Aiida

Latest version: v1.0.1

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0.11.0

Not secure
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- Documentation: updated outdated workflow examples [[948]](https://github.com/aiidateam/aiida-core/pull/948)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)

0.10.1

Not secure
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)

0.10.0

Not secure
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)

0.9.1

Not secure
Critical bug fixes
- Workchain steps will no longer be executed multiple times due to process pickles not being locked

Minor bug fixes
- Fix arithmetic operations for basic numeric types
- Fixed `verdi calculation cleanworkdir` after changes in `QueryBuilder` syntax
- Fixed `verdi calculation logshow` exception when called for `WorkCalculation` nodes
- Fixed `verdi import` for SQLAlchemy profiles
- Fixed bug in `reentry` and update dependency requirement to `v1.0.2`
- Made octal literal string compatible with python 3
- Fixed broken import in the ASE plugin

Improvements
- `verdi calculation show` now properly distinguishes between `WorkCalculation` and `JobCalculation` nodes
- Improved error handling in `verdi setup --non-interactive`
- Disable unnecessary console logging for tests

0.9.0

Not secure
Data export functionality
- A number of new functionalities have been added to export band structures to a number of formats, including: gnuplot, matplotlib (both to export a python file, and directly PNG or PDF; both with support of LaTeX typesetting and not); JSON; improved agr (xmgrace) output. Also support for two-color bands for collinear magnetic systems. Added also possibility to specify export-format-specific parameters.
- Added method get_export_formats() to know available export formats for a given data subclass
- Added label prettifiers to properly typeset high-symmetry k-point labels for different formats (simple/old format, seekpath, ...) into a number of plotting codes (xmgrace, gnuplot, latex, ...)
- Improvement of command-line export functionality (more options, possibility to write directly to file, possibility to pass custom options to exporter, by removing its DbPath dependency)

Workchains
- Crucial bug fix: workchains can now be run through the daemon, i.e. by using `aiida.work.submit`
- Enhancement: added an `abort` and `abort_nowait` method to `WorkChain` which allows to abort the workchain at the earliest possible moment
- Enhancement: added the `report` method to `WorkChain`, which allows a workchain developer to log messages to the database
- Enhancement: added command `verdi work report` which for a given `pk` returns the messages logged for a `WorkChain` through the `report` method
- Enhancement: workchain inputs ports with a valid default specified no longer require to explicitly set `required=False` but is overriden automatically

New plugin system
- New plugin system implemented, allowing to load aiida entrypoints, and working in parallel with old system (still experimental, though - command line entry points are not fully implemented yet)
- Support for the plugin registry

Code refactoring
- Refactoring of `Node` to move as much as possible of the caching code into the abstract class
- Refactoring of `Data` nodes to have the export code in the topmost class, and to make it more general also for formats exporting more than one file
- Refactoring of a number of `Data` subclasses to support the new export API
- Refactoring of `BandsData` to have export code not specific to xmgrace or a given format, and to make it more general

Documentation
- General improvements to documentation
- Added documentation to upgrade AiiDA from v0.8.0 to v0.9.0
- Added documentation of new plugin system and tutorial
- Added more in-depth documentation on how to export data nodes to various formats
- Added explanation on how to export band structures and available formats
- Added documentation on how to run tests in developer's guide
- Documented Latex requirements
- Updated WorkChain documentation for `WaitingEquationOfState` example
- Updated AiiDA installation documentation for installing virtual environment
- Updated documentation to use Jupyter

Enhancements
- Speedups the travis builds process by caching pip files between runs
- Node can be loaded by passing the start of its UUID
- Handled invalid verdi command line arguments; added help texts for same
- upgraded `Paramiko` to 2.1.2 and avoided to create empty file when remote connection is failed
- `verdi calculation kill` command is now available for `SGE plugin`
- Updated `Plum` from 0.7.8 to 0.7.9 to create a workchain inputs that had default value and evaluated to false
- Now QueryBuilder will be imported by default for all verdi commands

Bug Fixes
- Bug fixes in QE input parser
- Code.get() method accepts the pk in integer or string format whereas Code.get_from_string() method accepts pk only in string format
- `verdi code show` command now shows the description of the code
- Bug fix to check if computer is properly configured before submitting the calculation

Miscellaneous
- Replacing dependency from old unmantained `pyspglib` to new `spglib`
- Accept BaseTypes as attributes/extras, and convert them automatically to their value. In this way, for instance, it is now possible to pass a `Int`, `Float`, `Str`, ... as value of a dictionary, and store all into a `Dict`.
- Switch from `pkg_resources` to reentry to allow for much faster loading of modules when possible, and therefore allowing for good speed for bash completion
- Removed obsolete code for Sqlite
- Removed `mayavi2` package from dependencies

0.8.1

Not secure
Exporters
- Upgraded the TCODExporter to produce CIF files, conforming to the newest (as of 2017-04-26) version of cif_tcod.dic.

General
- Added dependency on six to properly re-raise exceptions

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