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cokelaer committed Jan 27, 2025
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41 changes: 20 additions & 21 deletions README.rst
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Expand Up @@ -20,7 +20,7 @@ BIOSERVICES: access to biological web services programmatically
.. image:: https://static.pepy.tech/personalized-badge/bioservices?period=month&units=international_system&left_color=black&right_color=orange&left_text=Downloads
:target: https://pepy.tech/project/bioservices

.. image:: https://anaconda.org/conda-forge/bioservices/badges/version.svg
.. image:: https://anaconda.org/conda-forge/bioservices/badges/version.svg
:target: https://anaconda.org/conda-forge/bioservices


Expand All @@ -29,14 +29,14 @@ BIOSERVICES: access to biological web services programmatically


:Python_version_available: BioServices is tested for Python 3.9, 3.10, 3.11, 3.12
:Contributions: Please join https://github.com/cokelaer/bioservices
:Contributions: Please join https://github.com/cokelaer/bioservices
:Issues: Please use https://github.com/cokelaer/bioservices/issues
:How to cite: Cokelaer et al. *BioServices: a common Python package to access biological Web Services programmatically*
`Bioinformatics <http://bioinformatics.oxfordjournals.org/content/29/24/3241>`_ (2013) 29 (24): 3241-3242
:Documentation: `RTD documentation <http://bioservices.readthedocs.io/>`_.

**Bioservices** is a Python package that provides access to many Bioinformatices Web Services (e.g.,
UniProt) and a framework to easily implement Web Services wrappers (based on
UniProt) and a framework to easily implement Web Services wrappers (based on
WSDL/SOAP or REST protocols).


Expand All @@ -48,12 +48,12 @@ One of the main philosophy of **BioServices** is to make use of the existing
biological databases (not to re-invent new databases) and to alleviates the
needs for expertise in Web Services for the developers/users.

BioServices provides access to about 40 Web Services.
BioServices provides access to about 40 Web Services.

Contributors
============

Maintaining BioServices would not have been possible without users and contributors.
Maintaining BioServices would not have been possible without users and contributors.
Each contribution has been an encouragement to pursue this project. Thanks to all:

.. image:: https://contrib.rocks/image?repo=cokelaer/bioservices
Expand All @@ -68,7 +68,7 @@ organism::

>>> from bioservices import UniProt
>>> u = UniProt(verbose=False)
>>> data = u.search("zap70+and+taxonomy_id:9606", frmt="tsv", limit=3,
>>> data = u.search("zap70+and+taxonomy_id:9606", frmt="tsv", limit=3,
... columns="id,length,accession, gene_names")
>>> print(data)
Entry name Length Entry Gene names
Expand All @@ -80,10 +80,10 @@ organism::
.. note:: major changes of UniProt API changed all columns names in June 2022. The code above is valid for bioservices
versions >1.10. Earlier version used::

>>> data = u.search("zap70+and+taxonomy:9606", frmt="tab", limit=3,
>>> data = u.search("zap70+and+taxonomy:9606", frmt="tab", limit=3,
... columns="entry name,length,id, genes")

Note that columns names have changed, the frmt was changed from tab to tsv
Note that columns names have changed, the frmt was changed from tab to tsv
and taxonomy is now taxonomy_id. Names correspondences can be found in::

u._legacy_names
Expand Down Expand Up @@ -177,7 +177,7 @@ wikipathway .. image:: https://github.com/cokelaer/bioservices/actions
:target: https://github.com/cokelaer/bioservices/actions/workflows/wikipathway.yml
==================== ================================================================================================

.. note:: Contributions to implement new wrappers are more than welcome.
.. note:: Contributions to implement new wrappers are more than welcome.
See `BioServices github page <https://github.com/cokelaer/bioservices/>`_
to join the development, and the Developer guide on how to implement new
wrappers.
Expand All @@ -187,7 +187,7 @@ Bioservices command

