0.5.0

Release 0.5.0 June 14, 2024

• JSON schema now used for validation of remodeling operations.
• hedId attributes added to all HED elements.
• representation of HED schemas with tsv files allowed.
• wordcloud visualization added.
• context representation

What's Changed (Details)

• Enable word cloud tests. Improve error reporter tests by @IanCa in #795
• Add support for loading multiple library schemas with the same prefix by @IanCa in #798
• Changed BidsDataset to not include participants for HED by default by @VisLab in #799
• Add a test for invalid header attributes by @IanCa in #802
• Raise exception if loading merged schemas with duplicate tags by @IanCa in #803
• Added initial version of the sequence map by @VisLab in #809
• Add linkchecker to documentation, and misc minor fixes to doc strings/templates by @IanCa in #817
• Add support for saving/loading in various RDF formats by @IanCa in #825
• Explicitly ban temporal tags when no onset column present by @IanCa in #826
• Add rdflib to setup.cfg by @IanCa in #829
• Validate remodeler file using json schema by @monique2208 in #828
• Add installer test for 3.7 and 3.10 by @IanCa in #830
• Add placeholder check for spaces in units by @IanCa in #832
• Added jsonschema to the docs requirements by @VisLab in #835
• Fix bug in column mapper dicts could be returned wrong by @IanCa in #844
• Remove some URL calls in test code, try to update token for workflow by @IanCa in #845
• Fix handling of optional remodeling arguments by @VisLab in #847
• Switch over most settings to .toml file by @IanCa in #848
• Implement context handling for factor by hed tags by @VisLab in #850
• Add wordcloud to setup requirements. Restore init file by @IanCa in #853
• Allow validation of files with out of order onsets. by @IanCa in #855
• Completely re-write schema comparison summary by @IanCa in #856
• Minor fixes and modifications to the def_expands. by @VisLab in #857
• Minor fixes to install/misc by @IanCa in #859
• Various cleanup of comments, removing some unused functions by @IanCa in #860
• Updating word cloud visualization in HED tag summary to have parameters by @VisLab in #861
• Remove new line from comment for now by @IanCa in #862
• Allow adjust size/color of svg contour in wordcloud by @IanCa in #863
• Allow tag cloud to take a transparent mask by @IanCa in #864
• Added minor logging facility for exceptions by @VisLab in #865
• Turn on allowed character support in > 8.3 by @IanCa in #867
• Update/improve deprecatedFrom support by @IanCa in #869
• WordCoud allows font_path and EventManager now checks for unsorted onsets. by @VisLab in #870
• Remove set_path parameter from word cloud creation by @VisLab in #873
• Update for mixed case extensions by @VisLab in #874
• Only flag spaces in units if they aren't deprecated by @IanCa in https://github.com/hed-standard/hed-python/pull/875Bump spec_tests/hed-examples from 64c7c94 to 0206613 by @dependabot in #876
• Update deprecatedFrom validation and tests by @IanCa in #877
