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Changelog

v1.2.1

In the fixing of three bugs, three minor features have been added along the way.

Features

  • Add config option daemon.worker_process_slots to configure the maximum number of concurrent tasks each daemon worker can handle [#3949]
  • Add config option daemon.default_workers to set the default number of workers to be started by verdi daemon start [#3949]
  • CalcJob: make submit script filename configurable through the metadata.options [#3948]

Bug fixes

  • CalcJob: fix bug in idempotency check of upload transport task [#3948]
  • REST API: reintroduce CORS headers, the lack of which was breaking the Materials Cloud provenance explorer [#3951]
  • Remove the equality operator of ExitCode which caused the serialization of workchains to fail if put in the workchain context [#3940]

Deprecations

  • The hookup argument of aiida.restapi.run_api and the --hookup option of verdi restapi are deprecated [#3951]

v1.2.0

Features

  • ExitCode: make the exit message parameterizable through templates [#3824]
  • GroupPath: a utility to work with virtual Group hierarchies [#3613]
  • Make Group sub classable through entry points [#3882][#3903][#3926]
  • Add auto-complete support for CodeParamType and GroupParamType [#3926]
  • Add export archive migration for Group type strings [#3912]
  • Add the -v/--version option to verdi export migrate [#3910]
  • Add the -l/--limit option to verdi group show [#3857]
  • Add the --order-by/--order-direction options to verdi group list [#3858]
  • Add prepend_text and append_text to aiida_local_code_factory pytest fixture [#3831]
  • REST API: make it easier to call run_api in wsgi scripts [#3875]
  • Plot bands with only one kpoint [#3798]

Bug fixes

  • Improved validation for CLI parameters [#3894]
  • Ensure unicity when creating instances of Autogroup [#3650]
  • Prevent nodes without registered entry points from being stored [#3886]
  • Fix the RotatingFileHandler configuration of the daemon logger[#3891]
  • Ensure log messages are not duplicated in daemon log file [#3890]
  • Convert argument to str in aiida.common.escaping.escape_for_bash [#3873]
  • Remove the return statement of RemoteData.getfile() [#3742]
  • Support for BandsData nodes without StructureData ancestors [#3817]

Deprecations

  • Deprecate --group-type option in favor of --type-string for verdi group list [#3926]

Documentation

  • Docs: link to documentation of other libraries via intersphinx mapping [#3876]
  • Docs: remove extra advanced_plotting from install instructions [#3860]
  • Docs: consistent use of "plugin" vs "plugin package" terminology [#3799]

Developers

  • Deduplicate code for tests of archive migration code [#3924]
  • CI: use GitHub Actions services for PostgreSQL and RabbitMQ [#3901]
  • Move aiida.manage.external.pgsu to external package pgsu [#3892]
  • Cleanup the top-level directory of the repository [#3738]
  • Remove unused orm.implementation.utils module [#3877]
  • Revise dependency management workflow [#3771]
  • Re-add support for Coverage reports through codecov.io [#3618]

v1.1.1

Changes

  • Emit a warning when input port specifies a node instance as default [#3466]
  • BaseRestartWorkChain: require process handlers to be instance methods [#3782]
  • BaseRestartWorkChain: add method to enable/disable process handlers [#3786]
  • Docker container: remove conda activation from configure-aiida.sh script [#3791]
  • Add fixtures to clear the database before or after tests [#3783]
  • verdi status: add the configuration directory path to the output [#3587]
  • QueryBuilder: add support for datetime.date objects in filters [#3796]

Bug fixes

  • Fix bugs in Node._store_from_cache and Node.repository.erase that could result in calculations not being reused [#3777]
  • Caching: fix configuration spec and validation [#3785]
  • Write migrated config to disk in Config.from_file [#3797]
  • Validate label string at code setup stage [#3793]
  • Reuse prepend_text and append_text in verdi computer/code duplicate [#3788]
  • Fix broken imports of urllib in various locations including verdi import [#3767]
  • Match headers with actual output for verdi data structure list [#3756]
  • Disable caching for the Data node subclass (this should not affect usual caching behavior) [#3807]

v1.1.0

Nota Bene: although this is a minor version release, the support for python 2 is dropped (#3566) following the reasoning outlined in the corresponding AEP001. Critical bug fixes for python 2 will be supported until July 1 2020 on the v1.0.* release series. With the addition of python 3.8 (#3719), this version is now compatible with all current python versions that are not end-of-life:

