pynucastro 2.2.0

2.2.0

• Switch to using math.fsum() instead of sum() for better python
  3.12 compatibility (#720)

• Some modernization of the AMReX-Astro C++ code output (#709, #714,
  #717)

• Documentation improvements, including references and contributing
  instructions, and NSE table (#669, #679, #695, #697, #706, #707)

• Clean-up up some plot interfaces to always take rho, T, comp in
  that order (#693)

• Performance improvements (#680, #685, #692)

• A new constants module was added to provide fundamental constants
  (#688)

• A new NumpyNetwork was added for use with the rate reduction
  algorithm (#684)

• Neutrino cooling routines based on Itoh et al. 1996 were added
  (#628)

• A new method for generating an NSE table was added (#676)

• A new NSENetwork class was added for dealing with NSE (#675)

• Moved some screening utilities out of RateCollection (#666)

• A PythonNetwork now write out a function to compute the energy
  release (#640)

pynucastro 2.1.1

2.1.1

• RateCollection.evaluate_energy_generation() can now return the
  neutrino losses from weak rates separately. (#665)

• AmrexAstroCxxNetwork now capitalizes the species names to be
  consistent with other AMReX-Astro Microphysics networks (#652)

• The pynucastro project configuration was updated and reorganized
  to pyproject.toml (#657, #660, #661)

• Library.get_rate_by_name no longer returns None if one of
  the input rate names is not found (#659)

• A C++ indexing error at the boundary of a weak rate table was
  fixed. (#654)

• The C++ AmrexAstroCxxNetwork for evaluating weak rate neutrino
  losses was cleaned up to fix a bounds error (#655)

• We now explicitly check in the C++ code if a weak rate table
  if found and contains data (#654)

• a RateCollection now enforces that there are no duplicate rates. A
  find_duplicate_links() method has been added to Library to allow
  one to construct a Library without duplicates and then create a
  RateCollection or other network from that. (#651)

• Some documentation updates (#643, #650)

• The positron rates in the Langanke weak rate tables have been
  merged with the corresponding electron rates and the n <-> p rate
  was added (#648)

• The Composition.bin_as() method now takes a list of nuclei
  to exclude from being binned into (#642)

• RateCollection.evaluate_ydots() now can take a filter to
  only evaluate a subset of the rates. (#641)

pynucastro 2.1.0

• add eval_zbar() to Composition (#632)

• fix get_rate_by_name to work with "pp" reactions (#632)

• created a method to reduce a Composition from one set
  of nuclei to another based on the nuclei masses and
  charge number (#625)

• switch AmrexAstroCxxNetwork to do bilinear interpolation
  in terms of log(T) and log(rhoY) (#592, #611)

• tabular rates in python now do linear interpolation (#602)

• added an example of creating a custom rate (#615)

• Rate now calls _set_q() to set the Q value if it is not
  passed in (#617)

• added a TableInterpolator that works both for interactive
  python and PythonNetwork (#612, 610, 609)

• added a RateCollection method to find duplicate links (#601)

• python networks with tabular rates now copy the table files (#605)

• added a get_nuclei_in_range method to return a range of
  nuclei (#593)

• we now do a binary search in the C++ partition function
  interpolation (#581)

• added a simple C++ network (SimpleCxxNetwork) (#591, #585)

• added the weak rates from Langanke 2001 (#536)

• cleaned up partition functions in C++ (#578, 573, 569, 565)

• converted the Suzuki tabular rates to be in terms of log (#550)

• fixed a bounds issue in C++ table interpolation (#566)

• eliminated a variable length array in the C++ table interpolation
  (#567)

• added rate indices to the C++ networks (#563)

• added a network reduction algorithm (#529, #528, #527, #526, #525,
  #523)

• added a molar fraction method to Composition (#546)

• added examples of interfacing with Julia (#539)

• added a code of conduct (#504)

• added gamma heating to tabular weak rates (#502)

pynucastro 2.0.3

2.0.3

• add functions to numerically evaluate the Jacobian (#467)

• Fix C++ compilation with partition functions and approximate
  rates and derived rates (#407, #494)

• The Explorer class now takes all of the options as
  RateCollection.plot() (#496)

• Rates edges can be highlighted via a user-defined function in the
  RateCollection plot (#486)

• All of the plot routines in RateCollection now return a
  matplotlib Figure object (#490)

• add get_rate_by_nuclei and add_rate to Library() (#484)

• RateCollection.remove_rates() can now act on a single rate and a
  new method, add_rates(), will add a rate directly to the
  collection.

