Changelog

Changelog#

2.8.0#

  • update CI artifact action version (#`#1160 <pynucastro/pynucastro#1160>`_)

  • update zenodo authors (#1155)

  • some optimization of AmrexAstroCxxNetwork C++ code (#1150)

  • allow NSENetwork and DerivedRate control over spin reliability (#1118)

  • add an error if ydot_cutoff_value is too high (#1154)

  • DRGEP reduction now supports screening (#1148)

  • symmetric screening support (using the same screening factor for forward and reverse rate) has been removed (#1147, #1158)

  • add the ability to convert a network into a different type (#1140)

  • add the ability to plot the net rate (forward - reverse) (#1135)

  • screening when evaluating rates in python is now handled by the Rate class instead of the RateCollection class. This fixes an issue where ApproximateRate child rates were not being screened (C++ and PythonNetwork were unaffected). (#1144)

  • fix pylint 4.0 compatibility (#1138)

  • network_helper now takes a verbose flag (#1134)

  • numerous redundant examples (from the examples/ directory) were removed (#1131)

  • He burning example has been updated (#1129, #1139)

  • RateCollection.plot can now use screening and take a matplotlib GridSpec that defines the axes (instead of creating them internally. (#1126)

  • RateCollection now takes a verbose option, and most informational prints are disabled by default (#1130)

  • Fix LaTeX rate rendering (#1128)

  • fix a mutability issue in Library addition (#1112)

  • add a method to Library to eliminate duplicate rates (#1111)

  • load all nuclear spins by default, even those that are “unreliable” (#1115)

  • fix a CI issue on DerivedRate (#1124)

  • for ReacLibRate, use r.derived_from_inverse instead of r.reverse (#938)

  • an electron-positron EOS was added. This directly integrates the Fermi-Dirac integrals and constructs n, p, and e. (#1076)

  • NumpyNetwork has been removed – it did not give much of a performance boost (#1109)

  • MPI utils have been moved from reduction/ to a higher-level for reuse (#1104)

  • Clean-up of the reduction code and new example documentation (#1098, #1103)

  • update links docs CI block list (#1113)

  • Composition can now zero out short-lived species (#1107)

  • Weak rates from Pruet & Fuller for A = 65 to 80 have been added (#1091, #1093)

  • RateFilter can now filter on an endpoint (#1106)

  • The write_to_file method has been moved from Library to ReacLibLibrary since it only works with those rates. (#1105)

  • A bounds issue has been fixed in the partition function C++ code (#1100, #1159)

  • CI fixes due to python or Microphysics library changes (#1086, #1092, #1094, #1099, #1102)

  • added an adaptived-difference method for differencing (#1075)

  • AmrexAstroCxxNetwork templates now use the new neutrino cooling method (#1069)

  • Binding energy example has been updated with a better example (#1087)

  • Doc and API docstring improvements (#1079, #1082, #1083, #1084, #1116, #1117, #1127, #1132, #1139, #1141, #1143, #1146, #1149, #1152, #1157)

  • pyproject.toml updated with license info (#1081)

  • plot_network_chart now uses a GridSpec for a better layout (#1060)

2.7.1#

  • fix a numba import for conda-forge (#1078)

2.7.0#

2.6.0#

  • Added a summary() method to RateCollection that gives details about the number of rates and nuclei (#954)

  • Added a new ModifiedRate class that allows for altering reactants, products, and stoichiometry while using an existing underlying rate (#950)

  • Drop requirement for sphinx_rtd_theme (#969)

  • SimpleCxxNetwork now stores and computes Y_e so it can work with weak rates (#965), and it also can take commandline arguments for rho and T (#970)

  • Fix README.md logo for PyPI (#973)

  • Add a new BaryonConservationError exception to Rate that ensures a rate is balanced with respect to baryons. (#975)

  • Added a new CI test that directly compares a PythonNetwork and SimpleCxxNetwork evaluation of dY/dt (#964)

  • SimpleCxxNetwork now allows for screening to be disabled (compile with DISABLE_SCREENING=TRUE). It also prints more precision in the test (#963)

  • Node colors in the RateCollection plot() can now be customized (#962)

  • Some helper functions for working with yt datasets have been added (#961)

  • update to the latest ReacLib database (#917)

