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Extensive revisions and updating of remodeling tools #605

Merged
merged 166 commits into from
Feb 11, 2023
Merged

Extensive revisions and updating of remodeling tools #605

merged 166 commits into from
Feb 11, 2023

Commits on Sep 12, 2022

  1. Minor correction to tests

    @VisLab
    VisLab committed Sep 12, 2022
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Commits on Sep 13, 2022

  1. Added datetime option on generate filenames

    @VisLab
    VisLab committed Sep 13, 2022
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  2. Fixed missing exclude_dirs in bids_file_group bug

    @VisLab
    VisLab committed Sep 13, 2022
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  3. Merge branch 'master' of https://github.com/hed-standard/hed-python i… 

    …nto develop
    @VisLab
    VisLab committed Sep 13, 2022
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Commits on Sep 14, 2022

  1. Corrected the hed type summary format

    @VisLab
    VisLab committed Sep 14, 2022
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  2. Added date to generate filename (#538) 

    * Minor correction to tests (#537)

* Added datetime option on generate filenames

* Fixed missing exclude_dirs in bids_file_group bug

* Corrected the hed type summary format
    @VisLab
    VisLab authored Sep 14, 2022
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Commits on Sep 18, 2022

  1. Started implementation of backup_manager

    @VisLab
    VisLab committed Sep 18, 2022
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  2. Fixed automerge issues

    @VisLab
    VisLab committed Sep 18, 2022
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Commits on Sep 22, 2022

  1. Updated tests for the CLI

    @VisLab
    VisLab committed Sep 22, 2022
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Commits on Sep 23, 2022

  1. Updated tests for remodel with hed

    @VisLab
    VisLab committed Sep 23, 2022
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  2. Replaced iteritems with items()

    @VisLab
    VisLab committed Sep 23, 2022
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  3. Updating the api docs - no success

    @VisLab
    VisLab committed Sep 23, 2022
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  4. Modified unit test

    @VisLab
    VisLab committed Sep 23, 2022
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Commits on Sep 24, 2022

  1. Test with windows path

    @VisLab
    VisLab committed Sep 24, 2022
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  2. Still testing get_path_components

    @VisLab
    VisLab committed Sep 24, 2022
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  3. Still working on the path normalization issue for windows paths on linux

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  4. Still not getting the current path correctly for path components

    @VisLab
    VisLab committed Sep 24, 2022
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  5. Updated the docs

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Commits on Sep 26, 2022

  1. Developed unit tests for cli for remodeling (#539) 

    * Minor correction to tests (#537)

* Added datetime option on generate filenames

* Fixed missing exclude_dirs in bids_file_group bug

* Corrected the hed type summary format

* Started implementation of backup_manager

* Updated tests for the CLI

* Updated tests for remodel with hed

* Replaced iteritems with items()

* Updating the api docs - no success

* Modified unit test

* Test with windows path

* Still testing get_path_components

* Still working on the path normalization issue for windows paths on linux

* Still not getting the current path correctly for path components

* Updated the docs
    @VisLab
    VisLab authored Sep 26, 2022
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  2. CLI branch testing (#540) 

    * Minor correction to tests (#537)

* Added datetime option on generate filenames

* Fixed missing exclude_dirs in bids_file_group bug

* Corrected the hed type summary format

* Started implementation of backup_manager

* Updated tests for the CLI

* Updated tests for remodel with hed

* Replaced iteritems with items()

* Updating the api docs - no success

* Modified unit test

* Test with windows path

* Still testing get_path_components

* Still working on the path normalization issue for windows paths on linux

* Still not getting the current path correctly for path components

* Updated the docs
    @VisLab
    VisLab authored Sep 26, 2022
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  3. generated docs

    @VisLab
    VisLab committed Sep 26, 2022
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Commits on Sep 27, 2022

  1. Updated rst

    @VisLab
    VisLab committed Sep 27, 2022
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  2. Correcting merge errors

    @VisLab
    VisLab committed Sep 27, 2022
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  3. Develop fixed the merge errors (#541) 

    * Minor correction to tests (#537)

* Added datetime option on generate filenames

* Fixed missing exclude_dirs in bids_file_group bug

* Corrected the hed type summary format

* Started implementation of backup_manager

* Updated tests for the CLI

* Updated tests for remodel with hed

* Replaced iteritems with items()