  • 3.5
  • 3.6
  • 3.7
  • 3.8

Features

  • Add the AiiDA Graph Explorer (AGE) a generic tool for traversing provenance graph [#3686]
  • Add the BaseRestartWorkChain which makes it easier to write a simple work chain wrapper around another process with automated error handling [#3748]
  • Add provenance_exclude_list attribute to CalcInfo data structure, allowing to prevent calculation input files from being permanently stored in the repository [#3720]
  • Add the verdi node repo dump command [#3623]
  • Add more methods to control cache invalidation of completed process node [#3637]
  • Allow documentation to be build without installing and configuring AiiDA [#3669]
  • Add option to expand namespaces in sphinx directive [#3631]

Performance

  • Add node_type to list of immutable model fields, preventing repeated database hits [#3619]
  • Add cache for entry points in an entry point group [#3622]
  • Improve the performance when exporting many groups [#3681]

Changes

  • CalcJob: move presubmit call from CalcJob.run to Waiting.execute [#3666]
  • CalcJob: do not pause when exception thrown in the presubmit [#3699]
  • Move CalcJob spec validator to corresponding namespaces [#3702]
  • Move getting completed job accounting to retrieve transport task [#3639]
  • Move last_job_info from JSON-serialized string to dictionary [#3651]
  • Improve SqlAlchemy session handling for QueryBuilder [#3708]
  • Use built-in open instead of io.open, which is possible now that python 2 is no longer supported [#3615]
  • Add non-zero exit code for verdi daemon status [#3729]

Bug fixes

  • Deal with unreachable daemon worker in get_daemon_status [#3683]
  • Django backend: limit batch size for bulk_create operations [#3713]
  • Make sure that datetime conversions ignore None [#3628]
  • Allow empty key_filename in verdi computer configure ssh and reuse cooldown time when reconfiguring [#3636]
  • Update pyyaml to v5.1.2 to prevent arbitrary code execution [#3675]
  • QueryBuilder: fix validation bug and improve message for in operator [#3682]
  • Consider 'AIIDA_TEST_PROFILE' in 'get_test_backend_name' [#3685]
  • Ensure correct types for QueryBuilder().dict() with multiple projections [#3695]
  • Make local modules importable when running verdi run [#3700]
  • Fix bug in upload_calculation for CalcJobs with local codes [#3707]
  • Add imports from urllib to dbimporters [#3704]

Developers

  • Moved continuous integration from Travis to Github actions [#3571]
  • Replace custom unit test framework for pytest and move all tests to tests top level directory [#3653][#3674][#3715]
  • Cleaned up direct dependencies and relaxed requirements where possible [#3597]
  • Set job poll interval to zero in localhost pytest fixture [#3605]
  • Make command line deprecation warnings visible with test profile [#3665]
  • Add docker image with minimal running AiiDA instance [#3722]

v1.0.1

Improvements

  • Improve the backup mechanism of the configuration file: unique backup written at each update [#3581]
  • Forward verdi code delete to verdi node delete [#3546]
  • Homogenize and improve output of verdi computer test [#3544]
  • Scheduler SLURM: support UNLIMITED and NOT_SET as values for requested walltimes [#3586]
  • Set default for the safe_interval option of verdi computer configure [#3590]
  • Create backup of configuration file before migrating [#3568]
  • Add python_requires to setup.json necessary for future dropping of python 2 [#3574]
  • Remove unused QB methods/functions [#3526]
  • Move pgtest argument of TemporaryProfileManager to constructor [#3486]
  • Add filename argument to SinglefileData constructor [#3517]
  • Mention machine in SSH connection exception message [#3536]
  • Docs: Expand on QB order_by information [#3548]
  • Replace deprecated pymatgen site.species_and_occu with site.species [#3480]
  • QueryBuilder: add deepcopy implementation and queryhelp property [#3524]

Bug fixes

  • Fix verdi calcjob gotocomputer when key_filename is missing [#3593]
  • Fix bug in database migrations where schema generation determination excepts for old databases [#3582]
  • Fix false positive for verdi database integrity detect-invalid-links [#3591]
  • Config migration: handle edge case where daemon key is missing from daemon_profiles [#3585]
  • Raise when unable to detect name of local timezone [#3576]
  • Fix bug for CalcJob dry runs with store_provenance=False [#3513]
  • Migrations for legacy and now illegal default link label _return, export version upped to 0.8 [#3561]
  • Fix REST API attributes_filter and extras_filter [#3556]
  • Fix bug in plugin Factory classes for python 3.7 [#3552]
  • Make PolishWorkChains checkpointable [#3532]
  • REST API: fix generator of full node namespace [#3516]

v1.0.0

Overview of changes

The following is a summary of the major changes and improvements from v0.12.* to v1.0.0.

