aiida.common package

Common data structures, utility classes and functions

Note

Modules in this sub package have to run without a loaded database environment

class aiida.common.CalcJobState

Bases: enum.Enum

The sub state of a CalcJobNode while its Process is in an active state (i.e. Running or Waiting).

PARSING = 'parsing'

RETRIEVING = 'retrieving'

SUBMITTING = 'submitting'

UPLOADING = 'uploading'

WITHSCHEDULER = 'withscheduler'

__module__ = 'aiida.common.datastructures'

class aiida.common.CalcInfo

Bases: aiida.common.extendeddicts.DefaultFieldsAttributeDict

This object will store the data returned by the calculation plugin and to be passed to the ExecManager.

In the following descriptions all paths have to be considered relative

• retrieve_list: a list of strings or tuples that indicate files that are to be retrieved from the remote

  after the calculation has finished and stored in the repository in a FolderData. If the entry in the list is just a string, it is assumed to be the filepath on the remote and it will be copied to ‘.’ of the repository with name os.path.split(item)[1] If the entry is a tuple it is expected to have the following format

  (‘remotepath’, ‘localpath’, depth)

  If the ‘remotepath’ is a file or folder, it will be copied in the repository to ‘localpath’. However, if the ‘remotepath’ contains file patterns with wildcards, the ‘localpath’ should be set to ‘.’ and the depth parameter should be an integer that decides the localname. The ‘remotepath’ will be split on file separators and the local filename will be determined by joining the N last elements, where N is given by the depth variable.

  Example: (‘some/remote/path/files/pattern*[0-9].xml’, ‘.’, 2)

  Will result in all files that match the pattern to be copied to the local repository with path

  ‘files/pattern*[0-9].xml’

• retrieve_temporary_list: a list of strings or tuples that indicate files that will be retrieved

  and stored temporarily in a FolderData, that will be available only during the parsing call. The format of the list is the same as that of ‘retrieve_list’

• retrieve_singlefile_list: a list of tuples with format

  (‘linkname_from calc to singlefile’, ‘subclass of singlefile’, ‘filename’) Each tuple represents a file that will be retrieved from cluster and saved in SinglefileData nodes

• local_copy_list: a list of tuples with format (‘node_uuid’, ‘filename’, relativedestpath’)

• remote_copy_list: a list of tuples with format (‘remotemachinename’, ‘remoteabspath’, ‘relativedestpath’)

• remote_symlink_list: a list of tuples with format (‘remotemachinename’, ‘remoteabspath’, ‘relativedestpath’)

• codes_info: a list of dictionaries used to pass the info of the execution of a code

• codes_run_mode: a string used to specify the order in which multi codes can be executed

__module__ = 'aiida.common.datastructures'

_default_fields = ('job_environment', 'email', 'email_on_started', 'email_on_terminated', 'uuid', 'prepend_text', 'append_text', 'num_machines', 'num_mpiprocs_per_machine', 'priority', 'max_wallclock_seconds', 'max_memory_kb', 'rerunnable', 'retrieve_list', 'retrieve_temporary_list', 'retrieve_singlefile_list', 'local_copy_list', 'remote_copy_list', 'remote_symlink_list', 'codes_info', 'codes_run_mode')

class aiida.common.CodeInfo

Bases: aiida.common.extendeddicts.DefaultFieldsAttributeDict

This attribute-dictionary contains the information needed to execute a code. Possible attributes are:

• cmdline_params: a list of strings, containing parameters to be written on the command line right after the call to the code, as for example:

  code.x cmdline_params[0] cmdline_params[1] ... < stdin > stdout
  

• stdin_name: (optional) the name of the standard input file. Note, it is only possible to use the stdin with the syntax:

  code.x < stdin_name
  

  If no stdin_name is specified, the string “< stdin_name” will not be passed to the code. Note: it is not possible to substitute/remove the ‘<’ if stdin_name is specified; if that is needed, avoid stdin_name and use instead the cmdline_params to specify a suitable syntax.

• stdout_name: (optional) the name of the standard output file. Note, it is only possible to pass output to stdout_name with the syntax:

  code.x ... > stdout_name
  

  If no stdout_name is specified, the string “> stdout_name” will not be passed to the code. Note: it is not possible to substitute/remove the ‘>’ if stdout_name is specified; if that is needed, avoid stdout_name and use instead the cmdline_params to specify a suitable syntax.

• stderr_name: (optional) a string, the name of the error file of the code.

• join_files: (optional) if True, redirects the error to the output file. If join_files=True, the code will be called as:

  code.x ... > stdout_name 2>&1
  

  otherwise, if join_files=False and stderr is passed:

  code.x ... > stdout_name 2> stderr_name
  

• withmpi: if True, executes the code with mpirun (or another MPI installed on the remote computer)

• code_uuid: the uuid of the code associated to the CodeInfo

__module__ = 'aiida.common.datastructures'

_default_fields = ('cmdline_params', 'stdin_name', 'stdout_name', 'stderr_name', 'join_files', 'withmpi', 'code_uuid')

class aiida.common.CodeRunMode

Bases: enum.IntEnum

Enum to indicate the way the codes of a calculation should be run.

For PARALLEL, the codes for a given calculation will be run in parallel by running them in the background:

code1.x &
code2.x &

For the SERIAL option, codes will be executed sequentially by running for example the following:

code1.x
code2.x

PARALLEL = 1

SERIAL = 0

__module__ = 'aiida.common.datastructures'

exception aiida.common.AiidaException

Bases: exceptions.Exception

Base class for all AiiDA exceptions.

Each module will have its own subclass, inherited from this (e.g. ExecManagerException, TransportException, …)

__module__ = 'aiida.common.exceptions'

__weakref__

list of weak references to the object (if defined)

exception aiida.common.NotExistent

Bases: aiida.common.exceptions.AiidaException

Raised when the required entity does not exist.

__module__ = 'aiida.common.exceptions'

exception aiida.common.MultipleObjectsError

Bases: aiida.common.exceptions.AiidaException

Raised when more than one entity is found in the DB, but only one was expected.

__module__ = 'aiida.common.exceptions'

exception aiida.common.RemoteOperationError

Bases: aiida.common.exceptions.AiidaException

Raised when an error in a remote operation occurs, as in a failed kill() of a scheduler job.

__module__ = 'aiida.common.exceptions'

exception aiida.common.ContentNotExistent

Bases: aiida.common.exceptions.NotExistent

Raised when trying to access an attribute, a key or a file in the result nodes that is not present

__module__ = 'aiida.common.exceptions'

exception aiida.common.FailedError

Bases: aiida.common.exceptions.AiidaException

Raised when accessing a calculation that is in the FAILED status

__module__ = 'aiida.common.exceptions'

exception aiida.common.StoringNotAllowed

Bases: aiida.common.exceptions.AiidaException

Raised when the user tries to store an unstorable node (e.g. a base Node class)

__module__ = 'aiida.common.exceptions'

exception aiida.common.ModificationNotAllowed

Bases: aiida.common.exceptions.AiidaException

Raised when the user tries to modify a field, object, property, … that should not be modified.

__module__ = 'aiida.common.exceptions'

exception aiida.common.IntegrityError

Bases: aiida.common.exceptions.AiidaException

Raised when there is an underlying data integrity error. This can be database related or a general data integrity error. This can happen if, e.g., a foreign key check fails. See PEP 249 for details.

__module__ = 'aiida.common.exceptions'

exception aiida.common.UniquenessError

Bases: aiida.common.exceptions.AiidaException

Raised when the user tries to violate a uniqueness constraint (on the DB, for instance).

__module__ = 'aiida.common.exceptions'

exception aiida.common.MissingEntryPointError

Bases: aiida.common.exceptions.AiidaException

Raised when the requested entry point is not registered with the entry point manager

__module__ = 'aiida.common.exceptions'

exception aiida.common.MultipleEntryPointError

Bases: aiida.common.exceptions.AiidaException

Raised when the requested entry point cannot uniquely be resolved by the entry point manager

__module__ = 'aiida.common.exceptions'

exception aiida.common.LoadingEntryPointError

Bases: aiida.common.exceptions.AiidaException

Raised when the class corresponding to requested entry point cannot be loaded

__module__ = 'aiida.common.exceptions'

exception aiida.common.MissingPluginError

Bases: aiida.common.exceptions.AiidaException

Raised when the user tries to use a plugin that is not available or does not exist.

__module__ = 'aiida.common.exceptions'

exception aiida.common.LoadingPluginFailed

Bases: aiida.common.exceptions.AiidaException

Raised when loading a plugin through the plugin loader fails

__module__ = 'aiida.common.exceptions'

exception aiida.common.InvalidOperation

Bases: aiida.common.exceptions.AiidaException

The allowed operation is not valid (e.g., when trying to add a non-internal attribute before saving the entry), or deleting an entry that is protected (e.g., because it is referenced by foreign keys)

__module__ = 'aiida.common.exceptions'

exception aiida.common.ParsingError

Bases: aiida.common.exceptions.AiidaException

Generic error raised when there is a parsing error

__module__ = 'aiida.common.exceptions'

exception aiida.common.InternalError

Bases: aiida.common.exceptions.AiidaException

Error raised when there is an internal error of AiiDA.

__module__ = 'aiida.common.exceptions'

exception aiida.common.PluginInternalError

Bases: aiida.common.exceptions.InternalError

Error raised when there is an internal error which is due to a plugin and not to the AiiDA infrastructure.