• Add support for Duration tag, and validation support for Delay by @IanCa in #879
• Update sidecar validation to check fully combined hed strings by @IanCa in #880
• Lazy load definition entries when creating tags by @IanCa in #882
• Allow mixed case in non unitsymbol units by @IanCa in #884
• Add validation/function to Delay and Duration tags. by @IanCa in #885
• Minor cleanup/documentation cleanup of schema and models by @IanCa in #887
• Added description fields to the remodeling JSON and removed get_assembled by @VisLab in #889
• Fix check if that should be top level when writing by @IanCa in #891
• Fix source_format when using a mix of xml/mediawiki sources by @IanCa in #892
• Update spec tests output by @IanCa in #893
• Improve schema character validation to match the new spec/utf8 support by @IanCa in #896
• Implement validation with new 83 schema properties/rules by @IanCa in #900
• Add support for caching prerelease schemas. by @IanCa in #901
• Initial commit of saving/loading .tsv. by @IanCa in #906
• Fix spec tests/minor error tweaks for tests by @IanCa in #907
• Correct argument on summarize column values by @VisLab in #90
• Include a str2_to_sidecars utility by @VisLab in #911
• Move cache test to spec_tests by @IanCa in #912
• Add utilities for accessing sidecars and tabular input by @VisLab in #913
• Add str_list to annotation_util to handle None for Matlab by @VisLab in #914
• Change the behavior of None in to_strlist by @VisLab in #915
• Remove tabs in wiki format by @IanCa in #916
• Second pass dataframe/omn schema handling by @IanCa in #919
• Replace removeprefix < 3.9 compatible by @IanCa in #920
• Add more robust hedID validation, minor ontology code tweaks by @IanCa in #922
• Make assigning ID's optional in script by @IanCa in #923
• Redo the imports to make MATLAB happier and avoid circular references by @VisLab in #924
• Revise the imports for MATLAB and added additional allowed font extensions by @VisLab in #925
• Delete test hed cache by @IanCa in #926
• Update dataframe loading/saving to allow passing a folder name by @IanCa in #928
• Move schema scripts over to hed-python by @IanCa in #929
• Minor tweaks to spreadsheet script/code by @IanCa in #931
• Fix for codespell and documentation errors by @IanCa in #933
• Ontology fixes by @IanCa in #934
• Fix tests on windows/with new 8.3 by @IanCa in #937
• First pass create_ontology script by @IanCa in #938
• Minor update to support hed web by @VisLab in #940
• First pass writing out ontology structure file by @IanCa in #944
• Improve validation of placeholders in schema compliance by @IanCa in #945
• Minor changes to change log. by @IanCa in #946
• Add 8.3.0 to built in schemas by @IanCa in #948
• Simplify some schema functions/minor refactoring by @IanCa in #950
• Replace and/or with &&/|| for searching by @IanCa in #951
• Optimize KeyMap:_remap by @IanCa in #953
• Update requirements to fix pycharm not recognizing one by @IanCa in #954
• Remove tools imports from top-level init by @VisLab in https://g...

