Skip to content
PEPkit

Changelog

[0.12.9] -- 2025-12-01

Section titled “[0.12.9] -- 2025-12-01”
  • Improved error handling
  • Fixed incorrect return for processed series metadata

[0.12.8] -- 2025-07-08

Section titled “[0.12.8] -- 2025-07-08”
  • Updated docs
  • Fixed parsing nested items. [143]
  • Added pypiper to requirements [142]
  • Fixed white spaces in reference genome string [141]
  • Added version in CLI help [135]
  • Updated SRA convert to use looper > 2.0.0 and fully automate process

[0.12.7] -- 2024-09-11

Section titled “[0.12.7] -- 2024-09-11”
  • Updated Python support 3.13
  • Cleaned code and Readme

[0.12.6] -- 2024-02-05

Section titled “[0.12.6] -- 2024-02-05”
  • Updated support for Windows in Prefetch (Note: Some functionality may still be unavailable on Windows)

[0.12.5] -- 2023-11-29

Section titled “[0.12.5] -- 2023-11-29”
  • Fixed bug, where description was not populated in PEP

[0.12.4] -- 2023-08-01

Section titled “[0.12.4] -- 2023-08-01”
  • Fixed SRA convert
  • Added how to convert SRA

[0.12.3] -- 2023-06-21

Section titled “[0.12.3] -- 2023-06-21”
  • Fixed preserving order of project keys (#119)

[0.12.2] -- 2023-04-25

Section titled “[0.12.2] -- 2023-04-25”
  • Added max-prefetch-size argument. #113
  • Improved code and logger structure.

[0.12.0] -- 2023-03-27

Section titled “[0.12.0] -- 2023-03-27”
  • Added functionality that saves gse metadata to config file
  • Fixed description in initialization of pepy object

[0.11.2] -- 2022-12-25

Section titled “[0.11.2] -- 2022-12-25”
  • Changed sample_name of PEP of processed files to file oriented
  • Added --max-soft-size argument, that sets size limit of soft files
    • Added functionality that skips downloading GEO tables that are in soft files
  • Fixed bug of creating unwanted empty folders
  • Fixed problem with missing data

[0.11.1] -- 2022-11-28

Section titled “[0.11.1] -- 2022-11-28”
  • Fixed requirements file
  • Fixed bug in expanding metadata list
  • Fixed bug in metadata links

[0.11.0] -- 2022-10-26

Section titled “[0.11.0] -- 2022-10-26”
  • Added initialization of peppy Project without saving any files (from within Python using an API)
  • Added Finder (searching GSE tool)
  • Added progress bar
  • Switched way of saving soft files to request library
  • Improved documentation
  • Refactored code
  • Added --add-convert-modifier flag
  • fixed looper amendments in the config file
  • Fixed special character bug in the config file
  • Fixed None issue in config file
  • Fixed saving raw peps bug

[0.10.1] -- 2022-08-04

Section titled “[0.10.1] -- 2022-08-04”
  • Updated metadata fetching requests from SRA database

[0.10.0] -- 2022-07-07

Section titled “[0.10.0] -- 2022-07-07”
  • Fixed subprocesses continuing to run during program interrupt.
  • Fixed issues with compatibility with NCBI API

[0.9.0] -- 2022-06-20

Section titled “[0.9.0] -- 2022-06-20”
  • Updated --pipeline-interface argument that adds it in for looper. --pipeline-interface argument was divided into: --pipeline-samples and --pipeline-project.
  • Fixed empty sample_name error while creating PEP.
  • Added --discard-soft argument.
  • Added --const-limit-project argument.
  • Added --const-limit-discard argument.
  • Added --attr-limit-truncate argument.
  • Added "--add-dotfile" argument.
  • Disabled creating combined pep when flag --acc-anno is set.
  • Improved finding and separating metadata keys and genome assembly information.
  • Added standardization of column names by replacing characters to lowercase and spaces by underscore.

[0.8.0] -- 2022-03-10

Section titled “[0.8.0] -- 2022-03-10”
  • Added --filter-size argument.
  • Added --data-source argument.
  • Removed --tar_re argument.
  • Added PEP for processed data.
  • Updated regex filter (case-insensitive update).
  • Changed way of downloading processed data (downloading each file separately).
  • Fixed code errors.
  • Separated sample and experiment processed data.

[0.7.0] -- 2020-05-21

Section titled “[0.7.0] -- 2020-05-21”
  • Fixed user interface for bam conversions
  • Added regex filter for processed data filenames, which will also auto-extract from tar archives
  • Updated output to PEP 2.0
  • Added --skip argument
  • Added more control over where to store results.
  • Integrate sraconvert into geofetch package.

[0.6.0] -- 2019-06-20

Section titled “[0.6.0] -- 2019-06-20”
  • Fixed a bug with specifying a processed data output folder
  • Added a pre-check and warning message for prefetch command

[0.5.0] -- 2019-05-09

Section titled “[0.5.0] -- 2019-05-09”
  • geofetch will now re-try a failed prefetch 3 times and warn if unsuccessful.
  • Fixed a bug that prevented writing metadata in python3.
  • More robust SOFT line parsing
  • Use logmuse for messaging
  • Improve modularity to facilitate non-CLI use if desired
  • Better documentation

[0.4.0] -- (2019-03-13)

Section titled “[0.4.0] -- (2019-03-13)”
  • Fixed a bug with default generic config template
  • Added --version option
  • Improved python 3 compatibility

[0.2.0] -- (2019-02-28)

Section titled “[0.2.0] -- (2019-02-28)”
  • Fixed bugs that prevented install from pypi

[0.1.0] -- (2019-02-27)

Section titled “[0.1.0] -- (2019-02-27)”
  • First official release
  • Enabled command-line usage
  • Packaged geofetch for release on PyPI

[0.0.0] -- (2017-10-24)

Section titled “[0.0.0] -- (2017-10-24)”
  • Legacy, unversioned development initiated