__module__ = 'aiida.common.exceptions'

exception aiida.common.ValidationError

Bases: aiida.common.exceptions.AiidaException

Error raised when there is an error during the validation phase of a property.

__module__ = 'aiida.common.exceptions'

exception aiida.common.ConfigurationError

Bases: aiida.common.exceptions.AiidaException

Error raised when there is a configuration error in AiiDA.

__module__ = 'aiida.common.exceptions'

exception aiida.common.ProfileConfigurationError

Bases: aiida.common.exceptions.ConfigurationError

Configuration error raised when a wrong/inexistent profile is requested.

__module__ = 'aiida.common.exceptions'

exception aiida.common.MissingConfigurationError

Bases: aiida.common.exceptions.ConfigurationError

Configuration error raised when the configuration file is missing.

__module__ = 'aiida.common.exceptions'

exception aiida.common.ConfigurationVersionError

Bases: aiida.common.exceptions.ConfigurationError

Configuration error raised when the configuration file version is not compatible with the current version.

__module__ = 'aiida.common.exceptions'

exception aiida.common.DbContentError

Bases: aiida.common.exceptions.AiidaException

Raised when the content of the DB is not valid. This should never happen if the user does not play directly with the DB.

__module__ = 'aiida.common.exceptions'

exception aiida.common.InputValidationError

Bases: aiida.common.exceptions.ValidationError

The input data for a calculation did not validate (e.g., missing required input data, wrong data, …)

__module__ = 'aiida.common.exceptions'

exception aiida.common.FeatureNotAvailable

Bases: aiida.common.exceptions.AiidaException

Raised when a feature is requested from a plugin, that is not available.

__module__ = 'aiida.common.exceptions'

exception aiida.common.FeatureDisabled

Bases: aiida.common.exceptions.AiidaException

Raised when a feature is requested, but the user has chosen to disable it (e.g., for submissions on disabled computers).

__module__ = 'aiida.common.exceptions'

exception aiida.common.LicensingException

Bases: aiida.common.exceptions.AiidaException

Raised when requirements for data licensing are not met.

__module__ = 'aiida.common.exceptions'

exception aiida.common.TestsNotAllowedError

Bases: aiida.common.exceptions.AiidaException

Raised when tests are required to be run/loaded, but we are not in a testing environment.

This is to prevent data loss.

__module__ = 'aiida.common.exceptions'

exception aiida.common.UnsupportedSpeciesError

Bases: exceptions.ValueError

Raised when StructureData operations are fed species that are not supported by AiiDA such as Deuterium

__module__ = 'aiida.common.exceptions'

__weakref__

list of weak references to the object (if defined)

exception aiida.common.DanglingLinkError

Bases: exceptions.Exception

Raised when an export archive is detected to contain dangling links when importing

__module__ = 'aiida.common.exceptions'

__weakref__

list of weak references to the object (if defined)

exception aiida.common.TransportTaskException

Bases: exceptions.Exception

Raised when a TransportTask, an task to be completed by the engine that requires transport, fails

__module__ = 'aiida.common.exceptions'

__weakref__

list of weak references to the object (if defined)

exception aiida.common.IncompatibleArchiveVersionError

Bases: exceptions.Exception

Raised when trying to import an export archive with an incompatible schema version.

__module__ = 'aiida.common.exceptions'

__weakref__

list of weak references to the object (if defined)

exception aiida.common.OutputParsingError

Bases: aiida.common.exceptions.ParsingError

Can be raised by a Parser when it fails to parse the output generated by a CalcJob process.

__module__ = 'aiida.common.exceptions'

class aiida.common.AttributeDict

Bases: dict

This class internally stores values in a dictionary, but exposes the keys also as attributes, i.e. asking for attrdict.key will return the value of attrdict[‘key’] and so on.

Raises an AttributeError if the key does not exist, when called as an attribute, while the usual KeyError if the key does not exist and the dictionary syntax is used.

__deepcopy__(memo=None)

Support deepcopy.

__delattr__(attr)

Delete a key as an attribute. Raise AttributeError on missing key.

__dict__ = dict_proxy({'__module__': 'aiida.common.extendeddicts', 'copy': <function copy>, '__setstate__': <function __setstate__>, '__deepcopy__': <function __deepcopy__>, '__setattr__': <function __setattr__>, '__getattr__': <function __getattr__>, '__delattr__': <function __delattr__>, '__repr__': <function __repr__>, '__dict__': <attribute '__dict__' of 'AttributeDict' objects>, '__getstate__': <function __getstate__>, '__weakref__': <attribute '__weakref__' of 'AttributeDict' objects>, '__doc__': "\n This class internally stores values in a dictionary, but exposes\n the keys also as attributes, i.e. asking for attrdict.key\n will return the value of attrdict['key'] and so on.\n\n Raises an AttributeError if the key does not exist, when called as an attribute,\n while the usual KeyError if the key does not exist and the dictionary syntax is\n used.\n ", '__dir__': <function __dir__>})

__dir__()

__getattr__(attr)

Read a key as an attribute. Raise AttributeError on missing key. Called only for attributes that do not exist.

__getstate__()

Needed for pickling this class.

__module__ = 'aiida.common.extendeddicts'

__repr__()

Representation of the object.

__setattr__(attr, value)

Set a key as an attribute.

__setstate__(dictionary)

Needed for pickling this class.

__weakref__

list of weak references to the object (if defined)

copy()

Shallow copy.

class aiida.common.FixedFieldsAttributeDict(init=None)

Bases: aiida.common.extendeddicts.AttributeDict

A dictionary with access to the keys as attributes, and with filtering of valid attributes. This is only the base class, without valid attributes; use a derived class to do the actual work. E.g.:

class TestExample(FixedFieldsAttributeDict):
    _valid_fields = ('a','b','c')

__dir__()

__init__(init=None)

x.__init__(…) initializes x; see help(type(x)) for signature

__module__ = 'aiida.common.extendeddicts'

__setattr__(attr, value)

Overridden to allow direct access to fields with underscore.

__setitem__(item, value)

Set a key as an attribute.

_valid_fields = ()

classmethod get_valid_fields()

Return the list of valid fields.

class aiida.common.DefaultFieldsAttributeDict

Bases: aiida.common.extendeddicts.AttributeDict

A dictionary with access to the keys as attributes, and with an internal value storing the ‘default’ keys to be distinguished from extra fields.

Extra methods defaultkeys() and extrakeys() divide the set returned by keys() in default keys (i.e. those defined at definition time) and other keys. There is also a method get_default_fields() to return the internal list.

Moreover, for undefined default keys, it returns None instead of raising a KeyError/AttributeError exception.

Remember to define the _default_fields in a subclass! E.g.:

class TestExample(DefaultFieldsAttributeDict):
    _default_fields = ('a','b','c')

When the validate() method is called, it calls in turn all validate_KEY methods, where KEY is one of the default keys. If the method is not present, the field is considered to be always valid. Each validate_KEY method should accept a single argument ‘value’ that will contain the value to be checked.

It raises a ValidationError if any of the validate_KEY function raises an exception, otherwise it simply returns. NOTE: the validate_* functions are called also for unset fields, so if the field can be empty on validation, you have to start your validation function with something similar to:

if value is None:
    return

Todo

Decide behavior if I set to None a field. Current behavior, if a is an instance and ‘def_field’ one of the default fields, that is undefined, we get:

• a.get('def_field'): None
• a.get('def_field','whatever'): ‘whatever’
• Note that a.defaultkeys() does NOT contain ‘def_field’

if we do a.def_field = None, then the behavior becomes

• a.get('def_field'): None
• a.get('def_field','whatever'): None
• Note that a.defaultkeys() DOES contain ‘def_field’

See if we want that setting a default field to None means deleting it.

__getitem__(key)

Return None instead of raising an exception if the key does not exist but is in the list of default fields.

__module__ = 'aiida.common.extendeddicts'

__setattr__(attr, value)

Overridden to allow direct access to fields with underscore.

_default_fields = ()

defaultkeys()

Return the default keys defined in the instance.

extrakeys()

Return the extra keys defined in the instance.

classmethod get_default_fields()

Return the list of default fields, either defined in the instance or not.

validate()

Validate the keys, if any validate_* method is available.

class aiida.common.LinkType

Bases: enum.Enum

A simple enum of allowed link types.

CALL_CALC = 'call_calc'

CALL_WORK = 'call_work'

CREATE = 'create'

INPUT_CALC = 'input_calc'

INPUT_WORK = 'input_work'

RETURN = 'return'

__module__ = 'aiida.common.links'

Submodules

Utility functions and classes to interact with AiiDA export archives.

class aiida.common.archive.Archive(filepath)

Bases: object

Utility class to operate on exported archive files or directories.

