rel-3-07-01

Fixing the incorrect naming of the rel-3-07 release

rel-3-07

What's Changed

• Implementation of percolator-reset by @percolator in #378
• Added RT to percolator output by @acquayefrank in #374

New Contributors

• @acquayefrank made their first contribution in #374

3.6.5

v3.06.5

• Allow empty pin-file with --no-terminate flag. (#371)
• Skip protein decoy pattern detection if --protein-decoy-pattern is specified. (#356)
• Delay tab file validation and decoy pattern detection to Caller::run().
• Cleaned up and refactored TabFileValidator.
• Deal with DefaultDirection row when merging multiple pin files.
• Better names for portable artifacts.

3.6.4

v3.06.4

• Fix assertion problem with ties in calculating PEPs. (#365)
• Upgrade to macos-12 on GH action builds. (#364, #366)

3.6.3

v3.06.3

• Add check and fallback for <4 bins in BaseSpline PEP estimation. (#362)

3.6.2

v3.06.2

• Take filename into account in TDC (#358)

3.6.1

v3.06.1

• Added checks for number of decoy PSMs<=1 (#337)
• Removing multiple warnings of decoyPrefix not being set (despite being set). (#338)
• #ifdef CRUX macros removed (#340)
• Fixed problem with missing protein IDs. (#342, #343, #329)
• Fix inconsistent behavior of --train-fdr-initial when --trainFDR is zero (#349)
• Extended fix for XercesC ICU dependency to Ubuntu 18.04 (#188)
• Clean up char pointers in tmpFile creation (#346)
• Removed binary reading mode and replace popen by subprocess (#330)
• Better triggered workflow for github actions
• Update GitHub MacOS runner to macos-11 because macos-10.15 is deprecated.

3.6

v3.06

• Added extended unit tests.
• Added code for quicker FDR calculation.
• Updated urls to xerces and google test
• Switched compiler to c++11
• Added basic pepXML support.
• Improved testing in Github actions:
  • Made separate stages for unit and system tests for Ubuntu
  • Introduced a test build for centos
  • Moved unit and system tests to release code.
  • Changed the dependency structure to gtest
• Added command-line argument to switch off reporting to analytics
• Added possibility to include spectrum file name in tab-delimited input, that is carried over to tab-delimited output.
• Added possibility to include retention time in tab-delimited input.
• Discontinued support of the Elude model
• Removed all retention time modeling and all other DOC features

3.5

v3.05

• Fixed problem with Elude model reading on windows (#249)
• Better error messages for converters (#251)
• Fixed several build errors (#188, #250)
• Parallel nested CV SVM training using a single OMP threadpool. Percolator can now handle up to 27 parallel threads to significantly speed up processing and uses parallel STL algorithms on linux (#254)
• Fixed TabReader error handling (#255)
• Continuous integration with GitHub Actions with nightly releases for Windows, OSX and Ubuntu (https://github.com/percolator/percolator/actions)

3.4

v3.04

• Added full support for static models (#247)