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Changelog

All notable changes to this project will be documented in this file.

The format is based on Keep a Changelog, and this project adheres to Semantic Versioning.

[v2_2_7] - todo

Added functionality for processing a subset of samples with a subset of components

Changed

  • bifrost_run_launcher/pipeline.py - added code for processing subset of samples/components
  • bifrost_run_launcher/launcher.py - added two more variables to parser
  • tests/test_simple.py - added variables in test_args

[v2_2_5] - 2021-06-09

Changed the way read files are found, from files matching a regex to filenames in the run_metadata.tsv file.

Changed

  • bifrost_run_launcher/pipeline.py

[v2_2_4] - 2021-04-09

Added pip install requirements.txt in prod environment

Changed

  • Dockerfile

[v2_2_3] - 2021-02-17

Updates to bifrostlib to fix datetime bug

Changed

  • setup.cfg

[v2_2_2] - 2021-01-11

Updates to bifrostlib to make it work with the tests and update to the tests so that they work with CI/CD which lacks access to bifrost/test_data

Changed

  • setup.cfg
  • .github/workflows/run_test.yml

[v2_2_1] - 2020-12-14

Notes

Development has adjusted from dev/prod on github to test/prod. Test for testing and prod for live code. Dev is now local and utilizes the whole bifrost folder structure while test/prod only utilizes the submodule structure. Currently tests have not been updated to reflect this change.

Added

For added version bump and test init

  • setup.cfg

Changed

  • tests moved from /bifrost_run_launcher/ to /tests
  • doc structure added but not set up

Adjusted format of docker to work in context to root folder of project for local development /bifrost/ and to the submodule to prod. New environment test also is created for testing prod ready code on github actions with CI.

  • Dockerfile
  • docker_build_and_push_to_dockerhub.yml
  • test_standard_workflow.yml Requirements are now for pytest and environmental values, actual required python libraries are included in setup.py and required programs in the Dockerfile
  • requirements.txt
  • setup.py Adjust code to reflect new bifrostlib==2.1.0 which has a new data structure and schema for the objects
  • main.py
  • config.yaml
  • launcher.py
  • test_1_standard_workflow.py

Removed

Development is now local and the dockerfile for compose on the root /bifrost/ folder instead of at each submodule

  • docker-compose.dev.yaml
  • docker-compose.yaml Now unnecessary as requirements merged with setup.py
  • requirements.dev.txt
  • .env

[2.2.0] - 2020-10-07 (Unreleased)

Added

  • CHANGELOG.md into repo

Changed

  • Templated files to be common for SSI maintained pipelines. All files use .env and <COMPONENT_NAME>/config.yaml as the source of all information. The config.yaml should be considered the primary source of all information regarding the component and it's settings. The .env file needs to contain the <COMPONENT_NAME> and install specific settings (currently just mongo_db connection).
    • docker-compose.dev.yaml
    • docker-compose.yaml
    • .env
      • This is being used for both Dockerfile and passing the values into the Docker image, not sure if that has any issues.
    • setup.py
      • This can't use libraries to extract config values, so right now it's hardcoded on what to look for. This can cause some potential issues.
  • The following files are also impacted by the changes
    • Dockerfile

Removed

  • Docker-compose files no longer point to a custom env file