Changelog

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

[0.13.0] -- 2026-07-01

• Migrated from peppy to peprs across all modules (project, sample, view, models, utils)
• Updated subsample key constant: SUBSAMPLE_RAW_LIST_KEY → SUBSAMPLE_RAW_DICT_KEY
• Added alembic database migration support; run_migrations parameter added to PEPDatabaseAgent and BaseEngine
• Fixed nullable fields in schema models (SchemaVersionAnnotation, SchemaRecordAnnotation, UpdateSchemaRecordFields, UpdateSchemaVersionFields)
• Added support for "latest" schema version resolution when uploading/updating projects
• Moved SAMPLE_NAME_ATTR and SAMPLE_TABLE_INDEX_KEY constants into pepdbagent/const.py
• Performed code cleanup and refactoring across modules, including modernization of the codestyle, installation and dependencies.
• ❗get_raw method (returning raw project) now returns keys: {config, samples, subsamples} instead of {config, sample_list, subsample_list}

[0.12.4] -- 2026-01-26

• Added project search by tag in annotation module
• Updated github actions workflows

[0.12.3] -- 2025-04-03

• Fixed models for schema records and versions

[0.12.2] -- 2025-03-27

• Fixed links between schema and project

[0.12.1] -- 2025-03-27

• Added alembic to the project
• Fixed errors in methods getting user stars

[0.12.0] -- 2025-03-27

• New database model for schemas
• Added schema version and schema record
• Added tags to schemas

[0.11.1] -- 2024-09-04

• Added archive table of namespaces
• Added sort by stars

[0.11.0] -- 2024-07-24

• Added validation schemas

[0.10.0] -- 2024-07-18

• Added user delete method
• Added project history and restoring projects

[0.9.0] -- 2024-06-25

• Introduced new sample ordering with linked list #133
• Efficiency improvements of project update function
• Test restructuring

[0.8.0] -- 2024-02-26

• Fixed forking schema
• Improved forking efficiency #129
• Added uploading project from dict
• Added get_config, get_samples, get_subsamples methods to project module #128
• Fixed error handling in views API #130
• Added no_fail to views API

[0.7.3] -- 2024-02-08

• Fixed POP update
• Improved error handling in views API
• Added stats method to Namespace module
• Updated docs
• Added coverage

[0.7.2] -- 2024-02-02

• Fixed Unique Constraint in the Views
• Fixed update project pop method
• Fixed bug in duplicating samples

[0.7.1] -- 2024-01-22

• Fixed bug in Stars annotation
• SQL efficiency improvements
• Added sort by date in stared projects

[0.7.0] -- 2024-01-17

• Added pop to project table and annotation model #107
• Added forked_from feature #73
• Switched to pydantic2 #105
• Updated requirements (psycopg2 -> psycopg3) #102
• Added sample module that contains functionality for updating, adding, and deleting samples in the project separately #111
• Added user and favorite tables with functionality #104
• Updated the sample update method when updating the whole project. Following this change, samples are updated without changing the ID in the database

[0.6.0] -- 2023-08-24

• Added date filter to project annotation

[0.5.5] -- 2023-07-19

• Updated requirements

[0.5.4] -- 2023-07-14

• Added namespaces info method that returns list of namespaces with

[0.5.3] -- 2023-07-13

• Fixed bugs in updating dates and descriptions

[0.5.2] -- 2023-07-13

• Fixed error in updating date in overwriting function

[0.5.1] -- 2023-07-10

• Fixed errors in updating projects, that caused Unique Constraint violation error

[0.5.0] -- 2023-07-07

• Introduced a new database schema (3 tables: projects, samples, subsamples)
• Added new tests
• Fixed the issue of sqlalchemy session already being closed

[0.4.3] -- 2023-06-30

• Changed the orientation of the raw project dictionary to "records" and updated peppy version to 0.35.6.
• Added description column
• Added sql description search
• Deleted unused files

[0.4.2] -- 2023-06-27

• Added validation of question mark in name and tag
• Fixed description and name in config file
• Fixed preserving order of columns in database

[0.4.1] -- 2023-06-09

• Fixed project.update function

[0.4.0] -- 2023-06-09

• Transitioned to SQLAlchemy ORM.
• Added a pep_schema column to the database.
• Implemented a new testing approach.
• Integrated sorting functionality into the annotations module.
• Temporarily disabled description-based searches to mitigate long processing times and reduce database load.
• Included timezone support in the database.
• Standardized namespace and names to lowercase for case-insensitivity.
• Streamlined the database schema creation process, with tables now created dynamically as needed.

[0.3.1] -- 2023-03-23

• Fixed bug with peppy const dependencies

[0.3.0] -- 2023-01-19

• Restructured pepdbagent:
  • Renamed Agent class to PEPDatabaseAgent
  • created subclasses (project, annotation, namespace).
  • Merged methods that have similar use case.
  • Removed unused methods.
  • Simplified pepdbagent API
• Restructured database (added columns: private, number_of_samples, submission_date, last_update_date)
• Improved logging
• Added new tests
• Improved documentation

[0.2.3] -- 2022-11-21

• Added more logging information in uploading project methods
• Added update_only argument upload_project method

[0.2.2] -- 2022-11-09

• Fixed error in pepannotation (privacy error)

[0.2.1] -- 2022-11-09

• Fixed error with namespace user if user is unknown

[0.2.0] -- 2022-11-08

• Added limits and offset to function: get_projects_in_namespace()

• Annotation changed to BaseModel from pydantic

• Added privacy information in annotations

• Added update feature to upload_project method with overwrite argument

• Added mock tests

• Deleted unused functions:

  • get_projects_in_list
  • get_projects_annotation_by_namespace
  • project_status
  • project_status_by_registry
  • get_registry_paths_by_digest

• Changed method names:

  • get_project_by_registry --> get_project_by_registry_path
  • get_project_annotation_by_registry --> get_project_annotation_by_registry_path

[0.1.0] -- 2022-08-18

• 🎉 first release!