Aiida-core

Improvements
- Documentation: AiiDA now has an automatically generated and complete API documentation (using `sphinx-apidoc`) [[1330]](https://github.com/aiidateam/aiida-core/pull/1330)
- Add JSON schema for connection of REST API to Materials Cloud Explore interface [[1336]](https://github.com/aiidateam/aiida-core/pull/1336)

Critical bug fixes
- `FINISHED_KEY` and `FAILED_KEY` variables were not known to `AbstractCalculation` [[1314]](https://github.com/aiidateam/aiida-core/pull/1314)

Minor bug fixes
- Make 'REST' extra lowercase, such that one can do `pip install aiida-core[rest]` [[1328]](https://github.com/aiidateam/aiida-core/pull/1328)
- `CifData` `/visualization` endpoint was not returning data [[1328]](https://github.com/aiidateam/aiida-core/pull/1328)

Deprecations
- `QueryTool` (was deprecated in favor of `QueryBuilder` since v0.8.0) [[1330]](https://github.com/aiidateam/aiida-core/pull/1330)

Miscellaneous
- Add `gource` config for generating a video of development history [[1337]](https://github.com/aiidateam/aiida-core/pull/1337)

Critical bug fixes
- Link types were not respected in `Node.get_inputs` for SqlAlchemy [[1271]](https://github.com/aiidateam/aiida-core/pull/1271)

Improvements
- Support visualization of structures and cif files with VESTA [[1093]](https://github.com/aiidateam/aiida-core/pull/1093)
- Better fallback when node class is not available [[1185]](https://github.com/aiidateam/aiida-core/pull/1185)
- `CifData` now supports faster parsing and lazy loading [[1190]](https://github.com/aiidateam/aiida-core/pull/1190)
- REST endpoint for `CifData`, API reports full list of available endpoints [[1228]](https://github.com/aiidateam/aiida-core/pull/1228)
- Various smaller improvements [[1100]](https://github.com/aiidateam/aiida-core/pull/1100) [[#1182]](https://github.com/aiidateam/aiida-core/pull/1182)

Critical bug fixes
- Restore attribute immutability in nodes [[1111]](https://github.com/aiidateam/aiida-core/pull/1111)
- Fix daemonization issue that could cause aiida daemon to be killed [[1246]](https://github.com/aiidateam/aiida-core/pull/1246)

Minor bug fixes
- Fix type column in `verdi calculation list` [[960]](https://github.com/aiidateam/aiida-core/pull/960) [[#1053]](https://github.com/aiidateam/aiida-core/pull/1053)
- Fix `verdi import` from URLs [[1139]](https://github.com/aiidateam/aiida-core/pull/1139)

Improvements

Core entities
- `Computer`: the shebang line is now customizable [[940]](https://github.com/aiidateam/aiida-core/pull/940)
- `KpointsData`: deprecate buggy legacy implementation of k-point generation in favor of Seekpath [[1015]](https://github.com/aiidateam/aiida-core/pull/1015)
- `Dict`: `to_aiida_type` used on dictionaries now automatically converted to `Dict` [[947]](https://github.com/aiidateam/aiida-core/pull/947)
- `JobCalculation`: parsers can now specify files that are retrieved locally for parsing, but only temporarily, as they are deleted after parsing is completed [[886]](https://github.com/aiidateam/aiida-core/pull/886) [[#894]](https://github.com/aiidateam/aiida-core/pull/894)

Plugins
- Plugin data hooks: plugins can now add custom commands to `verdi data` [[993]](https://github.com/aiidateam/aiida-core/pull/993)
- Plugin fixtures: simple-to-use decorators for writing tests of plugins [[716]](https://github.com/aiidateam/aiida-core/pull/716) [[#865]](https://github.com/aiidateam/aiida-core/pull/865)
- Plugin development: no longer swallow `ImportError` exception during import of plugins [[1029]](https://github.com/aiidateam/aiida-core/pull/1029)

Verdi
- `verdi shell`: improve tab completion of imports in [[1008]](https://github.com/aiidateam/aiida-core/pull/1008)
- `verdi work list`: projections for verdi work list [[847]](https://github.com/aiidateam/aiida-core/pull/847)

Miscellaneous
- Supervisor removal: dependency on unix-only supervisor package removed [[790]](https://github.com/aiidateam/aiida-core/pull/790)
- REST API: add server info endpoint, structure endpoint can return different file formats [[878]](https://github.com/aiidateam/aiida-core/pull/878)
- REST API: update endpoints for structure visualization, calculation (includes retrieved input & output list), add endpoints for `UpfData` and more [[977]](https://github.com/aiidateam/aiida-core/pull/977) [[#991]](https://github.com/aiidateam/aiida-core/pull/991)
- Tests using daemon run faster [[870]](https://github.com/aiidateam/aiida-core/pull/870)
- Documentation: updated outdated workflow examples [[948]](https://github.com/aiidateam/aiida-core/pull/948)
- Documentation: updated import/export [[994]](https://github.com/aiidateam/aiida-core/pull/994),
- Documentation: plugin quickstart [[996]](https://github.com/aiidateam/aiida-core/pull/996),
- Documentation: parser example [[1003]](https://github.com/aiidateam/aiida-core/pull/1003)

Minor bug fixes
- Fix bug with repository on external hard drive [[982]](https://github.com/aiidateam/aiida-core/pull/982)
- Fix bug in configuration of pre-commit hooks [[863]](https://github.com/aiidateam/aiida-core/pull/863)
- Fix and improve plugin loader tests [[1025]](https://github.com/aiidateam/aiida-core/pull/1025)
- Fix broken celery logging [[1033]](https://github.com/aiidateam/aiida-core/pull/1033)

