Changelog

This project adheres to Semantic Versioning and Keep a Changelog format.

[0.31.0] - 2020-10-07

Added

  • to_dict method in Sample class that can include or exclude Project reference

[0.30.3] - 2020-09-22

Changed

  • If there's just one subsample_table specified, Project.subsample_table property will return an object of pandas.DataFrame class rather than a list of ones

Fixed

  • TypeError when subsample_table is set to null

[0.30.2] - 2020-08-06

Added

  • Support for multiple subsample tables
  • License file to the package source distribution

[0.30.1] - 2020-05-26

Changed

  • Package authors list

[0.30.0] - 2020-05-26

This version introduced backwards-incompatible changes.

Added

  • attribute duplication functionality
  • config importing functionality
  • attribute removal functionality
  • possibility to define multi-attribute rules in attribute implication

Changed

  • Project configuration file to follow PEP2.0.0 specification. Browse the specification for changes related to config format
  • Do not require sample_name attribute in the sample table

[0.22.3] - 2019-12-13

Changed

  • Remove is_command_callable from utils module; instead, refer to ubiquerg.
  • It's now exceptional (rather than just a warning) for a sample table file to be missing a valid name column.

Fixed

  • Empty columns in subsample tables are treated just as empty columns in sample tables (respective attributes are not included rather than populated with nan)

[0.22.2] - 2019-06-20

Changed

  • Remove ngstk requirement.

[0.22.1] - 2019-06-19

Changed

  • Prohibit storing reference to full Project object on a Sample.

[0.22.0] -- (2019-06-06)

Changed

  • Deprecate Project constants in favor of constant_attributes.
  • Improved Project text representation for interactive/terminal display (__repr__): Issue 296

Fixed

  • Properly use constant_attributes if present from subproject. Issue 292
  • Fixed a bug with subproject activation paths
  • Revert deprecation of sample_name to name; so sample_name is again approved.

[0.21.0] -- (2019-05-02)

Added

  • Support for Snakemake projects (particularly SnakeProject)
  • Hook for get_arg_string on Project to omit some pipeline options/arguments from the returned argument string
  • sample_table and subsample_table functions, providing a functional syntax for requesting the respective attribute values from a Project
  • Hook on merge_sample for specifying name of subannotation column that stores name for each sample

Changed

  • Improved messaging: "Unmatched regex-like", "Missing and/or empty attribute(s)"
  • 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)

Added

  • subsample_table on a Project gives the table of sample subannotation / "units" if applicable.

Changed

  • 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)

New

  • Added activate_subproject method to Project.

Changed

  • 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)

Fixed

  • Made requirements more lenient to allow for newer versions of required packages.

[0.18.1] -- (2018-06-29)

Fixed

  • Fixed a bug that would cause sample attributes to lose order.
  • Fixed a bug that caused an install error with newer numexpr versions.

New

  • 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)

Fixed

  • Ensure data source path relativity is with respect to project config file's folder.

[0.17.1] -- (2017-12-21)

Changed

  • Version bump for first pypi release
  • Fixed bug with packaging for pypi release

[0.9.0] -- (2017-12-21)

New

  • Separation completed, peppy package is now standalone
  • looper can now rely on peppy

Changed

  • merge_table renamed to sample_subannotation
  • setup changed for compatibility with PyPI

[0.8.1] -- (2017-11-16)

New

  • Separated from looper into its own python package (originally called pep)

[0.7.2] -- (2017-11-16)

Fixed

  • Correctly count successful command submissions when not using --dry-run.

[0.7.1] -- (2017-11-15)

Fixed

  • 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)

New

  • 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

Changed

  • 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)

New

  • 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

  • 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)

New

  • 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
  • Colorize output
  • Complete rehaul of logging and test infrastructure, using logging and pytest packages

Changed

  • 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

  • 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.

Changed

  • 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