Usage

Installation

Under Construction!

Application settings

Settings for the application are shipped with the package in the application.yml file. There is also a test application.yml file used in tests. Most of what is included in the settings is a parameterization of options for the instrument. It may be desireable to override some of the settings which can be done via environment injection. For example

Example environment myenv.yml

environment: myenv

instrument:
  home: ~/snapred-testing/

Can be used to override the instrument.home directory to ~/snapred-testing/. At this time, only the instrument.home and samples.home directories will expand ~/ to a directory. This file can be supplied via command line injection

env=myenv.yml snapred

Using the Test Data Repo

When using the data repo for the very first time, be sure to run git lfs install outside the repo, otherwise the data will not show up correctly. You should not have to run this again later. To simply get the data, just run git submodule update --init --recursive and the data will appear under tests/data/snapred-data. You can now update the environmnet YAML file that you will use for tests and point to the test data using ${module.root}/data/snapred-data, assuming you are just running pytests. If you are just trying to run SNAPRed normally, you need to change the pathing to be ${module.root}/../../data/snapred-data or use the full absolute path. If you make any changes to the test repo, be sure to update the git LFS reference and commit it to this repo!

For more info about the test data repo, go to the readme here.