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CHANGELOG.md

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Change Log

All notable changes to this project will be documented in this file. This project adheres to Semantic Versioning.

[4.7.1] - 2024-06-05

Fixed

  • Added cryptography module among the dependencies

[4.7] - 2024-05-22

Added

  • github actions to publish the repo to PyPI and publish mkdocs on new release event

Changed

  • Replace ruamel.yaml with pyyaml lib
  • Updated GitHub actions
  • Replaced alchy lib with sqlservice
  • Unfreeze SQLAlchemy

Fixed

  • Add missing brew path to GitHub action. It has been removed from PATH variable in Ubuntu
  • Badges on README page

[4.6.1] - 2021-07-08

Fixed

  • Freeze SQLAlchemy to a version <1.4 to avoid report creation crashing
  • Fix links to documentation pages

[4.6] - 2020-11-20

Added

  • docker-compose and Makefile
  • adds link to publication

[4.5.0] - 2020-11-12

Added

  • Dockerfile
  • Added the Docker image build and push triggered by new releases
  • Added github action running pytest and coveralls
  • Software deployment instructions

[4.4.0] - 2020-02-12

Added

  • User can pass on file with row separated gene IDs for coverage calculation

[4.3.0] - 2020-02-05

Added

  • added CLI commands

[4.0.0] - 2016-08-02

Version 4 slims down Chanjo quite a bit.

Added

  • Lots of test, now 100% test coverage!
  • Cascade rules to make sure stats records get deleted with parent sample

Changed

  • Switched from Read the Docs to GitBook for documentation
  • Updated demo

Removed

  • Old database schema with explicit exon/gene records

[3.4.1] - 2016-03-08

Changed

  • setup and tear down session in Flask app usage

[3.4.0] - 2016-03-08

Added

  • All new transcript focused schema, generally activated by --transcript flag in CLI, this significantly reduces the database footprint and speeds up loading to only a few seconds for a full exome

[3.3.1] - 2016-02-23

Fixed

  • properly report if a CLI subcommand is not found
  • properly output results from "calculate region"
  • show error message for unknown region ids
  • fix sqlite issue when adding both exon_obj and exon_id

Changed

  • make schema more strict about which columns need to exist

[3.3.0] - 2016-02-15

Changed

  • add indexes to models, especially to exon_stat.metric to speed up queries
  • speed up loading by front-loading existing exons (~7 min)
  • update resources bundled in the bootstrap command, now includes database with exons + slicing sites

Fixed

  • travis-ci setup for testing

[3.2.1] - 2016-01-28

Changed

  • do a rollback of failed transactions on "save"

Added

  • show progress of load command on "info" level

[3.2.0] - 2015-12-22

Changed

  • diagnostic yield function now accepts "exon_ids" explicitly and requires "sample_id" to be given

[3.1.1] - 2015-11-19

Fixed

  • fixed bug in SQL relationship between gene and transcript

[3.1.0] - 2015-11-16

Added

  • sex subcommand for guessing sex from BAM alignment, see #158

[3.0.2] - 2015-11-04

Fixed

  • chanjo API: restrict converter queries to distinct/unique rows

[3.0.1] - 2015-10-26

Fixed

  • import from root init, use root logger

[3.0.0] - 2015-10-19

Code name: "Radical Red Panda"

This is a major new release. Please refer to the documentation for more details on what has been updated.

Added

  • Add functionality to run sambamba from chanjo
  • Add calulate command to get basic statistics from database
  • Add link command to specifically link genomic elements
  • Add db command to interface and perform maintainance on database

Removed

  • Support for older versions of Chanjo

Fixed

  • Changed way of logging
  • Added proper logstream handler

[2.3.2] - 2015-03-21

Fixed

  • Refactor EntryPointsCLI to allow for external subcommands
  • Updated documentation to reflect Chanjo 2.x CLI

[2.3.1] - 2015-03-05

Changed

  • use custom "multi command class" to load dynamic entry point plugins

Fixed

  • some pylint improvements

[2.3.0]

Added

  • New logging module accessible from the command line (-vvv)
  • Add SQL schema drawing to "Code walkthrough"

[2.2.1]

Fixed

  • Fix incorrectly references ID field in join statement (block_stats)

[2.2.0]

Added

  • Read sample ID from BAM header
  • Validate BED format in "annotate"
  • Enable getting config values from "chanjo.toml" (chanjo config annotate.cutoff)

Fixed

  • Fix issue with hardlinks in Vagrant shared folders (setup.py)
  • Change Travis CI setup using official guidelines
  • Fix typography in docs
  • Use io.open instead of codecs.open
  • Use .sqlite3 extension for SQLite databases
  • Better error message when overwriting existing databases

[2.1.3]

Fixed

  • Fix misstake in "import" subcommand so it's finally working!

