[JOSS] `protocol` version when installing from source vs install through pip

[htwangtw]

openjournals/joss-reviews#6269

• MRdataset version: 0.1.dev
• Python version: 3.10.12
• Operating System: Ubuntu 22.04.3 LTS

Description

This is part of the JOSS submission review.

In the installation instruction, the stable release will install a key dependency protocol version 0.3, however if we strictly follow the install from source instruction, it will be 0.1.

These two things should be consistent.

What I Did

virtualenv env-stable
source env-stable/bin/activate
pip install -U MRdataset
pip list

From source:

git clone git://github.com/Open-Minds-Lab/MRdataset
cd MRdataset
virtualenv env
source env/bin/activate
pip install git+https://github.com/sinhaharsh/protocol.git#egg=protocol
pip install -r requirements_dev.txt
pip install -e .
pip list

[raamana]

that's a great catch Hao, thank you. I guess we never attempted install from source :)

we will update the docs to make it they should use pip install -U MRdataset when possible, and only when they trying to contribute as a developer should they use the other instructions.

I personally don't understand the parameter #egg=protocol in this command in pip install git+https://github.com/sinhaharsh/protocol.git#egg=protocol but my guess is we don't need it. @sinhaharsh and I take a look and fix the docs asap.

[sinhaharsh]

Compiling protocol from source was initially required. It's surely not required anymore. The line for installing protocol is removed from the documentation. Thank you Hao.

[sinhaharsh]

The installation instructions are now updated. Installing MRdataset will also install latest protocol from PyPI

[htwangtw]

LGTM!