The main usage should be to construct the class with the filepath of the export archive as an argument. The contents will be lazily unpacked into a sand box folder which is constructed upon entering the instance within a context and which will be automatically cleaned upon leaving that context. Example:

with Archive('/some/path/archive.aiida') as archive:
    archive.version

FILENAME_DATA = 'data.json'

FILENAME_METADATA = 'metadata.json'

__dict__ = dict_proxy({'__module__': 'aiida.common.archive', 'ensure_unpacked': <function ensure_unpacked>, '__exit__': <function __exit__>, 'FILENAME_DATA': 'data.json', 'version_format': <property object>, 'version_aiida': <property object>, 'meta_data': <property object>, 'get_data_statistics': <function get_data_statistics>, '__dict__': <attribute '__dict__' of 'Archive' objects>, 'ensure_within_context': <function ensure_within_context>, 'data': <property object>, '__init__': <function __init__>, '__weakref__': <attribute '__weakref__' of 'Archive' objects>, '_read_json_file': <function _read_json_file>, 'filepath': <property object>, 'FILENAME_METADATA': 'metadata.json', 'unpack': <function unpack>, '__enter__': <function __enter__>, 'unpacked': <property object>, 'get_info': <function get_info>, 'conversion_info': <property object>, 'folder': <property object>, '__doc__': "\n Utility class to operate on exported archive files or directories.\n\n The main usage should be to construct the class with the filepath of the export archive as an argument.\n The contents will be lazily unpacked into a sand box folder which is constructed upon entering the instance\n within a context and which will be automatically cleaned upon leaving that context. Example::\n\n with Archive('/some/path/archive.aiida') as archive:\n archive.version\n\n "})

__enter__()

Instantiate a SandboxFolder into which the archive can be lazily unpacked.

__exit__(exc_type, exc_value, traceback)

Clean the sandbox folder if it was instatiated.

__init__(filepath)

x.__init__(…) initializes x; see help(type(x)) for signature

__module__ = 'aiida.common.archive'

__weakref__

list of weak references to the object (if defined)

_read_json_file(*args, **kwargs)

Read the contents of a JSON file from the unpacked archive contents.

Parameters:filename – the filename relative to the sandbox folder Returns:a dictionary with the loaded JSON content

conversion_info

Return information about migration events that were applied to this archive.

Returns:list of conversion notifications

data

Return the loaded content of the data file

Returns:dictionary with contents of data file

ensure_unpacked()

Decorator to ensure that the archive is unpacked before entering the decorated function.

ensure_within_context()

Decorator to ensure that the instance is called within a context manager.

filepath

Return the filepath of the archive

Returns:the archive filepath

folder

Return the sandbox folder

Returns:sandbox folder aiida.common.folders.SandboxFolder

get_data_statistics(*args, **kwargs)

Return a dictionary with statistics about data content, i.e. how many entries of each entity type it contains.

Returns:a dictionary with basic details

get_info(*args, **kwargs)

Return a dictionary with basic information about the archive.

Returns:a dictionary with basic details

meta_data

Return the loaded content of the meta data file

Returns:dictionary with contents of meta data file

unpack(*args, **kwargs)

Unpack the archive and store the contents in a sandbox.

unpacked

Return whether the archive has been unpacked into the sandbox folder.

version_aiida

Return the version of AiiDA the archive was created with.

Returns:version number

version_format

Return the version of the archive format.

Returns:version number

aiida.common.archive.extract_cif(infile, folder, nodes_export_subfolder='nodes', aiida_export_subfolder='aiida', silent=False)

Extract the nodes to be imported from a TCOD CIF file. TCOD CIFs, exported by AiiDA, may contain an importable subset of AiiDA database, which can be imported. This function prepares SandboxFolder with files required for import.

Parameters:

• infile – file path
• folder – a SandboxFolder, used to extract the file tree
• nodes_export_subfolder – name of the subfolder for AiiDA nodes
• aiida_export_subfolder – name of the subfolder for AiiDA data inside the TCOD CIF internal file tree
• silent – suppress debug print

aiida.common.archive.extract_tar(infile, folder, nodes_export_subfolder='nodes', silent=False)

Extract the nodes to be imported from a (possibly zipped) tar file.

Parameters:

• infile – file path
• folder – a SandboxFolder, used to extract the file tree
• nodes_export_subfolder – name of the subfolder for AiiDA nodes
• silent – suppress debug print

aiida.common.archive.extract_tree(infile, folder)

Prepare to import nodes from plain file system tree.

Parameters:

• infile – path
• folder – a SandboxFolder, used to extract the file tree

aiida.common.archive.extract_zip(infile, folder, nodes_export_subfolder='nodes', silent=False)

Extract the nodes to be imported from a zip file.

Parameters:

• infile – file path
• folder – a SandboxFolder, used to extract the file tree
• nodes_export_subfolder – name of the subfolder for AiiDA nodes
• silent – suppress debug print

Module to define the (physical) constants used throughout the code.

Module to define commonly used data structures.

class aiida.common.datastructures.CalcJobState

Bases: enum.Enum

The sub state of a CalcJobNode while its Process is in an active state (i.e. Running or Waiting).

PARSING = 'parsing'

RETRIEVING = 'retrieving'

SUBMITTING = 'submitting'

UPLOADING = 'uploading'

WITHSCHEDULER = 'withscheduler'

__module__ = 'aiida.common.datastructures'

class aiida.common.datastructures.CalcInfo

Bases: aiida.common.extendeddicts.DefaultFieldsAttributeDict

This object will store the data returned by the calculation plugin and to be passed to the ExecManager.

In the following descriptions all paths have to be considered relative

• retrieve_list: a list of strings or tuples that indicate files that are to be retrieved from the remote

  after the calculation has finished and stored in the repository in a FolderData. If the entry in the list is just a string, it is assumed to be the filepath on the remote and it will be copied to ‘.’ of the repository with name os.path.split(item)[1] If the entry is a tuple it is expected to have the following format

  (‘remotepath’, ‘localpath’, depth)

  If the ‘remotepath’ is a file or folder, it will be copied in the repository to ‘localpath’. However, if the ‘remotepath’ contains file patterns with wildcards, the ‘localpath’ should be set to ‘.’ and the depth parameter should be an integer that decides the localname. The ‘remotepath’ will be split on file separators and the local filename will be determined by joining the N last elements, where N is given by the depth variable.

  Example: (‘some/remote/path/files/pattern*[0-9].xml’, ‘.’, 2)

  Will result in all files that match the pattern to be copied to the local repository with path

  ‘files/pattern*[0-9].xml’

• retrieve_temporary_list: a list of strings or tuples that indicate files that will be retrieved

  and stored temporarily in a FolderData, that will be available only during the parsing call. The format of the list is the same as that of ‘retrieve_list’

• retrieve_singlefile_list: a list of tuples with format

  (‘linkname_from calc to singlefile’, ‘subclass of singlefile’, ‘filename’) Each tuple represents a file that will be retrieved from cluster and saved in SinglefileData nodes

• local_copy_list: a list of tuples with format (‘node_uuid’, ‘filename’, relativedestpath’)

• remote_copy_list: a list of tuples with format (‘remotemachinename’, ‘remoteabspath’, ‘relativedestpath’)

• remote_symlink_list: a list of tuples with format (‘remotemachinename’, ‘remoteabspath’, ‘relativedestpath’)

• codes_info: a list of dictionaries used to pass the info of the execution of a code

• codes_run_mode: a string used to specify the order in which multi codes can be executed

__module__ = 'aiida.common.datastructures'

_default_fields = ('job_environment', 'email', 'email_on_started', 'email_on_terminated', 'uuid', 'prepend_text', 'append_text', 'num_machines', 'num_mpiprocs_per_machine', 'priority', 'max_wallclock_seconds', 'max_memory_kb', 'rerunnable', 'retrieve_list', 'retrieve_temporary_list', 'retrieve_singlefile_list', 'local_copy_list', 'remote_copy_list', 'remote_symlink_list', 'codes_info', 'codes_run_mode')

class aiida.common.datastructures.CodeInfo

Bases: aiida.common.extendeddicts.DefaultFieldsAttributeDict

This attribute-dictionary contains the information needed to execute a code. Possible attributes are:

• cmdline_params: a list of strings, containing parameters to be written on the command line right after the call to the code, as for example:

  code.x cmdline_params[0] cmdline_params[1] ... < stdin > stdout
  

• stdin_name: (optional) the name of the standard input file. Note, it is only possible to use the stdin with the syntax:

  code.x < stdin_name
  

  If no stdin_name is specified, the string “< stdin_name” will not be passed to the code. Note: it is not possible to substitute/remove the ‘<’ if stdin_name is specified; if that is needed, avoid stdin_name and use instead the cmdline_params to specify a suitable syntax.

• stdout_name: (optional) the name of the standard output file. Note, it is only possible to pass output to stdout_name with the syntax:

  code.x ... > stdout_name
  

  If no stdout_name is specified, the string “> stdout_name” will not be passed to the code. Note: it is not possible to substitute/remove the ‘>’ if stdout_name is specified; if that is needed, avoid stdout_name and use instead the cmdline_params to specify a suitable syntax.

• stderr_name: (optional) a string, the name of the error file of the code.

• join_files: (optional) if True, redirects the error to the output file. If join_files=True, the code will be called as:

  code.x ... > stdout_name 2>&1
  

  otherwise, if join_files=False and stderr is passed:

  code.x ... > stdout_name 2> stderr_name
  

• withmpi: if True, executes the code with mpirun (or another MPI installed on the remote computer)

• code_uuid: the uuid of the code associated to the CodeInfo

__module__ = 'aiida.common.datastructures'

_default_fields = ('cmdline_params', 'stdin_name', 'stdout_name', 'stderr_name', 'join_files', 'withmpi', 'code_uuid')

class aiida.common.datastructures.CodeRunMode

Bases: enum.IntEnum

Enum to indicate the way the codes of a calculation should be run.

For PARALLEL, the codes for a given calculation will be run in parallel by running them in the background:

code1.x &
code2.x &

For the SERIAL option, codes will be executed sequentially by running for example the following:

code1.x
code2.x

PARALLEL = 1

SERIAL = 0

__module__ = 'aiida.common.datastructures'

Miscellaneous functions for escaping strings.

aiida.common.escaping.escape_for_bash(str_to_escape)

This function takes any string and escapes it in a way that bash will interpret it as a single string.

