Merged the remodeling into hedtools #535
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* Add accessors for definitions * Remove attribute columns. Anything that was one now defaults to an Ignore column * Tested the bids-dataset * Updated the definitions returned on assemble * Make ignored columns marked as HedTags show up Handle new schema versioning([prefix:][name_]version) Only process HedTag columns when converting to short Improve error handling of schema prefixes * Rename library_prefix -> schema_prefix * Updated the BIDS dataset to read in new schema format * Make load_schema_version take a list optionally Allow library names to be passed by themselves to load_schema_version * Updated bids dataset * Refactor column mapper function. Add a test for a column named 'HED' issue. Add optional parameters to column mapper to allow blank columns, or not warn on missing columns * fix unit test. Always ignore an unnamed column 0. Later index handling still TBD * Minor updates to docs * Make it a fatal error for columns to be blank. Further cleanups * Make columns return a list again * Having trouble with the unit tests for BidsTabularInput * Fixed tests after environment problem * Update default hed_cache location/tweak readme (hed-standard#520) * Only return default behavior on column mapper if nothing was requeste… (hed-standard#521) * Only return default behavior on column mapper if nothing was requested. If nothing was found, just return nothing * Update column mapper test * Updated the variable summary mechanism to get condition variables (hed-standard#523) * Added get_definitions to BaseInput * Wrote tests for onset_manager creation * Started work on the condition manager * Partial implementation of condition_manager * Updated the condition variable manager -- still incomplete * Updated the variable manager before changes levels * Updated the variable summary function * Update Input/Sidecar classes to take schema (hed-standard#522) * Update baseinput/sidecar derived classes to take a hed schema in constructor. If present, identify tags in definitions, and also use as the default schema if one isn't passed later. * Fix bad filename in tests Co-authored-by: VisLab <1189050+VisLab@users.noreply.github.com> * Updates to documentation and requirements (hed-standard#524) * Added get_definitions to BaseInput * Wrote tests for onset_manager creation * Started work on the condition manager * Partial implementation of condition_manager * Updated the condition variable manager -- still incomplete * Updated the variable manager before changes levels * Updated the variable summary function * Updated requirements to use >= * Updated the docs -- still failing to generate all docs files * Restored also_gather_defs * Working on filters (hed-standard#526) * Added get_definitions to BaseInput * Wrote tests for onset_manager creation * Started work on the condition manager * Partial implementation of condition_manager * Updated the condition variable manager -- still incomplete * Updated the variable manager before changes levels * Updated the variable summary function * Updated requirements to use >= * Updated the docs -- still failing to generate all docs files * Restored also_gather_defs * Updated the HED factorization * Reorganized the variable manager and variable summary * Updated the api documentation * Updated the filter concept * Experimental changes to variable management for summaries (hed-standard#527) * Added get_definitions to BaseInput * Wrote tests for onset_manager creation * Started work on the condition manager * Partial implementation of condition_manager * Updated the condition variable manager -- still incomplete * Updated the variable manager before changes levels * Updated the variable summary function * Updated requirements to use >= * Updated the docs -- still failing to generate all docs files * Restored also_gather_defs * Updated the HED factorization * Reorganized the variable manager and variable summary * Updated the api documentation * Updated the filter concept * Cleaned up the unit tests for the variable manager * Updated the variable manager * Got the unittests to run again * Minor updates to assemlby * Updated file summary for non-entity file naming (hed-standard#529) * Added get_definitions to BaseInput * Wrote tests for onset_manager creation * Started work on the condition manager * Partial implementation of condition_manager * Updated the condition variable manager -- still incomplete * Updated the variable manager before changes levels * Updated the variable summary function * Updated requirements to use >= * Updated the docs -- still failing to generate all docs files * Restored also_gather_defs * Updated the HED factorization * Reorganized the variable manager and variable summary * Updated the api documentation * Updated the filter concept * Cleaned up the unit tests for the variable manager * Updated the variable manager * Got the unittests to run again * Minor updates to assemlby * Added exclude_dirs option to get_dir_dictionary * Updated Bids File Summary to not require entitites * Moved the util under tools (hed-standard#530) * Added get_definitions to BaseInput * Wrote tests for onset_manager creation * Started work on the condition manager * Partial implementation of condition_manager * Updated the condition variable manager -- still incomplete * Updated the variable manager before changes levels * Updated the variable summary function * Updated requirements to use >= * Updated the docs -- still failing to generate all docs files * Restored also_gather_defs * Updated the HED factorization * Reorganized the variable manager and variable summary * Updated the api documentation * Updated