In version 1.8.2, we included a bioservices command. For now it has only one subcommand to download a NCBI accession number and possibly it genbank or GFF file (if available)::

bioservices download-accession --accession K01711.1 --with-gbk
bioservices download-accession --accession K01711.1 --with-gbk


Changelog
Expand All @@ -197,16 +197,15 @@ Changelog
========= ====================================================================
Version Description
========= ====================================================================
1.13.0 * Fix pyproject missing requirements
1.12.0 * Fix pyproject missing requirements
* Fix pkg_resources warning
* drop python 3.8, add py3.12
1.12.0 * migrating to pyproject
1.11.2 * Update COG service to be more user-friendly and return all pages
by default
* uniprot set progress to False in the search method
* Merged #250 and #249 user PRs (compress option in uniprot module
* Merged #250 and #249 user PRs (compress option in uniprot module
and logging issue in biodbnet)
1.11.1 * Fix regression i uniprot.mapping
1.11.1 * Fix regression i uniprot.mapping
(https://github.com/cokelaer/bioservices/issues/245)
1.11.0 * Fix uniprot limitation of 25 results only (
* For developers: all services are now refactorised to use services
Expand All @@ -218,7 +217,7 @@ Version Description
* remove biocarta (website not accesible anymore)
* Update Chembl (no API changes)
1.10.2 * Fix #226 and applied PR from Fix from @GianArauz
https://github.com/cokelaer/bioservices/pull/232 about UniProt
https://github.com/cokelaer/bioservices/pull/232 about UniProt
error
* Update MANIFEST to fix #232
1.10.1 * allow command line to download genbank and GFF
Expand All @@ -229,30 +228,30 @@ Version Description
1.8.4 * biomodels. Fix #208
* KEGG: fixed #204 #202 and #203
1.8.3 * Eutils: remove warning due to unreachable URL. Set REST as
attribute rather and inheritance.
attribute rather and inheritance.
* NEW biocontainers module
* KEGG: add save_pathway method. Fix parsing of structure/pdb entry
* remove deprecated function from Reactome
1.8.2 * Fix suds package in code and requirements
1.8.1 * Integrated a change made in KEGG service (DEFINITON was changed to
ORG_CODE)
* for developers: applied black on all modules
* switch suds-jurko to new suds community
1.8.0 * add main standalone application.
* switch suds-jurko to new suds community
1.8.0 * add main standalone application.
* moved chemspider and clinvitae to the attic
* removed picr service, not active anymore
1.4.X * NEW RNAseq from EBI in rnaseq_ebi module
* Replaced deprecated HGNC with the official web service from genenames.org
* Fully updated EUtils since WSDL is now down; implementation uses REST now.
* Removed the apps/taxonomy module now part of http://github.com/biokit.
* Removed the apps/taxonomy module now part of http://github.com/biokit.
1.3.X * CACHE files are now stored in a general directory in the home
* New REST class to use **requests** package instead of urllib2.
* New REST class to use **requests** package instead of urllib2.
* Creation of a global configuration file in .config/bioservice/bioservices.cfg
* NEW services: Reactome, Readseq, Ensembl, EUtils
1.2.X * NEW services: BioDBnet, BioDBNet, MUSCLE, PathwayCommons, GeneProf
1.1.X * NEW services: biocarta, pfam, ChEBI, UniChem
1.0.0: * first stable release
0.9.X: * NEW services: BioModels, Kegg, Reactome, Chembl, PICR, QuickGO,
0.9.X: * NEW services: BioModels, Kegg, Reactome, Chembl, PICR, QuickGO,
Rhea, UniProt,WSDbfetch, NCBIblast, PSICQUIC, Wikipath
========= ====================================================================

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2 changes: 1 addition & 1 deletion pyproject.toml
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Expand Up @@ -4,7 +4,7 @@ build-backend = "poetry.core.masonry.api"

[project]
name = "bioservices"
version = "1.13.0"
version = "1.12.0"
description = "Access to Biological Web Services from Python"
authors = [{name="Thomas Cokelaer", email="thomas.cokelaer@pasteur.fr"}]
license = "GPLv3"
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