Explanation:

At the end, in the return statement, the string is put within single quotes. Therefore, the only thing that I have to escape in bash is the single quote character. To do this, I substitute every single quote ‘ with ‘”’”’ which means:

First single quote: exit from the enclosing single quotes

Second, third and fourth character: “’” is a single quote character, escaped by double quotes

Last single quote: reopen the single quote to continue the string

Finally, note that for python I have to enclose the string ‘”’”’ within triple quotes to make it work, getting finally: the complicated string found below.

aiida.common.escaping.escape_for_sql_like(string)

Function that escapes % or _ symbols provided by user

SQL LIKE syntax summary:

• % -> match any number of characters
• _ -> match exactly one character

aiida.common.escaping.get_regex_pattern_from_sql(sql_pattern)

Convert a string providing a pattern to match in SQL syntax into a string performing the same match as a regex.

SQL LIKE syntax summary:

• % -> match any number of characters
• _ -> match exactly one character

Moreover, \ is the escape character (by default), so:

• \\ -> single backslash
• \% -> literal % symbol
• \_ -> literal _ symbol

and moreover the string should begin at the beginning of the line and end at the end of the line.

Parameters:sql_pattern – the string with the pattern in SQL syntax Returns:a string with the pattern in regex syntax

aiida.common.escaping.sql_string_match(string, pattern)

Check if the string matches the provided pattern, specified using SQL syntax.

See documentation of get_regex_pattern_from_sql() for an explanation of the syntax.

Parameters:

• string – the string to check
• pattern – the SQL pattern

Returns:

True if the string matches, False otherwise

Module that define the exceptions that are thrown by AiiDA’s internal code.

exception aiida.common.exceptions.AiidaException

Bases: exceptions.Exception

Base class for all AiiDA exceptions.

Each module will have its own subclass, inherited from this (e.g. ExecManagerException, TransportException, …)

__module__ = 'aiida.common.exceptions'

__weakref__

list of weak references to the object (if defined)

exception aiida.common.exceptions.NotExistent

Bases: aiida.common.exceptions.AiidaException

Raised when the required entity does not exist.

__module__ = 'aiida.common.exceptions'

exception aiida.common.exceptions.MultipleObjectsError

Bases: aiida.common.exceptions.AiidaException

Raised when more than one entity is found in the DB, but only one was expected.

__module__ = 'aiida.common.exceptions'

exception aiida.common.exceptions.RemoteOperationError

Bases: aiida.common.exceptions.AiidaException

Raised when an error in a remote operation occurs, as in a failed kill() of a scheduler job.

__module__ = 'aiida.common.exceptions'

exception aiida.common.exceptions.ContentNotExistent

Bases: aiida.common.exceptions.NotExistent

Raised when trying to access an attribute, a key or a file in the result nodes that is not present

__module__ = 'aiida.common.exceptions'

exception aiida.common.exceptions.FailedError

Bases: aiida.common.exceptions.AiidaException

Raised when accessing a calculation that is in the FAILED status

__module__ = 'aiida.common.exceptions'

exception aiida.common.exceptions.StoringNotAllowed

Bases: aiida.common.exceptions.AiidaException

Raised when the user tries to store an unstorable node (e.g. a base Node class)

__module__ = 'aiida.common.exceptions'

exception aiida.common.exceptions.ModificationNotAllowed

Bases: aiida.common.exceptions.AiidaException

Raised when the user tries to modify a field, object, property, … that should not be modified.

__module__ = 'aiida.common.exceptions'

exception aiida.common.exceptions.IntegrityError

Bases: aiida.common.exceptions.AiidaException

Raised when there is an underlying data integrity error. This can be database related or a general data integrity error. This can happen if, e.g., a foreign key check fails. See PEP 249 for details.

__module__ = 'aiida.common.exceptions'

exception aiida.common.exceptions.UniquenessError

Bases: aiida.common.exceptions.AiidaException

Raised when the user tries to violate a uniqueness constraint (on the DB, for instance).

__module__ = 'aiida.common.exceptions'

exception aiida.common.exceptions.MissingEntryPointError

Bases: aiida.common.exceptions.AiidaException

Raised when the requested entry point is not registered with the entry point manager

__module__ = 'aiida.common.exceptions'

exception aiida.common.exceptions.MultipleEntryPointError

Bases: aiida.common.exceptions.AiidaException

Raised when the requested entry point cannot uniquely be resolved by the entry point manager

__module__ = 'aiida.common.exceptions'

exception aiida.common.exceptions.LoadingEntryPointError

Bases: aiida.common.exceptions.AiidaException

Raised when the class corresponding to requested entry point cannot be loaded

__module__ = 'aiida.common.exceptions'

exception aiida.common.exceptions.MissingPluginError

Bases: aiida.common.exceptions.AiidaException

Raised when the user tries to use a plugin that is not available or does not exist.

__module__ = 'aiida.common.exceptions'

exception aiida.common.exceptions.LoadingPluginFailed

Bases: aiida.common.exceptions.AiidaException

Raised when loading a plugin through the plugin loader fails

__module__ = 'aiida.common.exceptions'

exception aiida.common.exceptions.InvalidOperation

Bases: aiida.common.exceptions.AiidaException

The allowed operation is not valid (e.g., when trying to add a non-internal attribute before saving the entry), or deleting an entry that is protected (e.g., because it is referenced by foreign keys)

__module__ = 'aiida.common.exceptions'

exception aiida.common.exceptions.ParsingError

Bases: aiida.common.exceptions.AiidaException

Generic error raised when there is a parsing error

__module__ = 'aiida.common.exceptions'

exception aiida.common.exceptions.InternalError

Bases: aiida.common.exceptions.AiidaException

Error raised when there is an internal error of AiiDA.

__module__ = 'aiida.common.exceptions'

exception aiida.common.exceptions.PluginInternalError

Bases: aiida.common.exceptions.InternalError

Error raised when there is an internal error which is due to a plugin and not to the AiiDA infrastructure.

__module__ = 'aiida.common.exceptions'

exception aiida.common.exceptions.ValidationError

Bases: aiida.common.exceptions.AiidaException

Error raised when there is an error during the validation phase of a property.

__module__ = 'aiida.common.exceptions'

exception aiida.common.exceptions.ConfigurationError

Bases: aiida.common.exceptions.AiidaException

Error raised when there is a configuration error in AiiDA.

__module__ = 'aiida.common.exceptions'

exception aiida.common.exceptions.ProfileConfigurationError

Bases: aiida.common.exceptions.ConfigurationError

Configuration error raised when a wrong/inexistent profile is requested.

__module__ = 'aiida.common.exceptions'

exception aiida.common.exceptions.MissingConfigurationError

Bases: aiida.common.exceptions.ConfigurationError

Configuration error raised when the configuration file is missing.

__module__ = 'aiida.common.exceptions'

exception aiida.common.exceptions.ConfigurationVersionError

Bases: aiida.common.exceptions.ConfigurationError

Configuration error raised when the configuration file version is not compatible with the current version.

__module__ = 'aiida.common.exceptions'

exception aiida.common.exceptions.DbContentError

Bases: aiida.common.exceptions.AiidaException

Raised when the content of the DB is not valid. This should never happen if the user does not play directly with the DB.

__module__ = 'aiida.common.exceptions'

exception aiida.common.exceptions.InputValidationError

Bases: aiida.common.exceptions.ValidationError

The input data for a calculation did not validate (e.g., missing required input data, wrong data, …)

__module__ = 'aiida.common.exceptions'

exception aiida.common.exceptions.FeatureNotAvailable

Bases: aiida.common.exceptions.AiidaException

Raised when a feature is requested from a plugin, that is not available.

__module__ = 'aiida.common.exceptions'

exception aiida.common.exceptions.FeatureDisabled

Bases: aiida.common.exceptions.AiidaException

Raised when a feature is requested, but the user has chosen to disable it (e.g., for submissions on disabled computers).

__module__ = 'aiida.common.exceptions'

exception aiida.common.exceptions.LicensingException

Bases: aiida.common.exceptions.AiidaException

Raised when requirements for data licensing are not met.

__module__ = 'aiida.common.exceptions'

exception aiida.common.exceptions.TestsNotAllowedError

Bases: aiida.common.exceptions.AiidaException

Raised when tests are required to be run/loaded, but we are not in a testing environment.

This is to prevent data loss.

__module__ = 'aiida.common.exceptions'

exception aiida.common.exceptions.UnsupportedSpeciesError

Bases: exceptions.ValueError

Raised when StructureData operations are fed species that are not supported by AiiDA such as Deuterium

__module__ = 'aiida.common.exceptions'

__weakref__

list of weak references to the object (if defined)

exception aiida.common.exceptions.DanglingLinkError

Bases: exceptions.Exception

Raised when an export archive is detected to contain dangling links when importing

__module__ = 'aiida.common.exceptions'

__weakref__

list of weak references to the object (if defined)

exception aiida.common.exceptions.TransportTaskException

Bases: exceptions.Exception

Raised when a TransportTask, an task to be completed by the engine that requires transport, fails

__module__ = 'aiida.common.exceptions'

__weakref__

list of weak references to the object (if defined)

exception aiida.common.exceptions.IncompatibleArchiveVersionError

Bases: exceptions.Exception

Raised when trying to import an export archive with an incompatible schema version.

