# Changelog

This project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html) and [Keep a Changelog](https://keepachangelog.com/en/1.0.0/) 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](https://github.com/pepkit/pipestat/issues/206)
- Fix [#212](https://github.com/pepkit/pipestat/issues/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](https://github.com/pepkit/pipestat/issues/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](https://github.com/pepkit/pipestat/issues/210)
- fix spaces in html files [#211](https://github.com/pepkit/pipestat/issues/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](https://github.com/pepkit/pipestat/issues/204)
- pipeline_name not setting correctly [#207](https://github.com/pepkit/pipestat/issues/207)
- bug with objects populating html report

## [0.10.2] - 2024-08-26
### Fixed
- add obtaining pephub_path from config file, [#202](https://github.com/pepkit/pipestat/issues/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](https://github.com/pepkit/pipestat/issues/189)
- fix pipestat summarize bugs re: inaccurate paths [#190](https://github.com/pepkit/pipestat/issues/190)
- add support for sqlite dbbackend [#192](https://github.com/pepkit/pipestat/issues/192)

## Added
- pephub backend [#125](https://github.com/pepkit/pipestat/issues/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](https://github.com/pepkit/looper/issues/471)
- Reduce overall verbosity when creating backends

## [0.9.1] - 2024-04-24
### Fixed
- Pipestat summarize html report columns now show stats only  [#148](https://github.com/pepkit/pipestat/issues/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](https://github.com/pepkit/pipestat/issues/150). 
- Add more complex schema during dependency check to mitigate false test failures regarding different output schemas [#181](https://github.com/pepkit/pipestat/issues/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](https://github.com/pepkit/pipestat/issues/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_time` now live under the `meta` 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](https://github.com/pepkit/pipestat/issues/159)

## [0.8.1] - 2024-02-07
### Changed
- Readme to reflect docker db configuration for testing. [#145](https://github.com/pepkit/pipestat/issues/145)
- Added dependency warning when attempting to run pytest suite without optional dependencies. [#146](https://github.com/pepkit/pipestat/issues/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](https://github.com/pepkit/pipestat/issues/149)
- Fix minor html report title bugs [#151](https://github.com/pepkit/pipestat/issues/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](https://github.com/pepkit/pipestat/issues/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](https://github.com/pepkit/pipestat/issues/1)

## [0.0.2] - 2021-02-22

### Added

- initial package release