0.4.0

Release 0.4.0 October 27, 2023

• Refactored the model classes to be based on DataFrame.
• Added additional command line options for remodeling tools.
• Restructured summaries for better reporting.
• Minor refactoring to reduce code complexity.
• Finalized and automated SPEC tests.
• Improvements to GitHub automation -- including adding CodeSpell.
• Improvements to API-Docs.

What's Changed (Details)

• Clean up some of the overly complex functions some, add a few unit tests by @IanCa in #705
• First pass word cloud for tag summaries by @IanCa in #706
• Started working on allowing multiple iteration of remodeling by @VisLab in #707
• Merging minor changes to the remodeling tools by @VisLab in #708
• Made the get_details_dict method return a uniform dict with Specifics by @VisLab in #709
• Updated the HedTagCounts --- minor count bug by @VisLab in #711
• Second pass word cloud by @IanCa in #710
• Update setup.cfg to limit pydantic version by @IanCa in #712
• Updated factor_hed_type_op to not include condition variable separate… by @VisLab in #713
• Revert inflect changes as it's fixed by @IanCa in #716
• Updated exception handling for invalid tabular and json files by @VisLab in #717
• Minor bug fixes, improved exception handling, inflect library conflicts resolved. by @VisLab in #718
• HedStrings now always require a Schema by @IanCa in #720
• Updated BaseInput dataframe input to convert to str by @VisLab in #721
• Updated BaseInput to always convert dfs to strings by @VisLab in #723
• Schema memory cache/inherited attribute support by @IanCa in #724
• add util functions for hed strings by @IanCa in #725
• Tag Schema Entries now know their children by @IanCa in #726
• Updates to schema loading and comparison by @IanCa in #727
• Cleanup pass of misc model/schema code by @IanCa in #728
• Corrrected HED column value summary error by @VisLab in #729
• Tweak format of errors and schema comparisons by @IanCa in #731
• Throw better error on deprecated xml files by @IanCa in #733
• Add HTML as a possible output format for printing errors by @IanCa in #734
• Add summary to top of schema comparisons by @IanCa in #735
• Minor code simplifications by @IanCa in #736
• Minor titling change to compare schemas by @VisLab in #737
• Started refactoring of event manager by @VisLab in #738
• Add support for validating deprecatedFrom. Improve other attribute validation by @IanCa in #740
• Handled nan conversion in df_to_hed by @VisLab in #741
• Allow dict as a parameter to DefinitionDict by @IanCa in #743
• Fix get_def_dict to return value if no sidecar by @IanCa in #744
• Add conversionFactor support. Improve default_unit handling and API by @IanCa in #746
• Update searching. by @IanCa in #747
• Tweak so it's easier to validate hed strings by @IanCa in #748
• Update HedString sort api. by @IanCa in #750
• Updated the event manager with context by @VisLab in #752
• Hopefully recovered from inadvertent rename of definition by @VisLab in #753
• Make HedGroup.replace work on non direct children by @IanCa in #754
• Add BaseInput.series_filtered by @IanCa in #755
• Minor corrections to the summaries by @VisLab in #758
• Add indented group printing from dungscout96 by @IanCa in #756
