Changelog¶

All notable changes to this project will be documented in this file.

The format is based on Keep a Changelog and this project adheres to Semantic Versioning

1.2.0 - 2017-03-15¶

Failed sample annotation: when a job fails, the result is annotated and forwarded until a SinkNode, where we can determine the status and possibly point of failure of the Sample.
Commandline tool fastr trace that can inspect a workflow run and help trace errors and print debug information
Supported for Lmod modules environment next to the old environmentmodules
BaseDataType descendants are now (un)picklable (including EnumTypes)
Option to use {extension} field in sink_data, which differs from {ext} in that it doesn’t include a leading dot.
Support for Docker targets. A Docker target will execute a command inside of a specified docker container, allowing Tools to use Docker for distribution
Using the right and left shift operator (<< and >>) for creating links to Inputs using input << output or output >> input.
In the FastrInterfaces, automatic outputs can have a prefix for a flag that should be set for the output to be actually generated.
Fastr is now able to limit the amount of SourceJobs that are allowed to run concurrently.
Ability to report progress to PIM (use the pim_host field in the config)

Version can now also accept a format based on a date (e.g. 2017-02-17_bananas) which will be parsed the same way as 2017.02.17_bananas
Work on the ExecutionPlugin and the corresponding API. Has better fall-backs and a mechanism to advertise plugin capabilities.
The collector plugins have the input and input_parts fields merged, and the output and output_parts fields merged.

In some cases the log directory was not created properly, causing an handled exception
A bug making the handling of Booleans incorrect for the FastrInterface, when a Boolean was given a flag would also appear when it was False
Serialization of the namespace of a Network was not correct
Check version of Fastr that creates and executes a Job against each other
load_gpickle helper can handle data with Enums that use to cause an AttributeError
Output validation of Jobs did not work correctly for automatic outputs

The example network in resources/networks/add_ints.json was using an old serialization format making it non-functions. Replaced by a new network file.

Network runs called from an interpreter (and not file) caused a crash because the network tried to report the file used. Better handling of these situations.

Namespaces for resources (tools and networks)
Network manager located at fastr.networklist
RQExecution plugin. This plugin uses python-rq to manage a job queue.
LinearExecution plugin. This plugin uses a background thread for execution.
BlockingExecution plugin. This plugin executes jobs in a blocking fashion.
Automatic generation of documentation for all plugins, the configuration fields and all commandline tools.

Provenance is updated with a network dump and used tool definitions.
New configuration system that uses python files
New plugin system that integrates with the new configuration system and enables automatic importing of plugins
The fastr command line tools now use an entrypoint which is located in fastr.utils.cmd. This code also dispatches the sub commands.