RELEASE

# Release history

## 5.8.2
- fix(tests): fix issues with test on Windows
- fix(rpthermo): add_thermo_info()
- chore(rplibs): make generic attributes reading
- chore(rplibs): 'ec' -> 'ec-code

## 5.8.1
- chore(rplibs): make generic attributes reading

## 5.8.0
- fix(rplibs): change dict struct for selenzy infos

## 5.7.5
- fix(tests/rpscore): handling temp files

## 5.7.4
- chore(rpSBML): fit speciesMatchWith() with specs
- fix(tests/rpextractsink): put back close() for temp files

## 5.7.3
- test(rpextractsink): modify temp file
- chore(rpSBML): change spec of speciesMatchWith()

## 5.7.2
- fix: fit to new rr_cache release

## 5.7.1
- fix(rpviz): allow missing thermo dGm prime value

## 5.7.0
- BREAK! feat: remove redis dependencies

## 5.6.1
- build: rm bioconda channel

## 5.6.0
- chore(rpcompletion): print out nb pathways
- BREAK! chore: change tmpl_rxn id into list of ids
- chore(rpSBML): simplify readSBML
- BREAK! (rpSBML): change the way values, lists, dicts are read/written
- fix(rpreport): typo
- feat(rpreport): add global_score
- feat(rpPathway): add get_mean_rule_score() method
- feat(rpreport): add rule score
- chore(rpreport): rename norm_rule_score into mean_rule_score
- BREAK! chore: change rule_id id into list of ids

## 5.4.1
- chore(rpscore): take only one single input pathway
- fix(rpthermo): add models in MANIFEST

## 5.4.0
- feat(rpscore): add scoring function based on learning

## 5.3.6
- chore(rplibs): change format for selenzy informations (single score into dictionnary)

## 5.3.5
- chore(rpthermo): handle __64__ suffix for substituted compounds

## 5.3.4
- fix(rpthermo): consider species are well-formed (i.e. without __64__)

## 5.3.3
- fix(rpthermo): handle the case where eQuilibrator cannot find any compound from an inchikey

## 5.3.2
- fix(rpreport): fit to new rpPathway version

## 5.3.1
- feat(rplibs): add MIRIAM infos
- feat(rplibs.rpReaction): add selenzy score
- feat(rplibs.rpSBML): handle lists in rpSBML files

## 5.3.0
- chore(rplibs): swap rpPathway methods from rpSBML to rpSBML methods into rpPathway

## 5.2.2
- fix(rpthermo): fix params naming
- chore(rpfba): add compartment synonyms for searching
- feat(rpthermo): when a species has not been found in the eQuilibrator cache, the first part of InChIKey is looked for
- chore(rplibs): generic methods to add group of species into a rpPathway
- feat(rpthermo): add 'rp_thermo_substituted_species' group in rpSBML file

## 5.2.1
- chore(rpfba): change units for fba fraction

## 5.2.0
- chore(rpfba): remove CLI args
- chore(rpfba): refactor code, push back 'fba' and 'pfba' sim types
- chore(rplibs): add fba and pfba methods
- fix(rpfba): CLI args name

## 5.1.4
- chore(rpfba): BREAK! make CLI option 'compartment_id' mandatory
- chore(rpfba): check first if compartment_id exists in the model
- chore(rpSBML): take compartment_id only from user CLI

## 5.1.3
- chore(rplibs): rename rpfba_ignored_species into rp_fba_ignored_species
- test(rpfba): rename rpfba_ignored_species into rp_fba_ignored_species

## 5.1.2
- chore(rpcompletion): rm compartment_id arg
- chore(rplibs): make 'c' the default compartment
- chore(rplibs): handle matched compartments
- chore(rpfba): add target consumption reaction

## 5.1.1
- chore(rpcompletion): add flux bounds
- chore(rpfba): create folder if does not exist
- chore(rpfba): add CLI args for flux bounds
- chore(rpfba): set flux bounds
- chore(rplibs): set flux bounds positive and reactions not reversible

## 5.1.0
- chore(rpfba): re-write cobra functions
- chore(rpSBML): re-write merging and add cobra methods
- chore(rpReaction): add constraints as attributes
- chore(rpPathway): create attributes for each rpSBML info
- chore(rpGraph): pass a list of species when searching isolated species
- feat(rpCompound): add compartment
- chore(rpfba): re-organize steps
- doc(README): add ignored species infos
- style(rpcompletion): do not assign rpCompound creation