  • Faster workflow engine: the new message-based engine powered by RabbitMQ supports tens of thousands of processes per hour and greatly speeds up workflow testing. You can now run one daemon per AiiDA profile.
  • Faster database queries: the switch to JSONB for node attributes and extras greatly improves query speed and reduces storage size by orders of magnitude.
  • Robust calculations: AiiDA now deals with network connection issues (automatic retries with backoff mechanism, connection pooling, ...) out of the box. Workflows and calculations are all Processes and can be "paused" and "played" anytime.
  • Better verdi commands: the move to the click framework brings homogenous command line options across all commands (loading nodes, ...). You can easily add new commands through plugins.
  • Easier workflow development: Input and output namespaces, reusing specs of sub-processes and less boilerplate code simplify writing WorkChains and CalcJobs, while also enabling powerful auto-documentation features.
  • Mature provenance model: Clear separation between data provenance (Calculations, Data) and logical provenance (Workflows). Old databases can be migrated to the new model automatically.
  • python3 compatible: AiiDA 1.0 is compatible with both python 2.7 and python 3.6 (and later). Python 2 support will be dropped in the coming months.

Detailed list of changes

Below a (non-exhaustive) list of changes by category. Changes between 1.0 alpha/beta releases are not included - for those see the changelog of the corresponding releases.

Engine and daemon

  • Implement the concept of an "exit status" for all calculations, allowing a programmatic definition of success or failure for all processes [#1189]
  • All calculations now go through the Process layer, homogenizing the state of work and job calculations [#1125]
  • Allow None as default for arguments of process functions [#2582]
  • Implement the new calcfunction decorator. [#2203]
  • Each profile now has its own daemon that can be run completely independently in parallel [#1217]
  • Polling based daemon has been replaced with a much faster event-based daemon [#1067]
  • Replaced Celery with Circus as the daemonizer of the daemon [#1213]
  • The daemon can now be stopped without loading the database, making it possible to stop it even if the database version does not match the code [#1231]
  • Implement exponential backoff retry mechanism for transport tasks [#1837]
  • Pause CalcJob when transport task falls through exponential backoff [#1903]
  • Separate CalcJob submit task in folder upload and scheduler submit [#1946]
  • Each daemon worker now respects an optional minimum scheduler polling interval [#1929]
  • Make the execmanager.retrieve_calculation idempotent'ish [#3142]
  • Make the execmanager.upload_calculation idempotent'ish [#3146]
  • Make the execmanager.submit_calculation idempotent'ish [#3188]
  • Implement a PluginVersionProvider for processes to automatically add versions of aiida-core and plugin to process nodes [#3131]

Processes

  • Implement the ProcessBuilder which simplifies the definition of Process inputs and the launching of a Process [#1116]
  • Namespaces added to the port containers of the ProcessSpec class [#1099]
  • Convention of leading underscores for non-storable inputs is replaced with a proper non_db attribute of the Port class [#1105]
  • Implement a Sphinx extension for the WorkChain class to automatically generate documentation from the workchain definition [#1155]
  • WorkChains can now expose the inputs and outputs of another WorkChain, which is great for writing modular workflows [#1170]
  • Add built-in support and API for exit codes in WorkChains [#1640], [#1704], [#1681]
  • Implement method for CalcJobNode to create a restart builder [#1962]
  • Add CalculationTools base and entry point aiida.tools.calculations [#2331]
  • Generalize Sphinx workchain extension to processes [#3314]
  • Collapsible namespace in sphinxext [#3441]
  • The retrieve_singlefile_list has been deprecated and is replaced by retrieve_temporary_list [#3041]
  • Automatically set CalcInfo.uuid in CalcJob.run [#2874]
  • Allow the usage of lambda functions for InputPort default values [#3465]

