[0.31.0] - 2020-10-07
Sampleclass that can include or exclude
[0.30.3] - 2020-09-22
- If there's just one
Project.subsample_tableproperty will return an object of
pandas.DataFrameclass rather than a
subsample_tableis set to
[0.30.2] - 2020-08-06
- Support for multiple subsample tables
- License file to the package source distribution
[0.30.1] - 2020-05-26
- Package authors list
[0.30.0] - 2020-05-26
This version introduced backwards-incompatible changes.
- attribute duplication functionality
- config importing functionality
- attribute removal functionality
- possibility to define multi-attribute rules in attribute implication
- Project configuration file to follow PEP2.0.0 specification. Browse the specification for changes related to config format
- Do not require
sample_nameattribute in the sample table
[0.22.3] - 2019-12-13
utilsmodule; instead, refer to
- It's now exceptional (rather than just a warning) for a sample table file to be missing a valid name column.
- Empty columns in subsample tables are treated just as empty columns in sample tables (respective attributes are not included rather than populated with
[0.22.2] - 2019-06-20
[0.22.1] - 2019-06-19
- Prohibit storing reference to full
Projectobject on a
[0.22.0] -- (2019-06-06)
constantsin favor of
Projecttext representation for interactive/terminal display (
__repr__): Issue 296
- Properly use
constant_attributesif present from subproject. Issue 292
- Fixed a bug with subproject activation paths
- Revert deprecation of
sample_nameis again approved.
[0.21.0] -- (2019-05-02)
- Support for Snakemake projects (particularly
- Hook for
Projectto omit some pipeline options/arguments from the returned argument string
subsample_tablefunctions, providing a functional syntax for requesting the respective attribute values from a
- Hook on
merge_samplefor specifying name of subannotation column that stores name for each sample
- Improved messaging: "Unmatched regex-like", "Missing and/or empty attribute(s)"
sheetis deprecated in favor of
sample_subannotationis deprecated in favor of
Sample, reference to
sample_nameis deprecated in favor of simply
[0.20.0] -- (2019-04-17)
Projectgives the table of sample subannotation / "units" if applicable.
fetch_samplesfunction to enable more general applicability. Additionally, the attribute value matching is more strict now -- requires perfect match.
- Remove Python 3.4 support.
attmapfor implementation of attribute-style access into a key-value collection.
sample_subannotationin favor of
[0.19.0] -- (2019-01-16)
Projectconstruction no longer requires sample annotations sheet.
- Specification of assembly/ies in project config outside of
derived_columnsare deprecated in favor of
[0.18.2] -- (2018-07-23)
- Made requirements more lenient to allow for newer versions of required packages.
[0.18.1] -- (2018-06-29)
- Fixed a bug that would cause sample attributes to lose order.
- Fixed a bug that caused an install error with newer
- Project names are now inferred with the
infer_namefunction, which uses a priority lookup to infer the project name: First, the
nameattribute in the
yamlfile; otherwise, the containing folder unless it is
metadata, in which case, it's the parent of that folder.
get_subsamplefunctions to both
- Subsamples are now objects that can be retrieved individually by name, with the
subsample_nameas the index column header.
[0.17.2] -- (2018-04-03)
- Ensure data source path relativity is with respect to project config file's folder.
[0.17.1] -- (2017-12-21)
- Version bump for first pypi release
- Fixed bug with packaging for pypi release
[0.9.0] -- (2017-12-21)
- Separation completed,
peppypackage is now standalone
loopercan now rely on
- setup changed for compatibility with PyPI
[0.8.1] -- (2017-11-16)
- Separated from looper into its own python package (originally called
[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
[0.7.0] -- (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
- Allow wildcard protocol_mapping for catch-all pipeline assignment
- 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'
- Improve user messages
- Simplifies command-line help display
[0.6.0] -- (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.yamlfiles, 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
runcan 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.
setuptoolsfor installation, and
pandas 0.20.2. If
numexpris installed, version
- Allows tilde in
[0.5.0] -- (2017-03-01)
- Add new looper version tracking, with
-Voptions 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
[0.4.0] -- (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
pipelinesrepository 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