Changelog for ppx



  • Fix links to MassIVE ccms_peak files. See this issue for details.



  • MassIVE and PRIDE links…again



  • Fix Test status badge.



  • Updated the ReadTheDocs configuration.



  • Linting and formatting is now performed with Ruff.

  • Migrated to pyproject.toml based build.


  • Fixed MassIVE FTP URLs using the MassIVE PROXI API.

  • Fixed PRIDE FTP URLs… again.

  • Updated unit tests with new PRIDE FTP URLs.

[1.3.0] - 2022-04-39


  • Support for cloud provider destinations. Thanks @sooheon!

[1.2.6] - 2022-03-16


  • Some PRIDE projects were still not working due to their recent URL change. This patch makes the our hotfix from v1.2.3 more robust.

[1.2.5] - 2021-11-05


  • Support for MassIVE reanalyses (accessions that start with RMSV)

[1.2.4] - 2021-11-23


  • New --timeout parameter for the command line interface, enabling custom timeout durations introduced in v1.2.0

  • New --version parameter for the command line interface to get the version number.

[1.2.3] - 2021-11-05


  • Hotfix for PRIDE’s recent FTP URL change (see #18 for details).


  • ppx progress bars now work much better in Jupyter environments. Under the hood we switched from from tqdm import tqdm to from import tqdm.

[1.2.2] - 2021-10-12


  • Lowered the Requests version requirement to 2.23.0. This resolves a problem installing ppx in Google Colab environments.

[1.2.1] - 2021-10-11


  • New file_info() method for MassIVE projects uses the GNPS API to get information about the files in a project.

[1.2.0] - 2021-09-14


  • New timeout parameter for most functions and classes. This specifies the maximum amount of time to wait for a response from the server.


  • The backend for MassIVE now uses the GNPS API to list files and projects, only falling back to scraping the FTP server on failure. This should make it much faster. Thanks @mwang87!

  • Files and projects are now returned in sorted order.


  • Poor connections with PRIDE were leading to a number of occasional errors. Multiple reconnect attempts are now tried for a wider variety of FTP operations.

[1.1.1] - 2021-07-02


  • Downloading files is now more robust. ppx will now retry FTP connections up to 10 times if the connection was dropped or refused.

  • Partial downloads are now continued automatically by comparing the local file size to the remote file size.

[1.1.0] - 2021-05-18


  • The PRIDE REST API was not yielding all of the available files on the their FTP server for a project. We changed the backend use the FTP server directly instead. Note that this may change the number, identity, and order of the file that were previously returned for PRIDE projects!

  • Small documentation updates.


  • Caching of the remote files and directories found for a project. If a project’s fetch attribute is False, then we’ll rely on this cached data, so long as it is available. Setting fetch=True will always refresh the data from the repository.

[1.0.0] - 2021-05-14


  • We did a complete rework of the API! This will break nearly all previous code using ppx, but greatly improves its versatility. See the docs for more details

  • Updated the build to align with PEP517


  • A command line interface for downloading files from PRIDE and MassIVE projects.

  • Additional unit tests.

  • A ppx logo

  • This changelog.

  • ppx is now available on bioconda!