…le that contains utility functions reused in the photosynthesis and fermi hubbard notebooks

….txt as pyproject now handles that

Merging in the initial QCA package structure

* pyliqrt 1.0 support up to qsp estimation

* complete translation to pyliqtr1.0.0 for the magneticlattices notebook

* fixed bug with qsp estimation and went through the notebook

* made the change to pyliqtr1.0 to HightemperatureSuperConductorExample jupyter notebook

* added output for the notebook

* removed old fermi hubbard notebook

* removed unused imports

* added hamiltonian utils file. Would proabbly be moved to some hamiltonian module in the future

* have the notebook use the packaged utility functions

* finalized adding additional features for fermi hubbard support

* fixed pyproject versioning

* successfull running of magnetic lattice using pyliqtr1.0 ontop of modularized functionality

* adding back fermihubbard notebook from main

* forgot to remove requirements file

* changed generate_square_hamiltonian to generate_square_hamiltonian and generate_triangle_hamiltonian to better seperate the two

* changed notebook to respond to PR comments, i.e, changed shape_graph to graph_shape and just manually imported all functions that are needed

* made the change to pyliqtr1.0 to HightemperatureSuperConductorExample jupyter notebook

* added output for the notebook

* removed old fermi hubbard notebook

* removed unused imports

* added hamiltonian utils file. Would proabbly be moved to some hamiltonian module in the future

* have the notebook use the packaged utility functions

* finalized adding additional features for fermi hubbard support

* fixed pyproject versioning

* translated  PyLIQTR1.0 to Photosynthesis example. GSE object was originally just a wrapped PE object, so had to explicitly specify PE objects now for GSEE

* made the change to pyliqtr1.0 to HightemperatureSuperConductorExample jupyter notebook

* added output for the notebook

* whitespace changes t photosynthesis

* removed old fermi hubbard notebook

* removed unused imports

* added hamiltonian utils file. Would proabbly be moved to some hamiltonian module in the future

* have the notebook use the packaged utility functions

* finalized adding additional features for fermi hubbard support

* fixed pyproject versioning

* finished modularizing qca with respect to photosynthesis notebook

* RuCl migration of pyLIQTR-1.0

* deleted old RuCl notebook

* Fix Trotter printing, update pyproject.toml to use pyLIQTR 1.0.0, update gitignore

* updated notebook to take out unused imports and fix unused colors issue

* structured RuCl notebook to use qca package, fixed plot_T_histogram header in qca.utils.utils

* removed unused functs and imports, changed the plot_histogram funct in qca, and reverted some previous changes, fixed plotting, changed assign_labels to allow generic x y z labels

* added default args to assign_hexagon_labels, removed the commented code for  plotting for qsp, made the labels uppercase

---------

Co-authored-by: Zain Mughal <zain@pn2401319.lanl.gov>
Co-authored-by: Zachary Alexander Morrell <zmorrell@lanl.gov>

* Add documentation to RuCl notebook, Pin pyLIQTR to version 1.0.0, add local field term for resource estimates

* Add explanation of terms in table.  Fix appearance of Heisenberg terms in VSCode

* Add Zeeman terms to Hamiltonian in RuCl, fix typos

* Add state preparation documentation and fix RNG seeding

* fixed time varying terms and added approprimate terms for rucl lattice

* Add resource estimate for state preparation and measurement

* Add state prep and measurement resource estimates section, attempt to fix figures

* Reduce image size of Figure 1

* Remove unused variable from prepare_measurement_rucl

---------

Co-authored-by: Jonhas Colina <jonhas@lanl.gov>

… and depth for GSEE in the fermihubbard notebook (#12)