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https://github.com/int-brain-lab/iblenv
Unified environment and Issue tracker for all IBL
https://github.com/int-brain-lab/iblenv
Last synced: about 1 month ago
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Unified environment and Issue tracker for all IBL
- Host: GitHub
- URL: https://github.com/int-brain-lab/iblenv
- Owner: int-brain-lab
- License: mit
- Created: 2020-03-03T14:17:48.000Z (almost 5 years ago)
- Default Branch: master
- Last Pushed: 2024-06-10T15:22:59.000Z (7 months ago)
- Last Synced: 2024-06-11T12:48:50.328Z (7 months ago)
- Language: HTML
- Size: 81 MB
- Stars: 10
- Watchers: 29
- Forks: 10
- Open Issues: 50
-
Metadata Files:
- Readme: README.md
- License: LICENSE
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README
# 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:
```bash
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](https://www.anaconda.com/distribution/#download-section) and [git](https://git-scm.com/downloads), 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:
```commandline
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](https://int-brain-lab.github.io/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](https://www.anaconda.com/blog/using-pip-in-a-conda-environment).
It is not recommended to use the Spyder IDE in conjunction with iblenv. Please seek alternatives, like
[PyCharm](https://www.jetbrains.com/pycharm/) or [Visual Studio Code](https://code.visualstudio.com/).
### 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 "", line 1, in
...
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](https://github.com/conda/conda/issues/9903).