Develop state class

[rburghol]

This PR includes an overhaul to the model state system, leveraging a new object-oriented version of state, which accomplishes the following:

• It streamlines the number of arguments passed to functions, so now, the arg state takes the place of state_ix, dict_ix, ts_ix, ...
• Declarations of the base containers for state attributes is moved outside of the function, living directly in the state.py file, which allows these to be cached, resulting in a huge improvement in performance (recent branches had seen start-up time double due to less optimal numba caching).
• An example of using dynamic equations has been added in tests/testcbp/HSP2results/ to test a 500 equation addon simulation (Use: cp PL3_5250_0001.json.manyeq PL3_5250_0001.json to test).
• Some cleanup of arguments in function like hydr() and sedtrn() to eliminate the argument io_manager as this is no longer used (I think this has been due for a while, I don't think it is due to any changes that I recall making to the code but it seems like a cleaner approach)

[rburghol]

Hey @PaulDudaRESPEC sorry in advance for the spam as I work out some last minute kinks revealed in the Git testing routines.

[rburghol]

OK - @PaulDudaRESPEC the running part is good, but there is a trouble with the tests, which I cannot tell if the values are not matching up? (my desktop tests have revealed the same values, but I can revisit if needed see Table 1).

• It looks more procedural, the error apears as: FAILED tests/test_regression.py::test_case[test10specl] - KeyError: '/STATE/timer'
  • I can confirm the entry /STATE/timer should be and IS in the in-memory simulation, is it saying that it needs to be in the hdf5?
• When I run manually with pytest -k test10specl according to the instructions (loosely following!) it appears to pass? (see pytest below)
• I realize now that the tests I am looking at likely stem from test_regression.py, rather than pytest. A more detailed excerpt is below as test_regression.py, and the full report is here: https://github.com/respec/HSPsquared/actions/runs/20860244981/job/59937734415?pr=202

test_regression.py

2026-01-09 17:39:07.65   Processing started for file /home/runner/work/HSPsquared/HSPsquared/tests/test10specl/HSPFresults/test10specl.h5; saveall=True
STATE initializing contexts.
=========================== short test summary info ============================
FAILED tests/test_regression.py::test_case[test10specl] - KeyError: '/STATE/timer'
=================== 1 failed, 3 passed in 190.44s (0:03:10) ====================
/opt/hostedtoolcache/Python/3.11.14/x64/lib/python3.11/site-packages/tables/file.py:130: UnclosedFileWarning: Closing remaining open file: /home/runner/work/HSPsquared/HSPsquared/tests/test10specl/HSPFresults/test10specl.h5
  warnings.warn(UnclosedFileWarning(msg))
Error: Process completed with exit code 1.

pytest

pytest -k test10specl
============================================== test session starts ==============================================
platform linux -- Python 3.9.5, pytest-8.4.2, pluggy-1.6.0
rootdir: /opt/model/HSPsquared
configfile: pyproject.toml
plugins: xdist-3.8.0, cov-7.0.0
collected 4 items / 3 deselected / 1 selected

tests/test_regression.py


.                                                                                [100%]

================================== 1 passed, 3 deselected in 148.34s (0:02:28) ==================================

Table 1

HSP2 no specl	HSPF no specl	HSPF w/specl	HSP2 w/specl	HSP2 w/EQ
167.012	167.013	167.035	167.033	167.033
180.398	180.397	227.732	227.636	227.636
212.764	212.763	307.26	307.219	307.219
223.543	223.541	365.287	365.215	365.215
229.247	244.982	418.175	418.135	418.135