CHANGELOG.md

v0.12.0

Improvements

• Hashing, caching and fast-forwarding [#652]
• Calculation no longer stores full source file [#1082]
• Delete nodes via verdi node delete [#1083]
• Import structures using ASE [#1085]
• StructureData - pymatgen - StructureData roundtrip works for arbitrary kind names [#1285] [#1306] [#1357]
• Output format of export file can now be defined for verdi export migrate [#1383]
• Automatic reporting of code coverage by unit tests has been added [#1422]

Critical bug fixes

• Add parser_name JobProcess options [#1118]
• Node attribute reads were not always up to date across interpreters for SqlAlchemy [#1379]

Minor bug fixes

• Cell vectors not printed correctly [#1087]
• Fix read-the-docs issues [#1120] [#1143]
• Fix structure/band visualization in REST API [#1167] [#1182]
• Fix verdi work list test [#1286]
• Fix _inline_to_standalone_script in TCODExporter [#1351]
• Updated reentry to fix various small bugs related to plugin registering [#1440]

Miscellaneous

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

v0.11.4

Improvements

• PyCifRW upgraded to 4.2.1 [#1073]

Critical bug fixes

• Persist and load parsed workchain inputs and do not recreate to avoid creating duplicates for default inputs [#1362]
• Serialize WorkChain context before persisting [#1354]

v0.11.3

Improvements

• Documentation: AiiDA now has an automatically generated and complete API documentation (using sphinx-apidoc) [#1330]
• Add JSON schema for connection of REST API to Materials Cloud Explore interface [#1336]

Critical bug fixes

• FINISHED_KEY and FAILED_KEY variables were not known to AbstractCalculation [#1314]

Minor bug fixes

• Make 'REST' extra lowercase, such that one can do pip install aiida-core[rest] [#1328]
• CifData /visualization endpoint was not returning data [#1328]

Deprecations

• QueryTool (was deprecated in favor of QueryBuilder since v0.8.0) [#1330]

Miscellaneous

• Add gource config for generating a video of development history [#1337]

v0.11.2:

Critical bug fixes

• Link types were not respected in Node.get_inputs for SqlAlchemy [#1271]

v0.11.1:

Improvements

• Support visualization of structures and cif files with VESTA [#1093]
• Better fallback when node class is not available [#1185]
• CifData now supports faster parsing and lazy loading [#1190]
• REST endpoint for CifData, API reports full list of available endpoints [#1228]
• Various smaller improvements [#1100] [#1182]

Critical bug fixes

• Restore attribute immutability in nodes [#1111]
• Fix daemonization issue that could cause aiida daemon to be killed [#1246]

Minor bug fixes

• Fix type column in verdi calculation list [#960] [#1053]
• Fix verdi import from URLs [#1139]

v0.11.0:

Improvements

Core entities

• Computer: the shebang line is now customizable [#940]
• KpointsData: deprecate buggy legacy implementation of k-point generation in favor of Seekpath [#1015]
• ParameterData: to_aiida_type used on dictionaries now automatically converted to ParameterData [#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] [#894]

Plugins

• Plugin data hooks: plugins can now add custom commands to verdi data [#993]
• Plugin fixtures: simple-to-use decorators for writing tests of plugins [#716] [#865]
• Plugin development: no longer swallow ImportError exception during import of plugins [#1029]

Verdi

• verdi shell: improve tab completion of imports in [#1008]
• verdi work list: projections for verdi work list [#847]

Miscellaneous

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

Minor bug fixes

• Fix bug with repository on external hard drive [#982]
• Fix bug in configuration of pre-commit hooks [#863]
• Fix and improve plugin loader tests [#1025]
• Fix broken celery logging [#1033]

Deprecations

• async from aiida.work.run has been deprecated because it can lead to race conditions and thereby unexpected behavior [#1040]

v0.10.1:

Improvements

• Improved exception handling for loading db tests [#968]
• verdi work kill on workchains: skip calculation if it cannot be killed, rather than stopping [#980]
• Remove unnecessary INFO messages of Alembic for SQLAlchemy backend [#1012]
• Add filter to suppress unnecessary log messages during testing [#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]
• Fix bug in verdi data list commands for SQLAlchemy backend [#1007]

Minor bug fixes

• Various bug fixes related to workflows for the SQLAlchemy backend [#952] [#960]

v0.10.0:

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
  • ASE
  • COD tools
  • 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). For a complete overview of available plugins you can visit the 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]
• New verdi command: verdi work kill to kill running workchains [#821]
• New verdi command: verdi data remote [ls,cat,show] to inspect the contents of RemoteData objects [#743]
• New verdi command: verdi export migrate allows the migration of existing export archives to new formats [#781]
• New verdi command: verdi profile delete [#606]
• Implemented a new option -m for the verdi work report command to limit the number of nested levels to be printed [#888]
• Added a running field to the output of verdi work list to give the current state of the workchains [#888]
• Implemented faster query to obtain database statistics [#738]
• Added testing for automatic SqlAlchemy database migrations through alembic [#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]

