4.0.0 - 2022-10-11

Added

• Anaconda environments. There are two anaconda environments included
  inside the source folder at the moment. anaconda-environment.yml and
  dev-environment.yml. These should provide a nice starting point for
  anyone wanting to work on or with PyPWA. Pull requests are welcomed
  if you think a package should be added to the base environment.
• Added PyTorch for GPU and Apple Metal support. Can be specified during
  install using pip install pypwa[torch]. Amplitude support is specified
  by setting the USE_TORCH flag to True.
• Added support for Python's Multithreading. You should only use this when
  computation is happening on separate nodes and/or your optimizer choice
  does not support passing it's values across an OS Pipe.
• Added support for Minuit's parameter array argument. Now amplitudes can
  be written to accept a single array containing all the array values.
• Debugging support for amplitudes is now explicit. You can set the DEBUG
  flag to True on your amplitude before simulation or fitting, and it'll run
  in the main process so traceback and errors will not be suppressed.
• Amplitudes can now know where they live. Amplitudes have a THREAD flag
  that is numbered from 0 to N-threads that will specify which thread the
  amplitude is running in. This is useful if you want to pair your
  processes/threads with external devices like GPUs or OpenMPI nodes.

Changed

• Data module will no longer bury the Cache object. The cache object will
  now reside in the same directory as the parsed data.
• Moves Emcee to an optional dependency so that PyPWA can function in a
  base anaconda environment. If Emcee is installed, or if emcee is
  specified during installation using pip install pypwa[emcee], the
  emcee functionality will be usable.
• iMinuit has changed their ABI entirely, so the iminuit function has
  been changed to adapt to the new ABI.
• Updated all dependencies around ReadTheDocs to avoid GitHub flagging
  the dependencies for exploits.

Removed

• Project manager. There were several bugs throughout the module, and as
  far as we are aware, no users using the module. If you're affected by
  this change, please open an issue in the issue tracker to let us know.
• Removed the command line Binning utility. The Jupyter-based and
  internal binning utilities remain unaffected. If this affects you,
  please open an issue.
• Removed appdirs as a dependency.
• Removed CuPy support, replaced by PyTorch.
• Removed PyYaml Configuration support.

Fixed

• The bin by range function was not sampling data correctly. The intended
  behaviour was for each bin to be sampled by N samples, and then those
  samples to be shuffled to add randomization. However, because the
  shuffling was improperly implemented, what would occur instead is a single
  random event would be dropped from the sample, and then returned. This
  no longer occurs, and the returned bins will now be the correct length,
  and will be correctly shuffled.

3.4.0 - 2021-7-23

Added

• Peter's emcee wrapper, available at PyPWA.mcmc

Changed

• System tests are now located in tests/system_tests
• PyMask will now return exit values on call

Removed

• PySimulate has been removed since it was limited in use, and it's functionality has been consumed by the PyPWA scripting libs.

3.3.0 - 2021-6-20

Added

• 2D Gauss introductory tutorial to the documentation
• CuPy support for Likelihoods and Simulation. This update means we now officially support NVIDIA GPU acceleration; however, for now, it is limited to a single GPU. If there is enough demand for multiple GPU support, we will expand processes to support deploying to GPUs.

Changed

• Particle now requires a charge to be supplied during the creation of the object. GAMP was also modified to support passing charge to the Particle
• Depreciated internal options Minuit options have been replaced with modern alternatives.

Fixed

• Likelihoods were spawning multiple processes with USE_MP set to false. Now Likelihoods will avoid creating additional processes as intended.

v3.2.3 - 2021-6-11

Added

• Particle Pools can now compared against other Particle Pools to see if they
  are storing the same content.

Fixed

• Regression from 3.2.0 where Gamp would not write out data to disk. This time
  by wrapping the data in a float, which should catch instances where the value
  stored is a pure scalar, verses instances where the data is an array with a
  len == 1

3.2.2 - 2021-6-11

Fixed

• Particles can now be masked again, the mask is no longer silently deleted
  when passed to the object.
• Numpy's warning about numpy.float being deprecation should be resolved.
• Any warnings about the LaTeX in the Likelihood's Docstrings being
  deprecated should be resolved as well.

v3.2.1 - 2021-6-10

Fixed

• Gamp no longer combines particles with the same ID
• Fixed issue where display_raw would fail in Jupyter with Particles

3.2.0 - 2021-6-1

Added

• Vectors now support iPython and Jupyter Pretty printing

Changed

• Vector sanitization function has improved handling of non-array inputs

Fixed

• FourVectors variable order is now in the correct order
• Vectors now work with inputs that aren't arrays
• Patched issue with GAMP failing to write to file

