Latest release

latest

Version bump

DuctApe-0.18.2

Version bump

DuctApe v0.17.8

UPGRADE URGENCY: HIGH, the KEGG data download step is now broken due to the retirement of the RPAIR database

BUGFIXES:

• kegg: the data contained in the now discontinued RPAIR database is retrieved from the KEGG reactions DB

DuctApe v0.17.6

UPGRADE URGENCY: HIGH if you have the latest version of networkx installed

BUGFIXES:

• dape start: newer versions of networkx do not cause crashes anymore
• Removed hardcoded KEGG API addresses (removes useless warning messages)

DuctApe v0.17.4

UPGRADE URGENCY: LOW if you are not experiencing crashes with the "dphenome stats" command

BUGFIXES:

• Do not smooth/compress PM signals when they are too few (manual experiments)
• dphenome stats: avoid crashes for unusual AV distributions

DuctApe v0.17.2

UPGRADE URGENCY: LOW if you are not experiencing crashes with the "dape start" command

BUGFIXES:

• dape start: avoid crashes when recent networkx versions are used
• dape/dgenome/dphenome: use "/usr/bin/env python" instead of "/usr/bin/python"

DuctApe v0.17.0

UPGRADE URGENCY: LOW if you are not interested in the new features
Please note that python 3 is still not supported

FEATURES:

• dphenome rings: use a parameter of choice instead of the activity
  • the new -r option can be used
• dphenome trim: the time at which perform the trim can be set by the user
• dgenome export: organisms are separated by tab (pangenome_category.tsv)

BUGFIXES:

• dgenome start: more information in the logs

DuctApe v0.16.4

UPGRADE URGENCY: LOW if you are not using PM experiments with a low number of time points

FEATURES:

• dphenome start: no smoothing/compressing when not enough time points
  • when the number of time points is below 33
  • "manual" phenomic experiments may have a very low number of time points

BUGFIXES:

• Full python3 compatibility
  • dgenome start still had some python2 bits
• dape/dgenome/dphenome start: option "-p" renamed to avoid conflicts
  • dape start -p --> dape start -s
  • dgenome start -p PREFIX --> dgenome start -x PREFIX
  • dphenome start -p --> dphenome start -s
• dphenome stats: do not exit if the AV has not been computed yet
  • The command may still output useful data

DuctApe v0.16.2

UPGRADE URGENCY: HIGH if you use the "dape map" command or have the latest matplolib library, LOW otherwise

BUGFIXES:

• dape map: could not get any colored pathway map
• Installation: NetworkX was missing in the setup file
• dphenome rings:
  • Memory-leak when many organisms are present
  • Different proportions when orgs > 10
  • Fix crashes w/ latest matplotlib version

DuctApe v0.16.0

UPGRADE URGENCY: MODERATE, one corner-case crash on dphenome plot has been fixed

FEATURES:

• dphenome plot: it is now possible to plot single plates/wells with one command
  • dphenome plot PM01 --> plots only plate PM01 (w/ heatmap)
  • dphenome plot PM01 A01 --> plots only well PM01 A01

BUGFIXES:

• dphenome plot: in some cases the creation of the legends caused a crash of the command