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Check out our Trello project page for more info.

Table Of Content

Unit tests

You can use pytest to run the tests

$ py.test -v test_kern_deriv.py

this automatically detects all the files and test functions with test_ prefixes.

If you need to debug the tests / code, instead run:

$ py.test --pdb -v test_kern_deriv.py

to trigger the python debugger pdb post mortem.

Python package prerequisites

See py_package_dependencies.txt for prerequisite packages to run this code. Here is a post on how to set up a virtualenv for this project.

Other dependencies

Note when setting up George

Don't compile HODLR, clone it and rename folder into hodlr in the github designated location.

$ git clone https://github.com/dfm/HODLR.git $GEORGE_FOLDER/hodlr

Then move into the george directory just do:

$ python setup.py develop

if you installed Eigen using a package manager. If not, if you have installed it in a weird location, do:

$ python setup.py build_ext -I/path/to/eigen3 develop

Shear_gp file organization

  • modules with functions for analyzing code are in this directory
  • code for calling the functions are in the subdirectories

File organization of George

Link to my fork of George

Note about ipynb magic

The autoreload magic automatically updates function definitions from imported modules, this requires the magic function %autoreload, if you are not Karen Ng you need to run

%load_ext autoreload

first, before you can use

%autoreload

in the notebook.