• Always copy definition contents in fully. by @IanCa in #759
• Add svg support for wordcloud by @IanCa in #760
• Updated the remodeler to allow separation by task by @VisLab in #762
• Corrected minor issues in various summaries by @VisLab in #763
• Minor corrections and testing by @VisLab in #766
• Create separate dispatcher for each task in remodeling comand line processing by @VisLab in #768
• Additional corrections to task separation in remodeling tools by @VisLab in #769
• Add a string based search first pass by @IanCa in #771
• Update basic_search to support words that must not appear by @IanCa in #774
• Make validation row numbers 1 based, and account for header by @IanCa in #775
• Corrected a format error in txt output of validation summary by @VisLab in #776
• Update to add 3.10/11 to tests by @IanCa in #777
• Add codespell/fix typos by @IanCa in #778
• Improve toctree in documentation by @IanCa in #779
• Updated the remodeling backup arguments by @VisLab in #781
• Merge develop in preparation for release by @VisLab in #782
• Add some attribute validator tests. Remove some unused code by @IanCa in #783
• Improve coverage/fix minor bugs in sidecar validator by @IanCa in #784
• Allow HED in sidecar lists again by @IanCa in #785
• Updated version in preparation for release by @VisLab in #786
• Further fixes/improvements to errors and error coverage by @IanCa in #787
• Merge develop with master in preparation for release by @VisLab in #788
• Raise error when loading schema with bad prefix by @IanCa in #789
• Update check for prefix/minor unit typos by @IanCa in #791

0.3.1

Overview of changes for tagged release 0.3.1

Released on PyPI on July 4, 2023

• Pinned the version of the pydantic and inflect libraries due to inflect conflict.
• Reorganized JSON output of remodeling summaries so that all of consistent form.
• Fixed summarize_hed_tags_op so that tags were correctly categorized for output.
• Minor refactoring to reduce code complexity.
• BaseInput and Sidecar now raise HedFileError if input could not be read.

What's changed (details)

• Updated changelog to release version by @VisLab in #703
• Updated changelog so all branches are synched by @VisLab in #704
• Clean up some of the overly complex functions some, add a few unit tests by @IanCa in #705
• First pass word cloud for tag summaries by @IanCa in #706
• Started working on allowing multiple iteration of remodeling by @VisLab in #707
• Merging minor changes to the remodeling tools by @VisLab in #708
• Made the get_details_dict method return a uniform dict with Specifics by @VisLab in #709
• Updated the HedTagCounts --- minor count bug by @VisLab in #711
• Second pass word cloud by @IanCa in #710
• Update setup.cfg to limit pydantic version by @IanCa in #712
• Updated factor_hed_type_op to not include condition variable separate… by @VisLab in #713
• Revert inflect changes as it's fixed by @IanCa in #716
• Updated exception handling for invalid tabular and json files by @VisLab in #717
• Minor bug fixes, improved exception handling, inflect library conflicts resolved. by @VisLab in #718
• Remodeling JSON summaries now have common output format. by @VisLab in #719