  • don’t use std::pow in constexpr in a SimpleCxxNetwork as that is C++23 and not yet widely supported. (#953)

  • allow the nodes in a network plot to have custom names (#946)

  • create a Nucleus .summary() method to display the information we know about a nucleus. (#949)

  • allow rates to support their own stoichiometry, instead of simply relying on the number of nuclei in the reactants or products list. (#947, #952)

  • Added a new network method, get_hidden_rates() that returns the rates that are not explicitly linked in the network but instead are used internally by ApproximateRate rates. (#943)

  • Clean up Library (#932)

  • Fix the binding energy notebook example – we don’t want to show negative binding energies (#939)

  • TabularLibrary() now takes a keyword argument ordering that can specify which sources to use and the order to read them. (#922)

  • Docstring updates (#892, #899, #926, #927, #928, #931, #933, #934, #935, #937, #956, #957, #960, #966, #967, #972, #977) and more API coverage (#929) and reorganization of the API docs (#955)

  • New codespell github action (#930)

  • mailmap updates (#924)

  • Add ruff settings to pyproject.toml (#923)

  • Added the Fuller, Fowler, & Newman weak rates (#910)

  • Updated the colors used for RateCollection plots (#921)

  • Added the ability to show a legend on a RateCollection network plot (#817, #942)

  • Documentation updates (#901, #902, #907, #913, #919, #920) and fixes (#941, #976)

  • PythonNetwork now pairs the forward and reverse rates when summing the ydot term, mirroring what we do in C++ (#784)

  • Highlighting of edges now uses better colors in RateCollection network plots (#904)

  • AmrexAstroCxxNetwork code cleaning (#909)

  • DerivedRate now sets reverse=True (#915)

  • Weak rate tables have been renamed to include the source in the filename (#912)

  • CI fixes (#905, #906)

  • RateCoillection class cleaning (#900)

2.5.0#

  • fix the zenodo authors (#898) and automate the zenodo bibtex in the docs (#880)

  • codespell fixes (#897)

  • AmrexAstroCxxNetwork now ifdefs out neutrinos (#884)

  • officially support python 3.13 (#860)

  • update package requirements (#896)

  • Implement Debye-Huckel screening (#870)

  • Fix a CODATA constants inconsistency between Nubase and SciPy (#877) and compatibility with SciPy < 1.15.0 (#889)

  • Address a new warning in matplotlib 3.10.0 (#879, #885)

  • Bump up jinja2 version (#871)

  • Added the ability to approximate A(n,gamma)X(n,gamma)B into an effective rate A(nn,gamma)B (#818)

  • SimpleCxxNetwork now includes electron screening using the prescription in Chugunov 2007 (#844)

  • added “NSE protons” that evaluate the same as a proton but can be used to decouple light and heavy reactions (#853, #854, #862, #863)

  • modify_products was moved to the base Rate class all rate classes can use it (#851)

  • Fix an issue with AMD HIP/ROCm memory access on the GPU in the partition functions (#859)

  • A FortranNetwork is now available that provides a wrapper around SimpleCxxNetwork with Fortran interfaces. (#841, #847)

  • Nucleus objects can now be added and subtracted (#835)

  • Fix a compiler issue with SimpleCxxNetwork and ReacLib weak rates (#846)

  • Documentation improvements (#782, #831, #832, #843, #848, #852, #855, #858, #861, #864, #866, #867, #874, #881, #887, #888), including new examples (#783, #800, #826) and build enhancements (#893)

  • Clean-up unused class data in SimpleCxxNetwork (#845)

  • Clean up the rate module by separating it into submodules (#840, #842)

  • Add the ability to label edges in network plots (#837)

  • Clean-up the make_ap_pg_approx code (#830, #850)

  • PartitionFunction.eval now returns a python float instead of a numpy float (#839)

  • Rates now store their source from publications (#822, #834)

  • Change some methods to properties in Composition, Library, and Rate (#829)

  • PythonNetwork rates now can take rho and Y. (#828)

  • CI fixes and updates (#827, #890)

  • Child rates in ApproximateRate are now stored as a dictionary (#824) + additional cleaning (#812)

  • Allow the identical particle factor in Rate to be disabled (#821)

  • Rate.eval() now take rho and comp (#820)

  • Update Zenodo authors (#815)