* Updating the api docs - no success

* Modified unit test

* Test with windows path

* Still testing get_path_components

* Still working on the path normalization issue for windows paths on linux

* Still not getting the current path correctly for path components

* Updated the docs

* generated docs

* Correcting merge errors
    @VisLab
    VisLab authored Sep 27, 2022
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  4. Merge branch 'develop' of https://github.com/hed-standard/hed-python … 

    …into develop
    @VisLab
    VisLab committed Sep 27, 2022
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  5. Made model required for remodel

    @VisLab
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  6. Develop updated model (#542) 

    * Minor correction to tests (#537)

* Added datetime option on generate filenames

* Fixed missing exclude_dirs in bids_file_group bug

* Corrected the hed type summary format

* Started implementation of backup_manager

* Updated tests for the CLI

* Updated tests for remodel with hed

* Replaced iteritems with items()

* Updating the api docs - no success

* Modified unit test

* Test with windows path

* Still testing get_path_components

* Still working on the path normalization issue for windows paths on linux

* Still not getting the current path correctly for path components

* Updated the docs

* generated docs

* Correcting merge errors

* Made model required for remodel
    @VisLab
    VisLab authored Sep 27, 2022
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  7. Merge branch 'develop' of https://github.com/hed-standard/hed-python … 

    …into develop
    @VisLab
    VisLab committed Sep 27, 2022
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Commits on Sep 28, 2022

  1. Corrected dispatcher archive save bug

    @VisLab
    VisLab committed Sep 28, 2022
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Commits on Sep 29, 2022

  1. Merge pull request #543 from VisLab/develop 

    Develop updated the archiving in dispatcher
    @VisLab
    VisLab authored Sep 29, 2022
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  2. Updated the gitignore to ignore summaries

    @VisLab
    VisLab committed Sep 29, 2022
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  3. Updated git ignore

    @VisLab
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  4. Merge branch 'develop' of https://github.com/hed-standard/hed-python … 

    …into develop
    @VisLab
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Commits on Sep 30, 2022

  1. Develop updating gitignore (#544) 

    * Updated the gitignore to ignore summaries

* Updated git ignore
    @VisLab
    VisLab authored Sep 30, 2022
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Commits on Oct 1, 2022

  1. Change remodeling commands to remodeling operations

    @VisLab
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  2. Merge branch 'develop' of https://github.com/hed-standard/hed-python … 

    …into develop
    @VisLab
    VisLab committed Oct 1, 2022
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  3. Merge pull request #545 from VisLab/develop 

    Updated remodeling terminology to use operation instead of command
    @VisLab
    VisLab authored Oct 1, 2022
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Commits on Oct 4, 2022

  1. Added get_formatted_version to schema for library handling

    @VisLab
    VisLab committed Oct 4, 2022
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  2. Merge branch 'develop' of https://github.com/hed-standard/hed-python … 

    …into develop
    @VisLab
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  3. Merge pull request #548 from VisLab/develop 

    Develop added get_formatted_versions
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Commits on Oct 7, 2022

  1. Updated the tests for the summary operations

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  2. Merge branch 'develop' of https://github.com/hed-standard/hed-python … 

    …into develop
    @VisLab
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Commits on Oct 8, 2022

  1. Merge pull request #549 from VisLab/develop 

    Updated tests for remodel summaries
    @VisLab
    VisLab authored Oct 8, 2022
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Commits on Oct 12, 2022

  1. Updated the testing added get_schema_versions for libraries

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  2. Merge branch 'develop' of https://github.com/hed-standard/hed-python … 

    …into develop
    @VisLab
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  3. Merge pull request #550 from VisLab/develop 

    Develop updated the tests-- added get_schema_versions
    @VisLab
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Commits on Oct 13, 2022

  1. Updated init for get_schema_versions

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  2. Merge branch 'develop' of https://github.com/hed-standard/hed-python … 

    …into develop
    @VisLab
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  3. Merge pull request #551 from VisLab/develop 

    Corrected init file in hed/schema for get_schema_versions
    @VisLab
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  4. Minor update to imports

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  5. Merge branch 'develop' of https://github.com/hed-standard/hed-python … 

    …into develop
    @VisLab
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  6. Merge pull request #552 from VisLab/develop 

    Updated httpd.conf to fix numpy deployment warning
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Commits on Oct 14, 2022

  1. Updates to testing -- commented out mains in tools

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  2. Merge branch 'develop' of https://github.com/hed-standard/hed-python … 

    …into develop
    @VisLab
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  3. Merge pull request #553 from VisLab/develop 

