On Project, sheet is deprecated in favor of sample_table.
On Project, sample_subannotation is deprecated in favor of subsample_table.
On Sample, reference to sample_name is deprecated in favor of simply name.
[0.20.0] -- (2019-04-17)
subsample_table on a Project gives the table of sample subannotation / "units" if applicable.
Add attribute parameter to fetch_samples function to enable more general applicability.
Additionally, the attribute value matching is more strict now -- requires perfect match.
Remove Python 3.4 support.
Use attmap for implementation of attribute-style access into a key-value collection.
Deprecate sample_annotation and sample_subannotation in favor of sample_table and subsample_table, respectively.
[0.19.0] -- (2019-01-16)
Added activate_subproject method to Project.
Project construction no longer requires sample annotations sheet.
Specification of assembly/ies in project config outside of implied_attributes is deprecated.
implied_columns and derived_columns are deprecated in favor of implied_attributes and derived_attributes.
[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 numexpr versions.
Project names are now inferred with the infer_name function, which uses a priority lookup to infer the project name: First, the name attribute in the yaml file; otherwise, the containing folder unless it is metadata, in which case, it's the parent of that folder.
Add get_sample and get_samples functions to Project objects.
Add get_subsamplesand get_subsample functions to both Project and Sample objects.
Subsamples are now objects that can be retrieved individually by name, with the subsample_name as 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, peppy package is now standalone
looper can now rely on peppy
merge_table renamed to sample_subannotation
setup changed for compatibility with PyPI
[0.8.1] -- (2017-11-16)
Separated from looper into its own python package (originally called pep)
[0.7.2] -- (2017-11-16)
Correctly count successful command submissions when not using --dry-run.
[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 pipeline_args section.
[0.7.0] -- (2017-11-15)
Add --lump and --lumpn options
Catch submission errors from cluster resource managers
Implied columns can now be derived
Now protocols can be specified on the command-line --include-protocols
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.yaml files, increasing flexibility, so this relaxes the specified folder structure that was previously used for pipelines_dir (with config subfolder).
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 pipelines_dir to pipeline_interfaces (but maintained backwards compatibility for now).
Changed name of run column to toggle, since 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.
Require setuptools for installation, and pandas 0.20.2. If numexpr is installed, version 2.6.2 is required.
Allows tilde in pipeline_interfaces
[0.5.0] -- (2017-03-01)
Add new looper version tracking, with --version and -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
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 all_input_files and required_input_files attributes
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 summarizePipelineStats.R script
New subcommand (looper check) replacing the flagCheck.sh script
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
From here you can search these documents. Enter
your search terms below.