Simmate

- fix pickling error for `workflow.run_cloud` command
- `simmate.website.third_parties` module is now the `data_explorer` module. With this, you can now specify custom database tables to appear in the "Data" section for the web UI

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- recover from `connection already closed` errors after long workflow runs
- fix bug where `simmate database reset` fails when there is no database `postgres` available
- update django regression of `django.db.backends.postgresql_psycopg2` to `django.db.backends.postgresql`
- fix bug where simmate cannot read vasp results due atypical number (e.g. -0.33328-312)
- fix bug where postgres cannot json serialize bs or dos results (int64 numbers)
- fix incorrect pointing of VASP potcars in matproj presets
- from `from_directory` method of the `Relaxation` database class
- fix HSE bandstructure and DOS kpoint file writing

**Enhancements**

- add `relax_bulk` and `relax_endpoints` parameters to optionally turn off pre-relaxations in NEB
- add CLEASE app for cluster expanison calculations (these workflows are highly experimental at the moment - so use with caution)
- update "bad-elf" workflow to accept an empty-atom template structure or a list
of empty sites
- add python 3.11 support
- `simmate database reset` now supports Postgres (requires admin user)
- docker images are now published to DockerHub and Github packages

**Refactors**

- `calculators` module is now the `apps` module and terminology is changed throughout the repo
- many dependencies are reworked to optional dependencies as all `apps` are now optional
- `workflow_engine` module has been renamed to `engine` to help shorten commands and import lines
- rework CI to use mamba instead of conda
- pull out dependencies for some apps that are now optional
- reorganize `Incar` class and move some functionality to general `utilities`
- NEB module is reorganized to help with building custom sets

**Fixes**

- fix site ordering in NEB supercell structures
- improve installation speed and guide users to conda alternatives like mamba
- clean up docs and fix several links
- apps are now registered to the web UI

!!! warning
The refactoring of simmate "apps" led to many breaking changes in the python API.
We strongly recommend clearing your `~/simmate/` directory, especially the
`my_env-apps.yaml` file because app names have changed.

**Enhancements**

- add structure creators for `ASE`, `GASP`, `PyXtal`, `AIRSS`, `CALYPSO`, `USPEX`, and `XtalOpt` as well as documentation for creators.
- add `simmate version` command
- changelog and update guide added to documentation website
- add `show-stats`, `delete-finished`, and `delete-all` commands to `workflow-engine`
- add `Cluster` base class + commands that allow submitting a steady-state cluster via subprocesses or slurm
- add `started_at`, `created_at`, `total_time`, and `queue_time` columns to `Calculation` tables
- add `exlcude_from_archives` field to workflows to optionally delete files when compressing outputs to zip archives
- various improvements added for evolutionary search workflows, such as parameter optimization, new output files, and website views
- add `Fingerprint` database table and integrate it with `Fingerprint` validator
- support >2 element hull diargrams and complex chemical systems

**Refactors**

- optimize `get_series` method of `relaxation.vasp.staged`
- reorganize `selectors` module for evolutionary structure prediction

**Fixes**

- fix dynamic loading of toolkit structures from third-party databases
- fix race condition with workers and empty queues
- increases default query rate for `state.result()` to lessen database load

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- fix transaction error with workers on a PostGres backend

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**Enhancements**

- REST API fields can now be specified directly with the `api_filters` attribute of any `DatabaseTable` class & fields from mix-ins are automatically added
- add `archive_fields` attribute that sets the "raw data" for the database table & fields from mix-ins are automatically added
- accept `TOML` input files in addition to `YAML`
- convergence plots and extras are now written for many workflow types (such as relaxations)
- when `use_database=True`, output files are automatically written and the workup method is directly paired with the database table.
- NEB workflow now accepts parameters to tune how distinct pathways are determined, including the max pathway length and cutoffs at 1D percolation.
- add `MatplotlibFigure` and `PlotlyFigure` classes to help with writing output files and also implementing these figures in the website UI
- update website to include workflow calculator types and add API links
- custom projects and database tables are now registered with Simmate and a intro guide has been added
- continued updates for `structure-prediction` workflows
- add inspection of methods for default input values and display them in metadata

**Refactors**

- the `website.core_components.filters` module has been absorbed into the `DatabaseTable` class/module
- yaml input for custom workflows now matches the python input format
- workup methods are largely depreciated and now database entries are returned when a workflow has `use_database=True`
- several NEB input parameters have been renamed to accurate depict their meaning.
- customized workflow runs now save in the original database table under the "-custom" workflow name
- `structure_string` column renamed to `structure` to simplify api logic
- clean up `toolkit.validators` module and establish fingerprint base class
- `calculators` and `workflows` modules are now based on simmate apps

**Fixes**

- fix bug in windows dev env where `simmate run-server` fails to find python path
- fix bug in `workflows explore` command where 'vasp' is the assumed calculator name
- fix broken example code in custom workflow docs
- fix broken website links and workflow views