Changelog

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

[0.13.1] - 2026-03-05

Changed

• Fixed import-time logging that overrode root logger configuration

[0.13.0] - 2026-02-25

Changed

• Renamed PipestatBoss to PipestatDualManager with .sample/.project attributes (replaces .samplemanager/.projectmanager)
• Removed MutableMapping inheritance from PipestatManager; fixed __len__ and __iter__ semantics to operate on records
• Added __contains__ method for record_identifier in psm checks
• Added classmethod constructors: from_file_backend(), from_db_backend(), from_pephub_backend(), from_config()
• Added validate_results and additional_properties options (replaces lenient mode)
• Added support for shared schema keys across sample and project levels
• Reframed as general-purpose pipeline results manager (updated keywords, classifiers, README)
• Migrated to yacman v1 API (YAMLConfigManager, write_lock context managers)
• Bumped yacman requirement to >=0.9.5
• Converted docstrings to Google style, added type hints
• PEPhub tests now gated by --pephub flag instead of hard skip
• Broke up monolithic test file into modular test files

[0.12.2] - 2025-09-25

Fixed

• Fix setting with copy warning for pephub backend #206
• Fix #212

[0.12.1] - 2025-02-10

Fixed

• fix checking for records during summarize failing because aggregate_results file had not yet been resolved #215

[0.12.0] - 2025-01-16

Fixed

• portable report now has proper file extension in messaging.
• add exception to pipestat summarize if there are no results to report #210
• fix spaces in html files #211
• add output_dir parameter to psm.table

[0.11.0] - 2024-10-02

Fixed

• for output schema, make samples an array type and nest under items #204
• pipeline_name not setting correctly #207
• bug with objects populating html report

[0.10.2] - 2024-08-26

Fixed

• add obtaining pephub_path from config file, #202

[0.10.1] - 2024-08-06

Fixed

• add pipestat summarize and link for pephub backend

[0.10.0] - 2024-07-18

Fixed

• allow for bool or boolean in schema #189
• fix pipestat summarize bugs re: inaccurate paths #190
• add support for sqlite dbbackend #192

Added

• pephub backend #125

[0.9.3] - 2024-06-06

Fixed

• fixed regression with summarizing or creating a table via aggregate_results.yaml and "{record_identifier}" in the results file path
• fix creating object summary when object is an array/list

[0.9.2] - 2024-06-03

Changed

• User can override pipeline name via parameter or config file, otherwise look at output_schema, then fall back on default as last resort.
• Allow pipestat to proceed without creating a results file backend IF using "{record_identifier}" in the file path, helps address Looper #471
• Reduce overall verbosity when creating backends

[0.9.1] - 2024-04-24

Fixed

• Pipestat summarize html report columns now show stats only #148.
• When creating HTML reports from both sample and project level results (multi results), only sample-level results show in the main index table #150.
• Add more complex schema during dependency check to mitigate false test failures regarding different output schemas #181.

[0.9.0] - 2024-04-19

Fixed

• Bug with rm_record for filebackend
• Bug when using record_identifier via env variable and the CLI

Added

• Added results history and history retrieval for both file and db backends via retrieve_history #177.
• Added remove_record to Pipestat manager object (it is no longer only on backend classes)
• Added meta key to each record for the file backend
• db backend will now create an additional sql history table
• Reporting history is toggleable

Changed

• Removing the last result no longer removes the entire record.
• pipestat_created_time, and pipestat_modified_timenow live under themeta` key.
• history lives under the meta key for the filebackend.

[0.8.2] - 2024-02-22

Changed

• Changed yacman requirement and using FutureYamlConfigManager.

Fixed

• Issue with retrieving similar record_identifiers, #159

[0.8.1] - 2024-02-07

Changed

• Readme to reflect docker db configuration for testing. #145
• Added dependency warning when attempting to run pytest suite without optional dependencies. #146
• Remove most docs in favor of new docs location: https://pep.databio.org/pipestat/

Fixed

• Ensure log files are gathered for portable reports, #149
• Fix minor html report title bugs #151

[0.8.0] - 2024-01-25

Added

• added portable flag to pipestat summarize to create a shareable version of the html report.
• added setting index: True within output schema to index specific results for DB backend.

