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

PyHDX version 0.4.0 beta4

Major changes to plotting: (#232)

• Added functions for making standard output plots in the plot.py module

• Added functions for default colormaps and normalizers; defined default colormaps for standard data types (rfu, dG, ddG)

• Added plotting class FitResultPlot which makes it easier to generate plots from a fit result

• Updated the pdf output class (now named FitReport) which allows all standard plots to be combined into a .pdf file

• SingleFitResult and BatchFitResult are now merged into one object.

Changes:

• Switched to pandas DataFrame instead of numpy structured arrays for data object's internal tables (#227)
• Refactored uptake_corrected to d_exp for FD-corrected D-uptake values (#227)
• Properties rfu_residues, rfu_peptides are now pandas Series objects (#227)
• Removed python 3.6 support (#227)
• Added option to filter input data (peptide table data) in batch processing (8fa9c5b)
• Fitting can be done on a specific device (ie CUDA GPU) and the fitting dtype can be specified (float32/float54) (#231)

PyHDX version 0.4.0 beta3

Changes:

• Refactored config; moved config files, refactored cluster to scheduler_address where applicable (#220)
• Changed Lagrangian squared error reduction from 'total' to 'mean' (affecting regularization values) (#221)
• Regularization components are treated separately and stored in losses dataframe (#222)
• Internal time units are now in seconds (73c387c)
• Added optimization loop callbacks and checkpoint (#222)
• Allow for saving of HDXMeasurementSet objects to .csv/.txt file (9cca09f)
• Allow for reading of 'HDXMeasurementSet` objects from .csv/.txt file (4e9fcac)
• Implemented __str__ for HDXMeassurement objects (5122d23)
• Updated yaml batch formatting format (7d94411, 7c71847)

PyHDX version 0.4.0 beta2

Changes:

• Added additional fit feedback panels; MSE per peptide, D-uptake curves + fit and losses/epoch #212
• Documentation and docstrings (#210, #213, #214)
• Updated pdf module, now requires proplot and generates figure subplots per page instead of per subplot

Fixes:

• Fixed mse and losses for single fits
• Extension for table export (#218 )

PyHDX 0.4.0 first beta release

Big changes in the new 0.4.0 version!
Major changes include an overhaul of the web interface and refactoring of major parts in the code.
Thanks for all contributions @sebaztiano @sajetan

Major changes:

Web interface

• Users can add multiple datasets ('state') at the same time and perform analysis in batch on these datasets. The datasets, operations on these datasets and the resulting views show in the web interface are now all based on lumen objects (Source, Filter, Transform, View) #188
• NGL viewer was implemented as a custom bokeh extension #201
• Classification control panel can now also apply matplotlib/colorcet colormaps

Refactoring of the PyHDX API

• Fitting API is now functional instead of object oriented; fit_gibbs_global(..), fit_gibbs_global_batch(..) #199
• KineticsSeries object was refactored to HDXMeasurement
• Added HDXMeasurementSet object
• The scores attribute (percentage D-uptake) was refactored to rfu (relative fractional uptake, 0-1)
• Updated fileIO functions, enable saving of kwargs to reload the file as well as saving metadata #205
• Allow saving and loading of fit results (#208) and HDXMeasurement objects #205

Minor changes:

• Versioning by versioneer instead of pbr (#207)
• Added k_obs as output variable of the fit (ce4f583)
• Added console script entry point to run the web interface (pyhdx serve) #191
• Export of all peptide uptake graphs + fitted curves in pdf format #209

Bugfixes:

• Alignment of exchanges and k_int (8301686)

Bugfix release 0.3.2

Minor release fixing a bug in requirements.txt

PyHDX version 0.3.1

Major changes:

• Estimate errors in ΔG fit from covariances obtained from the Hessian
• Allow fitting of multiple 'states' (conditions) in batch
• Allow fitting of 2 aligned (homologous) protein conditions in batch
• Added console entry script such that the pyhdx server can be started with pyhdx serve (#191)

Minor changes:

• Input/output data table formats are now in comma separated values (.csv) format
• Updated support for reloading and fitting data in batch from .yaml files
• Updated rgb_to_hex function to work on arrays (vectorized)
• Added a colorbar to plotting of peptides (in plot.py)
• Refactored k_series to series in KineticsFitting objects
• Refactored cov to coverage in KineticsSeries objects
• Updates to docstrings
• Protein full sequences can optionally be added to Protein objects
• Moved fitting loop to separate function outside of main fitting object
• Protein objects now more closely mimic pandas' dataframes

Web application updates:

• 'Scores' (RFU) can be obtained as a table from the GUI
• User feedback on relative contribution of regularizer to fit result
• Control sidebar is now formatted as accordions where only one can be opened at a time
• Panel requirement bumped to >= 0.11, fixing scrolling issues in sidebar
• Added config file, currently lists default Dask cluster address to use

• Various bug fixes!

Thanks to @sajetan for contributing (#191, #181)

PyHDX version 0.3.0

v0.3.0

capitalized PyHDX name

bioRxiv and bugfixes

This release accompanies submission to bioRxiv as well as various bugfixes.

• Updates to documentation (available as pdf)
• Refactored how the apps are created in apps.py
• Added all sub-controllers in controllers.py and main controllers in main_controllers.py

Bugfixes:

• Fixed bug where linking the x range of panels would cause an error (610d985)
• Removed unused .data attribute (#108)
• Fixed updates of figures, now via callback (#117)
• Fixed protein view not updating without switching between datasets (#114)

Protein Viewer and Themes

This release features an embedded Protein Viewer and implementation of Panel Themes / Templates.

Main features:

• NGL Protein viewer
• Streamlined layouts with Elvis (https://github.com/LeonvanKouwen/elvis) with Panel Templates (panel >0.10.0)
• Color protein by custom continuous color map (36e7070)
• Added Dark/Light themes
• Separate app for loading single state fitting results and applying classification (coloring)
• Separate app for comparing two protein states

Other changes:

• Added DataSource object which is now used for 'publishing' data
• Control and Figure panels are now supplied to controller as their `class`` rather than a string
• Added setup_hooks() method to couple Figures to Controllers
• Added a Logging panel
• Fixed ignoring prolines to always be True

Fixes:

• read_to_np can read files with two comment lines and with hex color codes (#000000)
• Fixed datapoints without coverage showing up (#89)
• Fixed coverage intervals (#91)
• Various bugfixes
• Improved documentation