Skip to content

Latest commit

 

History

History
86 lines (70 loc) · 4.12 KB

README.md

File metadata and controls

86 lines (70 loc) · 4.12 KB
Raw

IBLENV installation guide

Unified environment and issue tracker for IBL github repositories.

Update environment

In a terminal, navigate to your working directory, the one in you cloned the iblenv and iblapps repositories previously (typically something like int-brain-lab). Run the following commands in your terminal:

conda activate iblenv
cd iblapps
git pull
cd ..
cd iblenv
git pull
pip install -r requirements.txt --upgrade

If any errors are encountered, it is recommended to follow the "Removing an old installation" instructions and then the "Install from scratch" instructions.

Install from scratch

In order to create the unified environment for using IBL repositories, first download and install Anaconda and git, and follow their installer instructions to add each to the system path. Also, please ensure Anaconda is installed to your home directory. The below instructions will tell you how to set up and activate the unified conda environment (iblenv) and properly install multiple repositories within this environment.

In your git terminal, navigate to the directory in which you want to install the IBL repositories (e.g. create a folder named something like int-brain-lab and work from within it). Then run the following commands:

conda update -n base -c defaults conda
conda create --name iblenv python=3.10 --yes
conda activate iblenv
git clone https://github.com/int-brain-lab/iblapps
pip install --editable iblapps
git clone https://github.com/int-brain-lab/iblenv
cd iblenv
pip install --requirement requirements.txt

Removing an old installation

The following command will completely remove an anaconda environment and all of its packages: conda remove --name iblenv --all

Notes:

  • Whenever you run IBL code in Python you should activate the iblenv environment, i.e. conda activate iblenv
  • If you want to launch GUIs that rely on pyqt (e.g. the IBL data exploration gui or phy) from IPython, you should first run the IPython magic command %gui qt. Additional documentation here for working with iblenv

Troubleshooting:

Spyder

If using Anaconda's Spyder IDE, please take note. When installing Spyder in a virtual environment, like iblenv, conda will add many packages to that virtual environment. In the case of iblenv, some packages installed by spyder are in direct conflict with the pip installed packages. This will create an inconsistent and unstable environment, especially when attempting to perform any sort of update on those packages. For more information about how to work with pip within conda, please read the following article.

It is not recommended to use the Spyder IDE in conjunction with iblenv. Please seek alternatives, like PyCharm or Visual Studio Code.

brotli error

If attempting to set up this environment in older versions of anaconda or a version of anaconda that has been upgraded from an older version of anaconda, you may be presented with the following error when attempting to import the ONE api:

activate iblenv
python -c "from one.api import ONE"
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
...
File "C:\Users\username\Anaconda3\envs\iblenv\lib\site-packages\urllib3\response.py", line 396, in HTTPResponse
    DECODER_ERROR_CLASSES += (brotli.error,)
AttributeError: module 'brotli' has no attribute 'error'

The source of this issue looks to be with the way anaconda handled the brolipy package. One potential solution is to run the following:

activate iblenv
conda install brotlipy
python -c "from one.api import ONE"

If this results in the same error, a full removal of anaconda (windows uninstall followed by the manual removal of various files and directories hiding in several areas) and then a fresh install of Anaconda should correct the problem.

More details can be found in this github issue.