ORM

  • Implementat AuthInfo class which allows custom configuration per configured computer [#1184]
  • Add efficient count method for aiida.orm.groups.Group [#2567]
  • Speed up creation of Nodes in the AiiDA ORM [#2214]
  • Enable use of tuple in QueryBuilder.append for all ORM classes [#1608], [#1607]
  • Refactor the ORM to have explicit front-end and back-end layers [#2190][#2210][#2225][#2227][#2481]
  • Add support for indexing and slicing in orm.Group.nodes iterator [#2371]
  • Add support for process classes to QueryBuilder.append [#2421]
  • Change type of uuids returned by the QueryBuilder to unicode [#2259]
  • The AttributeDict is now constructed recursively for nested dictionaries [#3005]
  • Ensure immutability of CalcJobNode hash before and after storing [#3130]
  • Fix bug in the RemoteData._clean method [#1847]
  • Fix bug in QueryBuilder.first() for multiple projections [#2824]
  • Fix bug in delete_nodes when passing pks of non-existing nodes [#2440]
  • Remove unserializable data from metadata in Log records [#2469]

Data

  • Fix bug in parse_formula for formulas with leading or trailing whitespace [#2186]
  • Refactor Orbital code and fix some bugs [#2737]
  • Fix bug in the store method of CifData which would raise an exception when called more than once [#1136]
  • Allow passing directory path in FolderData constructor [#3359]
  • Add element X to the elements list in order to support unknown species [#1613]
  • Various bug and consistency fixes for CifData and StructureData [#2374]
  • Changes to Data class attributes and TrajectoryData data storage [#2310][#2422]
  • Rename ParameterData to Dict [#2530]
  • Remove the FrozenDict data sub class [#2532]
  • Remove the Error data sub class [#2529]
  • Make Code a real sub class of Data [#2193]
  • Implement the has_atomic_sites and has_unknown_species properties for the CifData class [#1257]
  • Change default library used in _get_aiida_structure (converting CifData to StructureData) from ase to pymatgen [#1257]
  • Add converter for UpfData from UPF to JSON format [#3308]
  • Fix potential inefficiency in aiida.tools.data.cif converters [#3098]
  • Fix bug in KpointsData.reciprocal_cell() [#2779]
  • Improve robustness of parsing versions and element names from UPF files [#2296]

Verdi command line interface

  • Migrate verdi to the click infrastructure [#1795]
  • Add a default user to AiiDA configuration, eliminating the need to retype user information for every new profile [#2734]
  • Implement tab-completion for profile in the -p option of verdi [#2345]
  • Homogenize the interface of verdi quicksetup and verdi setup [#1797]
  • Add the option --version to verdi to display current version [#1811]
  • verdi computer configure can now read inputs from a yaml file through the --config option [#2951]

External database importers

  • Add importer class for the Materials Platform of Data Science API, which hosts the Pauling file data [#1238]
  • Add an importer class for the Materials Project API [#2097]

Database

  • Add an index to columns of DbLink for SqlAlchemy [#2561]
  • Creating unique constraint and indexes at the db_dbgroup_dbnodes table for SqlAlchemy [#1680]
  • Performance improvement for adding nodes to group [#1677]
  • Make UUID columns unique in SqlAlchemy [#2323]
  • Allow PostgreSQL connections via unix sockets [#1721]
  • Drop the unused nodeversion and public columns from the node table [#2937]
  • Drop various unused columns from the user table [#2944]
  • Drop the unused transport_params column from the computer table [#2946]
  • Drop the DbCalcState table [#2198]
  • [Django]: migrate the node attribute and extra schema to use JSONB, greatly improving storage and querying efficiency [#3090]
  • [SqlAlchemy]: Improve speed of node attribute and extra deserialization [#3090]

Export and Import

  • Implement the exporting and importing of node extras [#2416]
  • Implement the exporting and importing of comments [#2413]
  • Implement the exporting and importing of logs [#2393]
  • Add export_parameters to the metadata.json in archive export files [#3386]
  • Simplify the data format of export archives, greatly reducing file size [#3090]
  • verdi import automatically migrates export files of old formats [#2820]

