Update Input/Sidecar classes to take schema #522
Merged
Conversation
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
…tructor. If present, identify tags in definitions, and also use as the default schema if one isn't passed later.
|
I am merging even though the tests fail. |
VisLab
added a commit
that referenced
this pull request
Sep 9, 2022
* 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>
VisLab
added a commit
that referenced
this pull request
Sep 12, 2022
* 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>
VisLab
added a commit
that referenced
this pull request
Sep 12, 2022
* 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>
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
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.
Also allow BaseInput to directly take a pandas dataframe.