If which pip does not show pip in the conda environment you can also create a local environment for which you can control the path and use its pip:

conda create --prefix ./<EnvName>

conda activate <path to EnvName>

<EnvName>/bin/pip install .

Pipenv

You can use pipenv to keep all dependencies together. You will need to install pipenv first. To install refineGEMs locally complete the following steps:

# install pipenv using pip
pip install pipenv

# clone or pull the latest source code
git clone https://github.com/draeger-lab/refinegems.git
cd refinegems

# install all dependencies from Pipfile
pipenv install .

# initiate a session in the virtual environment
pipenv shell

The pipenv package can also be installed via Anaconda (recommended if you are a Windows user).

Troubleshooting

  • If you get ImportError: DLL load failed while importing _sqlite3 when running main.py. Locate the sqlite3.dll file on you machine and add it to PATH.

  • If you run into a problem with pipenv not locking after f.ex. moving the repository try uninstalling pipenv and reinstalling it via pip. Then run pipenv install and it should work again.

  • If you use VSCode terminals and have trouble accessing the python from within your conda environment, deactivate base and reactivate again:

conda deactivate
conda deactivate
conda activate base
conda activate <your conda env>