Pynucastro

* 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)

* 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)

* 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)

* 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)

* `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)

* 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)