Ductape

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UPGRADE URGENCY: MODERATE, only feature improvements

IMPORTANT NOTE: this version introduces a backward incompatible change in dphenome
Users who want to analyze an old DuctApe project files should rebuilt it from scratch (or using the various "export" and "import" commands)

FEATURES:
* dphenome add: new parsing logic for plate IDs
* Before: PM03B --> the final letter was kept, causing confusion and failures
* After: PM03 --> more consistent and durable
* This is a backward incompatible change
* dphenome stats: output the tables to file (not just to the terminal)
* dgenome stats: output the tables to file (not just to the terminal)

BUGFIXES:
* dphenome add: yml files with "strange" plate IDs caused crashes
* Print functions compatible with python 3

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UPGRADE URGENCY: MODERATE, introduced some bugfixes in the KEGG API and in imported PM parameters handling

BUGFIXES:
* KEGG API: quote the URLs to avoid HTTP error 400 on some systems
* dphenome start: force negative parameters to zero for the clusterization
* The parameters stored in the database are left unchanged
* dape start: the maximum AV value in network reconstruction was still hard coded

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UPGRADE URGENCY: MODERATE, introduced some bugfixes in handling missing wells and in purging distinct replica

BUGFIXES:
* dphenome purge: replica id management bugfix
* dphenome add/add-multi/add-dir have been changed accordingly
* dphenome plot: handle missing strains
* dphenome: handle missing wells in mutation experiments
* dphenome: typo, "Sulfur" should be "Sulphur"

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UPGRADE URGENCY: HIGH, pangenome combined analysis have been changed to account for distant species

The pathway maps and combined analysis have been remodulated to consider also the presence of genes that are not orthologs but share the same metabolic function (i.e. KEGG reaction ID).
There are virtually no changes for pangenomic analyses on closely-related strains, as their metabolic variability is mainly based on orthology relationships.
The KEGG reaction IDs that are common to all strains are labelled as 'conserved', as opposed to the 'variable' ones.

FEATURES:
* dgenome stats/export: new outputs and graphs for conserved/variable reactions
* dape map: new pathway coloring policies for pangenomes
* Blue boxes means conserved reaction
* Orange boxes mean variable reactions (color intensity proportional to strains count)
* dape start: consider conserved/variable reactions in the analysis
* -n option removed

BUGFIXES:
* dphenome: the commands that need phenotypic data will exit if no PM plate is available

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UPGRADE URGENCY: MODERATE, crashes on CentOS have been fixed and new commands/options are available

FEATURES:
* dphenome trim: new command to cut all PM data to the same time step
* The 'area' parameter is greater in longer PM curves, even if the curve shape is equal
* dphenome purge: new purging policy ('replica') to remove a distinct replica by its ID
* dape, dgenome, dphenome start: new option (-y) to fetch kegg data with unstable connections

BUGFIXES:
* dphenome start: support older scipy versions
* dphenome start: support newer scikits.learn versions
* dape, dgenome, dphenome start: correctly exit when kegg data fetch fails

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UPGRADE URGENCY: HIGH, in some cases there were crashes during curve parameters estimation

FEATURES:
* dphenome start: new option to plot an elbow test (-e)
* dgenome export: more details in the reactions files

BUGFIXES:
* dphenome start: avoid crashes when estimating plateau and lag time for PM curves
* dape map: reduced risks of crashes when downloading KEGG maps