History¶
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.