v0.7.3

v0.7.3

• Fix nondeterministic behavior of decouple_connected_proteins

v0.7.2

v0.7.2

• Add --protein_group_fdr_threshold flag to set the protein group-level FDR cutoff for the rescuing procedure and logging messages
• Fix compatibility with Oktoberfest's new ProForma N-terminal notation
• Improved ProForma sequence format support
• Support new oktoberfest psmid with optional scan event number
• Use --psm_fdr_cutoff for "Peptide counts (unique)" column

v0.7.1

v0.7.1

• Switch to modified peptide instead of peptide in fragpipe parsing functions
• Make peptide flanking characters consistent across search engines. Fixes bug with percolator input used with --peptide_protein_map

v0.7.0

v0.7.0

• Less strict llvmlite dependency
• Add functionality to requantify fragpipe combined_protein.tsv
• Fix random number seed for mokapot
• Major refactoring and linting of multiple scripts
• Add system tests
• Fix peptide_protein_map input option for quantification.py
• Refactor picked_group_fdr.py, add some unit tests
• Add --suppress_missing_peptide_warning to all relevant modules
• Add readthedocs documentation
• Allow combining multiple Sage or FragPipe searches

v0.6.6

• Revert return type to List for ProteinGroups.get_protein_groups

v0.6.5

• Fix check for peptides not assigned to any protein group
• Fix for docker interactive mode

v0.6.4

• Add filename column for andromeda2pin
• Update mokapot to 0.10.0
• Update packages in poetry.lock
• Fix docker package version in greeter

v0.6.3

• Skip lfq if only 1 experiment is present
• Fix organism fasta parsing
• Added fractionated sample support for sage

v0.6.2

• Update job-pool to v0.2.6 to fix hanging maxlfq quant
• Fix gene_level support in quantification.py
• Speed optimizations for digest.py

v0.6.1

v0.6.1

• Fix --gene-level option
• Switch to job-pool package for multiprocessing
• Use specific libxml2 version to fix GUI build (#12)