Code

Expanded MPcule API#674

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munrojm merged 198 commits intomaterialsproject:mainmaterialsproject/emmet:mainfrom espottesmith:expanded_mpcule_apiespottesmith/emmet:expanded_mpcule_apiCopy head branch name to clipboardMar 14, 2023

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Commits

Commits on May 5, 2022

• Merge remote-tracking branch 'materialsproject/main' into main

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Commits on May 13, 2022

• Merge remote-tracking branch 'materialsproject/main' into main

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• Make bonding not mandatory

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Commits on Jun 10, 2022

• Fix bug for case where no tasks are valid

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• Small type change

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• Disallow certain task types in Q-Chem builder by default

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Commits on Jun 15, 2022

• Merge remote-tracking branch 'materialsproject/main' into molecules_update

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• Add graph hashes to molecule document format

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• Change SMD parameters for G2

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• change id format

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Commits on Jun 16, 2022

• Fixed bugs with graph hashes; added new ID class (needs to propagate through molecule world)

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Commits on Jun 22, 2022

• Working hard at getting new ID format working

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• Tests now pass on all builders; just need to make sure all corresponding tests pass in emmet-core (including remaking JSON files for summary)

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• Updated tests; everything (I think) passes; black

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• Now everything actually passes

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• Remove unused variable

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• mypy changes

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• ID didn't match - trying without?

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Commits on Jun 23, 2022

• Separate level of theory from solvent information; get rid of solvent names and instead create utility function to define a solvent string

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• Create composite lot_solvent concept (capturing what we used to do with LevelOfTheory with pre-defined solvents)

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• Updates to molecule doc (change to ID not done yet); now need to propagate to property documents

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• Core should be updated post-solvent LOT changes (surprisingly easy).

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Commits on Jul 1, 2022

• Merge branch 'main' into molecules_update

  

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Commits on Jul 14, 2022

• Merge remote-tracking branch 'origin/molecules_update' into molecules_update

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• Need to regenerate test files

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Commits on Aug 8, 2022

• Update thermo

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Commits on Aug 9, 2022

• Bundling networkx 2.8.5 networkx.algorithms.graph_hashing.py source code to ensure long-term fixity of graph hashes.

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• Tests

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• Add species as top-level attribute

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Commits on Aug 10, 2022

• Small change in filter_task_type; now arbitrary sorting functions can actually be used

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Commits on Aug 11, 2022

• Changes to ID helper function, molecule grouper helper function, and small associated changes to molecule association builder

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• Merge remote-tracking branch 'materialsproject/main' into molecules_update

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• MoleculeBuilder now updated to group based on the solvent used to optimize a molecule. Evaluation of different MoleculeDocs is based on the level of theory used to optimize as well as the overall "…

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• Small tweak

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Commits on Aug 12, 2022

• Mostly black-ing, but also working on adding more detail about property docs

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Commits on Aug 14, 2022

• Update all property docs (not builders yet) except Redox (which will be tricker)

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• Expanded list of metals; small changes to redox builder

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• Bugfixes to utils

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• Update PartialChargesBuilder to allow, for a given molecule, different docs in different charges

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• PartialSpinsBuilder updated

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• Updated BondingBuilder; also made check for NBO7 more general across all instances

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Commits on Aug 15, 2022

• Updated OrbitalBuilder

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• Updated VibrationBuilder

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Commits on Aug 23, 2022

• Progress on thermo builder; black in builders

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Commits on Aug 24, 2022

• Still not done with ThermoBuilder, but need to change tack and go back to reaction land for now

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Commits on Aug 26, 2022

• Merge remote-tracking branch 'materialsproject/main' into molecules_update

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• New thermo builder, allowing for single-point energy corrections, is finally done

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Commits on Sep 21, 2022

• Some fixes for bugs found by @samblau

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Commits on Oct 4, 2022

• Safety on BondingDoc creation to ensure that some method is always used

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• Merge remote-tracking branch 'materialsproject/main' into molecules_update

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• RedoxDoc rewrite done; now need to update builder

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• Some progress on RedoxBuilder; this one is kinda hairy, once again

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Commits on Oct 16, 2022

• Draft of RedoxBuilder done

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Commits on Oct 23, 2022

• Emergency backup commit

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Commits on Nov 11, 2022

• Think this should update SummaryDoc constructor?

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• Ready to start testing; that was less painful than I was expecting

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Commits on Nov 18, 2022

• Minor fixes to core test based on changes to MPculeID format

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• Small fixes

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• Fixed ThermoBuilder (specifically dealing with edge case of single atoms)

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• Fixed tricky bug in RedoxBuilder caused by use of defaultdict

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• SummaryBuilder works; now just need to (re)write tests for all builders

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Commits on Nov 19, 2022

• Weird bug: MongoDB really doesn't like doc keys to have periods in them

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• Patched test for molecule builders; next need to rewrite tests for property builders

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Commits on Nov 22, 2022

• bugfix in redox builder - IE/EA tasks weren't being populated properly

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Commits on Nov 25, 2022

• Fixed redox emmet-core test

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• Redox emmet-builder tests also finished

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• Fixed summary builder tests; now just one more

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• Summary test passes; we're golden

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Commits on Dec 28, 2022

• Merge remote-tracking branch 'materialsproject/main' into molecules_update

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• Remove enums

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• (hopefully) fix core linting issues

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Commits on Jan 3, 2023

• Linting

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• Merge remote-tracking branch 'materialsproject/main' into molecules_update

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• Trying to deal with mypy

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• Now another linting change

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• More mypy changes

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• Re-adding test files (for now)

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• Shuffling files around

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• Re-add conftest

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• Slight tweaks to fix SummaryBuilder for molecules

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• Merge remote-tracking branch 'materialsproject/main' into molecules_update

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Commits on Jan 4, 2023

• Super broke things yesterday. Hoping this fixes them

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• Realized I was a fool; updating tests now

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• I think last test?

