Bioservices

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* fix change in kegg (ORG_CODE replaces DEFINITION)



Revision 1.8.0 roadmap
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* removed chemspider,picr and clinvitae services due to deprecated services



Revision 1.7.12 (Jan 2021-July 2021)
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* continous integration revisited with github actions

* NEWS:

* COG services qdded
* New module: mygeneinfom pdbe
* added panther module (pantherdb.org)


* CHANGES

* update dbbionet to fulfill future new API
* Migrate to PDB new API (Jan 2021)
* Update Quickgo service
* Integration new Biomodels API following Combine/Harmony meetng
* Update ChEMBL after an ChEMBL API change

* BUGS and FIXES

* General fixes and update from thobalose (https://github.com/cokelaer/bioservices/pull/149) to
* PSICQUIC fix (https://github.com/cokelaer/bioservices/issues/189) to
* Fix ENA new API
* Fix NCBIBlast and Muscle services (new API)

* DEPRECATED:

* deprecated PICR and TCGA modules (the latter was not really available anyway)






Revision 1.7.11 (Dec 2020)
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* Fix https://github.com/cokelaer/bioservices/issues/183 (warning in uniprot
* Fix annoying warning https://github.com/cokelaer/bioservices/issues/184
* Implemented new PDB services (Update API changed in Nov/DEc 2020)

Revision 1.7.10 (Nov 2020)
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* Fix KEGG https://github.com/cokelaer/bioservices/issues/182 adding NETWORK field
* Fix Pathway common with new API https://github.com/cokelaer/bioservices/issues/135
* Update the PathwayCommon service with new API
* Update the Rhea service with new API

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* add missing field in KEgg Parser (REL_PATHWAY)
* fix panther.get_enrichment output (try/except)

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* Fix ENA new API
* fix missing plugin in requirements-dev.txt

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* small fix on pantherdb (autocorrect typo in pantherdb api)

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* Fixing ncbiblast and muscle services
* Fixing quickgo services by adding new methods
* Fixing chembl and all failing tests and modules (omicdi, seqret,etc)

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* NEW MODULE: mygeneinfo, pdbe
* Limits the request to 10 per seconds (3 for eutils). This fixes
https://github.com/cokelaer/bioservices/issues/7
* update quickgo
* Update PDB module (will not be maintained in the future, to usePDB instead.)
* Fix issue in Eutils/ECitMatch reported here https://github.com/cokelaer/bioservices/issues/169
and here https://tinyurl.com/y6u2cyjq on stackoverflow


Revision 1.7.4 (March 2020 Combine/Harmany2020 hackathon)
---------------------------------------------------------

* Integration of BioModels new API (REST instead of WSDL and different
functionalities) in coordination with Mihai Glont and Tung Nguyen at EMBL-EBI
during the Combine-Harmony hackathon.
* Integration of BiGG models service thanks to https://github.com/achillesrasquinha contribution.
* Fixing notebooks (biomodels and uniprot)
* Move the miriam services to the attic

Revision 1.7.3 (March 2020)
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* fixing chembl after API changed. Fix the get_status_resources method by
removing document_term and target_prediction. Changed acd_log into alogp: for
some reasons this was changed. There was a warning on 4th March 2020 telling
that changes may occur.



Revision 1.7.2 (March 2020)
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* Fixing ReadTheDocs online documentation and Changelog

Revision 1.7.1 (Feb 2020)
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* Just updating the README and setup metadata

Revision 1.7.0 (Feb 2020)
-------------------------

* Pull request
* from thobalose (https://github.com/cokelaer/bioservices/pull/149) to
update tests, travis recipes, pinned matplotlib to 3.0.3

* NEWS:
* panther module (pantherdb.org)
* add a test for the pubchem, pfam and eva modules, which are still
in draft version though

* CHANGES
* PICR module is fully commented. The service is most probably deprecated.
Not on EBI website anymore
* remove TCGA, which waws only a draft version with one method.

* BUGS and FIXES
* wikipathway: fixed getPathway, savePathway, getPathwayByLiterature and
coloredPathway methods. Some are failing due to some wikipathway
temporary failures.
* Fixed https://github.com/cokelaer/bioservices/issues/148 to have a more
informative error message (array express)
* Fixed KeggParser for the GENE entries to have the correct ID name.
https://github.com/cokelaer/bioservices/issues/151