v0.4.4

PyHDX version 0.4.5 is mostly a maintenance update, with additional pinned dependencies, style changes, and added examples.

What's Changed

• Bump jinja2 from 3.1.2 to 3.1.3 in /requirements by @dependabot[bot] in #340
• Bump pillow from 10.0.1 to 10.2.0 in /requirements by @dependabot[bot] in #341
• Bump idna from 3.4 to 3.7 in /requirements by @dependabot[bot] in #343
• Bump pillow from 10.2.0 to 10.3.0 in /requirements by @dependabot[bot] in #342
• Bump tqdm from 4.66.1 to 4.66.3 in /requirements by @dependabot[bot] in #344
• Bump jinja2 from 3.1.3 to 3.1.4 in /requirements by @dependabot[bot] in #345
• Bump requests from 2.31.0 to 2.32.0 in /requirements by @dependabot[bot] in #346
• Bump tornado from 6.3.3 to 6.4.1 in /requirements by @dependabot[bot] in #347
• update gitignore by @Jhsmit in #351
• Lint by @Jhsmit in #352
• Bump certifi from 2023.7.22 to 2024.7.4 in /requirements by @dependabot[bot] in #355
• Bump urllib3 from 2.0.7 to 2.2.2 in /requirements by @dependabot[bot] in #354
• Bump zipp from 3.16.2 to 3.19.1 in /requirements by @dependabot[bot] in #356
• changed default ddG colormap no coverage color to yellow by @Jhsmit in #360
• switch to uplot, py310 by @Jhsmit in #362
• Bump tornado from 6.4.1 to 6.4.2 in /requirements by @dependabot[bot] in #363
• Bump jinja2 from 3.1.4 to 3.1.5 in /requirements by @dependabot[bot] in #364

Full Changelog: v0.4.3...v0.4.4

PyHDX version 0.4.3

Features

• Integrates with hdxms-datasets, allows public dataset loading from web interface (#327)

Fixes

• Fixed RFU app file input, improvements to web app peptide input (#318 )
• Fixed changing norms after plotting linear bars (e86bf4d)
• Various minor fixes

Dependencies

• Switched to proplot == 0.9.7 version requirement.

Deprecations

• Removed the Protein object (#315).

Packaging and distribution:

• Switched to hatch for packaging (#331).
• Switched to mkdocs for documentation building (#314).

PyHDX version 0.4.2

• Added a peptide uptake simulation app (#285 )
• Updated configuration object to Omegaconf, allow users to select different configuration files (#291)
• Adding fitting of D-uptake values per timepoint (#296)
• Perform per-timepoint D-uptake fitting and calculate ΔD-uptake in the web application (#297)
• Added storing and exporting of user settings and logs from web application (#301)
• Refactored how data is loaded into PyHDX (#305)

Fixes:

• Fixed bug where sessions files do not reload graphs (#289)

PyHDX version 0.4.1

Bugfix release and some updates to documentation:

• Fixed progress bars (4f557b9)
• Moved pyyaml requirement to base requirements (57835ee)
• Updated the readme (57835ee)
• Add resources and citation section to docs (cfc50e0)

PyHDX version 0.4.0

Release v0.4.0 is the combination of 9 beta versions, spanning a total of ~10 months of PyHDX development.
Please refer to the individual beta releases for more detail.

Major improvements of the new version 0.4.0 release are:

Base PyHDX:

• Batch fitting of multiple large HDX datasets (+ GPU support)
• Batch processing of large HDX datasets through .yaml file spec
• Added $pyhdx process CLI command (early alpha feature)
• Added plotting and pdf output modules
• Major API changes

PyHDX-web:

• Two complete overhauls of the web interface, improving internal logic of the web interface
• Updated the GoldenLayout template to a combination of panel's GoldenLayout and the elvis golden layout
• Addition of the PDBeMolstar protein viewer, allowing direct export of colored structures
• Direct output of publication quality graphs from the web interface
• Create differential HDX datasets (ΔΔG / ΔRFU)

This release:

• Updated docs and docstrings, introduced PEP483 type hints (#271)
• Update to panel version 0.13.0 (#264)
• Added black, mypy, flake8, (isort) linters

PyHDX version 0.4.0 beta9

• Updated async handling of tasks, removed loop in main controller checking for new futures (#255)
• Fitting of multiple protein states individually through the web interface (#257)
• Allows for either rates or deltaG initial guesses (#257)
• Allows for one-to-one or one-to-many initial guesses (#257)
• Data input in web app in batch through yaml spec file (#258)
• Fixed web application not working in Chromium (#259)
• Added $ pyhdx process cli command (#267)

PyHDX version 0.4.0 beta8

Changes:

• Added ΔRFU in web interface
• Fixed bug where duplicate entries appeared in controls by using corrected start and end fields
• Initial guesses are now interpolated at fitting function and guesses are now broadcast over sample axis
• Added MultiTransform which takes multiple sources as input and SelectTransform for the protein view (3d21e4d)
• Reverted template back to GoldenTemplate #249
• Fixed initial guesses by association model (fbe9c23)
• Added PDBeMolstar protein viewer #252
• Minor tweaks to web app css #254

PyHDX version 0.4.0 beta7

Changes:

• Web interface performance improved by using hashes and caches (#242)
• Export of grouped rfu linear bars (f779201)
• Graph export bugfix (34552b0)
• Added RFU app and index page (#243)

PyHDX version 0.4.0 beta6

Patch release with bugfixes and packaging updates

PyHDX version 0.4.0 beta5

This release features mostly an overhaul of the web interface (#234).

Internal changes:

• Created new classes handling data/parameter flow within the web interface: Source, Transform, View, Opts
• Added a Constructor class which generates the web application from a yaml spec file
• Color transforms (colormap + normalize) are now defined on a per-datatype basis (ie one for rfu, dG, ddG, mse). Default color transforms can be changed with the ColorTransformControl control panel.
• The NGL protein viewer is now implemented as ReactiveHTML, obviating the need for custom bokeh models
• Timepoint zero is by default not selected
• The template was updated to the FastGridTemplate.

New features:

• Scatterplot of RFU values per residue.
• Create differential HDX ΔΔG comparisons directly.
• Download .zip session file and restore session from session file.
• Download ΔG/ΔΔG proplot/matplotlib graphs (linear_bars, scatter, rainbowclouds) in .png, .pdf. .svg or .eps format.
• Export data tables as hex color code tables (for supported tables)
• Export of pymol coloring scripts for RFU values

Refactors:

• deltaG was refactored to dG (ddG for deltadeltaG)

Other changes:

• csv_to_dataframe now also accepts BytesIO objects
• local_cluster.default_cluster now accepts additional kwargs
• Various bugfixes

Full Changelog: v0.4.0b4...v0.4.0b5