__module__ = 'aiida.common.exceptions'

__weakref__

list of weak references to the object (if defined)

exception aiida.common.exceptions.OutputParsingError

Bases: aiida.common.exceptions.ParsingError

Can be raised by a Parser when it fails to parse the output generated by a CalcJob process.

__module__ = 'aiida.common.exceptions'

Various dictionary types with extended functionality.

class aiida.common.extendeddicts.AttributeDict

Bases: dict

This class internally stores values in a dictionary, but exposes the keys also as attributes, i.e. asking for attrdict.key will return the value of attrdict[‘key’] and so on.

Raises an AttributeError if the key does not exist, when called as an attribute, while the usual KeyError if the key does not exist and the dictionary syntax is used.

__deepcopy__(memo=None)

Support deepcopy.

__delattr__(attr)

Delete a key as an attribute. Raise AttributeError on missing key.

__dict__ = dict_proxy({'__module__': 'aiida.common.extendeddicts', 'copy': <function copy>, '__setstate__': <function __setstate__>, '__deepcopy__': <function __deepcopy__>, '__setattr__': <function __setattr__>, '__getattr__': <function __getattr__>, '__delattr__': <function __delattr__>, '__repr__': <function __repr__>, '__dict__': <attribute '__dict__' of 'AttributeDict' objects>, '__getstate__': <function __getstate__>, '__weakref__': <attribute '__weakref__' of 'AttributeDict' objects>, '__doc__': "\n This class internally stores values in a dictionary, but exposes\n the keys also as attributes, i.e. asking for attrdict.key\n will return the value of attrdict['key'] and so on.\n\n Raises an AttributeError if the key does not exist, when called as an attribute,\n while the usual KeyError if the key does not exist and the dictionary syntax is\n used.\n ", '__dir__': <function __dir__>})

__dir__()

__getattr__(attr)

Read a key as an attribute. Raise AttributeError on missing key. Called only for attributes that do not exist.

__getstate__()

Needed for pickling this class.

__module__ = 'aiida.common.extendeddicts'

__repr__()

Representation of the object.

__setattr__(attr, value)

Set a key as an attribute.

__setstate__(dictionary)

Needed for pickling this class.

__weakref__

list of weak references to the object (if defined)

copy()

Shallow copy.

class aiida.common.extendeddicts.FixedFieldsAttributeDict(init=None)

Bases: aiida.common.extendeddicts.AttributeDict

A dictionary with access to the keys as attributes, and with filtering of valid attributes. This is only the base class, without valid attributes; use a derived class to do the actual work. E.g.:

class TestExample(FixedFieldsAttributeDict):
    _valid_fields = ('a','b','c')

__dir__()

__init__(init=None)

x.__init__(…) initializes x; see help(type(x)) for signature

__module__ = 'aiida.common.extendeddicts'

__setattr__(attr, value)

Overridden to allow direct access to fields with underscore.

__setitem__(item, value)

Set a key as an attribute.

_valid_fields = ()

classmethod get_valid_fields()

Return the list of valid fields.

class aiida.common.extendeddicts.DefaultFieldsAttributeDict

Bases: aiida.common.extendeddicts.AttributeDict

A dictionary with access to the keys as attributes, and with an internal value storing the ‘default’ keys to be distinguished from extra fields.

Extra methods defaultkeys() and extrakeys() divide the set returned by keys() in default keys (i.e. those defined at definition time) and other keys. There is also a method get_default_fields() to return the internal list.

Moreover, for undefined default keys, it returns None instead of raising a KeyError/AttributeError exception.

Remember to define the _default_fields in a subclass! E.g.:

class TestExample(DefaultFieldsAttributeDict):
    _default_fields = ('a','b','c')

When the validate() method is called, it calls in turn all validate_KEY methods, where KEY is one of the default keys. If the method is not present, the field is considered to be always valid. Each validate_KEY method should accept a single argument ‘value’ that will contain the value to be checked.

It raises a ValidationError if any of the validate_KEY function raises an exception, otherwise it simply returns. NOTE: the validate_* functions are called also for unset fields, so if the field can be empty on validation, you have to start your validation function with something similar to:

if value is None:
    return

Todo

Decide behavior if I set to None a field. Current behavior, if a is an instance and ‘def_field’ one of the default fields, that is undefined, we get:

• a.get('def_field'): None
• a.get('def_field','whatever'): ‘whatever’
• Note that a.defaultkeys() does NOT contain ‘def_field’

if we do a.def_field = None, then the behavior becomes

• a.get('def_field'): None
• a.get('def_field','whatever'): None
• Note that a.defaultkeys() DOES contain ‘def_field’

See if we want that setting a default field to None means deleting it.

__getitem__(key)

Return None instead of raising an exception if the key does not exist but is in the list of default fields.

__module__ = 'aiida.common.extendeddicts'

__setattr__(attr, value)

Overridden to allow direct access to fields with underscore.

_default_fields = ()

defaultkeys()

Return the default keys defined in the instance.

extrakeys()

Return the extra keys defined in the instance.

classmethod get_default_fields()

Return the list of default fields, either defined in the instance or not.

validate()

Validate the keys, if any validate_* method is available.

Utility functions to operate on filesystem files.

aiida.common.files.get_mode_string(mode)

Convert a file’s mode to a string of the form ‘-rwxrwxrwx’. Taken (simplified) from cpython 3.3 stat module: https://hg.python.org/cpython/file/3.3/Lib/stat.py

aiida.common.files.md5_file(filepath, block_size_factor=128)

Create the hexdigested md5 checksum of the contents from

Parameters:

• filepath – the filepath of the file for which we want the md5sum
• block_size_factor – the file is read at chunks of size block_size_factor * md5.block_size, where md5.block_size is the block_size used internally by the hashlib module.

Returns:

a string with the hexdigest md5.

Raises:

No checks are done on the file, so if it doesn’t exists it may raise IOError.

aiida.common.files.md5_from_filelike(filelike, block_size_factor=128)

Create the hexdigested md5 checksum of the contents from a filelike object.

Parameters:

• filelike – the filelike object for whose contents to generate the md5 checksum
• block_size_factor – the file is read at chunks of size block_size_factor * md5.block_size, where md5.block_size is the block_size used internally by the hashlib module.

Returns:

a string with the hexdigest md5.

Raises:

no checks are done on the filelike object, so it may raise IOError if it cannot be read from.

aiida.common.files.sha1_file(filename, block_size_factor=128)

Open a file and return its sha1sum (hexdigested).

Parameters:

• filename – the filename of the file for which we want the sha1sum
• block_size_factor – the file is read at chunks of size block_size_factor * sha1.block_size, where sha1.block_size is the block_size used internally by the hashlib module.

Returns:

a string with the hexdigest sha1.

Raises:

No checks are done on the file, so if it doesn’t exists it may raise IOError.

aiida.common.files.which(cmd, mode=1, path=None)

Given a command, mode, and a PATH string, return the path which conforms to the given mode on the PATH, or None if there is no such file.

mode defaults to os.F_OK | os.X_OK. path defaults to the result of os.environ.get(“PATH”), or can be overridden with a custom search path.

Utility functions to operate on filesystem folders.

class aiida.common.folders.Folder(abspath, folder_limit=None)

Bases: object

A class to manage generic folders, avoiding to get out of specific given folder borders.

Todo

fix this, os.path.commonprefix of /a/b/c and /a/b2/c will give a/b, check if this is wanted or if we want to put trailing slashes. (or if we want to use os.path.relpath and check for a string starting with os.pardir?)

Todo

rethink whether the folder_limit option is still useful. If not, remove it alltogether (it was a nice feature, but unfortunately all the calls to os.path.abspath or normpath are quite slow).

__dict__ = dict_proxy({'mode_dir': <property object>, '__module__': 'aiida.common.folders', 'exists': <function exists>, 'get_abs_path': <function get_abs_path>, 'abspath': <property object>, 'replace_with_folder': <function replace_with_folder>, 'create_symlink': <function create_symlink>, 'mode_file': <property object>, 'erase': <function erase>, 'insert_path': <function insert_path>, '__dict__': <attribute '__dict__' of 'Folder' objects>, 'remove_path': <function remove_path>, 'open': <function open>, '__init__': <function __init__>, 'isdir': <function isdir>, 'isfile': <function isfile>, 'create': <function create>, 'folder_limit': <property object>, '__weakref__': <attribute '__weakref__' of 'Folder' objects>, 'get_content_list': <function get_content_list>, 'create_file_from_filelike': <function create_file_from_filelike>, '__doc__': '\n A class to manage generic folders, avoiding to get out of\n specific given folder borders.\n\n .. todo::\n fix this, os.path.commonprefix of /a/b/c and /a/b2/c will give\n a/b, check if this is wanted or if we want to put trailing slashes.\n (or if we want to use os.path.relpath and check for a string starting\n with os.pardir?)\n\n .. todo::\n rethink whether the folder_limit option is still useful. If not, remove\n it alltogether (it was a nice feature, but unfortunately all the calls\n to os.path.abspath or normpath are quite slow).\n ', 'get_subfolder': <function get_subfolder>})

__init__(abspath, folder_limit=None)

x.__init__(…) initializes x; see help(type(x)) for signature

__module__ = 'aiida.common.folders'

__weakref__

list of weak references to the object (if defined)

abspath

The absolute path of the folder.

create()

Creates the folder, if it does not exist on the disk yet.

