Aiida

Improvements
- Always use a bash login shell to execute all remote SSH commands, overriding any system default shell [[1502]](https://github.com/aiidateam/aiida-core/pull/1502)
- Reduced the size of the distributed package by almost half by removing test fixtures and generating the data on the fly [[1645]](https://github.com/aiidateam/aiida-core/pull/1645)
- Removed the explicit dependency upper limit for `scipy` [[1492]](https://github.com/aiidateam/aiida-core/pull/1492)
- Resolved various dependency requirement conflicts [[1488]](https://github.com/aiidateam/aiida-core/pull/1488)

Minor bug fixes
- Fixed a bug in `verdi node delete` that would throw an exception for certain cases [[1564]](https://github.com/aiidateam/aiida-core/pull/1564)
- Fixed a bug in the `cif` endpoint of the REST API [[1490]](https://github.com/aiidateam/aiida-core/pull/1490)

Improvements
- Hashing, caching and fast-forwarding [[652]](https://github.com/aiidateam/aiida-core/pull/652)
- Calculation no longer stores full source file [[1082]](https://github.com/aiidateam/aiida-core/pull/1082)
- Delete nodes via `verdi node delete` [[1083]](https://github.com/aiidateam/aiida-core/pull/1083)
- Import structures using ASE [[1085]](https://github.com/aiidateam/aiida-core/pull/1085)
- `StructureData` - `pymatgen` - `StructureData` roundtrip works for arbitrary kind names [[1285]](https://github.com/aiidateam/aiida-core/pull/1285) [[#1306]](https://github.com/aiidateam/aiida-core/pull/1306) [[#1357]](https://github.com/aiidateam/aiida-core/pull/1357)
- Output format of archive file can now be defined for `verdi export migrate` [[1383]](https://github.com/aiidateam/aiida-core/pull/1383)
- Automatic reporting of code coverage by unit tests has been added [[1422]](https://github.com/aiidateam/aiida-core/pull/1422)

Critical bug fixes
- Add `parser_name` `JobProcess` options [[1118]](https://github.com/aiidateam/aiida-core/pull/1118)
- Node attribute reads were not always up to date across interpreters for SqlAlchemy [[1379]](https://github.com/aiidateam/aiida-core/pull/1379)

Minor bug fixes
- Cell vectors not printed correctly [[1087]](https://github.com/aiidateam/aiida-core/pull/1087)
- Fix read-the-docs issues [[1120]](https://github.com/aiidateam/aiida-core/pull/1120) [[#1143]](https://github.com/aiidateam/aiida-core/pull/1143)
- Fix structure/band visualization in REST API [[1167]](https://github.com/aiidateam/aiida-core/pull/1167) [[#1182]](https://github.com/aiidateam/aiida-core/pull/1182)
- Fix `verdi work list` test [[1286]](https://github.com/aiidateam/aiida-core/pull/1286)
- Fix `_inline_to_standalone_script` in `TCODExporter` [[1351]](https://github.com/aiidateam/aiida-core/pull/1351)
- Updated `reentry` to fix various small bugs related to plugin registering [[1440]](https://github.com/aiidateam/aiida-core/pull/1440)

Miscellaneous
- Bump `qe-tools` version [[1090]](https://github.com/aiidateam/aiida-core/pull/1090)
- Document link types [[1174]](https://github.com/aiidateam/aiida-core/pull/1174)
- Switch to trusty + postgres 9.5 on Travis [[1180]](https://github.com/aiidateam/aiida-core/pull/1180)
- Use raw SQL in sqlalchemy migration of `Code` [[1291]](https://github.com/aiidateam/aiida-core/pull/1291)
- Document querying of list attributes [[1326]](https://github.com/aiidateam/aiida-core/pull/1326)
- Document running `aiida` as a daemon service [[1445]](https://github.com/aiidateam/aiida-core/pull/1445)
- Document that Torque and LoadLever schedulers are now fully supported [[1447]](https://github.com/aiidateam/aiida-core/pull/1447)
- Cookbook: how to check the number of queued/running jobs in the scheduler [[1349]](https://github.com/aiidateam/aiida-core/pull/1349)

Improvements
- PyCifRW upgraded to 4.2.1 [[1073]](https://github.com/aiidateam/aiida-core/pull/1073)

Critical bug fixes
- Persist and load parsed workchain inputs and do not recreate to avoid creating duplicates for default inputs [[1362]](https://github.com/aiidateam/aiida-core/pull/1362)
- Serialize `WorkChain` context before persisting [[1354]](https://github.com/aiidateam/aiida-core/pull/1354)

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)