Fixed

• pipestat summarize: objects drop down now only shows sample-level

[0.7.0] - 2024-01-17

Added

• __iter__ now takes limit and cursor arguments to create an iterator from select_records

Changed

• updated pydantic requirement to be >= 2.5.3

Fixed

• Get summary files: Objects YAML button now works.

[0.6.0] - 2023-12-22

Added

• select_records, which allows for a single API for selecting attributes (result_identifiers) given filter_conditions and/or columns
• retrieve_one, and retrieve_many which allows for selecting one or multiple records given record_identifier
• pipestat reader submodule to read DB results via FastAPI endpoints: pipestat serve --config "config.yaml"
• ability to create SamplePipestatManager and ProjectSamplePipestatManager which are sample/project specific PipestatManager objects.
• PipestatBoss wrapper class which holds SamplePipestatManager and ProjectSamplePipestatManager classes.
• to_dict methods to parsed schema object.
• select_distinct function which retrieves unique results for a list of attributes.
• pipestat link which creates a directory of symlinks for reported results.
• list_recent_results which allows for retrieving records filtered via a start and end time.
• reporting and retrieving results via item access,e.g. psm["sample1", "name_of_something"] = "name_of_something_string" or result = psm["sample1"]
• pipestat now supports one results file per sample by using {record_identifier} in the results_file_path.

Fixed

• path expansion when creating database url.
• added jinja2 requirement.
• pipeline_name column not populating in postgres db backend.
• pipestat will now create subdirectories during results_file creation.
• fixed bugs and polished both report generation and stats table generation per https://github.com/pepkit/pipestat/pull/131

Changed

• Removed retrieve, get_one_record, get_records function.
• Removed get_orm and replace with get_model.
• Removed get_table_name function.
• Refactor:
  • sample_name -> record_identifier.
  • pipeline_type has been removed from most functions.
• added optional dependencies for the database backend and pipestat reader, e.g. pip install pipestat[dbbackend].

[0.5.2] - 2023-11-30

Fixed

• add jinja2 to requirements doc.

[0.5.1] - 2023-08-14

Fixed

• fix schema_path issue when building html reports and obtaining schema from config file.

[0.5.0] - 2023-08-08

Added

• Add summarize function to generate static html results report.

[0.4.1] - 2023-07-26

Fix

• ensure Pipestat uses proper versions of Pydantic, Yacman.

[0.4.0] - 2023-06-29

Changed

• Remove attmap dependency
• Migrate to SQLModel for Object–relational mapping (ORM)
• Renamed list_existing_results to list_results and allow for returning a subset of results.
• Refactor:
  • namespace -> project_name,
  • pipeline_id -> pipeline_name,
  • record_identifier -> sample_name

Added

• Add 'init -g' for creating generic configuration file.
• Add ability to pass function to format reported results.

[0.3.1] - 2022-08-18

Fix

• database connection error

[0.3.0] - 2021-10-30

Added

• select_distinct for select distinct values from given table and column(s)

[0.2.0] - 2021-10-25

Added

• optional parameter for specify returning columns with select_txt

[0.1.0] - 2021-06-24

This update introduces some backwards-incompatible changes due to database interface redesign

Changed

• database interface type from a driver to an Object–relational mapping (ORM) approach

Added

• results highlighting support
• database column parametrizing from the results schema
• static typing
• possibility to initialize the PipestatManager object (or use the pipestat status CLI) with no results schema defined for pipeline status management even when backed by a database; Issue #1

[0.0.4] - 2021-04-02

Added

• config validation
• typing in code

[0.0.3] - 2021-03-12

Added

• possibility to initialize the PipestatManager object (or use the pipestat status CLI) with no results schema defined for pipeline status management; Issue #1

[0.0.2] - 2021-02-22

Added

• initial package release