v1.0.0

This release sees a complete re-work of pgfinder with a fully featured WebUI for users to process their data.

Processing is now performed in pyodide, a Python WebAssembly framework and a new WebUI is provided using the Svelte framework.

The two pginder-gui is now part of the main repository and the Python backend now resides under the libdirectory.

PGFinder v0.0.3

Small but significant changes in this release.

myBinder has recently lost significant resources (see here for further details).

We have also found that uploading the .ftrs and maxquant files can take some time.

A new approach is therefore being adopted that uses JupyterLite which runs the notebook entirely in the users browser without the need to first start a server locally. This does have a slight downside in that it requires the installation of PGFinder and its dependencies when running the notebook which can take 30 seconds or longer depending on the connection. Users also have to be careful about not using a cached version of the PGFinder package, particularly if they wish to test new development versions.

There are expanded instructions on how to use the Notebook which can be viewed at mesnage-org.github.io/pgfinder-jupyterlite.

If you encounter problems please let us know by creating an issue.

What's Changed

• ruamel.yaml > pyYAML no longer depend on ruamel.yaml for reading and writing YAML files.
• Notebooks now redirect to mesnage-org.github.io/pgfinder-jupyterlite.
• README.md redirects to mesnage-org.github.io/pgfinder-jupyterlite.

Full Changelog: v0.0.2...v0.0.3

PGFinder v0.0.3-a3

Release candidate for v0.0.3

PGFinder v0.0.3-a2

What's Changed

• Remove the ruamel.yaml dependency from pyproject.toml by @ns-rse in #160

Full Changelog: v0.0.3-a1...v0.0.3-a2

PGFinder v0.0.3-a1

In attempting to get Interactive Notebooks running under JupyterLite (see #151 ) switching to pyYAML from ruamel.yaml.

What's Changed

• ruamel.yaml > pyYAML; testing and dev dependencies added by @ns-rse in #159

Full Changelog: v0.0.2...v0.0.3-a1

PGFinder v0.0.2

The PGFinder team are pleased to announce the release of v0.0.2

What's Changed

The majority of changes are internal and do not affect the user interface/Notebooks.

Internal Changes

• Improved logging and removal of print() statements.
• Improvements to tests.
• Keeps data in "long" format whilst processing, only reshapes to "wide" when writing output.
• Automatic versioning using setuptools_scm.
• Removed dependency on pysqlite3.
• Packages are built and deploy to PyPI and Sheffield ORDA automatically.

User visible Changes

• Introduction of entry point (Command Line Interface) to run PGFinder at the command line (see find_pg --help after installation for more details).
• Calculates Difference in PPM between observed and theoretical masses when there are matches.
• Determines best match based on smallest absolute difference in PPM, if there are multiple matches these are retained.

IMPORTANT The MyBinder service recently lost significant resources (see here for details). This means users may find that at times the Interactive Notebook will not launch as there are no available hosts to run the code. We are looking into alternative stable solutions.

New Contributors

• @ns-rse made their first contribution in #75
• @TheLostLambda made their first contribution in #138

Full Changelog: v0.1.0...v0.0.2

PGFinder

What's Changed

• Correct interactive notebook link by @bobturneruk in #55
• Add test for ftrs files by @bobturneruk in #59
• Better error message when no matches found. by @bobturneruk in #58
• Add test coverage report by @bobturneruk in #61
• Metadata by @bobturneruk in #60

Output files now contain metadata in the title of the first column, see readme for details.

Full Changelog: v0.02...v0.1.0

PGFinder

Added support for O-Acetylation (response to reviewers comments)
Code depreciation messages fixed

PGFinder

Initial release of PGFinder, this version is the one used in the citing paper