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Changelog

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

[0.40.0] -- 2023-12-18

This version introduced backwards-incompatible changes.

Changed

  • Replaced attmap with MutableMapping (which removes some attributes)
  • Replaced OrderedDict with dict
  • Deprecated support for Python versions <= 3.7

Due to the changes mentioned above, a few functionalities may be disabled. For example, the name and description project properties can no longer be accessed with getitem; use the getattr syntax instead

Added

  • Constructor methods: Project.from_dict, Project.from_pandas, Project.from_sample_yaml, Project.from_pep_config

[0.35.7] -- 2023-07-19

Fixed

  • incorrect setting of sample and subsample indexes using from_dict function (#452)
  • clarified debug messages

[0.35.6] -- 2023-06-27

Added

  • orient argument to to_dict method

Fixed

  • The name of the raw subsample object to match the actual name (list). Commit: #442

Changed

  • Reduced the number of items returned in the to_dict(extended=True) method to 3, with the name and description now stored in the config key.

[0.35.5] -- 2023-03-27

Fixed

  • A bug with custom sample ids
  • Improved performance for large tables dramatically

[0.35.4] -- 2023-01-17

Fixed

  • Fixed disabling rich progress on small datasets bug
  • Disabled progressbar if object variable progressbar is set False

[0.35.3] -- 2022-11-16

Fixed

  • Returning NaN value in initialization project from pandas df

[0.35.2] -- 2022-09-13

Fixed

  • Returning NaN value within to_dict method was fixed and method now returns None instead

[0.35.1] -- 2022-09-07

Changed

  • Organization of test files. Separated unittests from smoketests.

Fixed

  • The root cause of np.nan values showing up in Pandas dataframes. Replaced the values with None right after reading the database, which made it possible to remove all custom np.nan to None converters used later in the code.
  • Typing in some methods.
  • Code redundancy in fixtures in conftest.

Added

  • New test cases with test data

[0.35.0] -- 2022-08-25

Changed

  • Optimized converting Projects to and from dict. Now, to_dict(extended=True) returns only essential properties to save space and time.
  • Small refactors.

Fixed

  • Initialization of peppy.Project from pandas.DataFrame. Now from_pandas() can receive sample table, subsample table and config file
  • Multiple bugs introduced during initialization of the project with custom index column names

Added

  • New test cases and test data

[0.34.0] -- 2022-08-17

Changed

  • Way of initialization project from dictionary. Now it's possible as follows: Project().from_dict()

Fixed

  • Fix error that was raised when duplicated sample in sample_table had different read types (single-end mixed with paired-end).

Added

  • Feature of initializing peppy.Project from pandas.DataFrame

[0.33.0] -- 2022-07-25

Changed

  • pep_version is no longer a required parameter to create a peppy.Project instance from a configuration file.

Fixed

  • Performance issues during sample parsing. Two list comprehensions were combined to speed up this functionality.
  • KeyError is thrown when attempting to access the pep_version of a peppy.Project instance instatiated from a sample table (csv)

Added

  • Implementation of __eq__ for the peppy.Project class such that two instances of the class can be compared using python's equality operators (==, !=).
  • New from_dict function that lets a user instatiate a new peppy.Project object using an in-memory representation of a PEP (a dict). This supports database storage of PEPs.
  • New extended flag for the to_dict method on peppy.Project objects. This creates a richer dictionary representation of PEPs.
  • Better sample parsing

[0.32.0] -- 2022-05-03

Changed

  • Unify exceptions related to remote YAML file reading in read_yaml function. Now always a RemoteYAMLError is thrown.
  • Project dict representation

Added

  • Support for PEP 2.1.0, whichi includes support for no YAML configuration file component (CSV only), automatic sample merging if there are any duplicates in sample table index column, and new project attributes: sample_table_index and subsample_table_index.

Fixed

[0.31.2] -- 2021-11-04

Fixed

  • Bug with setuptools 58

[0.31.1] -- 2021-04-15

Added

  • Support for remote URL config files

Fixed

  • Error when accessing Project.subsample_table property when no subsample tables were defined

[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