It will also create top directories, if absent.

It is always safe to call it, it will do nothing if the folder already exists.

create_file_from_filelike(filelike, filename, mode='wb', encoding=None)

Create a file with the given filename from a filelike object.

Parameters:

• filelike – a filelike object whose contents to copy
• filename – the filename for the file that is to be created
• mode – the mode with which the target file will be written
• encoding – the encoding with which the target file will be written

Returns:

the absolute filepath of the created file

create_symlink(src, name)

Create a symlink inside the folder to the location ‘src’.

Parameters:

• src – the location to which the symlink must point. Can be either a relative or an absolute path. Should, however, be relative to work properly also when the repository is moved!
• name – the filename of the symlink to be created.

erase(create_empty_folder=False)

Erases the folder. Should be called only in very specific cases, in general folder should not be erased!

Doesn’t complain if the folder does not exist.

Parameters:create_empty_folder – if True, after erasing, creates an empty dir.

exists()

Return True if the folder exists, False otherwise.

folder_limit

The folder limit that cannot be crossed when creating files and folders.

get_abs_path(relpath, check_existence=False)

Return an absolute path for a file or folder in this folder.

The advantage of using this method is that it checks that filename is a valid filename within this folder, and not something e.g. containing slashes.

Parameters:

• filename – The file or directory.
• check_existence – if False, just return the file path. Otherwise, also check if the file or directory actually exists. Raise OSError if it does not.

get_content_list(pattern='*', only_paths=True)

Return a list of files (and subfolders) in the folder, matching a given pattern.

Example: If you want to exclude files starting with a dot, you can call this method with pattern='[!.]*'

Parameters:

• pattern – a pattern for the file/folder names, using Unix filename pattern matching (see Python standard module fnmatch). By default, pattern is ‘*’, matching all files and folders.
• only_paths – if False (default), return pairs (name, is_file). if True, return only a flat list.

Returns:

a list of tuples of two elements, the first is the file name and the second is True if the element is a file, False if it is a directory.

get_subfolder(subfolder, create=False, reset_limit=False)

Return a Folder object pointing to a subfolder.

Parameters:

• subfolder – a string with the relative path of the subfolder, relative to the absolute path of this object. Note that this may also contain ‘..’ parts, as far as this does not go beyond the folder_limit.
• create – if True, the new subfolder is created, if it does not exist.
• reset_limit – when doing b = a.get_subfolder('xxx', reset_limit=False), the limit of b will be the same limit of a. if True, the limit will be set to the boundaries of folder b.

Returns:

a Folder object pointing to the subfolder.

insert_path(src, dest_name=None, overwrite=True)

Copy a file to the folder.

Parameters:

• src – the source filename to copy
• dest_name – if None, the same basename of src is used. Otherwise, the destination filename will have this file name.
• overwrite – if False, raises an error on existing destination; otherwise, delete it first.

isdir(relpath)

Return True if ‘relpath’ exists inside the folder and is a directory, False otherwise.

isfile(relpath)

Return True if ‘relpath’ exists inside the folder and is a file, False otherwise.

mode_dir

Return the mode with which the folders should be created

mode_file

Return the mode with which the files should be created

open(name, mode='r', encoding='utf8', check_existence=False)

Open a file in the current folder and return the corresponding file object.

Parameters:check_existence – if False, just return the file path. Otherwise, also check if the file or directory actually exists. Raise OSError if it does not.

remove_path(filename)

Remove a file or folder from the folder.

Parameters:filename – the relative path name to remove

replace_with_folder(srcdir, move=False, overwrite=False)

This routine copies or moves the source folder ‘srcdir’ to the local folder pointed by this Folder object.

Parameters:

• srcdir – the source folder on the disk; this must be a string with an absolute path
• move – if True, the srcdir is moved to the repository. Otherwise, it is only copied.
• overwrite – if True, the folder will be erased first. if False, a IOError is raised if the folder already exists. Whatever the value of this flag, parent directories will be created, if needed.

Raises:

OSError or IOError: in case of problems accessing or writing the files.

Raises:

ValueError: if the section is not recognized.

class aiida.common.folders.RepositoryFolder(section, uuid, subfolder='.')

Bases: aiida.common.folders.Folder

A class to manage the local AiiDA repository folders.

__init__(section, uuid, subfolder='.')

Initializes the object by pointing it to a folder in the repository.

Pass the uuid as a string.

__module__ = 'aiida.common.folders'

get_topdir()

Returns the top directory, i.e., the section/uuid folder object.

section

The section to which this folder belongs.

subfolder

The subfolder within the section/uuid folder.

uuid

The uuid to which this folder belongs.

class aiida.common.folders.SandboxFolder(sandbox_in_repo=True)

Bases: aiida.common.folders.Folder

A class to manage the creation and management of a sandbox folder.

Note: this class must be used within a context manager, i.e.:

with SandboxFolder as f:

## do something with f

In this way, the sandbox folder is removed from disk (if it wasn’t removed already) when exiting the ‘with’ block.

Todo

Implement check of whether the folder has been removed.

__enter__()

Called when entering in the with statement

__exit__(exc_type, exc_value, traceback)

In exit, I remove the sandbox folder from disk, if it still exists

__init__(sandbox_in_repo=True)

Initializes the object by creating a new temporary folder in the sandbox.

Parameters:sandbox_in_repo (bool) – If True (default), creates the folder in the repository. If false, relies on the defaults of tempfile.mkdtemp

__module__ = 'aiida.common.folders'

aiida.common.folders.find_path(root, dir_name)

Iteratively recurse uopwards from a root folder to try and find a given directory.

Parameters:

• root – path to start from
• dir_name – name of the directory to try and find

Returns:

path of the directory if found

Raises:

OSError – if directory could not be found

Common password and hash generation functions.

aiida.common.hashing._(arr, **kwargs)

Hashing for Numpy arrays

aiida.common.hashing._make_hash(*args, **kw)

Implementation of the make_hash function. The hash is created as a 28 byte integer, and only later converted to a string.

aiida.common.hashing._single_digest(obj_type, obj_bytes='')

aiida.common.hashing.create_unusable_pass()

aiida.common.hashing.get_random_string(length=12, allowed_chars='abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ0123456789')

Returns a securely generated random string.

The default length of 12 with the a-z, A-Z, 0-9 character set returns a 71-bit value. log_2((26+26+10)^12) =~ 71 bits

aiida.common.hashing.is_password_usable(enc_pass)

check whether the passed password string is a valid hashed password

aiida.common.hashing.make_hash(object_to_hash, **kwargs)

Makes a hash from a dictionary, list, tuple or set to any level, that contains only other hashable or nonhashable types (including lists, tuples, sets, and dictionaries).

Parameters:object_to_hash – the object to hash Returns:a unique hash

There are a lot of modules providing functionalities to create unique hashes for hashable values. However, getting hashes for nonhashable items like sets or dictionaries is not easily doable because order is not fixed. This leads to the peril of getting different hashes for the same dictionary.

This function avoids this by recursing through nonhashable items and hashing iteratively. Uses python’s sorted function to sort unsorted sets and dictionaries by sorting the hashed keys.

aiida.common.hashing.truncate_array64(value, num_bits=4)

aiida.common.hashing.truncate_float64(value, num_bits=4)

reduce the number of bits making it into the hash to avoid rehashing due to possible truncation in float->str->float roundtrips

Abstracts JSON usage to ensure compatibility with Python2 and Python3.

Use this module prefentially over standard json to ensure compatibility. Also note the conventions for using io.open for dump and dumps.

aiida.common.json.dump(data, fhandle, **kwargs)

Write JSON encoded ‘data’ to a file-like object, fhandle In Py2/3, use io.open(filename, ‘wb’) to write. The utf8write object is used to ensure that the resulting serialised data is encoding as UTF8. Any strings with non-ASCII characters need to be unicode strings. We use ensure_ascii=False to write unicode characters specifically as this improves the readability of the json and reduces the file size.

aiida.common.json.dumps(data, **kwargs)

Write JSON encoded ‘data’ to a string. simplejson is useful here as it always returns unicode if ensure_ascii=False is used, unlike the standard library json, rather than being dependant on the input. We use also ensure_ascii=False to write unicode characters specifically as this improves the readability of the json and reduces the file size. When writing to file, use io.open(filename, ‘w’, encoding=’utf8’)

aiida.common.json.load(fhandle, **kwargs)

Deserialise a JSON file.

For Py2/Py3 compatibility, io.open(filename, ‘r’, encoding=’utf8’) should be used.

Raises:ValueError – if no valid JSON object could be decoded

aiida.common.json.loads(json_string, **kwargs)

Deserialise a JSON string.

Raises:ValueError – if no valid JSON object could be decoded

Utilities that extend the basic python language.

class aiida.common.lang.EmptyContextManager

Bases: object

A dummy/no-op context manager.

__dict__ = dict_proxy({'__module__': 'aiida.common.lang', '__exit__': <function __exit__>, '__enter__': <function __enter__>, '__dict__': <attribute '__dict__' of 'EmptyContextManager' objects>, '__weakref__': <attribute '__weakref__' of 'EmptyContextManager' objects>, '__doc__': '\n A dummy/no-op context manager.\n '})

__enter__()

__exit__(exc_type, exc_value, traceback)

__module__ = 'aiida.common.lang'

__weakref__

list of weak references to the object (if defined)

class aiida.common.lang.abstractclassmethod(callable)

Bases: classmethod

A decorator indicating abstract classmethods.

