v2.0.0a2

[2.0.0a2] -- 2024-09-30

This release breaks backwards compatibility for Looper versions < 2.0.0

Fixed

• divvy init #520
• replaced deprecated PEPHubClient function, _load_raw_pep with .load_raw_pep
• looper cli parameters now take priority as originally intended #518
• fix divvy inspect
• remove printed dictionary at looper finish #511

Changed

• --looper-config is now --config, -c. #455
• A pipeline interface now consolidates a sample_interface and a project_interface #493
• Updated documentation for Looper 2.0.0, removing previous versions pepspec PR #34
• remove position based argument for divvy config, must use --config or run as default config

Added

• looper init tutorial #466
• looper config allows for pephub_path in pipestat config section of .looper.yaml #519
• improve error messaging for bad/malformed looper configurations #515
• add shortform argument for --package (alias is now -p)

v1.9.1 release

[1.9.1] -- 2024-07-18

Changed

• ensure peppy requirement peppy>=0.40.0,<=0.40.2

v2.0.0a1

v2.0.0a1 pre-release

v1.9.0

[1.9.0] -- 2024-06-26

Added

• user can now add cli modifiers to looper config instead of PEP project #270
• pipeline interfaces no longer must be nested under sample and project keys within looper config file #465
• var_templates can now be hierarchical #334
• looper can now gracefully halt spawned subprocesses when the user sends a keyboard interrupt #37

v1.8.1

[1.8.1] -- 2024-06-06

Fixed

• added -v and --version to the CLI
• fixed running project level with --project argument

[1.8.0] -- 2024-06-04

Added

• looper destroy now destroys individual results when pipestat is configured: #469
• comprehensive smoketests: #464
• allow rerun to work on both failed or waiting flags: #463

Changed

• Migrated argparse CLI definition to a pydantic basis for all commands. See: #438
• during project load, check if PEP file path is a file first, then check if it is a registry path: #456
• Looper now uses FutureYamlConfigManager due to the yacman refactor v0.9.3: #452

Fixed

• inferring project name when loading PEP from csv: #484
• fix inconsistency resolving pipeline interface paths if multiple paths are supplied: #474
• fix bug with checking for completed flags: #470
• fix looper destroy not properly destroying all related files: #468
• looper rerun now only runs failed jobs as intended: #467
• looper inspect now inspects the looper config: #462
• Load PEP from CSV: #456
• looper now works with sample_table_index #458

v1.8.0a1

pre-release 1.8.0a1

v1.7.1

[1.7.1] -- 2024-05-28

Fixed

• pin pipestat version to be between pipestat>=0.8.0,<0.9.0 #494

v1.7.0

[1.7.0] -- 2024-01-26

Added

• --portable flag to looper report to create a portable version of the html report
• --lump-j allows grouping samples into a defined number of jobs

Changed

• --lumpn is now --lump-n
• --lump is now --lump-s

v1.7.0a1

v1.7.0a1

v1.6.0

Looper v1.6.0 - Major Release

[1.6.0] -- 2023-12-22

Added

• looper link creates symlinks for results grouped by record_identifier. It requires pipestat to be configured. #72
• basic tab completion.

Changed

• looper now works with pipestat v0.6.0 and greater.
• looper table, check now use pipestat and therefore require pipestat configuration. #390
• changed how looper configures pipestat #411
• initializing pipeline interface also writes an example output_schema.yaml and count_lines.sh pipeline

Fixed

• filtering via attributes that are integers.