    Incorporated rotating logs and minor updates to tests.
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Commits on Oct 23, 2022

  1. Updated the remodeling unit tests. Moved PARAMS inside ops classes

    @VisLab
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  2. Cleaned up some lint errors

    @VisLab
    VisLab committed Oct 23, 2022
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  3. Corrected a unit test

    @VisLab
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  4. Minor correction to error messages that are different for different v… 

    …ersions of Python
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Commits on Oct 25, 2022

  1. Merge pull request #555 from VisLab/develop 

    Updated the remodeling unit tests. Moved PARAMS inside ops classes
    @VisLab
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Commits on Oct 26, 2022

  1. Working on the summary

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  2. Merge branch 'develop' of https://github.com/hed-standard/hed-python … 

    …into develop
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  3. Merge pull request #556 from VisLab/develop 

    Improved error messages on remodeling ops.. started work on summaries
    @VisLab
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Commits on Nov 24, 2022

  1. Refactored BaseContext

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  2. Merge branch 'develop' of https://github.com/hed-standard/hed-python … 

    …into develop
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Commits on Nov 29, 2022

  1. Partial update so that remodeling includes file counts

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Commits on Dec 1, 2022

  1. Before hed_type_count update

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Commits on Dec 2, 2022

  1. Updated the hed type summary to include file breakdown

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  2. Merge pull request #561 from VisLab/develop 

    Reworked remodeling summary tools to keep individual file statistics
    @VisLab
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  3. Refactored BaseOp with checking parameters

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  4. Merge branch 'develop' of https://github.com/hed-standard/hed-python … 

    …into develop
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  5. Merge pull request #562 from VisLab/develop 

    Moved validation of parameters to BaseOp
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Commits on Dec 19, 2022

  1. Updated the summarizations with individual summaries

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Commits on Dec 20, 2022

  1. Updated the remodeling summaries

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  2. Merge pull request #565 from VisLab/develop 

    Develop
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Commits on Dec 22, 2022

  1. Updated the remodeling

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  2. Merge branch 'develop' of https://github.com/hed-standard/hed-python … 

    …into develop
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  3. Merge pull request #566 from VisLab/develop 

    Corrected some of the remodeling test datasets
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Commits on Jan 2, 2023

  1. Implemented the factor hed tags ops

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  2. Merge pull request #568 from VisLab/develop 

    Implemented the factor hed tags ops
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  3. Add line numbers to fatal wiki errors

    @IanCa
    IanCa committed Jan 2, 2023
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  4. Add back accidentally deleted junk files

    @IanCa
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  5. Add test files

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  6. Merge pull request #569 from hed-standard/dev_add_wiki_line_numbers 

    Add line numbers to fatal wiki errors
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Commits on Jan 4, 2023

  1. Allow searching by either terms or tags

    @IanCa
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  2. Merge pull request #570 from hed-standard/dev_update_search 

    Allow searching by either terms or tags
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Commits on Jan 9, 2023

  1. Added task argument to restore to address issue #567

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  2. Merge pull request #571 from VisLab/develop 

    Added task argument to restore to address issue #567
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Commits on Jan 11, 2023

  1. Add Wildcards to searching

    @IanCa
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  2. Tweak search code to get rid of portion that wasn't compatible with 3… 

    ….7 and 3.8
    @IanCa
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  3. Switch to 3.8 as read the docs doesn't like 3.9 or something.

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  4. Merge pull request #1 from IanCa/develop 

    Merge develop into master test
    @IanCa
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  5. Add alternate api.rst

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  6. Merge pull request #2 from IanCa/develop 

    Add alternate api.rst
    @IanCa
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Commits on Jan 12, 2023

  1. Add support for double quotes in search expressions

    @IanCa
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  2. Merge pull request #572 from hed-standard/dev_update_search2 

    Add Wildcards to searching
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  3. Merge pull request #573 from IanCa/master 

    First Pass Recursive docs
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Commits on Jan 14, 2023

  1. Remove hed group frozen

    @IanCa
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Commits on Jan 17, 2023

  1. Merge pull request #574 from hed-standard/dev_ian 

    Remove hed group frozen
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    VisLab authored Jan 17, 2023
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Commits on Jan 23, 2023

  1. Updated the version of Python for readthedocs

    @VisLab
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  2. Deleted the generated

    @VisLab
    VisLab committed Jan 23, 2023
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  3. Merge branch 'develop' of https://github.com/hed-standard/hed-python … 