Backported from python3.

__dict__ = dict_proxy({'__module__': 'aiida.common.lang', '__isabstractmethod__': True, '__dict__': <attribute '__dict__' of 'abstractclassmethod' objects>, '__weakref__': <attribute '__weakref__' of 'abstractclassmethod' objects>, '__doc__': '\n A decorator indicating abstract classmethods.\n\n Backported from python3.\n ', '__init__': <function __init__>})

__init__(callable)

x.__init__(…) initializes x; see help(type(x)) for signature

__isabstractmethod__ = True

__module__ = 'aiida.common.lang'

__weakref__

list of weak references to the object (if defined)

class aiida.common.lang.abstractstaticmethod(callable)

Bases: staticmethod

A decorator indicating abstract staticmethods.

Similar to abstractmethod. Backported from python3.

__dict__ = dict_proxy({'__module__': 'aiida.common.lang', '__isabstractmethod__': True, '__dict__': <attribute '__dict__' of 'abstractstaticmethod' objects>, '__weakref__': <attribute '__weakref__' of 'abstractstaticmethod' objects>, '__doc__': '\n A decorator indicating abstract staticmethods.\n\n Similar to abstractmethod.\n Backported from python3.\n ', '__init__': <function __init__>})

__init__(callable)

x.__init__(…) initializes x; see help(type(x)) for signature

__isabstractmethod__ = True

__module__ = 'aiida.common.lang'

__weakref__

list of weak references to the object (if defined)

class aiida.common.lang.classproperty(getter)

Bases: object

A class that, when used as a decorator, works as if the two decorators @property and @classmethod where applied together (i.e., the object works as a property, both for the Class and for any of its instance; and is called with the class cls rather than with the instance as its first argument).

__dict__ = dict_proxy({'__module__': 'aiida.common.lang', '__dict__': <attribute '__dict__' of 'classproperty' objects>, '__weakref__': <attribute '__weakref__' of 'classproperty' objects>, '__doc__': '\n A class that, when used as a decorator, works as if the\n two decorators @property and @classmethod where applied together\n (i.e., the object works as a property, both for the Class and for any\n of its instance; and is called with the class cls rather than with the\n instance as its first argument).\n ', '__init__': <function __init__>, '__get__': <function __get__>})

__get__(instance, owner)

__init__(getter)

x.__init__(…) initializes x; see help(type(x)) for signature

__module__ = 'aiida.common.lang'

__weakref__

list of weak references to the object (if defined)

class aiida.common.lang.combomethod(method)

Bases: object

A decorator that wraps a function that can be both a classmethod or instancemethod and behaves accordingly:

class A():

    @combomethod
    def do(self, **kwargs):
        isclass = kwargs.get('isclass')
        if isclass:
            print("I am a class", self)
        else:
            print("I am an instance", self)

A.do()
A().do()

>>> I am a class __main__.A
>>> I am an instance <__main__.A instance at 0x7f2efb116e60>

Attention: For ease of handling, pass keyword isclass equal to True if this was called as a classmethod and False if this was called as an instance. The argument self is therefore ambiguous!

__dict__ = dict_proxy({'__module__': 'aiida.common.lang', '__dict__': <attribute '__dict__' of 'combomethod' objects>, '__weakref__': <attribute '__weakref__' of 'combomethod' objects>, '__doc__': '\n A decorator that wraps a function that can be both a classmethod or\n instancemethod and behaves accordingly::\n\n class A():\n\n @combomethod\n def do(self, **kwargs):\n isclass = kwargs.get(\'isclass\')\n if isclass:\n print("I am a class", self)\n else:\n print("I am an instance", self)\n\n A.do()\n A().do()\n\n >>> I am a class __main__.A\n >>> I am an instance <__main__.A instance>\n\n Attention: For ease of handling, pass keyword **isclass**\n equal to True if this was called as a classmethod and False if this\n was called as an instance.\n The argument self is therefore ambiguous!\n ', '__init__': <function __init__>, '__get__': <function __get__>})

__get__(obj=None, objtype=None)

__init__(method)

x.__init__(…) initializes x; see help(type(x)) for signature

__module__ = 'aiida.common.lang'

__weakref__

list of weak references to the object (if defined)

aiida.common.lang.override(func)

aiida.common.lang.override_decorator(check=False)

Decorator to signal that a method from a base class is being overridden completely.

aiida.common.lang.protected(func)

aiida.common.lang.protected_decorator(check=False)

Decorator to ensure that the decorated method is not called from outside the class hierarchy.

aiida.common.lang.type_check(what, of_type, msg=None, allow_none=False)

Verify that object ‘what’ is of type ‘of_type’ and if not the case, raise a TypeError.

Parameters:

• what – the object to check
• of_type – the type (or tuple of types) to compare to
• msg – if specified, allows to customize the message that is passed within the TypeError exception
• allow_none – boolean, if True will not raise if the passed what is None

Module to define valid link types.

class aiida.common.links.LinkType

Bases: enum.Enum

A simple enum of allowed link types.

CALL_CALC = 'call_calc'

CALL_WORK = 'call_work'

CREATE = 'create'

INPUT_CALC = 'input_calc'

INPUT_WORK = 'input_work'

RETURN = 'return'

__module__ = 'aiida.common.links'

Module for all logging methods/classes that don’t need the ORM.

Functions to interactively or non-interactively set up the AiiDA instance and a profile.

aiida.common.setup.create_profile(config, profile_name='default')

Parameters:profile_name – The profile to be configured Returns:The populated profile that was also stored.

aiida.common.setup.create_profile_noninteractive(config, profile_name='default', force_overwrite=False, **kwargs)

Non-interactively creates a profile. :raises: a ValueError if the profile exists. :raises: a ValueError if one of the values not a valid input :param profile: The profile to be configured :param values: The configuration inputs :return: The populated profile that was also stored

aiida.common.setup.parse_repository_uri(repository_uri)

This function validates the REPOSITORY_URI, that should be in the format protocol://address

Note:At the moment, only the file protocol is supported. Returns:a tuple (protocol, address).

aiida.common.setup.validate_email(email)

Validate an email address using Django’s email validator.

Parameters:email – the email address Returns:boolean, True if email address is valid, False otherwise

Utility functions to operate on datetime objects.

aiida.common.timezone.delta(from_time, to_time=None)

Return the datetime object representing the different between two datetime objects.

Parameters:

• from_time – starting datetime object
• to_time – end datetime object

Returns:

the delta datetime object

aiida.common.timezone.get_current_timezone()

Return the current timezone.

Returns:current timezone

aiida.common.timezone.is_aware(value)

Return whether the given datetime object is timezone aware

Returns:boolean, True if aware, False otherwise

aiida.common.timezone.is_naive(value)

Return whether the given datetime object is timezone naive

Returns:boolean, True if naive, False otherwise

aiida.common.timezone.localtime(value, timezone=None)

Converts an aware datetime.datetime to local time. Local time is defined by the current time zone, unless another time zone is specified.

aiida.common.timezone.make_aware(value, timezone=None, is_dst=None)

Make the given datetime object timezone aware

Parameters:

• value (datetime.datetime) – The datetime to make aware
• timezone –
• is_dst –

Returns:

aiida.common.timezone.now()

Return the datetime object of the current time.

Returns:datetime object represeting current time

Miscellaneous generic utility functions and classes.

class aiida.common.utils.ArrayCounter

Bases: object

A counter & a method that increments it and returns its value. It is used in various tests.

__dict__ = dict_proxy({'__module__': 'aiida.common.utils', 'seq': None, 'array_counter': <function array_counter>, '__dict__': <attribute '__dict__' of 'ArrayCounter' objects>, '__weakref__': <attribute '__weakref__' of 'ArrayCounter' objects>, '__doc__': '\n A counter & a method that increments it and returns its value.\n It is used in various tests.\n ', '__init__': <function __init__>})

__init__()

x.__init__(…) initializes x; see help(type(x)) for signature

__module__ = 'aiida.common.utils'

__weakref__

list of weak references to the object (if defined)

array_counter()

seq = None

class aiida.common.utils.Capturing(capture_stderr=False)

Bases: object

This class captures stdout and returns it (as a list, split by lines).

Note: if you raise a SystemExit, you have to catch it outside. E.g., in our tests, this works:

import sys
with self.assertRaises(SystemExit):
    with Capturing() as output:
        sys.exit()

But out of the testing environment, the code instead just exits.

To use it, access the obj.stdout_lines, or just iterate over the object

Parameters:capture_stderr – if True, also captures sys.stderr. To access the lines, use obj.stderr_lines. If False, obj.stderr_lines is None.

__dict__ = dict_proxy({'__module__': 'aiida.common.utils', '__exit__': <function __exit__>, '__dict__': <attribute '__dict__' of 'Capturing' objects>, '__str__': <function __str__>, '__enter__': <function __enter__>, '__weakref__': <attribute '__weakref__' of 'Capturing' objects>, '__iter__': <function __iter__>, '__init__': <function __init__>, '__doc__': '\n This class captures stdout and returns it\n (as a list, split by lines).\n\n Note: if you raise a SystemExit, you have to catch it outside.\n E.g., in our tests, this works::\n\n import sys\n with self.assertRaises(SystemExit):\n with Capturing() as output:\n sys.exit()\n\n But out of the testing environment, the code instead just exits.\n\n To use it, access the obj.stdout_lines, or just iterate over the object\n\n :param capture_stderr: if True, also captures sys.stderr. To access the\n lines, use obj.stderr_lines. If False, obj.stderr_lines is None.\n '})

__enter__()

Enter the context where all output is captured.

