Release 6.5.0

6.5.0 (2023-11-29)

⚠ BREAKING CHANGES

• args: change arg name with_orphan_species

Features

• rplibs>rpSBML: add rm_isolated_species() (66895b1)

Bug Fixes

• rplibs: store group.getId() before removing (8263282)

Tests

• rpfba: fit to new arg (7483010)
• rplibs: add test to new rpSBML method (02a92e4)

chore

• args: change arg name with_orphan_species (b56cb0f)

Build Systems

• environment.yaml: python until 3.10 (7739b41)
• tag: put back jobs (784e0ed)

Release 6.4.1

6.4.1 (2023-11-21)

Bug Fixes

• rpfba: fit type for 'merge' option in tests (c535ebf)

Build Systems

• environment.yaml: fix pkg ver (aedc9af)

Release 6.4.0

6.4.0 (2023-11-20)

Features

• rpfba: add outfile name of rpfba merged model (cbf7e86)

Release 6.3.3

6.3.3 (2023-11-20)

Bug Fixes

• rpPathway: EC numbers list (2ea5ab8)
• rpPathwy: invert test Compound (89453a1)

Tests

• rplibs: change input dataset name attr (e9a442b)
• rplibs: rm import (acc2f1a)

Release 6.3.2

6.3.2 (2023-10-25)

Bug Fixes

• rprank: fix import (97629d5)
• rprank: import (6e761e1)

Build Systems

• environment: cobra >=0.26.3 (6066d0d)
• environment.yaml: rm pkgs (e902540)
• environment.yaml: update (e6f0f23)
• environment.yaml: update (1043fef)

Release 6.3.1

6.3.1 (2023-10-23)

Bug Fixes

• fit to new rpPathway specs (d69377d)

Release 6.3.0

6.3.0 (2023-10-20)

⚠ BREAKING CHANGES

• rpextractsink: genSink return a dict
• rpextractsink: stop converting spe id

Features

• rpextractsink: add standalone mode (7fd5f8b)

Bug Fixes

• rpextractsink: args typo (880cf87)
• rpfba: remove medium feature (0bd7bc3)
• rpfba: test (7476c2f)
• rplibs: fit to MIRIAM as list (972e2db)
• rplibs: fix MIRIAM cross-ref reading (070d05b)

Build Systems

• environment.yaml: rr_cache version (049e59e)
• tag: back to -latest (feb6949)
• tag: only do tagging (d4487f5)
• tag.yml: try ubuntu-20.04 (4981836)
• test: rm windows (c60c7b9)

Tests

• rpextractsink: clean up (76fd865)
• rpextractsink: reduce code (2a75589)
• rpextractsink: split tests + test wrong comp (76c98e7)
• rpscore: add tests (ee18a0e)

chore

• rpextractsink: genSink return a dict (08feb51)
• rpextractsink: stop converting spe id (3dc2012)

Styles

• rpfba: lint (1b9985f)

Release 6.2.3

6.2.3 (2023-03-17)

Release 6.2.2

6.2.2 (2023-02-15)

Bug Fixes

• rpextractsink: [WIP] detect more dead end metabolites (fa84570)
• rpextractsink.py: refine removal of dead end metabolites (e7e08a4)

Tests

• update sink data file (82e1398)

Release 6.2.1

6.2.1 (2023-02-09)

Bug Fixes

• rplibs: put back 'rp_' prefix for model ID (aa5af8c)

Tests

• rpcompletion: fit to 'rp_' (f5a685a)