Full Changelog: 0.3.0...0.3.1

0.3.0

Overview of changes for tagged release 0.3.0

Released on PyPI on June 20, 2023

• Introduction of partnered schema.
• Improved error handling for schema validation.
• Support of Inset tags.
• Support of curly brace notation in sidecars.
• Expanded remodeling functionality.
• Refactoring of models to rely on DataFrames.
• Expanded unit tests in conjunction with specification tests.

What's changed (details)

• Add with-standard schema header attribute by @IanCa in #614
• Add first draft conda stuff by @IanCa in #615
• fix spec tests workflow/tests by @IanCa in #617
• Redo spec tests to use github modules. Upload results as an artifact. Add sidecar/events tests by @IanCa in #618
• Minor doc corrections in remodeling by @VisLab in #619
• Updated tabular input and sidecar to always take schema in tools by @VisLab in #621
• Started on an event manager by @VisLab in #622
• First pass refactor of models by @IanCa in #623
• Updated unit tests by @VisLab in #624
• Add some df tests. Update hed_assemble. Make the df utils also work on series. by @IanCa in #625
• Fixed some of the refactoring errors by @VisLab in #626
• Add more unit tests. better nan and empty column handling by @IanCa in #627
• Revert "Add more unit tests. better nan and empty column handling" by @VisLab in #628
• Update nan and empty column handling by @IanCa in #629
• Fixed more unit tests by @VisLab in #630
• Fix hed_string.expand_defs issue by @IanCa in #631
• Corrected some of the refactored unit tests by @VisLab in #633
• Updated bids tests by @VisLab in #634
• Add squre bracket in column validation for spreadsheets. Update erro… by @IanCa in #632
• Block HED from appearing in sidecars by @IanCa in #635
• Updated the search in analysis tools by @VisLab in #636
• Fix sorting for hed string context by @IanCa in #637
• Merging the refactored model code into develop by @VisLab in #638
• Update def handling/validation by @IanCa in #639
• Add flatten schema function by @IanCa in #640
• Preliminary implement of definition summary by @VisLab in #641
• Update dependabot to also update submodules by @IanCa in #642
• dont' sort by hed strings by @IanCa in #643
• Remove dupes from flatten schema by @IanCa in #644
• Add more tests, handle more error cases for def gathering by @IanCa in #645
• Always add an issues list to HedFileError, even when it doesn't have one by @IanCa in #646
• Updated docs on summary ops by @VisLab in #647
• Removed from temporary tests by @VisLab in #649
• Refactoring of model code. by @VisLab in #648
• Added alternate work directory location for remodeling by @VisLab in #650
• Improve def-gatherer. Very much improve spec tests/related validator… by @IanCa in #651
• Update CHARACTER_INVALID and STYLE_WARNING tests. by @IanCa in #652
• Bump paambaati/codeclimate-action from 3.2.0 to 4.0.0 by @dependabot in #653
• Update merged schemas to support rooted tags by @IanCa in #654
• Added --no-summaries and --no-update options to run_remodel by @VisLab in #655
• Added badges to the README by @VisLab in #656
• Updated the imports for df_util by @VisLab in #657
• Fixed more incomplete imports in models by @VisLab in #658
• Added df_util to models init by @VisLab in #659
• Add sidecar brace support by @IanCa in #660
• Make sure setting hed strings can handle empty by @IanCa in #661
• Add Inset tag validation, enable inset spec tests by @IanCa in #662
• Remove werkzeug requirement, replace generate_filename by @IanCa in #663
• Refactored summary to pass op by @VisLab in #664
• Add 8.2.0 xml directly by @IanCa in #665
• Switch baseinput/column mapper back to 0 based. by @IanCa in #666
• Fix to_excel function for new system by @IanCa in #667
• Remove output_assembled parameter. Update requirements.txt by @IanCa in #668
• Fix saving library schemas lacking in the withStandard attribute. by @IanCa in #669
• Rewrite column mapper, add more unit tests for it by @IanCa in #670
• Change rooted implementation to new system by @IanCa in #672
• Develop updated cache directory tests setup by @VisLab in #674
• Minor updates to fix cache directory tests by @VisLab in #675
• Merging develop in preparation for new release by @VisLab in #676
• Bump spec_tests/hed-specification from d7d174f to 33f48d2 by @dependabot in #677
• Save rooted attribute in merged schema. Rename shecma_prefix->Namespace by @IanCa in #678
• Sort the schema tag list when saved by @IanCa in #679
• Develop updated the partnered schema merged ordering by @VisLab in #680
• Silently ignore libraries with no hedxml folder by @IanCa in #681
• Develop updated hedxml handling by @VisLab in #683
• Updated the handling of the hedxml directory by @VisLab in #684
• Made timestamp on filename for remodeling summaries optional by @VisLab in #685
• Timestamps are now optional on filenames for remodeling summary files. by @VisLab in #686
• Fix bug in caching library schema by @IanCa in #687
• Trying an experiment with the apidocs by @VisLab in #688
• Trying out the raises by @VisLab in #689
• Added the raises directive by @VisLab in #690
• Minor tweaks to docs by @VisLab in #691
• Updates to documentation fix to getting schema version by @VisLab in #692
• Update schema attribute validation by @IanCa in #693
• Moved get_schema_versions to hed-web by @VisLab in #694
• Fix issue with df_util. Also make them not return the modified df/series by @IanCa in #695
• Update documentation in models folder by @IanCa in #696
• Made sure all remodeling ops copied the df first by @VisLab in #697
• Final updates before release by @VisLab in #698
• Added zenodo DOI to README by @VisLab in #699
• Updated README and got DOIs by @VisLab in #700
• Prepare for release 0.3.0 by @VisLab in #701
• Updated the changelog by @VisLab in #702

