ioosbiodata_scripts

October 10, 2019 ยท View on GitHub

Bio data scripts & code samples related to the IOOS code sprint Biological Data Session.

examples

contribute

Each subdirectory is focuses on a particular problem/question. The subdirectories may contain R DESCRIPTION and/or python requirements.txt files to help with installing dependencies. Subdirectories can also contain their own README files.

There are no hard rules here; it's just a quick and easy place to drop your scripts/examples.

Installation: Python

If you're munging through data in Python, you might want to consider using a virtual environment to install your dependencies in.

Virtual Environment Using pip

On a Mac or Linux machine, you can quickly create a virtual environment with the commands below.

$ python3 -m venv env
$ source env/bin/activate # activate the environment
$ pip install -U pip # upgrade pip version
$ pip install -r requirements.txt

If you're installing and using jupyter notebooks this way, you'll also want to ensure that the user is specified so your installed packages are found properly:

python -m ipykernel install --user

Now, you should be ready to fire up Python and start exploring!

The install.sh (and install_*.sh) files in the root dir are helpers which comb through the subdirs and try to install all dependencies. They aren't pretty.

Highlights:

  • data_to_dwc : Abby's example data transformations
  • obis_subset : Pull data out of OBIS using robis then make some plots in R & in python.