Aiida-core

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

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

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

Installation and setup
- Simplified installation procedure by adopting standard python package installation method through
setuptools and pip
- Verdi install replaced by verdi setup
- New verdi command `quicksetup` to simplify the setup procedure
- Significantly updated and improved the installation documentation

General
- Significantly increased test coverage and implemented for both backends
- Activated continuous integration through Travis CI
- Application-wide logging is now abstracted and implemented for all backends
- Added a REST API layer with hook through verdi cli: `verdi restapi`
- Improved `QueryBuilder`
* Composition model instead of inheritance removing the requirement of determining the
implementation on import
* Added keyword `with_dbpath` that makes `QueryBuilder` switch between using the `DbPath`and not
using it.
* Updated and improved documentation
- The QueryTool as well as the `class Node.query()` method are now deprecated in favor of the
`QueryBuilder`
- Migration of verdi cli to use the `QueryBuilder` in order to support both database backends
- Added option `--project` to `verdi calculation list` to specify which attributes to print

Documentation
- Documentation is restructured to improve navigability
- Added pseudopotential tutorial

Database
- Dropped support for MySQL and SQLite to fully support efficient features in Postgres like JSONB
fields
- Database efficiency improvements with orders of magnitude speedup for large databases
[added indices for daemon queries and node UUID queries]
- Replace deprecated `commit_on_success` with atomic for Django transactions
- Change of how SQLAlchemy internally uses the session and the engine to work also with forks (e.g. in celery)

Workflows
- Finalized the naming for the new workflow system from `workflows2` to `work`
* `FragmentedWorkFunction` is replaced by `WorkChain`
* `InlineCalculation` is replaced by `Workfunction`
* `ProcessCalculation` is replaced by `WorkCalculation`
- Old style Workflows can still be called and run from a new style `WorkChain`
- Major improvements to the `WorkChain` and `Workfunction` implementation
- Improvements to `WorkChain`
* Implemented a `return` statement for `WorkChain` specification
* Logging to the database implemented through `WorkChain.report()` for debugging
- Improved kill command for old-style workflows to avoid steps to remaing in running state

Plugins
- Added finer granularity for parsing PW timers in output
- New Quantum ESPRESSO and scheduler plugins contributed from EPFL
* ASE/GPAW plugins: Andrea Cepellotti (EPFL and Berkeley)
* Quantum ESPRESSO DOS, Projwfc: Daniel Marchand (EPFL and McGill)
* Quantum ESPRESSO phonon, matdyn, q2r, force constants plugins: Giovanni Pizzi,
Nicolas Mounet (EPFL); Andrea Cepellotti (EPFL and Berkeley)
* Quantum ESPRESSO cp.x plugin: Giovanni Pizzi (EPFL)
* Quantum ESPRESSO neb.x plugin: Marco Gibertini (EPFL)
* LSF scheduler: Nicolas Mounet (EPFL)
- Implemented functionality to export and visualize molecular dynamics trajectories
(using e.g. matplotlib, mayavi)
- Improved the TCODExporter (some fixes to adapt to changes of external libraries, added some
additional TCOD CIF tags, various bugfixes)

Various fixes and improvements
- Fix for the direct scheduler on Mac OS X
- Fix for the import of computers with name collisions
- Generated backup scripts are now made profile specific and saved as `start_backup_<profile>.py`
- Fix for the vary_rounds warning

Functionalities
- Implemented support for Kerberos authentication in the ssh transport plugin.
- Added `_get_submit_script_footer` to scheduler base class.
- Improvements of the SLURM scheduler plugin.
- Fully functional parsers for Quantumespresso CP and PW.
- Better parsing of atomic species from PW output.
- Array classes for projection & xy, and changes in kpoints class.
- Added codespecific tools for Quantumespresso.
- `verdi code list`now shows local codes too.
- `verdi export` can now export non user-defined groups (from their pk).

Fixes
- Fixed bugs in (old) workflow manager and daemon.
- Improvements of the efficiency of the (old) workflow manager.
- Fixed JobCalculation text prepend with multiple codes.

This release introduces a lot and significant changes & enhancements.

We worked on our new backend and now AiiDA can be installed using SQLAlchemy too. Many of the verdi
commands and functionalities have been tested and are working with this backend. The full JSON
support provided by SQLAlchemy and the latest versions of PostgreSQL enable significant speed
increase in attribute related queries. SQLAlchemy backend choice is a beta option since some last
functionalities and commands need to be implemented or improved for this backend. Scripts are
provided for the transition of databases from Django backend to SQLAlchemy backend.

In this release we have included a new querying tool called `QueryBuilder`. It is a powerfull tool
allowing users to write complex graph queries to explore the AiiDA graph database. It provides
various features like selection of entity properties, filtering of results, combination of entities
on specific properties as well as various ways to obtain the final result. It also provides the
users an abstract way to query their data without enforcing them to write backend dependent queries.

Last but not least we have included a new workflow engine (in beta version) which is available
through the `verdi workflow2` command. The new workflows are easier to write (it is as close as
writing python as possible), there is seamless mixing of short running tasks with long running
(remote) tasks and they encourage users to write reusable workflows. Moreover, debugging of
workflows has been made easier and it is possible both in-IDE and through logging.

List of changes:
- Installation procedure works with SQLAlchemy backend too (SQLAlchemy option is still in beta).
- Most of the verdi commands work with SQLAlchemy backend.
- Transition script from Django schema of version 0.7.0 to SQLAlchemy schema of version 0.7.0.
- AiiDA daemon redesigned and working with both backends (Django & SQLAlchemy).
- Introducing new workflow engine that allows better debugging and easier to write workflows. It is
available under the `verdi workflows2` command. Examples are also added.
- Old workflows are still supported and available under the "verdi workflow" command.
- Introducing new querying tool (called `QueryBuilder`). It allows to easily write complex graph
queries that will be executed on the AiiDA graph database. Extensive documentation also added.
- Unifying behaviour of verdi commands in both backends.
- Upped to version 0.4.2 of plum (needed for workflows2)
- Implemented the validator and input helper for Quantum ESPRESSO pw.x.
- Improved the documentation for the pw (and cp) input plugins (for all the flags in the Settings
node).
- Fixed a wrong behavior in the QE pw/cp plugins when checking for the parser options and checking
if there were further unknown flags in the Settings node. However, this does not solve yet
completely the problem (see issue 219).
- Implemented validator and input helper for Quantum ESPRESSO pw.x.
- Added elements with Z=104-112, 114 and 116, in `aiida.common.constants`.
- Added method `set_kpoints_mesh_from_density` in `KpointsData` class.
- Improved incremental backup documentation.
- Added backup related tests.
- Added an option to `test_pw.py` to run also in serial.
- SSH transport, to connect to remote computers via SSH/SFTP.
- Support for the SGE and SLURM schedulers.
- Support for Quantum ESPRESSO Car-Parrinello calculations.
- Support for data nodes to store electronic bands, phonon dispersion and generally arrays defined
over the Brillouin zone.