3.1.0 - 2020-10-2

Added

• Helper functions pwa.pandas_to_numpy to convert Pandas data types to
  Numpy Structured Arrays, and pwa.to_contiguous to convert DataFrames
  and Structured Arrays columns to contiguous arrays for quicker
  processing and C/Fortran Support
• New experimental file format ParticleGZ, a direct-to-memory file format
  using pickle, csv, and Tar/GZ to compress data into a single archive for
  easy use.
• Reference documentation to the Read The Docs for the various modules
  in PyPWA.
• Initial examples section added.

Changed

• Users now have to option to request structured Numpy arrays or Pandas
  DataFrames from pwa.read and pwa.get_reader
• pwa.cache now defaults to intermediate caching, and has to be disabled
  for use with caching files
• Vectors str and repr field now output the mean of their theta, phi, as well
  as particle id and mass if they are available.
• Vectors now wrap individual numpy arrays instead of a single structured
  array or DataFrame. This was done to improve performance of the vector
  as well as to make it C contiguous.

Fixed

• pwa.write would fail to write CSV Numpy Arrays
• pwa.write would occasionally fail to detect DataFrames
• Vectors would occasionally replace their fields with just their x values.

Release: 3.0.0 - 2020-6-4

Added

• ProjectDatabase has been added handle large data manipulation on disk
  instead of in memory.
• Reader/Writer now share path of the file being operated on.
• Binning now works in both fixed count and ranges, and can be done
  entirely in memory.
• Initial Jupyter and IPython support.
• Adding lego plotting.
• Likelihoods are now standalone objects that can be combined with any
  optimizer.
• Resonance support now builtin using DataFrames as a backbone.
  Resonances are now saved as a two sheet excel file, and can be modified
  using the supplied wave and resonance objects.
• Adds support for Numexpr to accelerate computation.
• Simulation can be done as two separate parts through PyPWA.simulate
• Github Templates to help users and developers contribute to PyPWA

Changed

• Separate release tag from version info
• Package info is now stored in PyPWA.info
• pydata has officially been updated to PyPWA 3.0.
• Structured Arrays have been replaces for Pandas DataFrames in some
  cases. Vectors still wrap regular numpy arrays to maintain performance.
• Reactions have been merged into ParticlePool.
• Vectors have been simplified to be easier to test while still being
  powerful to use.
• ProcessInterfaces now must be closed after use. This includes all
  Likelihood objects.
• Cache has been refactored to be easier to be completely usable by
  itself.

Removed

• SlotTable has been removed in favor of Project. Both use PyTables
  for the backend.
• Unsupported Python versions removed from package's classifiers.

Fixed

• GAMP no longer claims that it can read PF files.
• Cache will correctly report invalid when it's contents differ from the
  source file.
• monte_carlo_simulation and likelihoods now correctly handle exceptions
  that occur in the child processes.
• Pipes are correctly closed now.
• Extended Log-likelihood is now correctly calculated
• Sv Writer will now write data.
• Kv Reader will now read data.

Release v3.0.0a1

Added

• Added numpy reader and writer.
• Adds a helper script to clean the project directory of caches.
• Adds initial documentation for PyPWA.
• Added support for 3 Vectors, 4 Vectors, and Particles
• Added ParticlePool to aid in working with multiple Particles
• Added a binning utility that supports multiple binning variables and
  dimensions
• Added PyTables support, so that large datasets can be easily managed

Changed

• All program names have been lowercased
• Configuration package has been compressed into a single module
• PySimulate now is a library that has no UI, and has a UI portion
  that exclusively works with interfacing
• Fuzzywuzzy is now optional
• Process package is now a single module. Interface no longer uses IS_DUPLEX
• Bulk of program functionality moved to libs, progs being just for UI
• Builtin Plugins moved to libs, old plugin's plugins have still reside
  in plugins, but under a package with the appropriate name. I.E. data
  plugins are in plugins/data.
• All file related libs have been moved to libs/file
• Combined optimizers with fit library
• GAMP was updated to use Particles and ParticlePool
• Files with extra newline should parse correctly now
• CSV and TSV files will be lf instead of crlf on linux systems now

Removed

• Nestle Minimization. There is currently no clear way to have Minuit and
  Nestle to operate with each other nicely. Implementation for multiple
  optimizers will remain, as well as new associated issues created.
• Removed support for all version of Python before 3.7