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Recent Releases of primerForge

primerForge - primerForge v1.5.3

What's new

  • Fixed a bug in --check_install to handle non-integer patch versions (eg. 2.0.0a3)

Full Changelog: https://github.com/dr-joe-wirth/primerForge/compare/v1.5.2...v1.5.3

Scientific Software - Peer-reviewed - Python
Published by dr-joe-wirth about 1 year ago

primerForge - primerForge v1.5.2

What's Changed

  • better error code documentation
  • better inline documentation
  • added example showing how to obtain target-specific PCR primers using bedtools

Full Changelog: https://github.com/dr-joe-wirth/primerForge/compare/v1.5.1...v1.5.2

Scientific Software - Peer-reviewed - Python
Published by dr-joe-wirth over 1 year ago

primerForge - primerForge v1.5.1

What's Changed

  • improved documentation
  • now writes a BED file containing each primer's position in the ingroup genomes
  • user's can specify the BED file location (optional)
  • added additional unit tests to validate BED file creation

Full Changelog: https://github.com/dr-joe-wirth/primerForge/compare/v1.4.3...v1.5.1

Scientific Software - Peer-reviewed - Python
Published by dr-joe-wirth over 1 year ago

primerForge - primerForge v1.4.3

What's Changed

  • added --advanced options (#29)
  • avoiding filename collisions (#37)
  • better checkpointing
  • better github CI
  • Pixi by @lskatz in https://github.com/dr-joe-wirth/primerForge/pull/36

Full Changelog: https://github.com/dr-joe-wirth/primerForge/compare/v1.3.7...v1.4.3

Scientific Software - Peer-reviewed - Python
Published by dr-joe-wirth over 1 year ago

primerForge - primerForge v1.3.7

What's changed

  • parallelized calls to isPcr during primer validation (#30)
  • primer pairs are sorted before writing to file (#31)
  • removed unnecessary read/write operations
  • cleanup of intermediate files is more stable

Full Changelog: https://github.com/dr-joe-wirth/primerForge/compare/v1.3.6...v1.3.7

Scientific Software - Peer-reviewed - Python
Published by dr-joe-wirth over 1 year ago

primerForge - primerForge v1.3.6

What's changed

  • addressed redundant operations during kmer evaluation
  • reduced memory footprint
  • improved documentation

Full Changelog: https://github.com/dr-joe-wirth/primerForge/compare/v1.3.5...v1.3.6

Scientific Software - Peer-reviewed - Python
Published by dr-joe-wirth over 1 year ago

primerForge - primerForge v1.3.5

What's changed

  • modified isPcr parameters to improve primer pair filtering
  • updated manuscript to match this version

Full Changelog: https://github.com/dr-joe-wirth/primerForge/compare/v1.3.4...v1.3.5

Scientific Software - Peer-reviewed - Python
Published by dr-joe-wirth over 1 year ago

primerForge - primerForge v.1.3.4

What's changed

  • Better checkpointing (#25)
  • Added additional unit test (#25)
  • Improved stability

Full Changelog: https://github.com/dr-joe-wirth/primerForge/compare/v1.3.3...v1.3.4

Scientific Software - Peer-reviewed - Python
Published by dr-joe-wirth over 1 year ago

primerForge - primerForge v.1.3.3

What's Changed

  • updated manuscript
  • updated README
  • better logging
  • Footnote madness by @lskatz in https://github.com/dr-joe-wirth/primerForge/pull/28

Full Changelog: https://github.com/dr-joe-wirth/primerForge/compare/v1.3.2...v1.3.3

Scientific Software - Peer-reviewed - Python
Published by dr-joe-wirth over 1 year ago

primerForge - primerForge v1.3.2

Several minor changes and quality of life improvements: * better cleanup of intermediate files * improved logging and status reporting * added contributing instructions * updated manuscript to include isPcr

Full Changelog: https://github.com/dr-joe-wirth/primerForge/compare/v1.3.1...v1.3.2

Scientific Software - Peer-reviewed - Python
Published by dr-joe-wirth over 1 year ago

primerForge - primerForge v1.3.1

Full Changelog: https://github.com/dr-joe-wirth/primerForge/compare/v1.2.7...v1.3.1

Scientific Software - Peer-reviewed - Python
Published by dr-joe-wirth over 1 year ago

primerForge - primerForge v1.2.7

Overview

Many changes in this release that drastically improved runtimes, performance, and maintenance.

Major changes

  • Overhaul of ingroup kmer retrieval
    • increased efficiency
    • faster runtimes (~5x faster)
    • requires pyahocorasick package
  • Overhaul of outgroup primer pair filtering
    • increased efficiency
    • faster runtimes (~60x faster)
    • requires pyahocorasick package
  • Unit tests use Mycoplasma mycoides genomes by default; Escherichia coli tests still available
  • Added unit testing to github CI workflow

  Full Changelog: https://github.com/dr-joe-wirth/primerForge/compare/v1.2.5...v1.2.7

Scientific Software - Peer-reviewed - Python
Published by dr-joe-wirth over 1 year ago

primerForge - primerForge v1.2.5

Reduced memory footprint (#23), improved performance, and decreased runtimes.