## 5.0.0
- chore(rpthermo):
    - switch functions I/O from rpSBML to rpPathway
    - remove intermediate components and compute thermo for the pathway net reaction
- chore(rpfba):
    - switch functions I/O from rpSBML to rpPathway
    - hide metabolites not compliant with Cobra
- chore(rpObject, rpCompound, rpReaction, rpPathway):
    - add access methods
    - rewrite to_dict() methods
- fix(rpcompletion):
    - merge sublists of transfos with same ID (multiple identical reactions in a pathway)

## 4.7.0
- chore(rpcompletion): re-write almost all code
- feat(rpcompletion): ability to write out pathways as JSON files

## 4.6.0
- use rxn_rebuild to add cofactors
- test(rpreport): add tests

## 4.5.0
- chore(rplibs): add fields in toDict(): 'central_species', 'rp_sink_species', 'ignored_species_for_FBA', 'rp_target_species'
- chore(rplibs.rpSBML): make checklibSBML() returns a value rather than exit
- chore(rplibs.rpSBML): make readGroupMembers() returns None if group not found
- chore(rplibs.rpSBML): remove default group_id in readGroupMembers()
- chore(rplibs.rpSBML): BREAK! put 'left' end 'right' keys from 'brsynth' to reaction level
- refactor: switch from rpCache to rrCache

## 4.4.5
- chore(rpcompletion): change out filenames nomenclature
- style(printout): change printout display

## 4.4.4
- fix(rpSBML): do not check SBML when creating an empty rpSBML

## 4.4.3
- chore(rpSBML): add 'nb_reactions' key in output of toDict()

## 4.4.2
- fix(rpSBML): fix input file control (TypeError + FileNotFoundError)

## 4.4.1
- rpSBML: modify getGroup() method arguments
- rpSBML: add getListOfGroups() method

## 4.4.0
- rpFBA: ignore metabolites that are ony consumed/producted to avoid null scores

## 4.3.0
- rpRanker: ability to rename output files
- rpFBA: switch '--dont_merge' CLI argument into '--merge' (default: False)
- rpSBML: add build_filename_from_name()

## 4.2.3
- rpRanker: rename outfiles properly (.xml)

## 4.2.2
- rpRanker: add --data_outdir option

## 4.2.1
- New feature (rpSBML): add checkSBML() method
- Check SBML format in methods: __init__(), mergeModels()
- Bypass completeHeterologousPathway() when merging rpSBML models

## 4.2.0
- New feature (rpRanker): ability to store either pathway files or only the ranking result

## 4.1.0
- New feature (rpRanker): provides an .tar.gz file with selected pathways in

## 4.0.0
- New module: rpranker
- rpSBML: add optional 'keys' arg in toDict() to specify part of rpSBML to parse

## 3.0.0
- New module: rpscore

## 2.4.0
- rpSBML: rewrite methods
- rpFBA: rewrite functions
- add test datasets
- add the ability of rpSBML class to read file from gzip format
- method mergeModels() returns the merged model rather than modify objects passed as arguments

## 2.3.0
- fix rpfba tool
- refactor datasets to save disk space

## 2.2.1
- Clean code in rpcompletion

## 2.2.0
- rename in rpSBML format:
    + step -> rxn_idx

## 2.1.0
- rename in rpSBML format:
    + path_id     -> path_base_idx
    + alt_path_id -> path_variant_idx
- 'path_id' is now used to really store the id of the pathway
- remove 'value' field from simple tag in rpSBML file for: path_base_id, path_variant_idx
- rpCompletion:
    + functions
    + compare dictionnaries for tests

## 2.0.0
- rename reaction ids in rpSBML format:
    + RP1      -> rxn_1
    + RP1_sink -> rxn_target
- change reactions order from reverse to forward
- rename methods in rpSBML class:
    + createPathway()            -> createGroup()
    + readRPpathwayIDs()         -> readGroupMembers()
    + genJSON()                  -> toDict()
    + convert_pathways_to_dict() -> convert_pathway_to_dict()
- move annotations from reaction nodes to pathway node:
    + path_id
    + sub_step_id
- rename 'sub_step_id' to 'alt_path_id'

## 1.2.0
- add global_score to rpSBML

## 1.1.0
- add __init__.py and __main__.py into files to embed in package. 'python -m rptools --help' is possible

## 1.0.0
- first release of rpTools