OpenMSToffee

Contents

• OpenMSToffee: C++
  • OpenSwathWorkflow
  • Internal Class Structure
• OpenMSToffee: Python
  • Working with toffee files
  • Converting SRLs
  • Internal Class Structure

|| Master: || Dev:

OpenMSToffee is a wrapper around OpenSwath that allows us to use the toffee file format. It is available as a Docker image at cmriprocan/openms-toffee.

We follow the OpenVDB style guide for the C++ and PEP-8 for our python code, so please aim to stay consistent with the rest of the code base. Contributions will be pass through peer review and style will be one element that is reviewed.

Changes

Change Log

0.14

0.14.1

• Changed license to MIT and fixed documentation for https://openms-toffee.readthedocs.io
• Bumped version of toffee to 0.13.1, also MIT licensed

0.13

0.13.12

• Bumped version of toffee to 0.12.16, which now includes the mzML to toffee to mzML conversions
• Removed all mzML to toffee conversions from this package and deleted tests

0.13.11

• Bumped version of toffee to 0.12.9, which now includes the toffee to mzML conversion (PD-793)

0.13.10

• Bumped version of toffee to 0.12.4
• Many fixes to accommodate change in structure of the dia-test-data repository

0.13.9

• Added ability to convert toffee files to Spectra HDF5 files (PD-793)

0.13.8

• Bumped version of toffee to 0.11.1

0.13.6

• Bumped version of toffee to 0.10.6 (that fixes PD-749) and added unit test

0.13.5

• Bumped version of toffee to 0.10.5 (that fixes PD-735)

0.13.4

• Pinned version of toffee to 0.10.4 (that fixes PD-727)

0.13.3

• A few bug fixes for the mzML to toffee conversion

0.13.2

• Updated to version 1.2.4 of cmriprocan/openms.

0.13.1

• Significant refactor of the XML to toffee conversion process. This has been pulled apart into smaller modules such that individual parts can be tested. Importantly, the code that converts mzML and mzXML to HDF5 is now shared by the process that then converts these to toffee. This improves memory performance, and means that we can test both conversions.

0.12

0.12.1

• Directly linking to upstream image in Dockerfile: cmriprocan/openms:1.2.3 which:
  • Updated OpenMS to version CMRI-ProCan-v1.1.2
  • Updated PyProphet to 2.0.2

0.11

0.11.1

• Updated OpenMS to version CMRI-ProCan-v1.1.1 with hot-fix to solve https://github.com/OpenMS/OpenMS/issues/3860

0.10

0.10.1

• Updated OpenMS to version CMRI-ProCan-v1.1.0 that incorporates upstream Release2.4.0 with our changes that enable toffee files to be used on the command line

License

MIT Copyright (c) 2017-2019 Children’s Medical Research Institute (CMRI)

Indices and tables

• Index
• Module Index
• Search Page