0.2.0

Overview of changes for tagged release 0.2.0

Actual release of 0.2.0 on PyPi February 14, 2023

• First release of the HED remodeling tools.
• Reorganization of branches to reflect stages of development.
• Updated schema cache with local copies.
• Improved schema validation and error messages.
• First pass at search and summarization.

What's changed (details)

• Add accessors for definitions by @IanCa in #507
• Develop added definitions to assemble return by @VisLab in #509
• Handle new schema versioning([prefix:][name_]version) by @IanCa in #510
• Updated the BIDS dataset to read in new schema format by @VisLab in #511
• Make load_schema_version take a list optionally by @IanCa in #512
• Refactor column mapper function. by @IanCa in #513
• Minor updates to documentation by @VisLab in #514
• Make it a fatal error for columns to be blank. Further cleanups by @IanCa in #515
• Fixed tests after environment problem. by @VisLab in #516
• Update default hed_cache location/tweak readme by @IanCa in #520
• Only return default behavior on column mapper if nothing was requeste… by @IanCa in #521
• Updated the variable summary mechanism to get condition variables by @VisLab in #523
• Update Input/Sidecar classes to take schema by @IanCa in #522
• Updates to documentation and requirements by @VisLab in #524
• Working on filters by @VisLab in #526
• Experimental changes to variable management for summaries by @VisLab in #527
• Updated file summary for non-entity file naming by @VisLab in #529
• Moved the util under tools by @VisLab in #530
• Develop moved the util directory under tools by @VisLab in #531
• Reorganized the directory structure of tools by @VisLab in #532
• Moved utils into tools by @VisLab in #533
• Merging the remodeling tools by @VisLab in #534
• Merged the remodeling into hedtools by @VisLab in #535
• Merging preliminary version of remodeling tools by @VisLab in #536
• Minor correction to tests by @VisLab in #537
• Added date to generate filename by @VisLab in #538
• Developed unit tests for cli for remodeling by @VisLab in #539
• CLI branch testing by @VisLab in #540
• Develop fixed the merge errors by @VisLab in #541
• Develop updated model by @VisLab in #542
• Develop updated the archiving in dispatcher by @VisLab in #543
• Develop updating gitignore by @VisLab in #544
• Updated remodeling terminology to use operation instead of command by @VisLab in #545
• Develop added get_formatted_versions by @VisLab in #548
• Updated tests for remodel summaries by @VisLab in #549
• Develop updated the tests-- added get_schema_versions by @VisLab in #550
• Corrected init file in hed/schema for get_schema_versions by @VisLab in #551
• Updated httpd.conf to fix numpy deployment warning by @VisLab in #552
• Incorporated rotating logs by @VisLab in #553
• Updated the remodeling unit tests. Moved PARAMS inside ops classes by @VisLab in #555
• Improved error messages on remodeling ops.. started work on summaries by @VisLab in #556
• Reworked remodeling summary tools to keep individual file statistics by @VisLab in #561
• Moved validation of parameters to BaseOp by @VisLab in #562
• Develop by @VisLab in #565
• Corrected some of the remodeling test datasets by @VisLab in #566
• Implemented the factor hed tags ops by @VisLab in #568
• Add line numbers to fatal wiki errors by @IanCa in #569
• Allow searching by either terms or tags by @IanCa in #570
• Added task argument to restore to address issue #567 by @VisLab in #571
• Add Wildcards to searching by @IanCa in #572
• First Pass Recursive docs by @IanCa in #573
• Remove hed group frozen by @IanCa in #574
• Develop updating python version for readthedocs to 3.8 by @VisLab in #575
• Fix sort function. Might need tweaking later. Minor test fixes. by @IanCa in #576
• Updated the summaries to dump individual files by @VisLab in #577
• Update requirements/docs requirements by @IanCa in #578
• Corrected doc ref error and added subfolders to summary saving by @VisLab in #579
• Added option for individual file saving in remodeling summaries by @VisLab in #580
• Add access token for github auth. Update urls for schemas by @IanCa in #581
• Corrected the summary generation for single files by @VisLab in #582
• Pass down token to coverage by @IanCa in #583
• Corrected the remap function by @VisLab in #584
• Updated the tests for remap by @VisLab in #585
• Split code coverage upload out of main build job. by @IanCa in #586
• Add a 'not in line' symbol to search by @IanCa in #587
• Fixed bug in run_direct and shortened summary file names by @VisLab in #590
• Add dependabot file by @IanCa in #588
• Add better load_schema_version error by @IanCa in #591
• Finished renaming the split_events op by @VisLab in #592
• Worked on remodeling api docs by @VisLab in #593
• Experimented with different format for class documentation by @VisLab in #594
• Experimenting with documentation formats by @VisLab in #595
• Updated docs and modified name of TagExpressionParser by @VisLab in #596
• Updated some of the remodeling docs by @VisLab in #597
• Updated the documentation format for remodeling again by @VisLab in #598
• Add some default schemas to schema folder. Cache from there first. by @IanCa in #599
• Update workflow to check for secrets before trying to publish coverages by @IanCa in #600
• Corrected the save_context structure for individual files by @VisLab in #601
• Updated the name of 3645 to correct for digit reversal by @VisLab in #602
• Corrected the counts in columns value summary by @VisLab in #603
• Minor updates to remodeling formats by @VisLab in #604
• Extensive revisions and updating of remodeling tools by @VisLab in #605
• Minor changes to the README by @VisLab in #606
• Minor update to the README by @VisLab in #607
• Make sure we try to get from the local cache before we hit the internet by @ian...

Initial release of hedtools on PyPi

This is the first release of HEDTOOLS that supports HED-3G features such as long and short tags and definitions.