v1.1.3

Updates viennarna dependency to 2.6.4
More flexible python api for calibrated constants
New PyPI's attestation release pipeline for improved software supply chain accountability
New docker configuration files for ease of installation

Thank you to the following community contributors for their contributions since the last release:
@yiduo-wang-32 for the updated constants api
@luilver for docker configuration files

v1.1.2

Changes in verbosity to allow for different levels, rather than all or nothing.

OSTIR v1.1.0

The major change in this version is the implementation of ViennaRNA's python API, which has the effect of reducing file IO (including eliminating the need for temp files, see #5) and dramatically reducing runtime. Single core performance is improved by ~16x on a 4.700GHz 11th Gen Intel i7-1165G7 as benchmarked by analyzing the T7 genome 100 times (17 minutes 48 seconds in version 1.1.0 versus 4 hours 42 minutes 16 seconds in version 1.0.6), but this pegs the used core at 100% so real gains may be higher.

This version also introduces folding constraints which are passed to ViennaRNA, available only through python and not the command line script for advanced usage.

Change log:

• Implements ViennaRNA python API in place of subprocess calls #7
• Implements constraints (python usage only) #6, #7
• Caches ViennaRNA parameters (reducing IO to RNA hybridization files) #7
• Better install location identification to find RNA hybridization files #7
• General code readability / PEP improvements #7

OSTIR v1.0.6

Change log:
Updated version number for JOSS publication and archiving

OSTIR v1.0.5

Changelog:

• Fix line ending mismatch to make unit tests OS-independent

OSTIR v1.0.4

Changelog:

• Updated command line help descriptions
• Added --version option
• Updated command line output column order for consistency.

OSTIR v1.0.3

Bug fixes:
Added sorting to viennaRNA post processing to make consistent output across linux/mac
Fixed command line output failing due to outdated expected variables
Fixed string input expecting undocumented CLI flag
Additional proofing for user input
Additional consistency tests

Initial Release

Initial public release for OSTIR