This project adheres to Semantic Versioning and Keep a Changelog format.
[0.12.4] -- 2019-07-18
- Ability to declare
required_executables in a
PipelineInterface, to trigger a naive "runnability" check for a sample submission
- A possibility to opt out of status page inclusion in the navbar
- The status tables now use DataTables jQuery plugin to make them interactive
[0.12.3] -- 2019-06-20
- Bug in
Sample YAML naming, whereby a base
Sample was being suffixed as a subtype would be, leading to a pipeline argument based on
yaml_file that did not exist on disk.
[0.12.2] -- 2019-06-06
- Fixed various bugs related to populating derived attributes, including using attributes like
sample_name as keys.
- Fixed a bug related to singularity attributes not being passed from a pipeline interface file.
- Fixed several bugs with incorrect version requirements.
[0.12.1] -- 2019-05-20
looper.Sample include more specific functionality from
- Status table creation is possible outside of
- In the summary index page the plottable columns list is now scrollable
- Status page relies on the
profile.tsv file rather than
*.log; Issue 159
- In HTML reporting module, do not ignore objects which are neither HTMLs nor images in the summary, e.g. CSVs
- Restore parsing and application of pipeline-level computing resource specification from a pipeline interface file; Issue 184
ignore_flags to properly modulate submission messaging; Issue 179
- Do not display time-like summary columns as the plottable ones; Issue 182
[0.12.0] -- 2019-05-03
- First implementation of pipeline interface 'outputs', so pipeline authors can specify items of interest produced by the pipeline.
- Functions and attributes on
Project to support "outputs" (
- Start "compute" --> "compute_packages" transition
get_logger moved to
- Prevent CLI option duplication in pipeline commands generated
- Make functional CLI spec of particular attribute on which to base selection of a subset of a project's samples (
[0.11.1] -- 2019-04-17
- Improved documentation
- Improved interaction with
[0.11] -- 2019-04-17
looper rerun command.
- Support use of custom
resources in pipeline's
- Listen for itemized compute resource specification on command-line with
- Support pointing to
Project config file with folder path rather than full filepath
selector-attribute parameter for more generic sample selection.
- Switched to a Jinja-style templating system for summary output
- Made various UI changes to adapt to
attmap for "attribute-style key-vale store" implementation
- Removed Python 3.4 support.
- UI: change parameter names
[0.10.0] -- 2018-12-20
PipelineInterface now derives from
PipelineInterface, iteration over pipelines now is with
build_parser, which returns
- Integers in HTML reports are made more human-readable by including commas.
- Column headers in HTML reports are now stricly for sorting; there's a separate list for plottable columns.
- More informative error messages
- HTML samples list is fully populated.
- Existence of an object lacking an anchor image is no longer problematic for
- Basic package test in Python 3 now succeeds:
python3 setup.py test.
[v0.9.2] -- 2018-11-12
- Fixed bugs with
looper summarize when no summarizers were present
- Added CLI flag to force
looper destroy for programmatic access
- Fixed a bug for samples with duplicate names
- Added new display features (graphs, table display) for HTML summary output.
[0.9.1] -- 2018-06-30
- Fixed several bugs with
looper summarize that caused failure on edge cases.
[0.9.0] -- 2018-06-25
- Support for custom summarizers
allow-duplicate-names command-line options
- Allow any variables in environment config files or other
compute sections to be used in submission templates. This allows looper to be used with containers.
- Add nice universal project-level HTML reporting
[0.8.1] -- 2018-04-02
- Minor documentation and packaging updates for first Pypi release.
- Fix a bug that incorrectly mapped protocols due to case sensitive issues
- Fix a bug with
report_figure that made it output pandas code
[0.8.0] -- 2018-01-19
- Use independent
peppy package, replacing
models module for core data types.
ProtocolInterface functionality into
[0.7.2] -- 2017-11-16
- Correctly count successful command submissions when not using
[0.7.1] -- 2017-11-15
- No longer falsely display that there's a submission failure.
- Allow non-string values to be unquoted in the
[0.7] -- 2017-11-15
- Catch submission errors from cluster resource managers
- Implied columns can now be derived
- Now protocols can be specified on the command-line
- Add rudimentary figure summaries
- Simplifies command-line help display
- Allow wildcard protocol_mapping for catch-all pipeline assignment
- Improve user messages
- New sample_subtypes section in pipeline_interface
- Sample child classes are now defined explicitly in the pipeline interface. Previously, they were guessed based on presence of a class extending Sample in a pipeline script.
- Changed 'library' key sample attribute to 'protocol'
[0.6] -- 2017-07-21
- Add support for implied_column section of the project config file
- Add support for Python 3
- Merges pipeline interface and protocol mappings. This means we now allow direct pointers to
pipeline_interface.yaml files, increasing flexibility, so this relaxes the specified folder structure that was previously used for
- Allow URLs as paths to sample sheets.
- Allow tsv format for sample sheets.
- Checks that the path to a pipeline actually exists before writing the submission script.
- Changed LOOPERENV environment variable to PEPENV, generalizing it to generic models
- Changed name of
pipeline_interfaces (but maintained backwards compatibility for now).
- Changed name of
run column to
run can also refer to a sequencing run.
- Relaxes many constraints (like resources sections, pipelines_dir columns), making project configuration files useful outside looper. This moves us closer to dividing models from looper, and improves flexibility.
- Various small bug fixes and dev improvements.
setuptools for installation, and
pandas 0.20.2. If
numexpr is installed, version
2.6.2 is required.
- Allows tilde in
[0.5] -- 2017-03-01
- Add new looper version tracking, with
-V options and printing version at runtime
- Add support for asterisks in file paths
- Add support for multiple pipeline directories in priority order
- Revamp of messages make more intuitive output
- Colorize output
- Complete rehaul of logging and test infrastructure, using logging and pytest packages
- Removes pipelines_dir requirement for models, making it useful outside looper
- Small bug fixes related to
- More robust installation and more explicit requirement of Python 2.7
[0.4] -- 2017-01-12
- New command-line interface (CLI) based on sub-commands
- New subcommand (
looper summarize) replacing the
- New subcommand (
looper check) replacing the
- New command (
looper destroy) to remove all output of a project
- New command (
looper clean) to remove intermediate files of a project flagged for deletion
- Support for portable and pipeline-independent allocation of computing resources with Looperenv.
- Removed requirement to have
pipelines repository installed in order to extend base Sample objects
- Maintenance of sample attributes as provided by user by means of reading them in as strings (to be improved further)
- Improved serialization of Sample objects