MesoHOPS v1.2.0

This is large update to the MesoHOPS code that includes a variety of cosmetic updates as well as:
1. More efficient memory management, particularly for large systems
2. Faster execution, particularly when there are a large number of auxiliaries
3. An adaptive linear absorption equation-of-motion
4. An improved algorithm for constructing hierarchies when using both a large hierarchy depth and aggressive static filters
5. Improved efficiency of Markovian filtration during adaptive basis updates
6. A noise indexing scheme that ensures two trajectories of different lengths with the same seed will have the same raw noise in the time region where they overlap
7. A larger variety of options for inputing noise trajectories
8. Improved random number seeding for noise trajectories of large aggregates
9. A generalized class for saving data during a trajectory
10. A helper function for defining Matsubara modes of Drude-Lorentz spectral density
11. Generalized auxiliary indexing to manage arbitrary size of absolute hierarchy

This update also includes the following bug fixes:
1. _determine_error_thresh: removed an error for the edge case when, if all error was below error threshold, all basis elements were included in basis
2. _error_sflux_state: removed a bug that resulted in overestimating error terms
3. _error_flux_down: removed a bug that could result in underestimated error terms

Author: digbennett

mesohops/docs/Makefile

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+# Minimal makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line, and also
+# from the environment for the first two.
+SPHINXOPTS    ?=
+SPHINXBUILD   ?= sphinx-build
+SOURCEDIR     = source
+BUILDDIR      = build
+
+# Put it first so that "make" without argument is like "make help".
+help:
+	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+.PHONY: help Makefile
+
+# Catch-all target: route all unknown targets to Sphinx using the new
+# "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
+%: Makefile
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)

mesohops/docs/build/doctrees/basis.doctree

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+# Sphinx build info version 1
+# This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
+config: c02f26641aba381581aa5677b22a8f48
+tags: 645f666f9bcd5a90fca523b33c5a78b7