Used to document all changes from previous releases and collect changes until the next release.
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pprint methods have been added to both Section and Property
to print whole Section trees with their child sections and properties.
The __repr__ style of Section and Property has been changed to
be more similar to the nixpy __repr__ style.
Printing a Section now also features the immediate Property child count
in addition to the immediate Section child count. See #309.
To make working with odML more similar to working with the
metadata part of nixpy, the Property.value
attribute has been marked deprecated and the Property.values
attribute has been added. See #308.
Uncertainty is now limited to float only. See #294.
The VersionConverter dealt with an edge case of XML test files with opening tags that were missing their closing tag rendering them broken. Catching this one edge case circumvented opening XML files via lxml, leaving the resulting document open to various encoding problems.
Support to resolve the specific tag edge cases is dropped in favour of properly opening XML files via lxml. See #301.
The odmlconversion convenience console script has been added to convert multiple
previous odML version files to the latest odML version.
When cloning a Section or a Property by default the id of any object is changed
to a new UUID. The cloning methods now feature a new keep_id attribute. If set to
True, the cloned object and any cloned children retain their original id. This
is meant to create exact copies of Section-Property trees in different documents.
When a document is saved, a new validation check makes sure, that a document contains only unique UUIDs this is required due to the introduction of creating clones with identical ids.
pyyaml was version fixed on 3.13 to circumvent introduced breaking changes in the library. See #291, #292, #296, #298.docopt was added to support console scriptsVersionConverter XML parser. See #288, #296.XMLParser that when reading a single string value from csv which contains commata, it now remains a single value and is not split up at each comma. See #295, #296.XMLParser any leading or trailing whitespaces are removed from any string values when it is written to csv. Along the same lines, multiple values that are saved to file via the VersionConverter do not contain leading whitespaces any longer. See #296.unicode has been introduced to all Parsers and Converters to avoid encoding errors with Python 2 and Python 3. See #297.Section and Property SmartListSmartList.sort(). By default Document and Section child lists will retain the order in which child elements were added, but now a sort by name can be manually triggered. See #290.SmartList comparison magic methods to partially address #265. The introduction of the RDF backend led to an issue when comparing odML entities. The used RDF library rdflib does not respect child order upon loading of a file, odML entities with children can not be compared without sorting the child elements. The added magic methods sort child elements by name before comparison without changing the actual order of the child elements. This only addresses the issue for Section and Property child lists, but does not solve the problem for the order of Property.values. See #290._origin_file_name is added to the Document entity. When an odML document is loaded from file, this attribute is now set with the file name from whence the document was loaded. See #297.Seq is now used instead of Bag to store odml.Property values to respect the order of values. See #292.rdflib currently does not support proper Seq behaviour with RDF li items, for now the index of the value items will be manually written as RDF properties, which rdflib supports when reading an RDF file. See #292._origin_file_name, the value is exported as odml:hasFileName. See #297.xml is now the default ODMLWriter format when writing a document to RDF since the XML format of RDF is still the format with the broadest acceptance. See #297.odmltordf convenience console script has been added to convert multiple odML files to the RDF format from any odML format or version. See #298.The switch from odML version 1.3 to 1.4 contains many cool updates which should make work more comfortable, but also includes some breaking changes.
base._baseobj class, leaving BaseObject as the root odML class.doc.Document class, leaving BaseDocument as the only odML Document class.section.Section class, leaving BaseSection as the only odML Section class.property.Property class leaving BaseProperty as the only odML Property class.baseobject and sectionable are renamed to BaseObject and Sectionable respectively.base.SafeList and base.SmartList have been merged, base.SafeList has been removed.base.SmartList can now only contain Sections or Properties. See #272.reorder method is moved from the base to the Section class. See #267.Value class has been removed.Property.value now always holds a list of uniform values. Property.value always
returns a copy of the actual value list. See #227.__setitem__ method of a PropertyValue attributes uncertainty, unit, dtype and reference have been moved to
Property and now apply to all values of the Property.value list.Value attributes filename, encoder and checksum have been removed.binary dtype has been removed. Providing binary content via odML files is
discouraged in favor of providing a reference to the origin files using the URL
dtype instead.mapping functionality has been removed.XMLReader.fromFile() and .fromString() have been renamed to .from_file() and .from_string() respectively.odml.format where changed: Section.name,
Section.type and Property.name are the only attributes set to be required for
their respective odML entities. See #240.Section.name and Property.name can now be None on init. If this is the case, the
entities' id value is used as name value.name attributes in the XML Parser are removed. Only