the filter concept * Cleaned up the unit tests for the variable manager * Updated the variable manager * Got the unittests to run again * Minor updates to assemlby * Added exclude_dirs option to get_dir_dictionary * Updated Bids File Summary to not require entitites * Updated the init for some utilities * Develop moved the util directory under tools (hed-standard#531) * Added get_definitions to BaseInput * Wrote tests for onset_manager creation * Started work on the condition manager * Partial implementation of condition_manager * Updated the condition variable manager -- still incomplete * Updated the variable manager before changes levels * Updated the variable summary function * Updated requirements to use >= * Updated the docs -- still failing to generate all docs files * Restored also_gather_defs * Updated the HED factorization * Reorganized the variable manager and variable summary * Updated the api documentation * Updated the filter concept * Cleaned up the unit tests for the variable manager * Updated the variable manager * Got the unittests to run again * Minor updates to assemlby * Added exclude_dirs option to get_dir_dictionary * Updated Bids File Summary to not require entitites * Updated the init for some utilities * Moved the util directory under tools * Reorganized the directory structure of tools (hed-standard#532) * Added get_definitions to BaseInput * Wrote tests for onset_manager creation * Started work on the condition manager * Partial implementation of condition_manager * Updated the condition variable manager -- still incomplete * Updated the variable manager before changes levels * Updated the variable summary function * Updated requirements to use >= * Updated the docs -- still failing to generate all docs files * Restored also_gather_defs * Updated the HED factorization * Reorganized the variable manager and variable summary * Updated the api documentation * Updated the filter concept * Cleaned up the unit tests for the variable manager * Updated the variable manager * Got the unittests to run again * Minor updates to assemlby * Added exclude_dirs option to get_dir_dictionary * Updated Bids File Summary to not require entitites * Updated the init for some utilities * Moved the util directory under tools * Moved utils into tools (hed-standard#533) * Added get_definitions to BaseInput * Wrote tests for onset_manager creation * Started work on the condition manager * Partial implementation of condition_manager * Updated the condition variable manager -- still incomplete * Updated the variable manager before changes levels * Updated the variable summary function * Updated requirements to use >= * Updated the docs -- still failing to generate all docs files * Restored also_gather_defs * Updated the HED factorization * Reorganized the variable manager and variable summary * Updated the api documentation * Updated the filter concept * Cleaned up the unit tests for the variable manager * Updated the variable manager * Got the unittests to run again * Minor updates to assemlby * Added exclude_dirs option to get_dir_dictionary * Updated Bids File Summary to not require entitites * Updated the init for some utilities * Moved the util directory under tools * Updated the summary output for design matrices * Revising the summary format * Minor doc updates plus elimination of BidsTabularySummary Co-authored-by: IanCa <ianrcallanan@gmail.com> Co-authored-by: IanCa <30812436+IanCa@users.noreply.github.com>
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* Add accessors for definitions * Remove attribute columns. Anything that was one now defaults to an Ignore column * Tested the bids-dataset * Updated the definitions returned on assemble * Make ignored columns marked as HedTags show up Handle new schema versioning([prefix:][name_]version) Only process HedTag columns when converting to short Improve error handling of schema prefixes * Rename library_prefix -> schema_prefix * Updated the BIDS dataset to read in new schema format * Make load_schema_version take a list optionally Allow library names to be passed by themselves to load_schema_version * Updated bids dataset * Refactor column mapper function. Add a test for a column named 'HED' issue. Add optional parameters to column mapper to allow blank columns, or not warn on missing columns * fix unit test. Always ignore an unnamed column 0. Later index handling still TBD * Minor updates to docs * Make it a fatal error for columns to be blank. Further cleanups * Make columns return a list again * Having trouble with the unit tests for BidsTabularInput * Fixed tests after environment problem * Update default hed_cache location/tweak readme (#520) * Only return default behavior on column mapper if nothing was requeste… (#521) * Only return default behavior on column mapper if nothing was requested. If nothing was found, just return nothing * Update column mapper test * Updated the variable summary mechanism to get condition variables (#523) * Added get_definitions to BaseInput * Wrote tests for onset_manager creation * Started work on the condition manager * Partial implementation of condition_manager * Updated the condition variable manager -- still incomplete * Updated the variable manager before changes levels * Updated the variable summary function * Update Input/Sidecar classes to take schema (#522) * Update baseinput/sidecar derived classes to take a hed schema in constructor. If present, identify tags in definitions, and also use as the default schema if one isn't passed later. * Fix bad filename in tests Co-authored-by: VisLab <1189050+VisLab@users.noreply.github.com> * Updates to documentation and requirements (#524) * Added get_definitions to BaseInput * Wrote tests for onset_manager creation * Started work on the condition manager * Partial implementation of condition_manager * Updated the condition variable manager -- still incomplete * Updated the variable manager before changes levels * Updated the variable summary function * Updated requirements to use >= * Updated the docs -- still failing to generate all docs files * Restored also_gather_defs * Working on filters (#526) * Added get_definitions to BaseInput * Wrote tests for onset_manager creation * Started work on the condition manager * Partial implementation of condition_manager * Updated the condition variable manager -- still incomplete * Updated the variable manager before changes levels * Updated the variable summary function * Updated requirements to use >= * Updated the docs -- still failing to generate all docs files * Restored also_gather_defs * Updated the HED factorization * Reorganized the variable manager and variable summary * Updated the api documentation * Updated the filter concept * Experimental changes to variable management for summaries (#527) * Added get_definitions to BaseInput * Wrote tests for onset_manager creation * Started work on the condition manager * Partial implementation of condition_manager * Updated the condition variable manager -- still incomplete * Updated the variable manager before changes levels * Updated the variable summary function * Updated requirements to use >= * Updated the docs -- still failing to generate all docs files * Restored also_gather_defs * Updated the HED factorization * Reorganized the variable manager and variable summary * Updated the api documentation * Updated the filter concept * Cleaned up the unit tests for the variable manager * Updated the variable manager * Got the unittests to run again * Minor updates to assemlby * Updated file summary for non-entity file naming (#529) * Added get_definitions to BaseInput * Wrote tests for onset_manager creation * Started work on the condition manager * Partial implementation of condition_manager * Updated the condition variable manager -- still incomplete * Updated the variable manager before changes levels * Updated the variable summary function * Updated requirements to use >= * Updated the docs -- still failing to generate all docs files * Restored also_gather_defs * Updated the HED factorization * Reorganized the variable manager and variable summary * Updated the api documentation * Updated the filter concept * Cleaned up the unit tests for the variable manager * Updated the variable manager * Got the unittests to run again * Minor updates to assemlby * Added exclude_dirs option to get_dir_dictionary * Updated Bids File Summary to not require entitites * Moved the util under tools (#530) * Added get_definitions to BaseInput * Wrote tests for onset_manager creation * Started work on the condition manager * Partial implementation of condition_manager * Updated the condition variable manager -- still incomplete * Updated the variable manager before changes levels * Updated the variable summary function * Updated requirements to use >= * Updated the docs -- still failing to generate all docs files * Restored also_gather_defs * Updated the HED factorization * Reorganized the variable manager and variable summary * Updated the api documentation * Updated the filter concept * Cleaned up the unit tests for the variable manager * Updated the variable manager * Got the unittests to run again * Minor updates to assemlby * Added exclude_dirs option to get_dir_dictionary * Updated Bids File Summary to not require entitites * Updated the init for some utilities * Develop moved the util directory under tools (#531) * Added get_definitions to BaseInput * Wrote tests for onset_manager creation * Started work on the condition manager * Partial implementation of condition_manager * Updated the condition variable manager -- still incomplete * Updated the variable manager before changes levels * Updated the variable summary function * Updated requirements to use >= * Updated the docs -- still failing to generate all docs files * Restored also_gather_defs * Updated the HED factorization * Reorganized the variable manager and variable summary * Updated the api documentation * Updated the filter concept * Cleaned up the unit tests for the variable manager * Updated the variable manager * Got the unittests to run again * Minor updates to assemlby * Added exclude_dirs option to get_dir_dictionary * Updated Bids File Summary to not require entitites * Updated the init for some utilities * Moved the util directory under tools * Reorganized the directory structure of tools (#532) * Added get_definitions to BaseInput * Wrote tests for onset_manager creation * Started work on the condition manager * Partial implementation of condition_manager * Updated the condition variable manager -- still incomplete * Updated the variable manager before changes levels * Updated the variable summary function * Updated requirements to use >= * Updated the docs -- still failing to generate all docs files * Restored also_gather_defs * Updated the HED factorization * Reorganized the variable manager and variable summary * Updated the api documentation * Updated the filter concept * Cleaned up the unit tests for the variable manager * Updated the variable manager * Got the unittests to run again * Minor updates to assemlby * Added exclude_dirs option to get_dir_dictionary * Updated Bids File Summary to not require entitites * Updated the init for some utilities * Moved the util directory under tools * Moved utils into tools (#533) * Added get_definitions to BaseInput * Wrote tests for onset_manager creation * Started work on the condition manager * Partial implementation of condition_manager * Updated the condition variable manager -- still incomplete * Updated the variable manager before changes levels * Updated the variable summary function * Updated requirements to use >= * Updated the docs -- still failing to generate all docs files * Restored also_gather_defs * Updated the HED factorization * Reorganized the variable manager and variable summary * Updated the api documentation * Updated the filter concept * Cleaned up the unit tests for the variable manager * Updated the variable manager * Got the unittests to run again * Minor updates to assemlby * Added exclude_dirs option to get_dir_dictionary * Updated Bids File Summary to not require entitites * Updated the init for some utilities * Moved the util directory under tools * Updated the summary output for design matrices * Revising the summary format * Minor doc updates plus elimination of BidsTabularySummary * Merged the remodeling into hedtools (#535) * Added get_definitions to BaseInput * Wrote tests for onset_manager creation * Started work on the condition manager * Partial implementation of condition_manager * Updated the condition variable manager -- still incomplete * Updated the variable manager before changes levels * Updated the variable summary function * Updated requirements to use >= * Updated the docs -- still failing to generate all docs files * Restored also_gather_defs * Updated the HED factorization * Reorganized the variable manager and variable summary * Updated the api documentation * Updated the filter concept * Cleaned up the unit tests for the variable manager * Updated the variable manager * Got the unittests to run again * Minor updates to assemlby * Added exclude_dirs option to get_dir_dictionary * Updated Bids File Summary to not require entitites * Updated the init for some utilities * Moved the util directory under tools * Updated the summary output for design matrices * Revising the summary format * Minor doc updates plus elimination of BidsTabularySummary * Merged the remodeling tools into the repo * Merging the remodeling tools (#534) * Add accessors for definitions * Remove attribute columns. Anything that was one now defaults to an Ignore column * Tested the bids-dataset * Updated the definitions returned on assemble * Make ignored columns marked as HedTags show up Handle new schema versioning([prefix:][name_]version) Only process HedTag columns when converting to short Improve error handling of schema prefixes * Rename library_prefix -> schema_prefix * Updated the BIDS dataset to read in new schema format * Make load_schema_version take a list optionally Allow library names to be passed by themselves to load_schema_version * Updated bids dataset * Refactor column mapper function. Add a test for a column named 'HED' issue. Add optional parameters to column mapper to allow blank columns, or not warn on missing columns * fix unit test. Always ignore an unnamed column 0. Later index handling still TBD * Minor updates to docs * Make it a fatal error for columns to be blank. Further cleanups * Make columns return a list again * Having trouble with the unit tests for BidsTabularInput * Fixed tests after environment problem * Update default hed_cache location/tweak readme (#520) * Only return default behavior on column mapper if nothing was requeste… (#521) * Only return default behavior on column mapper if nothing was requested. If nothing was found, just return nothing * Update column mapper test * Updated the variable summary mechanism to get condition variables (#523) * Added get_definitions to BaseInput * Wrote tests for onset_manager creation * Started work on the condition manager * Partial implementation of condition_manager * Updated the condition variable manager -- still incomplete * Updated the variable manager before changes levels * Updated the variable summary function * Update Input/Sidecar classes to take schema (#522) * Update baseinput/sidecar derived classes to take a hed schema in constructor. If present, identify tags in definitions, and also use as the default schema if one isn't passed later. * Fix bad filename in tests Co-authored-by: VisLab <1189050+VisLab@users.noreply.github.com> * Updates to documentation and requirements (#524) * Added get_definitions to BaseInput * Wrote tests for onset_manager creation * Started work on the condition manager * Partial implementation of condition_manager * Updated the condition variable manager -- still incomplete * Updated the variable manager before changes levels * Updated the variable summary function * Updated requirements to use >= * Updated the docs -- still failing to generate all docs files * Restored also_gather_defs * Working on filters (#526) * Added get_definitions to BaseInput * Wrote tests for onset_manager creation * Started work on the condition manager * Partial implementation of condition_manager * Updated the condition variable manager -- still incomplete * Updated the variable manager before changes levels * Updated the variable summary function * Updated requirements to use >= * Updated the docs -- still failing to generate all docs files * Restored also_gather_defs * Updated the HED factorization * Reorganized the variable manager and variable summary * Updated the api documentation * Updated the filter concept * Experimental changes to variable management for summaries (#527) * Added get_definitions to BaseInput * Wrote tests for onset_manager creation * Started work on the condition manager * Partial implementation of condition_manager * Updated the condition variable manager -- still incomplete * Updated the variable manager before changes levels * Updated the variable summary function * Updated requirements to use >= * Updated the docs -- still failing to generate all docs files * Restored also_gather_defs * Updated the HED factorization * Reorganized the variable manager and variable summary * Updated the api documentation * Updated the filter concept * Cleaned up the unit tests for the variable manager * Updated the variable manager * Got the unittests to run again * Minor updates to assemlby * Updated file summary for non-entity file naming (#529) * Added get_definitions to BaseInput * Wrote tests for onset_manager creation * Started work on the condition manager * Partial implementation of condition_manager * Updated the condition variable manager -- still incomplete * Updated the variable manager before changes levels * Updated the variable summary function * Updated requirements to use >= * Updated the docs -- still failing to generate all docs files * Restored also_gather_defs * Updated the HED factorization * Reorganized the variable manager and variable summary * Updated the api documentation * Updated the filter concept * Cleaned up the unit tests for the variable manager * Updated the variable manager * Got the unittests to run again * Minor updates to assemlby * Added exclude_dirs option to get_dir_dictionary * Updated Bids File Summary to not require entitites * Moved the util under tools (#530) * Added get_definitions to BaseInput * Wrote tests for onset_manager creation * Started work on the condition manager * Partial implementation of condition_manager * Updated the condition variable manager -- still incomplete * Updated the variable manager before changes levels * Updated the variable summary function * Updated requirements to use >= * Updated the docs -- still failing to generate all docs files * Restored also_gather_defs * Updated the HED factorization * Reorganized the variable manager and variable summary * Updated the api documentation * Updated the filter concept * Cleaned up the unit tests for the variable manager * Updated the variable manager * Got the unittests to run again * Minor updates to assemlby * Added exclude_dirs option to get_dir_dictionary * Updated Bids File Summary to not require entitites * Updated the init for some utilities * Develop moved the util directory under tools (#531) * Added get_definitions to BaseInput * Wrote tests for onset_manager creation * Started work on the condition manager * Partial implementation of condition_manager * Updated the condition variable manager -- still incomplete * Updated the variable manager before changes levels * Updated the variable summary function * Updated requirements to use >= * Updated the docs -- still failing to generate all docs files * Restored also_gather_defs * Updated the HED factorization * Reorganized the variable manager and variable summary * Updated the api documentation * Updated the filter concept * Cleaned up the unit tests for the variable manager * Updated the variable manager * Got the unittests to run again * Minor updates to assemlby * Added exclude_dirs option to get_dir_dictionary * Updated Bids File Summary to not require entitites * Updated the init for some utilities * Moved the util directory under tools * Reorganized the directory structure of tools (#532) * Added get_definitions to BaseInput * Wrote tests for onset_manager creation * Started work on the condition manager * Partial implementation of condition_manager * Updated the condition variable manager -- still incomplete * Updated the variable manager before changes levels * Updated the variable summary function * Updated requirements to use >= * Updated the docs -- still failing to generate all docs files * Restored also_gather_defs * Updated the HED factorization * Reorganized the variable manager and variable summary * Updated the api documentation * Updated the filter concept * Cleaned up the unit tests for the variable manager * Updated the variable manager * Got the unittests to run again * Minor updates to assemlby * Added exclude_dirs option to get_dir_dictionary * Updated Bids File Summary to not require entitites * Updated the init for some utilities * Moved the util directory under tools * Moved utils into tools (#533) * Added get_definitions to BaseInput * Wrote tests for onset_manager creation * Started work on the condition manager * Partial implementation of condition_manager * Updated the condition variable manager -- still incomplete * Updated the variable manager before changes levels * Updated the variable summary function * Updated requirements to use >= * Updated the docs -- still failing to generate all docs files * Restored also_gather_defs * Updated the HED factorization * Reorganized the variable manager and variable summary * Updated the api documentation * Updated the filter concept * Cleaned up the unit tests for the variable manager * Updated the variable manager * Got the unittests to run again * Minor updates to assemlby * Added exclude_dirs option to get_dir_dictionary * Updated Bids File Summary to not require entitites * Updated the init for some utilities * Moved the util directory under tools * Updated the summary output for design matrices * Revising the summary format * Minor doc updates plus elimination of BidsTabularySummary Co-authored-by: IanCa <ianrcallanan@gmail.com> Co-authored-by: IanCa <30812436+IanCa@users.noreply.github.com> * Minor change in the remodeling tools * Merged the master * Removed verbose flag from do-op Co-authored-by: IanCa <ianrcallanan@gmail.com> Co-authored-by: IanCa <30812436+IanCa@users.noreply.github.com> Co-authored-by: IanCa <ianrcallanan@gmail.com> Co-authored-by: IanCa <30812436+IanCa@users.noreply.github.com>
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