  • Use python’s pathlib.Path throughout (#811)

  • Nucleus now stores the halflife (#801)

2.4.0#

  • expanded documentation on exporting networks (#805) and physical constants (#793)

  • some doc test fixes (#806, #807, #809)

  • expanded unit testing (#802)

  • update pylint disabled features (#794)

  • dropped support for python 3.9 (#787)

  • we now compute the Q value for rates from masses instead of binding energies if it is not available (#797)

  • updated the nuclear properties to all be based on Nubase 2020, with the mass excesses being the primary quantity used and binding energies now derived from the mass excesses. (#788, #792, #796)

  • added a get_all_nuclei() method that returns every nucleus for which we have a mass (#798)

  • removed unused scripts in the nucdata module (#789)

  • fixed the labels for trace nuclei in a Composition pie chart (#781)

2.3.0#

  • added a warning if we use the ReacLib n decay rate (#778)

  • doc updates, including an example of dealing with duplicate rates (#777), new theme (#775), axis label fixes (#774), some examples of nuclear astrophysics concepts (#762, #766)

  • fix the limits for TabularRate plots (#779)

  • created a new alternate_rates module and added the de Boer et al. 2017 C12(a,g)O16 rate (#769)

  • the minimum version of python supported is now 3.8 (#768)

  • some test fixes (#755, #757, #760, #763)

  • C++ autodiff changes / cleanups (#752, #759)

  • AmrexAstroCxxNetwork now create a ydot_weak function that evaluates the weak rate contributions to compute dYe/dt (#739)

2.2.1#

  • numpy 2.0 support added (#748)

  • new logo! (#744, #746)

  • pynucastro can now be installed by conda (#741, #743)

  • minor test fixes (#729, #735, #740, #745)

  • doc fixes (#737)

  • pylint fixes (#733)

  • Composition now allows for direct key-value indexing (#731), and has a new set_random() method (#728)

  • The screen5 screening routine has been added (#730)

  • C++ partition function interpolation is now cached (#726)

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)

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)

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)

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)

2.0.2#

  • Fix the installation of the C++ templates via setup.py (#460)

2.0.1#

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

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

  • Support historical ReacLib format (#449)

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 calculations (#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::vector<std::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 indices 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 now 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)

1.6.0#

  • added support for C++ StarKiller / AMReX Microphysics networks (#152, #151, #149)

  • centralized sympy code generation and removed common subexpression support from network generation (#145)

  • added an example on integrating a python network

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

1.4.1#

  • Improvements for locating rate files in directories also containing python scripts or Jupyter notebooks

  • Fixed a warning when using Numba

  • Updates to the StarKiller Microphysics format for compile time variables

  • Enhancements for the RateCollection Explorer to use NetworkX 2.5

  • Updated the requirements

1.4.0#

  • Added general support for tabulated weak rates from Suzuki, et al. 2016

  • Added a simple pp network example

  • Updated StarKiller Microphysics output to track latest changes in Microphysics network API

  • Added a core developers policy in the Readme

1.3.0#

  • Replace double precision reals in StarKiller networks with custom real type _rt

  • Incorporate modifications to thermal neutrino Jacobian contributions from Microphysics (#210) in StarKiller networks

  • Simplify rate evaluation code in StarKiller networks

  • Deprecated standalone Fortran output with VODE integration.

  • BaseFortranNetwork is now an abstract class to require users to either use StarKillerNetwork or provide templates

1.2.0#

  • Fix tabular rate bug where electron chemical potential contributions were not included

  • Update documentation and code comments

  • Add Numba support for Python networks

  • Enable sparse Jacobian (CSR) for StarKiller networks

  • Incorporate CUDA Fortran port for StarKiller networks including tabulated rates

  • Optimize rate screening evaluation for StarKiller networks

  • Fix bug to include the electron fraction and correct density dependence for Reaclib electron capture rates

  • Allow a nuclide to be both reactant and product

  • Updates an error message for multiple degenerate rates

  • Add example code generating a 160-isotope network

  • Fix table compilation issue for StarKiller networks

  • Moved energy generation subroutine into RHS module for StarKiller networks

1.1.1#

  • pynucastro published on JOSS is archived to Zenodo

1.1.0#

  • JOSS reviewer changes merged and pynucastro accepted to JOSS

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