    …into develop
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  4. Just using api2.rst

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  5. Merge pull request #575 from VisLab/develop 

    Develop updating python version for readthedocs to 3.8
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    VisLab authored Jan 23, 2023
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Commits on Jan 25, 2023

  1. Fix sort function. Might need tweaking later. Minor test fixes.

    @IanCa
    IanCa committed Jan 25, 2023
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Commits on Jan 27, 2023

  1. Fix for some cases based on new unit tests

    @IanCa
    IanCa authored Jan 27, 2023
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  2. Fix sort with regards to other unit test

    @IanCa
    IanCa committed Jan 27, 2023
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  3. Merge pull request #576 from hed-standard/dev_fixes 

    Fix sort function.  Might need tweaking later.  Minor test fixes.
    @VisLab
    VisLab authored Jan 27, 2023
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  4. Updated the summaries to dump individual files

    @VisLab
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  5. Merge pull request #577 from VisLab/develop 

    Updated the summaries to dump individual files
    @VisLab
    VisLab authored Jan 27, 2023
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Commits on Jan 28, 2023

  1. Update requirements/docs requirements

    @IanCa
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  2. Merge pull request #578 from hed-standard/dev_update_reqs2 

    Update requirements/docs requirements
    @VisLab
    VisLab authored Jan 28, 2023
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  3. Corrected doc ref error and added subfolders to summary saving

    @VisLab
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  4. Merge pull request #579 from VisLab/develop 

    Corrected doc ref error and added subfolders to summary saving
    @VisLab
    VisLab authored Jan 28, 2023
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Commits on Jan 29, 2023

  1. Changed the include_individual and separate_files into one option

    @VisLab
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Commits on Jan 30, 2023

  1. Updated various docs

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  2. Merge pull request #580 from VisLab/develop 

    Added option for individual file saving in remodeling summaries
    @VisLab
    VisLab authored Jan 30, 2023
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  3. Add access token for github auth. Update urls for schemas

    @IanCa
    IanCa committed Jan 30, 2023
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  4. Rename env variable to avoid conflict

    @IanCa
    IanCa committed Jan 30, 2023
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  5. Merge pull request #581 from hed-standard/dev_update_github 

    Add access token for github auth. Update urls for schemas
    @VisLab
    VisLab authored Jan 30, 2023
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Commits on Jan 31, 2023

  1. Corrected the summary generation for single files

    @VisLab
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  2. Merge pull request #582 from VisLab/develop 

    Corrected the summary generation for single files
    @VisLab
    VisLab authored Jan 31, 2023
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  3. Pass down token to coverage

    @IanCa
    IanCa committed Jan 31, 2023
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  4. Merge pull request #583 from hed-standard/dev_update_github3 

    Pass down token to coverage
    @VisLab
    VisLab authored Jan 31, 2023
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  5. Corrected the remap function

    @VisLab
    VisLab committed Jan 31, 2023
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  6. Merge pull request #584 from VisLab/develop 

    Corrected the remap function
    @VisLab
    VisLab authored Jan 31, 2023
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  7. Updated the tests for remap

    @VisLab
    VisLab committed Jan 31, 2023
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  8. Merge pull request #585 from VisLab/develop 

    Updated the tests for remap
    @VisLab
    VisLab authored Jan 31, 2023
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Commits on Feb 1, 2023

  1. Split code coverage upload out of main build job. Cache the python en… 

    …v for a minor speedup.
    @IanCa
    IanCa committed Feb 1, 2023
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  2. Merge pull request #586 from hed-standard/dev_update_workflow 

    Split code coverage upload out of main build job.
    @VisLab
    VisLab authored Feb 1, 2023
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  3. Add a 'not in line' symbol to search

    @IanCa
    IanCa committed Feb 1, 2023
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Commits on Feb 2, 2023

  1. Merge pull request #587 from hed-standard/dev_update_search 

    Add a 'not in line' symbol to search
    @VisLab
    VisLab authored Feb 2, 2023
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Commits on Feb 3, 2023

  1. Add dependabot file 

    Check pip/github action dependencies.  Note: I don't believe this will be active until pulled to master branch.
    @IanCa
    IanCa authored Feb 3, 2023
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  2. Fixed bug in run_direct and shortened summary file names

    @VisLab
    VisLab committed Feb 3, 2023
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  3. Corrected the HedFileError format in the remodeller

    @VisLab
    VisLab committed Feb 3, 2023
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  4. Merge pull request #590 from VisLab/develop 

