catalystneuro/nwb-conversion-tools issues and pull requests

#609 - [pre-commit.ci] pre-commit autoupdate

Pull Request - State: closed - Opened by pre-commit-ci[bot] about 2 years ago

#608 - [pre-commit.ci] pre-commit autoupdate

Pull Request - State: closed - Opened by pre-commit-ci[bot] about 2 years ago

#607 - [pre-commit.ci] pre-commit autoupdate

Pull Request - State: closed - Opened by pre-commit-ci[bot] about 2 years ago

#605 - Add deep lab cut interface

Pull Request - State: closed - Opened by h-mayorquin over 2 years ago - 5 comments
Labels: enhancement, testing

#604 - [Testing]: Bypass git-annex install if unneeded

Pull Request - State: closed - Opened by CodyCBakerPhD over 2 years ago
Labels: bug, testing

#603 - Refactor write segmentation III (add summary images)

Pull Request - State: closed - Opened by h-mayorquin over 2 years ago - 2 comments
Labels: testing, refactoring

#602 - Refactor write segmentation II (use `add_devices`)

Pull Request - State: closed - Opened by h-mayorquin over 2 years ago - 1 comment
Labels: testing, refactoring

#601 - Refactor write segmentation I

Pull Request - State: closed - Opened by h-mayorquin over 2 years ago - 3 comments
Labels: testing, refactoring

#600 - [Do not merge] Test roi extractors changes

Pull Request - State: closed - Opened by h-mayorquin over 2 years ago
Labels: testing

#599 - testing CI from fork

Pull Request - State: closed - Opened by CodyCBakerPhD over 2 years ago - 3 comments

#598 - [Gallery] Pin SpikeInterface to dev branch

Pull Request - State: closed - Opened by CodyCBakerPhD over 2 years ago - 2 comments

#597 - Fix typos

Pull Request - State: closed - Opened by JuliaSprenger over 2 years ago - 7 comments

#596 - [neuralynx] Exploit metadata exposed from neo neuralynxrawio

Pull Request - State: closed - Opened by JuliaSprenger over 2 years ago - 6 comments

#595 - Prepare for v0.11.37 release

Pull Request - State: closed - Opened by CodyCBakerPhD over 2 years ago - 3 comments

#592 - Bump PyNWB version

Pull Request - State: closed - Opened by CodyCBakerPhD over 2 years ago - 2 comments

#591 - Bump lxml from 4.6.5 to 4.9.1

Pull Request - State: closed - Opened by dependabot[bot] over 2 years ago
Labels: dependencies

#590 - Discussion: transposing images in `roiextractors`

Issue - State: closed - Opened by weiglszonja over 2 years ago - 3 comments
Labels: discussion

#588 - [pre-commit.ci] pre-commit autoupdate

Pull Request - State: closed - Opened by pre-commit-ci[bot] over 2 years ago

#587 - Update spikeextractors version to latest

Pull Request - State: closed - Opened by h-mayorquin over 2 years ago
Labels: dependencies, warnings

#586 - Scan image interface to use proper roiextractor

Pull Request - State: closed - Opened by h-mayorquin over 2 years ago - 8 comments
Labels: enhancement

#585 - Add optical physiology interfaces to conversion gallery I

Pull Request - State: closed - Opened by h-mayorquin over 2 years ago - 2 comments
Labels: documentation

#583 - Pre-select channels to load in `CEDRecordingInterface`

Issue - State: open - Opened by h-mayorquin over 2 years ago - 2 comments

#582 - Add spikeinterface support and and gin test for `CEDRecordingInterface`

Pull Request - State: closed - Opened by h-mayorquin over 2 years ago - 3 comments
Labels: enhancement, testing

#581 - Gin test for scan image

Pull Request - State: closed - Opened by h-mayorquin over 2 years ago
Labels: testing

#580 - Refactor metadata extraction for `ScanImageImagingInterface`

Pull Request - State: closed - Opened by h-mayorquin over 2 years ago - 4 comments
Labels: warnings, testing, refactoring

#578 - Add spike interface support to neuralynx

Pull Request - State: closed - Opened by h-mayorquin over 2 years ago - 2 comments
Labels: enhancement, testing

#577 - Refactor neuralynx before adding support for spikeinterface

Pull Request - State: closed - Opened by h-mayorquin over 2 years ago - 1 comment
Labels: refactoring

#576 - Remove optional typing in neuroscope

Pull Request - State: closed - Opened by h-mayorquin over 2 years ago - 1 comment
Labels: low priority

