Bug fixes, continuing PEP585 support, PropertyDoc schema

[esoteric-ephemera]

Bug fixes:

• Ensure OSZICAR is parsed by file discovery, was unintentionally removed in Update VASP file discovery #1223 (only affects MD runs by parsing temperature) - thanks @mcgalcode for the fix!
• Allow for TaskDoc to still parse VASP calcs with missing projected DOS data

PEP 585

• Remove typing.Set in favor of set, and migrate objects like typing.Sequence to collections.abc.Sequence per the migration guide

Schema Changes:

• Per internal discussion: made structure an optional top-level on PropertyDoc that is instantiated with from_structure. However, this field is by default both excluded from the model_dump and the JSON schema
  • Any class that already had a top-level structure, like SummaryDoc, overrides this behavior and includes the field in model_dump / JSON schema

[codecov-commenter]

Codecov Report

Attention: Patch coverage is 73.93617% with 49 lines in your changes missing coverage. Please review.

Project coverage is 89.18%. Comparing base (2542a26) to head (2a628ab).
Report is 1 commits behind head on main.

Files with missing lines	Patch %	Lines
...et-builders/emmet/builders/materials/elasticity.py	60.00%	2 Missing ⚠️
emmet-builders/emmet/builders/molecules/redox.py	60.00%	2 Missing ⚠️
emmet-builders/emmet/builders/molecules/summary.py	60.00%	2 Missing ⚠️
emmet-builders/emmet/builders/qchem/molecules.py	80.00%	2 Missing ⚠️
emmet-core/emmet/core/material_property.py	75.00%	2 Missing ⚠️
emmet-core/emmet/core/molecules/summary.py	71.42%	2 Missing ⚠️
emmet-core/emmet/core/mpid.py	50.00%	2 Missing ⚠️
emmet-core/emmet/core/utils.py	33.33%	2 Missing ⚠️
emmet-core/emmet/core/vasp/calculation.py	60.00%	2 Missing ⚠️
...rs/emmet/builders/materials/absorption_spectrum.py	75.00%	1 Missing ⚠️
... and 30 more

Additional details and impacted files

@@            Coverage Diff             @@
##             main    #1253      +/-   ##
==========================================
- Coverage   89.42%   89.18%   -0.24%     
==========================================
  Files         151      151              
  Lines       15632    15735     +103     
==========================================
+ Hits        13979    14034      +55     
- Misses       1653     1701      +48     

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[tsmathis]

Okay guys, what is going on between this, #1252, and #1230

@mcgalcode your submission is for MLMD trajectory parsing, but has a patch for oszicar discovery?

@esoteric-ephemera you cherry-picked (?) 9c636d6 which only adds the "oszicar" to the vasp discovery? But not the relative file path patch for the parsing? I thought all of the oszicar stuff was in #1230. Is the file discovery the only missing piece?
You also have DOS parsing here?

[esoteric-ephemera]

This is mostly patch / bug fixes for TaskDoc, related to changes in 1223. I left out the oszicar_file from the file discovery unintentionally, as it's not used in production data. Cherry picked Max's commit to give credit there

The DOS parsing changes here allow TaskDoc to still parse when complete DOS info is missing, before it would throw an exception and fail

Max's 1252 is mostly expanding the scope of TaskDoc to handle different run / task types (an MLMD run, something that's not in production data yet)

Also still need to add tests for these since I think we're missing coverage