CHANGELOG¶
This project uses semantic versioning. This change log uses principles from keep a changelog.
[0.7.0] - 2017-06-19¶
Added¶
- Option to sketchjob CLI to use overlay as a filter for which identifiers will be processed
Changed¶
- JobSketcher.sketch() now takes a list of identifiers to process, and checks that those identifiers are in the dataset.
[0.6.0] - 2017-06-15¶
Added¶
- Agent now creates the output directory that it will pass to the “smart” tool
via the
--output-directory
Changed¶
- “Smart” tool interface parameter name changed from
--output-path
to--output-directory
- Singularity template
Fixed¶
- Naming of
sketchjob
input argument
[0.5.0] - 2017-06-15¶
Added¶
- Ability to access file level metadata from dataset items when running a Python analysis script
Changed¶
- Tools now need to comply with a specific command line interface to
be able to run using scripts produced by
sketchjob
. The command line interface of such “smart” scripts should have no positional arguments and has three required named arguments:--dataset-path
,--identifier
, and--output-path
. Furthermore, such “smart” analysis scripts should only work on one item in a dataset as it is the responsibility ofsketchjob
and the jobarchitectagent
to split the dataset into individual jobs. - For jobs that do not adhere to the command line interface above one will
have to write thin Python wrappers, for examples have a look at the scripts
in
tests/sample_smart_tools/
- Requiring the use of “smart” tools removes the need to make use of CWL, so its support has been removed
- See the Design document for more details about the thought process that led to this redesign
Removed¶
- CWL support
[0.4.0] - 2017-06-08¶
Changed¶
- Now using CWL (Common Workflow Language) to specify program to be run on dataset.
[0.3.0] - 2017-02-07¶
Changed¶
- Move
JobSpec
fromjobarchitect
tojobarchitect.backends
module JobSpec
class now stores absolute paths- Update Dockerfile to set entrypoint to sketchjob
[0.2.0] - 2017-02-06¶
Added¶
- singularity job command backend
- sketchjob CLI options for selecting wrapper script
- Templates for both job command and wrapper script creation
jobarchitect.backends.render_script
function- Hosting of docs on readthedocs
- API documentation to sphinx generated docs
- Change log to sphinx generated docs
- Better docstrings
[0.1.0] - 2017-02-03¶
Added¶
sketchjob
CLI_analyse_by_ids
CLI- Support script and files to build docker image
jobarchitect.JobSpec
classjobarchitect.agent.analyse_by_identifiers
functionjobarchitect.agent.Agent
classjobarchitect.backends.generate_docker_job
backendjobarchitect.sketchjob.generate_jobspecs
functionjobarchitect.sketchjob.sketch
functionjobarchitect.sketchjob.JobSketcher
classjobarchitect.utils.mkdir_parents
functionjobarchitect.utils.output_path_from_hash
functionjobarchitect.utils.split_dataset
functionjobarchitect.utils.path_from_hash
function