Simmate

**Enhancements**

- add guide for installing VASP v5 to Ubuntu v22.04 ([scott-materials](https://github.com/scott-materials), [#183](https://github.com/jacksund/simmate/issues/183))
- add `simmate database load-remote-archives` command and `load_remote_archives` utility that populates all tables from `database.third_parties`
- add `load_default_sqlite3_build` utility that downloads a pre-built database with all third-party data present. This is an alternative to calling `load_all_remote_archives` if you are using sqlite3 and saves a significant amount of time for users.
- standardize workflow naming. Note this breaks from python naming conventions for classes ([150](https://github.com/jacksund/simmate/issues/150))
- dynamically determine `register_kwargs` and rename property to `parameters_to_register`
- add full-run unittests that call workflows and vasp (without emulation)
- add walltime error handler that properly shuts down calculations when a SLURM job is about to expire
- add option to restart workflows from a checkpoint
- automatically build api documentation using github actions

**Refactors**

- refactor `start-worker` command to use prefect instead of the experimental django executor
- remove experimental `workflow_engine.executor`
- move contents of `configuration.django.database` to `database.utilities`
- upgraded to Prefect v2 ("Orion"). This involved the refactoring the entire `workflow_engine` module, and therefore the entire workflow library. ([185](https://github.com/jacksund/simmate/pull/185)).

**Enhancements**

- add `AflowPrototypes` to the `database.third_parties` module (only includes data distributed through pymatgen)
- add new modules to `toolkit.structure_prediction` and `toolkit.creation`, including ones to provide `known`, `substitution`, and `prototype` based structures.
- add `created_at` and `updated_at` columns to all database tables
- check if there is a newer version of Simmate available and let the user know about the update
- add experimental `badelf` workflow for determining electride character
- add `electronic-structure` workflow which carries out both DOS and BS calculations
- add `database_obj` attribute to the `toolkit.Structure` base class that is dynamically set

**Refactors**

- standardize `database_table` attribute for workflows by merging `calculation_table` and `result_table` attributes ([102](https://github.com/jacksund/simmate/issues/102))
- removed use of `-s`, `-c`, and `-d` shortcuts from the `workflows` commands
- refactor `relaxation/staged` workflow to run in single parent directory
- refactor evolutionary search algorithm (alpha feature)
- condense where parsing/deserialization of workflow parameters occurs to the refactored the `load_input_and_register` task. Originally, this would occur in multiple places (e.g. in the CLI module before submission, in the workflow run_cloud method, in the LoadInputAndRegister task, etc.) and involved boilerplate code. ([173](https://github.com/jacksund/simmate/pull/173))
- refactor experimental features `register_kwargs` and `customized` workflows
- refactor `LoadInputAndRegister` and `SaveOutputTask` to `load_input_and_register` and `save_result`

**Fixes**

- fix import for `visualization.structure.blender` module ([bocklund](https://github.com/bocklund), [#180](https://github.com/jacksund/simmate/issues/180))
- fix bug where `command` or `directory` improperly passes `None` when they are not set in the `simmate workflows run` command
- fix bug where `update_all_stabilities` grabs incomplete calculations ([177](https://github.com/jacksund/simmate/pull/177))
- fix bug where SCF calculation is not completed before the non-SCF DOS or BS calculation and causes the workflows to fail ([171](https://github.com/jacksund/simmate/issues/171))
- fix bug for Bader workflow by registering the prebader workflow ([174](https://github.com/jacksund/simmate/pull/174))
- fix bug where `source` is not determined with yaml-file submissions ([172](https://github.com/jacksund/simmate/issues/172))

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- update CI to test all OSs and pin pytest<7.1 as temporary fix for [162](https://github.com/jacksund/simmate/issues/162)
- fix spelling typos in `keyword_modifiers` ([laurenmm](https://github.com/laurenmm), [#165](https://github.com/jacksund/simmate/pull/165))
- users can now apply their own unique keyword modifiers to Incars -- such as how we allow "__per_atom" or "__smart_ismear" tags on Incar settings. This change involved refactoring how `keyword_modifiers` are implemented for the `vasp.inputs.Incar` class. Rather than static methods attached to the base class, modifiers are now dynamically applied using the `add_keyword_modifier` classmethod.
- large update of `calculators.vasp.tasks` module where many new presets are reimplemented from [`pymatgen.io.vasp.sets`](https://pymatgen.org/pymatgen.io.vasp.sets.html). This includes robust unit testing to confirm that generated inputs match between simmate and pymatgen (see [#157](https://github.com/jacksund/simmate/issues/157) for a list of presets)
- catch error with vasp freezing when `Brmix` handler switches to kerker mixing ([becca9835](https://github.com/becca9835), [#159](https://github.com/jacksund/simmate/issues/159))

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- add `description_doc_short` + `show_parameters` to workflows and use these to update the UI
- add django-allauth dependency for account management and google/github sign-ins
- archive directory as `simmate_attempt_01.zip` whenever an error handler is triggered
- depreciate the workflow parameter `use_prev_directory` in favor of `copy_previous_directory`

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- add highly customizable VASP workflow
- add Bader analysis and ELF workflows
- update module readmes to warn of experimental features
- reorganize `toolkit` module

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- start the CHANGELOG!
- refactor API views and add `SimmateAPIViewSet` class
- refactor `simmate start-project` command and underlying methods
- refactor `simmate workflow-engine run-cluster` command and underlying methods
- continue outlining `file_converters` module

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