Earth Observations for Crop Performance (Phenotype) Prediction

private repo made public after the work on the EU HORIZON20 PARSEC grant was completed (2020-2021). Sensitive trial information and stale branches were removed. This is a Python-based project dealing with spatial-temporal geographical datasets. Exploring the scientific concept of GxE (Genotype x Environment interaction). Some initial work was done in 2007 by Larisa Golovko, then at RiceTec Inc see

Git collab ground rules

If you just started using GitHub, some ground rules. Assuming Win OS, for Mac - adjust accordingly. Install VS Code (recommended, can use other code editors but stay away from Anaconda, we would use pip install in our project). Install Git (Mac has it) from https://git-scm.com/book/en/v2/Getting-Started-Installing-Git. Install Python 3 (this repo would not work for Python 2) - Mac has Python 2 by default installed, make sure you switch to Python 3 if on Mac (and ALWAYS use a separate Virtual Environment for each project, that will save you some headaches later on;).

• Clone the repo to your machine:

git clone https://github.com/Landviser-LLC/eo-data.git. #[url of this repo]

• Create new local branch for your work and switch to it:

git checkout -b branchname    # anything you want, but identifying YOU

• work on your local branch, use commands

git add [file]  # file modified
git status   # to check for commits and changes
git commit -m "something about what was done on this commit - changes etc"

• when done, push your branch back to this repo using

git push origin

then submit pull request here on GitHub for others to review and approve the merge of your branch with master. You can then delete your branch here or keep for your continued work. When you return to project after awhile, always do pull master/branch from here using

git pull origin    # this is on your local terminal when navigated to the project folder, 
                   # also depends on which branch are you - switch to master to pull master updates

Set local coding environment

Assuming you installed Python, VS Code (or other IDE), Git and cloned repo as described above, checked out you branch. In the terminal (PS - Power Shell) check which version of Python you have on your PC by typing py -0 make sure you are on Python 3.8 or 3.9 (latest).

py -0
Installed Pythons found by C:\Windows\py.exe Launcher for Windows
 -3.9-64 *
 -3.8-64
 -3.6-64
 -2.7-32

Install Virtual Environment for the Project - you can use exactly the same name for your environment, repo is setup not to pull files in the environment - they are specific to your machine, no use to share those. If you name your environment differently, it is ok, just setup .gitignore file yourself for it ;) so, type

python -m venv .env39eo

Finally, activate your coding environment by typing

.env39eo/scripts/activate

Notice how the prompt changed showing that you are in your Python environment - with core Python modules copied into environment folder and activated

(.env39eo) PS C:\Users\laris\OneDrive\PY3\eo_crops> 

Installing Python Modules for the project

The modules used in the project are listed in the file requirements.txt type the following to install all

pip install -r requirements.txt

Now you should have no problem using Jupyter Notebooks and Python files in this repo. If in the course of your development, you need an additional module you would pip install [module] do not forget to add it in requirements.txt so others (or yourself) working after you can quickly reinstall all modules in the repo.

That's All for Now! Welcome to Landviser's Team! Happy Coding