Major changes

  • evaluating only one primer pair per bin pair to reduce memory usage
  • several changes to how multithreading is managed to reduce overhead
  • using khmer for efficient k-mer retrieval; added this to the manuscript

Minor changes

  • added instructions for running unit tests
  • manual installation works with strict channel priority
  • fixed bug in results_test.py that inadvertently caused a TimeoutError
  • updated mermaid diagram

Full Changelog: https://github.com/dr-joe-wirth/primerForge/compare/v1.1.1...v1.2.5

Scientific Software - Peer-reviewed - Python
Published by dr-joe-wirth over 1 year ago

primerForge - primerForge v1.1.1

made unit tests easier to run

Full Changelog: https://github.com/dr-joe-wirth/primerForge/compare/v1.1.0...v1.1.1

Scientific Software - Peer-reviewed - Python
Published by dr-joe-wirth over 1 year ago

primerForge - primerForge v1.1.0

Major overhaul to code base to improve performance and user interface.

Performance improvements

  • removed plotting and matplotlib requirement
    • plotting was not very informative but took a significant amount of time to complete
    • future versions will create BED files to enable users to easily generate plots
  • parallelized kmer retrieval for both ingroup and outgroup sequences
    • more significant decreases in runtimes as the number of ingroup genomes increases
    • more significant decreases in runtimes as the number of outgroup contigs increases
  • decreased time complexity of primer pair identification
    • previously, retrieved primer pairs for each ingroup genome
    • now retrieve primer pairs for one genome then reduce to those pairs present in all other ingroup genomes
  • reduced memory footprint

User interface improvements

  • more informative and better formatted status messages
  • added templates for submitting issues

Miscellaneous changes

  • fixed CI for automatically updating pypi
  • revised Clock class to enable more flexibility in its application

Full Changelog: https://github.com/dr-joe-wirth/primerForge/compare/v1.0.2...v1.1.0

Scientific Software - Peer-reviewed - Python
Published by dr-joe-wirth over 1 year ago

primerForge - primerForge v1.0.2

minor changes to ensure --check_install is compatible with the conda installation.

Full Changelog: https://github.com/dr-joe-wirth/primerForge/compare/v1.0.1...v1.0.2

Scientific Software - Peer-reviewed - Python
Published by dr-joe-wirth almost 2 years ago

primerForge - primerForge v1.0.1

several small changes: * updated installation instructions * added a logo * added a --check_install job

Full Changelog: https://github.com/dr-joe-wirth/primerForge/compare/v1.0.0...v1.0.1

Scientific Software - Peer-reviewed - Python
Published by dr-joe-wirth almost 2 years ago

primerForge - primerForge v1.0.0

ready for the first release! * improved installation instructions * updated workflow diagram * added manuscript

What's Changed

  • Update paper.md by @lskatz in https://github.com/dr-joe-wirth/primerForge/pull/16
  • Update paper.md by @jchen232 in https://github.com/dr-joe-wirth/primerForge/pull/17

New Contributors

  • @jchen232 made their first contribution in https://github.com/dr-joe-wirth/primerForge/pull/17

Full Changelog: https://github.com/dr-joe-wirth/primerForge/compare/v0.7.4...v1.0.0

Scientific Software - Peer-reviewed - Python
Published by dr-joe-wirth almost 2 years ago

primerForge - primerForge v0.7.4

major changes: * now using primer3-py to calculate melting temperatures and evaluate hairpin potential, homodimer potential, and heterodimer potential * now pip installable

minor changes: * fixed and updated unit tests * fixed potential memory leak that could occur under specific conditions when checkpointing * revised primer binning and splitting large bins * fixed bug in outgroup primer pair removal * updated README.md

Full Changelog: https://github.com/dr-joe-wirth/primerForge/compare/v0.6.2...v0.7.4

Scientific Software - Peer-reviewed - Python
Published by dr-joe-wirth almost 2 years ago

primerForge - primerForge v0.6.2

What's Changed

  • installation and usage doc by @lskatz in https://github.com/dr-joe-wirth/primerForge/pull/12
  • Added basic CI testing by @lskatz in https://github.com/dr-joe-wirth/primerForge/pull/13
  • Added checkpointing
  • Improved logging
  • Added plotting
  • Better documentation
  • Added primer dimer predictions

New Contributors

  • @lskatz made their first contribution in https://github.com/dr-joe-wirth/primerForge/pull/12

Full Changelog: https://github.com/dr-joe-wirth/primerForge/compare/v0.2.0...v0.6.2

Scientific Software - Peer-reviewed - Python
Published by dr-joe-wirth almost 2 years ago

primerForge - primerForge v0.2.0

Providing an initial release. Passes all unit tests, but still pre-release

Scientific Software - Peer-reviewed - Python
Published by dr-joe-wirth about 2 years ago