    Fixed bug in run_direct and shortened summary file names
    @VisLab
    VisLab authored Feb 3, 2023
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Commits on Feb 4, 2023

  1. Add better load_schema_version error

    @IanCa
    IanCa committed Feb 4, 2023
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  2. Merge pull request #588 from hed-standard/dev_add_dependabot 

    Add dependabot file
    @VisLab
    VisLab authored Feb 4, 2023
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  3. Merge pull request #591 from IanCa/develop 

    Add better load_schema_version error
    @VisLab
    VisLab authored Feb 4, 2023
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  4. Finished renaming the split_events op

    @VisLab
    VisLab committed Feb 4, 2023
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  5. Merge pull request #592 from VisLab/develop 

    Finished renaming the split_events op
    @VisLab
    VisLab authored Feb 4, 2023
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  6. Worked on remodeling api docs

    @VisLab
    VisLab committed Feb 4, 2023
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  7. Merge pull request #593 from VisLab/develop 

    Worked on remodeling api docs
    @VisLab
    VisLab authored Feb 4, 2023
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  8. Experimented with different format for class documentation

    @VisLab
    VisLab committed Feb 4, 2023
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  9. Merge pull request #594 from VisLab/develop 

    Experimented with different format for class documentation
    @VisLab
    VisLab authored Feb 4, 2023
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Commits on Feb 5, 2023

  1. Experimenting with documentation formats

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    VisLab committed Feb 5, 2023
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  2. Merge pull request #595 from VisLab/develop 

    Experimenting with documentation formats
    @VisLab
    VisLab authored Feb 5, 2023
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  3. Updated docs and modified name of TagExpressionParser

    @VisLab
    VisLab committed Feb 5, 2023
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  4. Merge pull request #596 from VisLab/develop 

    Updated docs and modified name of TagExpressionParser
    @VisLab
    VisLab authored Feb 5, 2023
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Commits on Feb 6, 2023

  1. Updated some of the remodeling docs

    @VisLab
    VisLab committed Feb 6, 2023
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  2. Merge pull request #597 from VisLab/develop 

    Updated some of the remodeling docs
    @VisLab
    VisLab authored Feb 6, 2023
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  3. Updated the documentation format for remodeling again

    @VisLab
    VisLab committed Feb 6, 2023
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  4. Merge pull request #598 from VisLab/develop 

    Updated the documentation format for remodeling again
    @VisLab
    VisLab authored Feb 6, 2023
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Commits on Feb 7, 2023

  1. Add some default schemas to schema folder. Cache from there first.

    @IanCa
    IanCa committed Feb 7, 2023
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  2. Merge pull request #599 from IanCa/dev_add_schema_data 

    Add some default schemas to schema folder.  Cache from there first.
    @VisLab
    VisLab authored Feb 7, 2023
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Commits on Feb 8, 2023

  1. Update workflow to check for secrets before trying to publish coverages

    @IanCa
    IanCa committed Feb 8, 2023
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  2. Merge pull request #600 from hed-standard/dev_check_for_id 

    Update workflow to check for secrets before trying to publish coverages
    @VisLab
    VisLab authored Feb 8, 2023
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Commits on Feb 9, 2023

  1. Corrected the save_context structure for individual files

    @VisLab
    VisLab committed Feb 9, 2023
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  2. Merge pull request #601 from VisLab/develop 

    Corrected the save_context structure for individual files
    @VisLab
    VisLab authored Feb 9, 2023
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  3. Updated the name of 3645 to correct for digit reversal

    @VisLab
    VisLab committed Feb 9, 2023
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Commits on Feb 10, 2023

  1. Updated summarize hed tags to include overall event counts

    @VisLab
    VisLab committed Feb 10, 2023
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  2. Merge pull request #602 from VisLab/develop 

    Updated the name of 3645 to correct for digit reversal
    @VisLab
    VisLab authored Feb 10, 2023
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  3. Corrected the counts in columns value summary

    @VisLab
    VisLab committed Feb 10, 2023
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  4. Merge pull request #603 from VisLab/develop 

    Corrected the counts in columns value summary
    @VisLab
    VisLab authored Feb 10, 2023
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Commits on Feb 11, 2023

  1. Minor updates to remodeling formats

    @VisLab
    VisLab committed Feb 11, 2023
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  2. Merge pull request #604 from VisLab/develop 

    Minor updates to remodeling formats
    @VisLab
    VisLab authored Feb 11, 2023
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