• Fixed printing of TabularLibrary (#479)

• Documentation updates (#473)

• added get_rate_by_name to RateCollection (#468)

• added tabular rates to PythonNetwork (#451)

• fixed NSE state for network without protons (#463)

pynucastro 2.0.2

fix a setup.py install issue for the C++ templates

pynucastro 2.0.1

2.0.1

-- Fix some setup.py metadata for PyPI (#453)

-- Change how tabular rate tables are stored and read (#450)

-- Support historial ReacLib format (#449)

pynucastro 2.0.0

2.0.0

-- Added a method to get a rate by short name: A(x,y)B (#438)

-- Added the option to show rate links hidden by ydot <
ydot_cutoff_value (#436)

-- Added a TabularLibrary (#429)

-- Moved validate into RateCollection (#433)

-- renamed StarKillerCxxNetwork to AmrexAstroCxxNetwork (#426)

-- Fixed formatting of tabular rate strings (#421)

-- Fixed normalization of colorbar in grid_plot (#424)

-- Added the ability to plot neutrino loss for tabular rates (#422)

-- Added support for partition functions in C++ networks (#404)

-- NSE solver now can return chemical potentials (#415)

-- Add spins to NSE calculatons (#405)

-- Separate the Coulomb calculation from the NSE screening, make it
switchable (#398, #380)

-- Fixed StarKillerCxxNetwork output directory (#400)

-- Added Potekhin screening (#385)

-- Added screening to python networks (#383)

-- Numba accelerated screening (#373)

-- Fixed C++ approximate rate screening (#384)

-- Added RateCollection remove_rates() (#368), and allow
remove_rates to operate on dictionary keys (#375)

-- Added NSE solver (#339, #364, #377)

-- added find_unimportant_rates method (#367, #369, #374)

-- added spins to partition functions (#371)

-- Split rate up into several classes, including ReacLibRate (#362)
and TabularRate (#360)

-- added partition function support to python networks (#358)

-- fixed definition of inverse rate for symmetric screening (#363)

-- Moved Nucleus into nucdata (#346)

-- Added screening to RateCollection (#344)

-- Added approximate rate support to C++ (#333)

-- C++ networks now hardcode the coefficients in a function to
compute the rates instead of storing a metadata table that is
read at runtime (#329)

1.7.0

-- the Rate class now knows how to make its function string in
python and C++ (#328)

-- C++ networks now have a std::vectorstd::string of rate names
(#326)

-- support for Fortran networks was removed (#324)

-- numerous optimizations (#263, #264, #321, #331)

-- a DerivedRate class was added (#272)

-- approximate rate support was added to python networks (#316, #315, #313, #271)

-- energy generation was added to python networks (#301)

-- support for inert nuclei was added (#307)

-- the ability to disable rates in C++ networks was added (#304, #290)

-- methods for finding reverse rates were added (#303)

-- a method to find neutrino loss energy from tabulated rates was added (#302)

-- the ability to run without Numba was added (#300)

-- weak rate table units in the header were fixed (#297)

-- python nuclei variable indicies now begin with 'j' (#296)

-- python implementations of screening were added (#281)

-- the network chart plot was added (#202)

-- a rate filter for the network plot was added (#187)

-- the Explorer class was expanded to have more options (#251)

-- the rate plot now returns a matplotlib Figure object (#231)

-- added the ability to modify rate products (#252)

-- allow for the edges between nodes to be curved (#257)

-- add a RatePair object that groups forward and reverse rates (#212)

-- updated the ReacLib rate library (#248)

-- added nuclear spin tables (#238)

-- added partition function tables (#241, #204)

-- a Nucleus no knows its binding energy (#220)

-- many improvements to C++ output (#246, #214, #185, #183)

-- added a diff method to a Library (#194)

-- fixed rate sorting so it is more deterministic (#216)

-- added forward() and backward() methods to Library (#207)

-- added a default ReacLibLibrary function (#206)

-- added a validate() method for a library to find potentially
important missing rates (#188, #172)

-- added a method to get the number of rates in a library (#173)

-- add a method to remove a rate from a library (#199)

-- libraries are now sorted when printed, with more information
shown (#195, #168)

-- added a symmetric screening option (#178)

-- a "rotated" plot type for the network structure was added (#161)

-- versioning is now managed by setuptools_scm (#158)

pynucastro 1.6.0

pynucastro 1.6.0

pynucastro 1.5.0

1.5.0

-- Added gridplot function for plotting nuclides on a grid and
coloring the cells by X, Y, Xdot, Ydot or activity

-- Created a notebook and a script for generating rp-process
networks. The script allows an arbitrary endpoint to be specified.

-- Added a filter_function option to RateFilter and to the plotting
functions that allows for filtering rates or nuclei using a
user-defined Boolean map.

-- Fixed a write_network crash if the RateCollection contains
multiple rates with the same name.

-- Deleted unused BLAS and VODE files previously used for the standalone
Fortran outputs. These have been deprecated in favor of the StarKiller
Microphysics network output as of v1.3.0.

-- fixed screening for the 3-alpha rate