Critical bug fixes

• Export will now write the link types to the archive and import will properly recreate the link [#760]
• Fix bug in workchain persistence that would lead to crashed workchains under certain conditions being resubmitted [#728]
• Fix bug in the pickling of WorkChain instances containing an _if logical block in the outline [#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]
• Fixed a problem with the states of the direct scheduler that was causing the daemon process to hang during submission [#879]
• Various bug fixes related to the old workflows in combination with the SqlAlchemy backend [#889] [#898]
• Fixed bug in TCODexporter [#761]
• verdi profile delete now respects the configured dbport setting [#713]
• Restore correct help text for verdi --help [#704]
• Fixed query in the ICSD importer element that caused certain structures to be erroneously skipped [#690]

Miscellaneous

• Added a "quickstart" to plugin development in the documentation, structured around the new plugintemplate [#818]
• Improved and restructured the developer documentation [#818]

v0.9.1:

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

v0.9.0

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 ParameterData.
• 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

v0.8.1

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

v0.8.0

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 DbPathand 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

v0.7.1

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 listnow 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.

v0.7.0

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.

v0.6.0

We performed a lot of changes to introduce in one of our following releases a second
object-relational mapper (we will refer to it as back-end) for the management of the used DBMSs and
more specifically of PostgreSQL. SQLAlchemy and the latest version of PostgreSQL allows AiiDA to
store JSON documents directly to the database and also to query them. Moreover the JSON query
optimization is left to the database including also the use of the JSON specific indexes. There was
major code restructuring to accommodate the new back-end resulting to abstracting many classes of
the orm package of AiiDA.

Even if most of the needed restructuring & code addition has been finished, a bit of more work is
needed. Therefore even in this version, Django is the only available back-end for the end user.

However, the users have to update their AiiDA configuration files by executing the migration file
that can be found at YOUR_AIIDA_DIR/aiida/common/additions/migration.py as the Linux user that
installed AiiDA in your system. (e.g. python YOUR_AIIDA_DIR/aiida/common/additions/migration.py)

List of changes:

• Back-end selection (Added backend selection). SQLAlchemy selection is disabled for the moment.
• Migration scripts for the configuration files of AiiDA (SQLAlchemy support).
• Enriched link description in the database (to enrich the provenance model).
• Corrections for numpy array and cell. List will be used with cell.
• Fixed backend import. Verdi commands load as late as possible the needed backend.
• Abstraction of the basic AiiDA orm classes (like node, computer, data etc). This is needed to
  support different backends (e.g. Django and SQLAlchemy).
• Fixes on the structure import from QE-input files.
• SQLAlchemy and Django benchmarks.
• UltraJSON support.
• requirements.txt now also include SQLAlchemy and its dependencies.
• Recursive way of loading JSON for SQLAlchemy.
• Improved way of accessing calculations and workflows attached to a workflow step.
• Added methods to programmatically create new codes and computers.

v0.5.0

General

• Final paper published, ref: G. Pizzi, A. Cepellotti, R. Sabatini, N. Marzari, and B. Kozinsky,
  AiiDA: automated interactive infrastructure and database for computational science,
  Comp. Mat. Sci 111, 218-230 (2016)
• Core, concrete, requirements kept in requirements.txt and optionals moved to
  optional_requirements.txt
• Schema change to v1.0.2: got rid of calc_states.UNDETERMINED

Import/export, backup and code interaction

• [non-back-compatible] Now supporting multiple codes execution in the same submission script.
  Plugin interface changed, requires adaptation of the code plugins.
• Added import support for XYZ files
• Added support for van der Waals table in QE input
• Restart QE calculations avoiding using scratch using copy of parent calc
• Adding database importer for NNIN/C Pseudopotential Virtual Vault
• Implemented conversion of pymatgen Molecule lists to AiiDA's TrajectoryData
• Adding a converter from pymatgen Molecule to AiiDA StructureData
• Queries now much faster when exporting
• Added an option to export a zip file
• Added backup scripts for efficient incremental backup of large AiiDA repositories

API

• Added the possibility to add any kind of Django query in Group.query
• Added TCOD (Theoretical Crystallography Open Database) importer and exporter
• Added option to sort by a field in the query tool
• Implemented selection of data nodes and calculations by group
• Added NWChem plugin
• Change default behaviour of symbolic link copy in the transport plugins: "put"/"get"
  methods -> symbolic links are followed before copy; "copy" methods -> symbolic links are not
  followed (copied "as is").

Schedulers

• Explicit Torque support (some slightly different flags)
• Improved PBSPro scheduler
• Added new num_cores_per_machine and num_cores_per_mpiproc fields for pbs and torque schedulers
  (giving full support for MPI+OpenMP hybrid codes)
• Direct scheduler added, allowing calculations to be run without batch system
  (i.e. directly call executable)

verdi

• Support for profiles added: it allows user to switch between database configurations using the verdi profile command
• Added verdi data structure import --file file.xyz for importing XYZ
• Added a verdi data upf exportfamily command (to export an upf pseudopotential family into a folder)
• Added new functionalities to the verdi group command (show list of nodes, add and remove nodes
  from the command line)
• Allowing verdi export command to take group PKs
• Added ASE as a possible format for visualizing structures from command line
• Added possibility to export trajectory data in xsf format
• Added possibility to show trajectory data with xcrysden
• Added filters on group name in verdi group list
• Added possibility to load custom modules in the verdi shell (additional property
  verdishell.modules created; can be set with verdi devel setproperty verdishell.modules)
• Added verdi data array show command, using json_date serialization to display the contents of ArrayData
• Added verdi data trajectory deposit command line command
• Added command options --computer and --code to verdi data * deposit
• Added a command line option --all-users for verdi data * list to list objects, owned by all users