Version 1.5.4

What's Changed

• test_doc_examples.py: initialize examples_path. by @emollier in #538
• use python3 in shebang. by @emollier in #539
• Numpy > 2.0 compatibility by @jgrewe in #542
• Removed Python2 leftovers by @a-detiste in #541
• fix test warnings by @jgrewe in #543

New Contributors

• @emollier made their first contribution in #538
• @a-detiste made their first contribution in #541

Full Changelog: 1.5.3...1.5.4

Version 1.5.3

This release fixes two issues

• When reading string data from the dataset, the strings were implicitly converted to np.str_ data type. They are ensured to be kept as native str now (pr #536)

• When reading data slices with data_array.get_slice method from an event array in SliceMode.Data that did not contain any events, a OutOfBounds exception was thrown. This is now caught and instead an empty DataView is returned.

Version 1.5.2

• fixes a problem with DataArray.get_slice in combination with a RangeDimension (#529 )
• fixes an issue with reading more than 1d string data (#531)
• old-style metadata string values are now read and returned as proper strings and no longer byte strings (#530)
• sets the maximum recursion depth of the Section.pprint to unlimited (max_depth = -1) as default (#523
• aligns the internal version numbers with the realease version number (#528)
• solves an inconsistency in error handling #525
• corrects the block creating without name and type #524
• manifests the long-ago drop of python 2 support in the setup.py #465

Version 1.5.1

Changes in 1.5.1

• adds a method to the DataArray that adds a RangeDimension that links to the DataArray itself. (What has been an AliasRangeDimension before 1.5, issue #500
• reintroduces RangeDimension.is_alias method and allows to read before 1.2 AliasRangeDimension ticks (pr #503)
• fixes an issue to access the parent Block of a Source (issue #498)
• adds a method to find the parent source in a nested tree of Sources (issue #498)
• updates the full documentation https://nixpy.readthedocs.io/en/master/ (pr #512)
• adds an overload to SampledDimension.axis that allows to start at a position not only an index (pr #504)
• add optional arguments to Block.create_data_array to set label and unit directly upon creation (pr #505)
• improves the print output of DataFrame entities.
• empty data slices no longer lead to an exception but return an empty array (issue #502, pr #516)
• fixes bugs in upgrade script (issue #509, issue #511)
• fixes a bug in command line tool occurring in 3.6 (we used an argparse argument introduced in 3.7+ versions, pr #519)
• makes file_upgrade function available via nixio package import (pull request #512)
• allows to pass other iterables to SetDimension.labels than just lists (pr #520)
• adds a Label to the SetDimension (pr #522)
• fixes a downward compatibility issue with AliasRangeDimensions (pr #521)

Data model changes

• Pull request #522 introduces a non-breaking change to the model. Model version was bumped to 1.2.1

Version 1.5.0

Changes

• adds new functionality to the nixio command line tool to explore nix files:

nixio explore --help

• changes the default way of retrieving data from a Tag or MultiTag, this now follows the numpy behavior, old behavior is available via flag
• Allows to link to DataFrames in as Features in Tags and MultiTags
• Drops Python2 support

Fixes

• Adapts to changes in h5py string handling
• Fixes an issue reading data from a DataView object
• Fixes how strings are handled in DataFrames
• Lots of tiny code-style fixes
• Improved testing of data access functions

Relevant PRs:

#495 Tag retrieval: Inclusive and Exclusive stop rule
#478 Support linking DataFrames to Tags via Features
#477 RangeDimension: Replace ticks with link and vice versa when setting
#475 Command line: Top level nixio command with subcommands for command line scripts
#471 Add nixexplore command line tool

Version 1.5.0 beta 6

Changes

• File format upgrade script changes AliasRangeDimension to RangeDimension with DimensionLink to DataArray.

Relevant PRs

• #470: Upgrade dimension

Version 1.5.0 beta 5

Changes

• Dimension links: Dimensions can now be linked to data objects (DataArray or DataFrame). This links a Dimension object to a specific vector of data, which is either a single vector of a DataArray's data or a single column of a DataFrame.
  • This removes the AliasRangeDimension object. The same functionality can be achieved by adding a RangeDimension and then linking it back to the parent DataArray.
  • The FILE FORMAT version is now 1.2.0.
• New script nixio-upgrade: Upgrades files to newest version if there are file format changes.
• Every NIX object holds a reference to the open file object it belongs to and can be accessed via obj.file.
• Storage optimisation: Dataset and property creation was causing large per-object overhead which made files with a large number of small objects take up too much space. We changed the way these are initialised so file sizes should be much smaller going forward.
• MultiTags can have extents specified in the constructor.
• MultiTags can now be created by supplying an array or a list for the positions and extents arguments. This will result in the automatic creation of DataArrays to hold these values.
• DataArray now has an iter_dimensions() method which, when iterated upon, generates a 1-based index along with each dimension of the array.
• Changed the structure of the information returned by the File.validate() method. The information is now organised in a dictionary with two keys, "errors" and "warnings". Each contains dictionary that maps NIX objects to a list of error or warning messages respectively.

Bug fixes

• Fixed the behaviour of the object modification time and the option which disables it.
• Fixed several bugs in the validator module.
• Fixed DataFrame creation using a compound (structured) data type without specifying column names.

Relevant PRs

• #421: Validator part 2
• #423: Validator script
• #432: Add shape when initializing properties to optimize storage
• #434: Fix bug for h5group.root
• #436: Allow supplying np_arrays or list for multi_tags positions
• #438: Add method that returns 1-based index dimension iterators
• #440: Change the search method of index_of() for range_dim
• #442: Enforce unique column names for DataFrame
• #445: Fix bug when create dataframe from compound arrays and add test
• #452: Upgrade script
• #462: File references
• #464: Fixes and simplifications for DataTypes and DataType mappings
• #469: Dimension links

Version 1.5.0 beta 4

Changes

• DataFrame: The new table-like DataFrame object has been available since beta 3, but now it has been improved and better tested. There are still some planned features before it can be considered complete.
• New file open argument: auto_update_time. When enabled, updates the modification time for objects whenever they are modified. This may become the default behaviour in a future release.
• Incremented file format version: 1.1.1
• Properties now have an extend_values() method for adding values to an existing Property.
• Pretty print from file root: File object now has a pprint() method which combines the data and metadata pretty print methods.
• Validator method method and command line script: Added a full reimplementation of the NIX validator. this can be called from a file object using the validate() method or from the command line with the command nix-validate followed by one or more NIX file paths.

Bug fixes

• Fixed unicode support in Property values.
• Fixed reading and writing data through DataView objects.

Relevant PRs

• #322: Validator for No bindings dev branch
• #385: Add auto-time-update flag to NIXpy file
• #386: File format version: 1.1.1
• #392: Add append_values method for modifying values
• #393: Add pprint function for file
• #408: Support unicode in Property values
• #414: Fix DataView reading and writing

Version 1.5.0 beta 3

Changes

• Dropped retrieve_ prefix from data access methods in Tag and MultiTag. Old method names still work but warn that they are deprecated.
  • retrieve_data → tagged_data
  • retrieve_feature_data → feature_data
• New pretty print function pprint() for the data tree. The function can be run from any Block object to print a tree representation of its contained objects.

Bug fixes

• Fixed a bug where an error would occur when searching for objects from a metadata Section and some objects did not have defined metadata.

Relevant PRs

• #373: Retrieve rename
• #376: Pretty Print for Data Tree
• #381: Inverse search fix

Version 1.4.9

Bugfixes

• Fixed bug in metadata pretty print function pprint()

Relevant PRs

• #350 Fix argument order in recursive calls to pprint()