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• All (relevant) tests pass

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• Fix lint - also, really need to prevent enums from being added in changes

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• Going for it

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• mypy makes me want to break things sometimes

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Commits on Jan 5, 2023

• Pin numpy in emmet-api

  

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Commits on Jan 9, 2023

• Merge branch 'main' into molecules_update

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Commits on Jan 10, 2023

• Initial structuring of MPcules API

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Commits on Jan 17, 2023

• First attempt at an API for the MPcules molecules collection

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• Added some hint schemes; API for MPcules tasks collection

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Commits on Jan 27, 2023

• Builder bugfix

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Commits on Jan 31, 2023

• Merge branch 'main' into molecules_update

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• Testing import issues

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• Modify requirements

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• Seems the root of the issue is that eigen is missing?

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• One more attempt before I call in the big guns

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• Last try before I just gut these tests; not worth it

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• jkjk

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Commits on Feb 3, 2023

• Trying to figure out new bug on property builders - task docs apparently with no orig???

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• Use debugger more effectively

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• Trying to catch an error again

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• Resolved issue?

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• Reverting testing change; think all is well in the world.

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• Floating validation on partial charges/spin docs

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• Fix for H1 specifically (I think)

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Commits on Feb 4, 2023

• Remove unnecessary printing

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Commits on Feb 5, 2023

• Merge branch 'testing' into molecules_update

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• Merge branch 'main' into molecules_update

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• Merge branch 'molecules_update' into molapi

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• Starting work on bond query

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• Fix mypy issue

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• Draft MPcules bonds API

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• (limited) API for partial charges and spins (better API requires more detail in emmet-core docs)

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• Merge branch 'molecules_update' into molapi

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• Begun work on NBO query operators

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Commits on Feb 7, 2023

• Orbital query WIP

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• Merge branch 'main' into molapi

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Commits on Feb 8, 2023

• First-draft, very simple summary API

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Commits on Feb 9, 2023

• Working summary api endpoint

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• Merge branch 'main' into molapi

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• Rewriting MoleculeBuilder to collapse MoleculeDocs from different solvents

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Commits on Feb 21, 2023

• WIP - changing molecules builder

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• (for now) commenting out orbital routes;

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• Tests for mpcules/molecule route pass

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• Test for mpcules/bond query operators

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• Lint issues

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• Linters make code better and my life worse

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• Fix mypy issue

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• Merge branch 'main' into molapi

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Commits on Feb 23, 2023

• mypy issues

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• Linting

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• Mypy is a pain point

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• Pain continues

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• mypy was a mistake

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• Merge branch 'molapi' into fix_multi_solvent

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• What happened to duck typing?

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• Merge branch 'main' into molapi

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• Merge branch 'main' into molapi

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• Merge branch 'molapi' into fix_multi_solvent

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• Incorporating some changes from Sam Blau (@samblau); one bugfix, a couple of small tweaks

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• Merge branch 'main' into molapi

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• Small bugfixes to resources; made a new MPcules app

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• Merge branch 'molapi' into fix_multi_solvent

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• Fix mpcule_app

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• Draft of new molecule builder written; needs testing (tests need to be rewritten in general)

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• Merge branch 'main' into fix_multi_solvent

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Commits on Feb 24, 2023

• Small tweaks to property builders

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• Bugfix from Sam; debugging some weirdness with MoleculesBuilder

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• Fixed AssociationBuilder; deprecated molecules now processed appropriately

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• New MoleculesBuilder works as expected!

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• Looks like SummaryBuilders is working correctly now as well, though property builders may not be

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• I think we got it! Just had to change update keys for property builders

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• Updated builder tests

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• Linting

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• Found some more lint

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• mypy nonsense

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• The mypy gods were furious; hopefully this prayer appeases them

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• Fix failing test

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• Remove superfluous test file

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• remove debugging tools

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Commits on Feb 25, 2023

• Accounting for multiple possible task ID formats

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• Merge branch 'main' into fix_multi_solvent

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• Lint

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• Small bugfix

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Commits on Mar 3, 2023

• Merge branch 'main' into expanded_mpcule_api

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• Back at work on orbital operators

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• (Hopefully) reduce computational burden of MoleculeBuilder prechunk

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• Same thing elsewhere

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Commits on Mar 6, 2023

• Continued WIP: orbital endpoint

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• NBO is an immense pain; also realized that I needed a new query operator to grab property docs with SPECIFIC levels of theory

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• Finally done rough draft query objects for OrbitalDocs

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Commits on Mar 7, 2023

• redox query operator and resource

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• Add thermo resource

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• Think everything is set up for the new API endpoints/resources

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• Still need to write tests, but app deployment looks good

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• Reorganizing

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• Reorganize core

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• More reorganizing, now in emmet-builders

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• More renaming; mysterious problem popping up with species_hash

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• Giving up on testing builders; trying API again

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• Back to square 1

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• MPcules API tests pass

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• Small formatting change

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Commits on Mar 8, 2023

• Add SMD synonyms dictionary in emmet-core

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• Small quality of life tweaks, mostly

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• Fix tests; minor bugfix in SummaryBuilder

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Commits on Mar 9, 2023

• Association endpoint

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• Merge branch 'main' into expanded_mpcule_api

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• Linting

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• Small bugfix reflecting name change

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• Another small bugfix

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• mypy continues to hurt me

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• linting issue

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• BURN MYPY

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Commits on Mar 11, 2023

• Small bugs in resources; whoops!

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