Aiida-core

Improvements
- Added new endpoint in rest api to get list of distinct node types [[2745]](https://github.com/aiidateam/aiida-core/pull/2745)
- Travis: port the deploy stage from the development branch [[2816]](https://github.com/aiidateam/aiida-core/pull/2816)

Minor bug fixes
- Corrected the graph export set expansion rules [[2632]](https://github.com/aiidateam/aiida-core/pull/2632)

Miscellaneous
- Backport streamlined quick install instructions from `provenance_redesign` [[2555]]( https://github.com/aiidateam/aiida_core/pull/2555)
- Remove useless chainmap dependency [[2799]](https://github.com/aiidateam/aiida-core/pull/2799)
- Add aiida-core version to docs home page [[3058]](https://github.com/aiidateam/aiida-core/pull/3058)
- Docs: add note on increasing work_mem [[2952]](https://github.com/aiidateam/aiida-core/pull/2952)

Improvements
- Fast addition of nodes to groups with `skip_orm=True` [[2471]](https://github.com/aiidateam/aiida-core/pull/2471)
- Add `environment.yml` for installing dependencies using conda; release of `aiida-core` on conda-forge channel [[2081]](https://github.com/aiidateam/aiida-core/pull/2081)
- REST API: io tree response now includes link type and node label [[2033]](https://github.com/aiidateam/aiida-core/pull/2033) [[#2511]](https://github.com/aiidateam/aiida-core/pull/2511)
- Backport postgres improvements for quicksetup [[2433]](https://github.com/aiidateam/aiida-core/pull/2433)
- Backport `aiida.get_strict_version` (for plugin development) [[2099]](https://github.com/aiidateam/aiida-core/pull/2099)

Minor bug fixes
- Fix security vulnerability by upgrading `paramiko` to `2.4.2` [[2043]](https://github.com/aiidateam/aiida-core/pull/2043)
- Disable caching for inline calculations (broken since move to ``workfunction``-based implementation) [[1872]](https://github.com/aiidateam/aiida-core/pull/1872)
- Let `verdi help` return exit status 0 [[2434]](https://github.com/aiidateam/aiida-core/pull/2434)
- Decode dict keys only if strings (backport) [[2436]](https://github.com/aiidateam/aiida-core/pull/2436)
- Remove broken verdi-plug entry point [[2356]](https://github.com/aiidateam/aiida-core/pull/2356)
- `verdi node delete` (without arguments) no longer tries to delete all nodes [[2545]](https://github.com/aiidateam/aiida-core/pull/2545)
- Fix plotting of `BandsData` objects [[2492]](https://github.com/aiidateam/aiida-core/pull/2492)

Miscellaneous
- REST API: add tests for random sorting list entries of same type [[2106]](https://github.com/aiidateam/aiida-core/pull/2106)
- Add various badges to README [[1969]](https://github.com/aiidateam/aiida-core/pull/1969)
- Minor documentation improvements [[1955]](https://github.com/aiidateam/aiida-core/pull/1955)
- Add license file to MANIFEST [[2339]](https://github.com/aiidateam/aiida-core/pull/2339)
- Add instructions when `verdi import` fails [[2420]](https://github.com/aiidateam/aiida-core/pull/2420)

Improvements
- Support the hashing of `uuid.UUID` types by registering a hashing function [[1861]](https://github.com/aiidateam/aiida-core/pull/1861)
- Add documentation on plugin cutter [[1904]](https://github.com/aiidateam/aiida-core/pull/1904)

Minor bug fixes
- Make exported graphs consistent with the current node and link hierarchy definition [[1764]](https://github.com/aiidateam/aiida-core/pull/1764)
- Fix link import problem under SQLA [[1769]](https://github.com/aiidateam/aiida-core/pull/1769)
- Fix cache folder copying [[1746]](https://github.com/aiidateam/aiida-core/pull/1746) [[1752]](https://github.com/aiidateam/aiida-core/pull/1752)
- Fix bug in mixins.py when copying node [[1743]](https://github.com/aiidateam/aiida-core/pull/1743)
- Fix pgtest failures (release-branch) on travis [[1736]](https://github.com/aiidateam/aiida-core/pull/1736)
- Fix plugin: return testrunner result to fail on travis, when tests don't pass [[1676]](https://github.com/aiidateam/aiida-core/pull/1676)

Miscellaneous
- Remove pycrypto dependency, as it was found to have sercurity flaws [[1754]](https://github.com/aiidateam/aiida-core/pull/1754)
- Set xsf as default format for structures visualization [[1756]](https://github.com/aiidateam/aiida-core/pull/1756)
- Delete unused `utils/create_requirements.py` file [[1702]](https://github.com/aiidateam/aiida-core/pull/1702)

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)