Version 0.15.0
==============

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

Version 0.14.2
==============

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

Version 0.14.0
==============

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"

Version 0.13.0
==============

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

Version 0.12.0
==============   

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

Version 0.10.0
==============

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

Version 0.9.6
=============

UPGRADE URGENCY: LOW, only a few improvements for BBH searches

FEATURES:
* dgenome start: two new options to modulate the BBH search
    * -m to change the Blast scoring matrix (i.e. BLOSUM62)
    * -e to change the Blast E-value threshold 
* Slightly faster threads

Version 0.9.4
=============

UPGRADE URGENCY: LOW, only a style fix has been added

BUGFIXES:
* dphenome rings: thicker categories legend

Version 0.9.2
=============

UPGRADE URGENCY: LOW, the bug fixed in this version affects only users importing curve parameters from other softwares

BUGFIXES:
* dphenome start: bugfix when considering parameters with NAN values in all wells

Version 0.9.0
=============

UPGRADE URGENCY: HIGH, some compounds were discarded in network reconstructions

FEATURES:
* dape start: new outputs to higlight relevant genome/phenome combinations
    * pangenome: high genomic/phenomic variability are highlighted
    * mutants: high phenomic variability in pathways w/ mutated genes are highlighted
    * single organisms: all the genomic/phenomic data is showed

BUGFIXES:
* dape start: some compounds (w/ AV=0) were excluded from the network construction
* dape start: discard the analysis on the general pathways
* database: some queries have been optimized for pangenome analysis
* Other small bugfixes

Version 0.8.2
=============

UPGRADE URGENCY: HIGH, the curve parameters extraction and clustering have been improved

FEATURES:
* dphenome start: slight changes to parameters calculation
    * the smoothing algorithm is now less aggressive
    * the recursive attempts on curve parameters estimation are reduced two
* dphenome start: clustering improvements
    * the curve parameters are normalized prior to clusterization, in order to give all the parameters the same weight
    * added a new option (-n) to set the number of clusters (and therefore tha maximum AV)

BUGFIXES:
* dape start: give the right number of distinct reaction IDs in the metabolic network tables
* Other small bugfixes and speed improvements

Version 0.8.0
=============

UPGRADE URGENCY: LOW, if you work exclusively with DuctApe and use the standard bacterial PM plates

FEATURES:
* dphenome import-plates: the user can now analyze even custom plates
    * the table in test/input/newplate.tsv contains an example
* dphenome add/add-multi: PM data analyzed by different programs (i.e. opm) can now be imported
    * YAML/JSON file formats are supported
    * Curve parameters calculated by other programs are considered: they may be overridden by using dphenome start -r
* dgenome export: PM data can now be exported in YAML/JSON format

BUGFIXES:
* dape init: if something goes wrong during DB creation raise an error
* Other small bugfixes

Version 0.7.0
=============

UPGRADE URGENCY: MODERATE; many features have changed, especially for the genomic analysis

FEATURES:
* Reactions copy number is no more analyzed: for pangenome and mutants experiments the program now focus on exclusive and distinct reaction IDs
    * dgenome stats/export, dape start/map have been changed accordingly
* dgenome annotate: new command to transfer kegg annotations inside an orthologous group
* dgenome deannotate: revert the annotation transfer
* Added a test directory with a simple script to test the three modules

BUGFIXES:
* PM data: prevent crashes in the clusterization step
* PM data: prevent crashes when parsing csv files
* kegg: final fix to handle correctly HTMLs from kegg 
* DB: speed improvements on big pangenomes
* Other small bugfixes

Version 0.6.2
=============

UPGRADE URGENCY: HIGH; in some cases the KEGG html maps could not be retrieved correctly

kegg:
BUGFIX: the preparation of some kegg html maps resulted in failures

dgenome start:
FEATURE: roughly 3X speed improvements on BBH pangenome calculation, thanks to in-memory Blast searches


Version 0.6.1
=============

UPGRADE URGENCY: HIGH; in some cases the KEGG data could not be retrieved correctly

kegg:
FEATURE: an improved connectivity check
BUGFIX: the insertion in the database of some kegg maps resulted in failures

dgenome start:
BUGFIX: in a corner case the pangenome calculation was performed twice

Version 0.6.0
=============

UPGRADE URGENCY: HIGH; the control signal subtraction has been fixed on PM plate PM04A

dgenome start
FEATURE: roughly 3X speed improvements on BBH pangenome calculation 

dphenome zero
BUGFIX: the control signal subtraction has been fixed on PM plate PM04A

dphenome export
BUGFIX: the table with the average AV shouldn't contain the column "replica"

kegg:
FEATURE: fetch also the EC numbers for the Kegg reactions
BUGFIX: add some spaces when a tag retrieved with the "info" request spans multiple lines

dape start
BUGFIX: fixing again the compound duplication bug when creating metabolic networks

Version 0.5.4
=============

UPGRADE URGENCY: HIGH; dphenome users may be unable to load some PM data 

dphenome
FEATURE: import/export plates data
BUGFIX: biolog parser shouldn't fail on unknown plates
BUGFIX: handle new possible plate names some plates names

dape
FEATURE: add-multi lets the user to provide multiple orgID
Fixed some typos

dape/dgenome/dphenome start:
FEATURE: added options to skip kegg map and phenomics parameters calculation

kegg:
FEATURE: internet connectivity is checked before the kegg mapping is performed

Version 0.5.3
=============

dape start
FEATURE: added AV color to KEGG compounds (GML graph output)
BUGFIX: avoid duplicated nodes in the metabolic graphs

Version 0.5.2
=============

dape start
BUGFIX: pangenome network analysis improvements

dphenome add
BUGFIX: handle csv files with a different OrgID than expected
BUGFIX: calculate the correct number of added plates

dphenome plot
FEATURE: added the ability to generate plots in svg formats (-s option)

Version 0.5.1
=============

BUGFIX: The net file was absent from the kegg module

Version 0.5.0
=============

First release
