testkraken

Test workflows in a matrix of computational environments.


License
Apache-2.0
Install
pip install testkraken==0.1.4

Documentation

TestKraken

Use TestKraken to test workflows in a matrix of parametrized environments.

Installation

TestKraken can be installed with pip:

$ pip install testkraken

Developers should use the development installation:

$ pip install -e .[dev]

Preparing the workflow for testing

Here is a directory tree of a valid TestKraken workflow:

workflows4regtests/basic_examples/sorting_list_fixedenv
├── data
│    ├── avg_list.json	
│    ├── list2sort.json
│    └── list_sorted.json
│        
├── scripts
│    ├── my_test_obj_eq.py	
│    └── sorting.py
│        
└── testkraken_spec.yml

  • The scripts subdirectory is the deafult place for the directory that contains the analysis script with command line interface; it can also include user defined tests.
  • The data subdirectory is the deafult place for the directory that contains all input data needed to run the workflow and all reference results.
  • Each workflow should have testkraken_spec.yml to describe environments, input data, script and command to run the workflow, and chosen tests for the workflow outputs.

TestKraken Specification

Specification should be included in testkraken_spec.yml file, that should be in the main workflow directory (see above).

Specification of the computational environments

The computational environments for the tested analysis can be described in env or fixed_env (one or both elements have to be specified in the specification). The Dockerfiles to generate the images will be created using Neurodocker, so the components of both entries, env and fixed_env, are specified in the Neurodocker specification. There is one difference, that base part should contain image and pkg-manager in one dictionary.

env and fixed_env elements

Both env and fixed_env are used to specify multiple environments. In the env part, each Neurodocker key (e.g. base, miniconda, fsl) can be a list, and TestKraken will create all desired combinations of environment specifications. The fixed_env can provide an additional specification for an environment or a list of complete specifications. The Neurodocker keys must be the same for env and all elements of the fixed_env part.

This is an example of the environment specification that makes use of env and fixed_env elements:

# List all desired combinations of environment specifications. This
# configuration, for example, will produce four different Docker images:
#  1. ubuntu 16.04 + python=3.5, numpy
#  2. ubuntu 16.04 + python=2.7, numpy
#  3. debian:stretch + python=3.5, numpy
#  4. debian:stretch + python=2.7, numpy
env:
  base:
  - {image: ubuntu:16.04, pkg-manager: apt}
  - {image: debian:stretch, pkg-manager: apt}
  miniconda:
  - {conda_install: [python=3.5, numpy]}
  - {conda_install: [python=2.7, numpy]}


# One or more fixed environments to test. These environments are built as defined
# and are not combined in any way. This configuration, for example, will
# produce one Docker image.
fixed_env:
  base: {image: debian:stretch, pkg-manager: apt}
  miniconda: {conda_install: [python=3.7, numpy]}

Example that uses the concept can be found here

common and varied parts

In order to eliminate repetition in the env part, for each Neurodocker key the additional structure can be added to describe common and varied parts. The previous example could also look like this:

env:
  base:
  - {image: ubuntu:16.04, pkg-manager: apt}
  - {image: debian:stretch, pkg-manager: apt}
  miniconda:
    common: {pip_install: [numpy]}
    varied:
    - {conda_install: [python=3.5]}
    - {conda_install: [python=2.7]}

Example that uses the concept can be found here

Data and Scripts locations

There is a default location where TestKraken tries to find all the data files and all the scripts files - this is the root directory of the tested workflow. However, these default locations can be changed via the testkraken_spec.yml.

data element

In order to specify how to get the data, the data entry has to have two keys - type and location. For now, only one type is implemented - workflow_path, but in the future this might be used to specify external repositories. For type=workflow_path, the location is simply the relative directory path to the workflow path. An example can look like this:

data:
  type: workflow_path
  location: my_data

scripts element

The scripts entry requires only the relative directory path to the workflow path. An example can look like this:

scripts: my_scripts

Example that uses the concept can be found here

Analysis part

The analysis element contains all the information required to run the workflow with the analysis. There is one required element - command, and two optional elements - script and inputs. These are assembled as command script input1 input2 .... When the command is a shell or interpreter (e.g., "bash", "python"), then the script is needed. However, the command can be an executable (e.g., "ssh", "bc") and then the script option is not required. The inputs part contains all the inputs needed to complete the command required to run the analysis. Each element of the inputs entry should have type, argstr (if a flag is needed) and value, and might have additional metadata that can be used by pydra (a dataflow engine used by TestKraken). If type is File, the file is assumed to be relative to the the data directory location. If script is provided, the script file is expected to be in the scripts directory. An example can look like this:

# The analysis part: inputs to the analysis script,
# the command to run the script and the script with the analysis.
analysis:
  inputs:
  - {type: File, argstr: -f, value: list2sort.json}
  command: python
  script: sorting.py

Tests part

The tests part contains all information regarding testing the analysis output. It is assumed that the output file is compared to the reference file that is available in the data directory (with the same name). If the tests part is not present or it's empty, no tests will be run after the analysis. There could be multiple entries for tests, but each element has to contain file with the name of the output file, name with the user defined name of the test, and script with the name of the script that should be used for running the test. The script can be saved in the script directory (checked first) or it can be an existing test from the TestKraken testing_functions directory. Any user provided tests have to follow the same template as the tests from TestKraken and define a command line interface. Example:

# Tests to compare the output of the script to reference data.
# The scripts are available under the user defined `script` subdirectory
# or the `testkraken/testing_functions` directory.
tests:
- {file: list_sorted.json, name: regr1, script: test_obj_eq.py}
- {file: list_sorted.json, name: regr1a, script: my_test_obj_eq.py}
- {file: avg_list.json, name: regr2, script: test_obj_eq.py}

Example that uses the concept can be found here

Thanks

Huge thanks to Puck Reeders for creating the logo and Anisha Keshavan for help with the dashboard.