Meta refactor

[ggmarshall]

Closes #69
Closes #66
Closes #57

[ggmarshall]

Closes #66 debug mode added as config option and flag for hit and pht

[ggmarshall]

#57 done, why did I even do this @gipert

[gipert]

oh george......

[gipert]

Maybe rename branch just to refactor?

[ggmarshall]

Have started adding docs to fix #71, if @gipert could take a look at configuring that would be great

[gipert]

Ok so pushed a commit and activated readthedocs.org (not sure it will work until this PR is merged). Anyways there are a couple of things to fix. These error messages when building:

WARNING: autodoc: failed to import module 'blinding_calibration' from module 'scripts'; the following exception was raised:
cannot import name 'hpge_find_E_peaks' from 'pygama.pargen.energy_cal' (/user/.local/lib/python3.11/site-packages/pygama/pargen/energy_cal.py) [autodoc.import_object]
WARNING: autodoc: failed to import module 'build_dsp' from module 'scripts'; the module executes module level statement and it might call sys.exit(). [autodoc.import_object]
WARNING: autodoc: failed to import module 'build_evt' from module 'scripts'; the module executes module level statement and it might call sys.exit(). [autodoc.import_object]
WARNING: autodoc: failed to import module 'build_fdb' from module 'scripts'; the module executes module level statement and it might call sys.exit(). [autodoc.import_object]
WARNING: autodoc: failed to import module 'build_hit' from module 'scripts'; the module executes module level statement and it might call sys.exit(). [autodoc.import_object]
WARNING: autodoc: failed to import module 'build_raw' from module 'scripts'; the module executes module level statement and it might call sys.exit(). [autodoc.import_object]
WARNING: autodoc: failed to import module 'build_raw_blind' from module 'scripts'; the module executes module level statement and it might call sys.exit(). [autodoc.import_object]
WARNING: autodoc: failed to import module 'build_skm' from module 'scripts'; the module executes module level statement and it might call sys.exit(). [autodoc.import_object]
WARNING: autodoc: failed to import module 'build_tcm' from module 'scripts'; the module executes module level statement and it might call sys.exit(). [autodoc.import_object]
WARNING: autodoc: failed to import module 'check_blinding' from module 'scripts'; the module executes module level statement and it might call sys.exit(). [autodoc.import_object]
WARNING: autodoc: failed to import module 'complete_run' from module 'scripts'; the following exception was raised:
Traceback (most recent call last):
  File "/user/.local/lib/python3.11/site-packages/sphinx/ext/autodoc/importer.py", line 143, in import_module
    return importlib.import_module(modname)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/opt/anaconda3/lib/python3.11/importlib/__init__.py", line 126, in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "<frozen importlib._bootstrap>", line 1204, in _gcd_import
  File "<frozen importlib._bootstrap>", line 1176, in _find_and_load
  File "<frozen importlib._bootstrap>", line 1147, in _find_and_load_unlocked
  File "<frozen importlib._bootstrap>", line 690, in _load_unlocked
  File "<frozen importlib._bootstrap_external>", line 940, in exec_module
  File "<frozen importlib._bootstrap>", line 241, in _call_with_frames_removed
  File "/home/gipert/sw/src/legend/legend-dataflow/scripts/complete_run.py", line 253, in <module>
    file_db_config["tier_dirs"] = {k: tdirs(k) for k in snakemake.params.setup["table_format"]}
                                                        ^^^^^^^^^
NameError: name 'snakemake' is not defined
 [autodoc.import_object]
WARNING: autodoc: failed to import module 'create_chankeylist' from module 'scripts'; the module executes module level statement and it might call sys.exit(). [autodoc.import_object]
WARNING: autodoc: failed to import module 'merge_channels' from module 'scripts'; the module executes module level statement and it might call sys.exit(). [autodoc.import_object]
WARNING: autodoc: failed to import module 'par_psp' from module 'scripts'; the module executes module level statement and it might call sys.exit(). [autodoc.import_object]
WARNING: autodoc: failed to import module 'pars_dsp_build_svm' from module 'scripts'; the module executes module level statement and it might call sys.exit(). [autodoc.import_object]
WARNING: autodoc: failed to import module 'pars_dsp_dplms' from module 'scripts'; the module executes module level statement and it might call sys.exit(). [autodoc.import_object]
WARNING: autodoc: failed to import module 'pars_dsp_eopt' from module 'scripts'; the module executes module level statement and it might call sys.exit(). [autodoc.import_object]
WARNING: autodoc: failed to import module 'pars_dsp_nopt' from module 'scripts'; the module executes module level statement and it might call sys.exit(). [autodoc.import_object]
WARNING: autodoc: failed to import module 'pars_dsp_svm' from module 'scripts'; the module executes module level statement and it might call sys.exit(). [autodoc.import_object]
WARNING: autodoc: failed to import module 'pars_dsp_tau' from module 'scripts'; the module executes module level statement and it might call sys.exit(). [autodoc.import_object]
WARNING: autodoc: failed to import module 'pars_hit_aoe' from module 'scripts'; the module executes module level statement and it might call sys.exit(). [autodoc.import_object]
WARNING: autodoc: failed to import module 'pars_hit_lq' from module 'scripts'; the module executes module level statement and it might call sys.exit(). [autodoc.import_object]
WARNING: autodoc: failed to import module 'pars_tcm_pulser' from module 'scripts'; the module executes module level statement and it might call sys.exit(). [autodoc.import_object]

and installing dependencies for readthedocs, which is at the moment done explicitly in .readthedocs.yaml.