[2.1.2]

Fixed

  • Fix bug in "import" where the program didn't flush the session before committing.
  • Change "build_interval_data" to only create model without adding to the session.
  • Use "scoped_session" with "sessionmaker".
  • Flush session before each commit call in chanjo.Store.save()

[2.1.1]

Fixed

  • Fix interval assertion that didn't allow intervals to start and end on the same chromosomal position.

[2.1.0]

Added

  • Add lazy loading of chanjo.Store` through new chanjo.Store.connect` method
  • Much improved documentation of changes between releases

Fixed

  • Fix case where "demo" subcommand fails (``package` not set)

[2.0.2]

Fixed

  • Rename misspelled method (non-breaking): chanjo.Store.tare_down` to chanjo.Store.tear_down`

Fixed

  • Fix some CSS selectors in theme
  • Reorder API references in API docs

[2.0.1]

Fixed

  • Fixes broken symlinked demo/fixture files
  • Adds validation to check that stdin isn't empty
  • Fixes link to logo on front page
  • Adds John Kern as collaborator
  • Adds link to Master's Thesis paper for reference in README
  • Adds more FAQ

[2.0.0]

Code name: "Wistful Weasel"

Being a major release, expect previous scripts written for Chanjo 1.x to be incompatible with Chanjo 2.x.

Added

  • New built-in "demo" subcommand in the CLI

  • New public setuptools entry point for Chanjo plugins (CLI subcommands)

  • New of cial public Python API (stable until 3.x release). Read more in the new API documentation.

  • New "sex-checker" bonus command to guess gender from BAM alignment.

  • Command line interface updates

    • --out option removed across CLI. Use >| to redirect STDOUT instead.
    • --prepend` is now known as --prefix``
    • --db and --dialect must be supplied directly after "chanjo" on the command line (not after the subcommand). Like: chanjo --db ./coverage.sqlite import annotations.bed.
    • --extend-by is now --extendby

  • Config file format has changed from JSON to TOML. It's a more readable format (think INI) that also supports comments!

  • Improves BED-format compliance. Chanjo will now expect the "score" field to be in position 5 (and strand in position 6). The Chanjo specific fields start from position 7.

  • Major internal code restructuring. Essentially everything is built as plugins/self-contained components. Since no official Python API existed pre Chanjo 2, I won't go into any details here.

  • Improves documentation.

  • Last but not least, Chanjo will now code name releases according to animals in the Musteloidea superfamily :)

  • Introduces a new compat module to better support Python 2+3.

  • Trades command line framework from "docopt" to "click" to build more flexible nested commands.

  • Adds a first hand BaseInterval object to unify handling of intervals inside Chanjo.

  • BamFile no-longer requires numpy as a hard dependency. You still likely want to keep it though for performance reasons.

[1.0.0]

Code name: "Rebel Raccoon"

First and current stable version of Chanjo.

[0.6.0]

Added

  • BREAKING: changes group_id field to string instead of int.
  • Exposes the threshold option to the CLI for optimizing BAM-file reading with SAMTools, fixes #58

[0.5.0]

Fixed

  • UPDATE: Small updates to the command line interface
  • UPDATE: New tests for new functions

Added

  • NEW: MySQL support added
  • CHANGE: A lot of internal restructuring from classes to functions
  • IMPROV ENT: New structure seems to significantly improve speed Documentation
  • UPDATE: New documentation covering new features/structure

[0.4.0]

  • NEW: Table with Sample meta-data
  • UPDATE: CLI creates sample entries
  • UPDATE: SQL structure in docs
  • UPDATE: Updated tests
  • UPDATE: included test data (MANIFEST.in) - more on this later...

[0.3.0]

  • NEW: API - annotate: splice sites option
  • NEW: CLI - annotate: splice sites option
  • UPDATE: Much improved documentation
  • UPDATE: Modern setuptools only installation
  • UPDATE: New cleaner banner
  • NEW: travis integration

[0.2.0]

New CLI!

  • New Command Line: "chanjo" replaces "chanjo-autopilot"
  • Ability to save a temporary JSON file when running Chanjo in parallel (avoids writing to SQLite in several instances)
  • New command line option: peaking into a database
  • New command line option: building a new SQLite database skeleton
  • New command line option: import temporary JSON files
  • New command line option: reading coverage from any interval from BAM-file
  • Many small bugfixes and minor improvements
  • New dependency: path.py