Merge pip modularization changes to "end of may work in progress"#16

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jonathanhhb wants to merge 31 commits intojbloedow/end_of_may_wipfrom jb_modulify

+1,602-1,200

Commits on Jun 19, 2024

Converting to pip installable package.
Jonathan Bloedow
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Tidy up data files that were moved into the module src dir. Moved them to data outside of idmlaser.
Jonathan Bloedow
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Don't want large data files in repo; can get from idm-data.
Jonathan Bloedow
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Commits on Jun 20, 2024

Added some startup checks for existence of settings files and useful error messages to user about what to do. The idea is to enable users to get going by trial and error. The build_template_workspa…
Jonathan Bloedow
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Commits on Jun 26, 2024

Added build_template_workspace script to new package and fixed issues that came up in testing.
Jonathan Bloedow
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Commits on Jul 1, 2024

Adding README for pip package.
Jonathan Bloedow
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Added section to README to show all the code references for an example column/attribute/property (age).
Jonathan Bloedow
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Tweaking README for pip package.
Jonathan Bloedow
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Commits on Jul 2, 2024

Removed some placeholder doc string from cli.py. Should really add more but at least what's there isn't wrong.
Jonathan Bloedow
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Removed some placeholder doc string from __main__.py. Should really add more but at least what's there isn't wrong.
Jonathan Bloedow
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Fixes and changes to support running in COMPS.
Jonathan Bloedow
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Commits on Jul 3, 2024

Adding script and SIF asset collection id to run a version of laser on COMPS.
Jonathan Bloedow
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Commits on Jul 4, 2024

Added ability to get pre-created fits_ew.npy from idm-data.
Jonathan Bloedow
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Commits on Jul 5, 2024

Got pip dev install working.
Jonathan Bloedow
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Commits on Jul 6, 2024

Make fits.npy file optional. User can model without eulas if they want. This runs without errors but I'm not sure if we need more clarity to user.
Jonathan Bloedow
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Commits on Jul 9, 2024

Commits on Jul 10, 2024

Rev to 0.0.7.
Jonathan Bloedow
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Added missing MANIFEST.in file
Jonathan Bloedow
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Code wasn't use dont_import_after setting. And the import_cases setting is no longer really being used.
Jonathan Bloedow
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Removed duplicate get_beta_samples function from sir_numpy.py. Using one in sir_sql.
Jonathan Bloedow
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Removed unused code from the all sql model. And an unused function in the c code. Also starting adding ability to pass in incubation duration to C function which does new infections.
Jonathan Bloedow
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Added capabliity to set incubation_period in settings.py. This is useful for calibratoin.
Jonathan Bloedow
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Commits on Jul 13, 2024

Adding scripts & files to run idmlaser on COMPS.
Jonathan Bloedow
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Some cleanup.
Jonathan Bloedow
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Cleaned up some doc strings with ChatGPT.
Jonathan Bloedow
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Commits on Jul 16, 2024

Don't treat settings.py not being in INPUT_ROOT directory as an error anymore. (After getting sweeps working in COMPS.)
Jonathan Bloedow
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Commits on Jul 22, 2024

Was using wrong datatype.
Jonathan Bloedow
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Removed more currently unused code from update_ages.cpp and revved version.
Jonathan Bloedow
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Commits on Jul 24, 2024

Got .so building and installing working with both wheel and develop installs. That was hard.
Jonathan Bloedow
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