__exit__(*args)

Exit the context where all output is captured.

__init__(capture_stderr=False)

x.__init__(…) initializes x; see help(type(x)) for signature

__iter__()

__module__ = 'aiida.common.utils'

__str__() <==> str(x)

__weakref__

list of weak references to the object (if defined)

class aiida.common.utils.ErrorAccumulator(*error_cls)

Bases: object

Allows to run a number of functions and collect all the errors they raise

This allows to validate multiple things and tell the user about all the errors encountered at once. Works best if the individual functions do not depend on each other.

Does not allow to trace the stack of each error, therefore do not use for debugging, but for semantical checking with user friendly error messages.

__dict__ = dict_proxy({'__module__': 'aiida.common.utils', 'run': <function run>, 'result': <function result>, 'success': <function success>, '__dict__': <attribute '__dict__' of 'ErrorAccumulator' objects>, 'raise_errors': <function raise_errors>, '__weakref__': <attribute '__weakref__' of 'ErrorAccumulator' objects>, '__doc__': '\n Allows to run a number of functions and collect all the errors they raise\n\n This allows to validate multiple things and tell the user about all the\n errors encountered at once. Works best if the individual functions do not depend on each other.\n\n Does not allow to trace the stack of each error, therefore do not use for debugging, but for\n semantical checking with user friendly error messages.\n ', '__init__': <function __init__>})

__init__(*error_cls)

x.__init__(…) initializes x; see help(type(x)) for signature

__module__ = 'aiida.common.utils'

__weakref__

list of weak references to the object (if defined)

raise_errors(raise_cls)

result(raise_error=<type 'exceptions.Exception'>)

run(function, *args, **kwargs)

success()

class aiida.common.utils.Prettifier(format)

Bases: object

Class to manage prettifiers (typically for labels of kpoints in band plots)

__dict__ = dict_proxy({'_prettify_label_agr_simple': <classmethod object>, '__module__': 'aiida.common.utils', 'prettify': <function prettify>, '_prettify_label_gnuplot': <classmethod object>, '_prettify_label_latex_simple': <classmethod object>, '_prettify_label_agr': <classmethod object>, '_prettify_label_pass': <classmethod object>, 'prettifiers': <aiida.common.lang.classproperty object>, '_prettify_label_gnuplot_simple': <classmethod object>, 'get_prettifiers': <classmethod object>, '__dict__': <attribute '__dict__' of 'Prettifier' objects>, '_prettify_label_latex': <classmethod object>, '__weakref__': <attribute '__weakref__' of 'Prettifier' objects>, '__doc__': '\n Class to manage prettifiers (typically for labels of kpoints\n in band plots)\n ', '__init__': <function __init__>})

__init__(format)

Create a class to pretttify strings of a given format

Parameters:format – a string with the format to use to prettify. Valid formats are obtained from self.prettifiers

__module__ = 'aiida.common.utils'

__weakref__

list of weak references to the object (if defined)

classmethod _prettify_label_agr(label)

Prettifier for XMGrace

Parameters:label – a string to prettify

classmethod _prettify_label_agr_simple(label)

Prettifier for XMGrace (for old label names)

Parameters:label – a string to prettify

classmethod _prettify_label_gnuplot(label)

Prettifier for Gnuplot

Note:uses unicode, returns unicode strings (potentially, if needed) Parameters:label – a string to prettify

classmethod _prettify_label_gnuplot_simple(label)

Prettifier for Gnuplot (for old label names)

Note:uses unicode, returns unicode strings (potentially, if needed) Parameters:label – a string to prettify

classmethod _prettify_label_latex(label)

Prettifier for matplotlib, using LaTeX syntax

Parameters:label – a string to prettify

classmethod _prettify_label_latex_simple(label)

Prettifier for matplotlib, using LaTeX syntax (for old label names)

Parameters:label – a string to prettify

classmethod _prettify_label_pass(label)

No-op prettifier, simply returns the same label

Parameters:label – a string to prettify

classmethod get_prettifiers()

Return a list of valid prettifier strings

Returns:a list of strings

prettifiers = {'agr_seekpath': <bound method type._prettify_label_agr of <class 'aiida.common.utils.Prettifier'>>, 'agr_simple': <bound method type._prettify_label_agr_simple of <class 'aiida.common.utils.Prettifier'>>, 'gnuplot_seekpath': <bound method type._prettify_label_gnuplot of <class 'aiida.common.utils.Prettifier'>>, 'gnuplot_simple': <bound method type._prettify_label_gnuplot_simple of <class 'aiida.common.utils.Prettifier'>>, 'latex_seekpath': <bound method type._prettify_label_latex of <class 'aiida.common.utils.Prettifier'>>, 'latex_simple': <bound method type._prettify_label_latex_simple of <class 'aiida.common.utils.Prettifier'>>, 'pass': <bound method type._prettify_label_pass of <class 'aiida.common.utils.Prettifier'>>}

prettify(label)

Prettify a label using the format passed in the initializer

Parameters:label – the string to prettify Returns:a prettified string

aiida.common.utils.are_dir_trees_equal(dir1, dir2)

Compare two directories recursively. Files in each directory are assumed to be equal if their names and contents are equal.

@param dir1: First directory path @param dir2: Second directory path

@return: True if the directory trees are the same and

there were no errors while accessing the directories or files, False otherwise.

aiida.common.utils.export_shard_uuid(uuid)

Sharding of the UUID for the import/export

aiida.common.utils.get_class_string(obj)

Return the string identifying the class of the object (module + object name, joined by dots).

It works both for classes and for class instances.

aiida.common.utils.get_new_uuid()

Return a new UUID (typically to be used for new nodes). It uses the UUID version specified in aiida.backends.settings.AIIDANODES_UUID_VERSION

aiida.common.utils.get_object_from_string(class_string)

Given a string identifying an object (as returned by the get_class_string method) load and return the actual object.

aiida.common.utils.get_repository_folder(subfolder=None)

Return the top folder of the local repository.

aiida.common.utils.get_unique_filename(filename, list_of_filenames)

Return a unique filename that can be added to the list_of_filenames.

If filename is not in list_of_filenames, it simply returns the filename string itself. Otherwise, it appends a integer number to the filename (before the extension) until it finds a unique filename.

Parameters:

• filename – the filename to add
• list_of_filenames – the list of filenames to which filename should be added, without name duplicates

Returns:

Either filename or its modification, with a number appended between the name and the extension.

aiida.common.utils.grouper(n, iterable)

Given an iterable, returns an iterable that returns tuples of groups of elements from iterable of length n, except the last one that has the required length to exaust iterable (i.e., there is no filling applied).

Parameters:

• n – length of each tuple (except the last one,that will have length <= n
• iterable – the iterable to divide in groups

aiida.common.utils.join_labels(labels, join_symbol='|', threshold=1e-06)

Join labels with a joining symbol when they are very close

Parameters:

• labels – a list of length-2 tuples, in the format(position, label)
• join_symbol – the string to use to join different paths. By default, a pipe
• threshold – the threshold to decide if two float values are the same and should be joined

Returns:

the same list as labels, but with the second value possibly replaced with strings joined when close enough

aiida.common.utils.prettify_labels(labels, format=None)

Prettify label for typesetting in various formats

Parameters:

• labels – a list of length-2 tuples, in the format(position, label)
• format – a string with the format for the prettifier (e.g. ‘agr’, ‘matplotlib’, …)

Returns:

the same list as labels, but with the second value possibly replaced with a prettified version that typesets nicely in the selected format

aiida.common.utils.str_timedelta(dt, max_num_fields=3, short=False, negative_to_zero=False)

Given a dt in seconds, return it in a HH:MM:SS format.

Parameters:

• dt – a TimeDelta object
• max_num_fields – maximum number of non-zero fields to show (for instance if the number of days is non-zero, shows only days, hours and minutes, but not seconds)
• short – if False, print always max_num_fields fields, even if they are zero. If True, do not print the first fields, if they are zero.
• negative_to_zero – if True, set dt = 0 if dt < 0.

aiida.common.utils.strip_prefix(full_string, prefix)

Strip the prefix from the given string and return it. If the prefix is not present the original string will be returned unaltered

Parameters:

• full_string – the string from which to remove the prefix
• prefix – the prefix to remove

Returns:

the string with prefix removed

aiida.common.utils.validate_list_of_string_tuples(val, tuple_length)

Check that:

1. val is a list or tuple
2. each element of the list:

1. is a list or tuple
2. is of length equal to the parameter tuple_length
3. each of the two elements is a string

Return if valid, raise ValidationError if invalid

Define warnings that can be thrown by AiiDA.

exception aiida.common.warnings.AiidaDeprecationWarning

Bases: exceptions.Warning

Class for AiiDA deprecations.

It does not inherit, on purpose, from DeprecationWarning as this would be filtered out by default. Enabled by default, you can disable it by running in the shell:

verdi config warnings.showdeprecations False

__module__ = 'aiida.common.warnings'

__weakref__

list of weak references to the object (if defined)

exception aiida.common.warnings.AiidaEntryPointWarning

Bases: exceptions.Warning

Class for warnings concerning AiiDA entry points.

It does not inherit, on purpose, from DeprecationWarning as this would be filtered out by default.

__module__ = 'aiida.common.warnings'

__weakref__

list of weak references to the object (if defined)