attributes set as required in format are now used to check for missing required odML
entity attributes. See #241.name attribute of a Section or a Property can now only be rewritten if there
is no sibling with the same name on the same hierarchical level. See #283.Document, Section and Property now have an id attribute to uniquely identify any
entity. If no valid id is provided when an entity is initialized, an id is
automatically generated and assigned.new_id() method to Document, Section and Property which generates
and sets a new valid id for any entity. See #262.None or ""."false", "f", 0, False, "true", "t", 1 or True
will now raise a ValueError. See #224base.Sectionable.extend method for child Sections and Properties. See #237.base.Sectionable.insert and .append methods. Only proper
BaseSections with a unique name can be added to the Section child list of a
Sectionable.append method to
mirror Property append functionality and since extend now serves this need.Property now provides a merge method to merge two properties. This will sync all but
the dependency and dependencyValue attributes. ValueErrors are raised, if information
is set in both properties but are in conflict. See #221.Section.merge_check() method which validates whether a Section including all
its sub-sections and sub-properties can properly be merged. A ValueError is raised
if any potential merge problem arises. This is necessary since a recursive Section
merge cannot be easily rolled back once begun.reference and definition from the "source" Section if they
were None in the "destination" Section. See #273.strict flag to any merge method. Now all Section and Property attribute
checks during a merge will only be done, if strict=True. On strict=False a
Section or Property attribute will only be replaced with the "source" value, if
the "destination" value is None. Otherwise the "destination" value will be kept and
the "source" value lost. See #270.Section or a Property is cloned, a new id is set for the clone and of any
cloned children. See #259.Document.append since
Document.extend should be used to add multiple new Sections to a Document.Section.extend method.Property has the new attribute value_origin which may contain the origin of the
property's value e.g. a filename.Property init now supports setting all attributes as well as its parent.Property now provides append, extend and remove methods to change the actual
value list. This approach is required to ensure DType checks when adding new values
to an existing list. See #223.Property init. See #253.http://portal.g-node.org/odml/terminologies/v1.1/terminologies.xml.XMLParser can now be run in warning mode: any errors encountered during parsing
will just print a warning, but will not stop and exit during the parsing process.tools.RDFWriter and toosl.RDFReader classes, which enable the export of
odML documents to RDF and also provides the used ontology OWL file at doc/odml_terminology/.tools.ODMLWriter and tools.ODMLReader classes which serve as an easy
entry point to saving and loading for all the supported file formats XML, YAML,
JSON and RDF.tools.DictWriter and tools.DictReader classes which convert Python
dictionary data to odML data and vice versa, which in turn is required for both YAML
and JSON format loading and saving.tools.jsonparser file which is no longer required due to the classes in
tools.odmlparser and tools.dict_parser.tools.FormatConverter class which enables batch conversion of one odML
format into another.tools.VersionConverter class which enables conversion of pre-v1.4 odML files
into valid v1.4 odML.
VersionConverter converts XML, JSON and YAML based odML files of odML file
version 1.0 to odML file version 1.1.Document, Section and Property are exported. Any
non supported attribute will produce a warning message, the content will be
discarded.Value object to its parent Property value list.unit or uncertainty of values of a Property will be moved
to its parent Property. Any differing subsequent unit or uncertainty of
values of the same Property will produce a warning message, the content will be
discarded.filename attribute content of a Value is moved to the value_origin
attribute of its parent Property.repository or link is updated from v1.0 to their
v1.1 counterparts if available.VersionConverter object provides a .conversion_log list attribute to access all
info and warning messages after a conversion has taken place. See #234.False as well as F are now properly converted to bool values in both
Python 2 and 3. See #222.XMLParser.Document now properly uses the dtypes date setter on init. See #249.None boolean and datetime related values. See #245.id when comparing odML entities for equality. See #260.Property is cloned, the parent of the clone is now properly set to None.AttributeError on get_path() when a Property has no parent. See #256.AttributeError on get_merged_equivalent() when a Property
has no parent. See #257.Property.append(), if the dtype was not set. See #266.Property.append() exits on empty values but accepts 0 and False.Property.uncertainty to None if an empty string is passed to it.Property.__init__ set attributes order: In the previous set attribute
order, the repository attribute was overwritten with None by the super.__init__
after it had been set.Property.parent = None bugs in remove() and insert() methods.ODMLParser class. See #199.BaseSection or BaseDocument for isinstance checks throughout
base instead of a mixture of BaseSection and Section.info.py.Version, Format version, Contact,
Homepage, Author, PyPI Classifiers, Copyright.setup.py. The license text interfered with the PyPI
process in a way, that the description was not displayed on PyPI.json or yaml files; #191.json or yaml files when Section.repository, Section.link or Section.include are present; #194.backend argument that specifies the parser or writer.
Can be one of XML, JSON, or YAML.