Ductape

==============

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

==============

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"

==============

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

==============

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

==============

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

==============

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