Miscellaneous

  • Refactor unit test managers and add basic fixtures for pytest [#3319]
  • REST API v4: updates to conform with aiida-core==1.0.0 [#3429]
  • Improve decorators using the wrapt library such that function signatures are properly maintained [#2991]
  • Allow empty enabled and disabled keys in caching configuration [#3330]
  • AiiDA now enforces UTF-8 encoding for text output in its files and databases. [#2107]

Backwards-incompatible changes (only a sub-set)

  • Remove aiida.tests and obsolete aiida.backends.tests.test_parsers entry point group [#2778]
  • Implement new link types [#2220]
  • Rename the type strings of Groups and change the attributes name and type to label and type_string [#2329]
  • Make various protected Node methods public [#2544]
  • Rename DbNode.type to DbNode.node_type [#2552]
  • Rename the ORM classes for Node sub classes JobCalculation, WorkCalculation, InlineCalculation and FunctionCalculation [#2184][#2189][#2192][#2195][#2201]
  • Do not allow the copy or deepcopy of Node, except for Data nodes [#1705]
  • Remove aiida.control and aiida.utils top-level modules; reorganize aiida.common, aiida.manage and aiida.tools [#2357]
  • Make the node repository API backend agnostic [#2506]
  • Redesign the Parser class [#2397]
  • [Django]: Remove support for datetime objects from node attributes and extras [#3090]
  • Enforce specific precision in clean_value for floats when computing a node's hash [#3108]
  • Move physical constants from aiida.common.constants to external qe-tools package [#3278]
  • Add type checks to all plugin factories [#3456]
  • Disallow pickle when storing numpy array in ArrayData [#3434]
  • Remove implementation of legacy workflows [#2379]
  • Implement CalcJob process class that replaces the deprecated JobCalculation [#2389]
  • Change the structure of the CalcInfo.local_copy_list [#2581]
  • QueryBuilder: Change 'ancestor_of'/'descendant_of' to 'with_descendants'/'with_ancestors' [#2278]

v0.12.4

Improvements

  • Added new endpoint in rest api to get list of distinct node types [#2745]
  • Travis: port the deploy stage from the development branch [#2816]

Minor bug fixes

  • Corrected the graph export set expansion rules [#2632]

Miscellaneous

  • Backport streamlined quick install instructions from provenance_redesign [#2555]
  • Remove useless chainmap dependency [#2799]
  • Add aiida-core version to docs home page [#3058]
  • Docs: add note on increasing work_mem [#2952]

v0.12.3

Improvements

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

Minor bug fixes

  • Fix security vulnerability by upgrading paramiko to 2.4.2 [#2043]
  • Disable caching for inline calculations (broken since move to workfunction-based implementation) [#1872]
  • Let verdi help return exit status 0 [#2434]
  • Decode dict keys only if strings (backport) [#2436]
  • Remove broken verdi-plug entry point [#2356]
  • verdi node delete (without arguments) no longer tries to delete all nodes [#2545]
  • Fix plotting of BandsData objects [#2492]

Miscellaneous

  • REST API: add tests for random sorting list entries of same type [#2106]
  • Add various badges to README [#1969]
  • Minor documentation improvements [#1955]
  • Add license file to MANIFEST [#2339]
  • Add instructions when verdi import fails [#2420]

v0.12.2

Improvements

  • Support the hashing of uuid.UUID types by registering a hashing function [#1861]
  • Add documentation on plugin cutter [#1904]

Minor bug fixes

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

Miscellaneous

  • Remove pycrypto dependency, as it was found to have sercurity flaws [#1754]
  • Set xsf as default format for structures visualization [#1756]
  • Delete unused utils/create_requirements.py file [#1702]

v0.12.1

Improvements

  • Always use a bash login shell to execute all remote SSH commands, overriding any system default shell [#1502]
  • Reduced the size of the distributed package by almost half by removing test fixtures and generating the data on the fly [#1645]
  • Removed the explicit dependency upper limit for scipy [#1492]
  • Resolved various dependency requirement conflicts [#1488]

Minor bug fixes

  • Fixed a bug in verdi node delete that would throw an exception for certain cases [#1564]
  • Fixed a bug in the cif endpoint of the REST API [#1490]

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

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]
  • Dict: to_aiida_type used on dictionaries now automatically converted to Dict [#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:

    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

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 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

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