Deprecations
- async from aiida.work.run has been deprecated because it can lead to race conditions and thereby unexpected behavior [[1040]](https://github.com/aiidateam/aiida-core/pull/1040)

Improvements
- Improved exception handling for loading db tests [[968]](https://github.com/aiidateam/aiida-core/pull/968)
- `verdi work kill` on workchains: skip calculation if it cannot be killed, rather than stopping [[980]](https://github.com/aiidateam/aiida-core/pull/980)
- Remove unnecessary INFO messages of Alembic for SQLAlchemy backend [[1012]](https://github.com/aiidateam/aiida-core/pull/1012)
- Add filter to suppress unnecessary log messages during testing [[1014]](https://github.com/aiidateam/aiida-core/pull/1014)

Critical bug fixes
- Fix bug in `verdi quicksetup` on Ubuntu 16.04 and add regression tests to catch similar problems in the future [[976]](https://github.com/aiidateam/aiida-core/pull/976)
- Fix bug in `verdi data` list commands for SQLAlchemy backend [[1007]](https://github.com/aiidateam/aiida-core/pull/1007)

Minor bug fixes
- Various bug fixes related to workflows for the SQLAlchemy backend [[952]](https://github.com/aiidateam/aiida-core/pull/952) [[#960]](https://github.com/aiidateam/aiida-core/pull/960)

Major changes
- The `DbPath` table has been removed and replaced with a dynamic transitive closure, because, among others, nested workchains could lead to the `DbPath` table exploding in size
- Code plugins have been removed from `aiida-core` and have been migrated to their own respective plugin repositories and can be found here:
* [Quantum ESPRESSO](https://github.com/aiidateam/aiida-quantumespresso)
* [ASE](https://github.com/aiidateam/aiida-ase)
* [COD tools](https://github.com/aiidateam/aiida-codtools)
* [NWChem](https://github.com/aiidateam/aiida-nwchem)

Each can be installed from `pip` using e.g. `pip install aiida-quantumespresso`.
Existing installations will require a migration (see [update instructions in the documentation](https://aiida-core.readthedocs.io/en/v0.10.0/installation/updating.html#plugin-migration)).
For a complete overview of available plugins you can visit [the registry](https://aiidateam.github.io/aiida-registry/).

Improvements
- A new entry `retrieve_temporary_list` in `CalcInfo` allows to retrieve files temporarily for parsing, while not having to store them permanently in the repository [[903]](https://github.com/aiidateam/aiida-core/pull/903)
- New verdi command: `verdi work kill` to kill running workchains [[821]](https://github.com/aiidateam/aiida-core/pull/821)
- New verdi command: `verdi data remote [ls,cat,show]` to inspect the contents of `RemoteData` objects [[743]](https://github.com/aiidateam/aiida-core/pull/743)
- New verdi command: `verdi export migrate` allows the migration of existing export archives to new formats [[781]](https://github.com/aiidateam/aiida-core/pull/781)
- New verdi command: `verdi profile delete` [[606]](https://github.com/aiidateam/aiida-core/pull/606)
- Implemented a new option `-m` for the `verdi work report` command to limit the number of nested levels to be printed [[888]](https://github.com/aiidateam/aiida-core/pull/888)
- Added a `running` field to the output of `verdi work list` to give the current state of the workchains [[888]](https://github.com/aiidateam/aiida-core/pull/888)
- Implemented faster query to obtain database statistics [[738]](https://github.com/aiidateam/aiida-core/pull/738)
- Added testing for automatic SqlAlchemy database migrations through alembic [[834]](https://github.com/aiidateam/aiida-core/pull/834)
- Exceptions that are triggered in steps of a `WorkChain` are now properly logged to the `Node` making them visible through `verdi work report` [[908]](https://github.com/aiidateam/aiida-core/pull/908)

Critical bug fixes
- Export will now write the link types to the archive and import will properly recreate the link [[760]](https://github.com/aiidateam/aiida-core/pull/760)
- Fix bug in workchain persistence that would lead to crashed workchains under certain conditions being resubmitted [[728]](https://github.com/aiidateam/aiida-core/pull/728)
- Fix bug in the pickling of `WorkChain` instances containing an `_if` logical block in the outline [[904]](https://github.com/aiidateam/aiida-core/pull/904)

Minor bug fixes
- The logger for subclasses of `AbstractNode` is now properly namespaced to `aiida.` such that it works in plugins outside of the `aiida-core` source tree [[897]](https://github.com/aiidateam/aiida-core/pull/897)
- Fixed a problem with the states of the direct scheduler that was causing the daemon process to hang during submission [[879]](https://github.com/aiidateam/aiida-core/pull/879)
- Various bug fixes related to the old workflows in combination with the SqlAlchemy backend [[889]](https://github.com/aiidateam/aiida-core/pull/889) [[#898]](https://github.com/aiidateam/aiida-core/pull/898)
- Fixed bug in `TCODexporter` [[761]](https://github.com/aiidateam/aiida-core/pull/761)
- `verdi profile delete` now respects the configured `dbport` setting [[713]](https://github.com/aiidateam/aiida-core/pull/713)
- Restore correct help text for `verdi --help` [[704]](https://github.com/aiidateam/aiida-core/pull/704)
- Fixed query in the ICSD importer element that caused certain structures to be erroneously skipped [[690]](https://github.com/aiidateam/aiida-core/pull/690)

Miscellaneous
- Added a "quickstart" to plugin development in the [documentation](http://aiida-core.readthedocs.io/en/v0.10.0/developer_guide/plugins/quickstart.html),
structured around the new [plugintemplate](https://github.com/aiidateam/aiida-plugin-template) [[#818]](https://github.com/aiidateam/aiida-core/pull/818)
- Improved and restructured the developer documentation [[818]](https://github.com/aiidateam/aiida-core/pull/818)