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History

2.0.3 (2021-02-03)

  • BUGFIX: shutil.move can lead to "operation not permitted" error
  • Allow to download small GSE object by using how parameter

2.0.2 (2020-08-26)

  • Allow to pass kwargs to open function to controll eg. encoding

2.0.1 (2020-02-20)

  • prevent installation on old python versions

2.0.0 (2020-02-20)

  • Drop support for python 2
  • Fix issue with SRR entiries not being available through FTP server
  • Better error message if entry is not available
  • Better code formatting
  • Some small improvements

1.2.0 (2019-08-21)

  • Remove BioPython dependency - use requests instead
  • Replace wget with custom file downloader
  • Allow to parse GSE file partially
  • Support for parallel-fastq-dump
  • Allow to use proxy server (FTP)
  • Fix Travis-CI issues with FTP download
  • Various bugfixes

1.1.0 (2018-09-10)

  • Allow parallel download of supplementary files
  • Add timeout to urlopen callsq
  • Bugfix: Keep logger as a module name and rename logger object to geoparse_logger. This is a breaking change.
  • Bugfix: Some samples do not have table data error in python 3
  • Bugfix: broken download when supplementary_files is empty or contains invalid URLs
  • Some small bugfixes

1.0.5 (2018-01-12)

  • Bugfix: Some samples do not have table data error in python 3

1.0.4 (2018-01-08)

  • Bugfix: Empty line in the SOFT file caused an error in python 3

1.0.3 (2017-11-01)

  • Bugfix: Fixed the FTP link

1.0.2 (2017-11-01)

  • Bugfix: type name was depended on the order of entries

1.0.1 (2017-08-10)

  • Hotfix: wrong path split in Windows

1.0.0 (2017-07-21)

  • Many small bug fixes: * unknown subset types added to columns * silent=True is really silent * correct treatment of duplicated columns * illegal file names and no filtering of user input from GEO to create the file names * platform was not imported but used * fixed issues of python 2 and 3 compatibility
  • Logging replaced stdout and stderr + ability to set verbosity and log file
  • Return downloaded paths from download functions
  • Updated documentation according to Google docstring style guide
  • Tests update
  • Code refactored to be more PEP-8 friendly

0.1.10 (2017-03-27)

  • Important fix for SRA download
  • Fix duplicated columns issue
  • Python 2 and 3 open compatibility

0.1.9 (2017-03-10)

  • Added property phenotype_data to access phenotype data of GSE
  • Fixed windows issue with file names
  • replaced default download function with wgetter
  • Update documentation
  • Various bugfixes

0.1.8 (2016-11-02)

Thanks to Tycho Bismeijer:

  • Python 3 Compatibility
  • Bio.Entrez dependency optional

0.1.7 (2016-05-30)

Thanks to Simon van Heeringen:

  • bugfix in datasets with multiple associated relations
  • --split-files to fastq-dump to support paired-end experiments by default
  • parse a GPL that also contains series and sample information
  • gsm2fastq command to make download easier
  • initial Aspera download support

0.1.6 (2016-04-12)

  • Bugfixes
  • SRA function of GSE can now filter GSMs

0.1.5 (2016-02-03)

  • Added functions to download supplementary files including raw files from SRA

0.1.4 (2015-09-27)

  • Updated documentation including example
  • Updated tests: they now cover 80% of library with all important functions
  • Added pivot_and_annotate method to GSE object
  • Bugfixes

0.1.3 (2015-08-30)

  • Updated documentation
  • Added pivot_samples to GSE object
  • Code of GEOTypes was refactored
  • All objects now have to_soft function
  • Various bugfixes

0.1.2 (2015-08-23)

  • Added GDS support
  • Added to_soft methods to GSE, GSM and GPL
  • Added DATABASE entry support to GSE and GDS

0.1.1 (2015-08-16)

  • Brown-Bag release

0.1.0 (2015-08-16)

  • First release on PyPI.