#575 - Add ImagingExtractorDataChunkIterator

Pull Request - State: closed - Opened by weiglszonja over 2 years ago - 16 comments

#574 - Added timezone to session start time in add_units_table tests

Pull Request - State: closed - Opened by h-mayorquin over 2 years ago
Labels: warnings

#573 - Add spikeinterface support for `SpikeGadgetsRecordingInterface`

Pull Request - State: closed - Opened by h-mayorquin over 2 years ago - 2 comments
Labels: enhancement, testing

#572 - Add spikeinterface support for `NeuroscopeSortingInterface`

Pull Request - State: closed - Opened by h-mayorquin over 2 years ago - 1 comment
Labels: enhancement, testing

#571 - Remove optional typing in blackrock data interface

Pull Request - State: closed - Opened by h-mayorquin over 2 years ago

#570 - Remove optional types in pphy sorting data interface

Pull Request - State: closed - Opened by h-mayorquin over 2 years ago - 1 comment

#569 - Fix #566

Pull Request - State: closed - Opened by CodyCBakerPhD over 2 years ago - 1 comment
Labels: bug

#568 - Add test for `ScanImageImagingInterface` in `test_gin_ophys.py`.

Issue - State: closed - Opened by h-mayorquin over 2 years ago - 10 comments
Labels: coverage, testing

#567 - Add spikeinterface support to `PhySortingInterface`

Pull Request - State: closed - Opened by h-mayorquin over 2 years ago - 2 comments
Labels: enhancement, testing

#566 - The new command line interface with YAML introduced a bug.

Issue - State: closed - Opened by h-mayorquin over 2 years ago
Labels: bug

#565 - Update conversion gallery to new parameters

Pull Request - State: closed - Opened by h-mayorquin over 2 years ago - 1 comment
Labels: warnings, deprecation fix

#564 - Add spikeinterface support to `OpenEphysRecordingExtractorInterface`

Pull Request - State: closed - Opened by h-mayorquin over 2 years ago - 1 comment
Labels: enhancement, testing

#563 - Add spikeinterface support to `BlackrockRecordingExtractorInterface`

Pull Request - State: closed - Opened by h-mayorquin over 2 years ago - 1 comment
Labels: enhancement, testing

#562 - Added docstring and refactor metadata to `IntanRecordingInterface`

Pull Request - State: closed - Opened by h-mayorquin over 2 years ago - 3 comments
Labels: documentation, testing, refactoring

#561 - Add spikeinterface support to intan

Pull Request - State: closed - Opened by h-mayorquin over 2 years ago - 2 comments
Labels: enhancement, testing

#560 - Debug new ephy_testing_data

Pull Request - State: closed - Opened by CodyCBakerPhD over 2 years ago - 2 comments

#559 - Make imaging extrator interface an abstract class

Pull Request - State: closed - Opened by h-mayorquin over 2 years ago - 5 comments

#558 - Refactor intan data interface

Pull Request - State: closed - Opened by h-mayorquin over 2 years ago - 4 comments
Labels: code reduction

#557 - this class should be abstract

Issue - State: closed - Opened by bendichter over 2 years ago - 1 comment

#556 - `get_metadata_schema` in BaseImagingExtractorInterface needs a small refactor

Issue - State: closed - Opened by weiglszonja over 2 years ago - 9 comments

#555 - Synchronize with latest changes in roiextractors

Pull Request - State: closed - Opened by h-mayorquin over 2 years ago - 2 comments
Labels: dependencies, testing

#554 - Bump numpy from 1.21.0 to 1.22.0

Pull Request - State: closed - Opened by dependabot[bot] over 2 years ago - 4 comments
Labels: dependencies

#553 - added debugged Dockerfile

Pull Request - State: open - Opened by CodyCBakerPhD over 2 years ago - 1 comment
Labels: enhancement

#551 - [pre-commit.ci] pre-commit autoupdate

Pull Request - State: closed - Opened by pre-commit-ci[bot] over 2 years ago

#550 - YAML conversion specification CLI

Pull Request - State: closed - Opened by CodyCBakerPhD over 2 years ago - 9 comments
Labels: enhancement

#549 - Further ophys metadata fixes

Pull Request - State: closed - Opened by h-mayorquin over 2 years ago - 1 comment

#548 - Added stubbing for write imaging

Pull Request - State: closed - Opened by h-mayorquin over 2 years ago - 1 comment
Labels: enhancement

#547 - Correct order of writing in `add_two_photon_series`

Pull Request - State: closed - Opened by h-mayorquin over 2 years ago - 5 comments
Labels: high priority

#546 - Unit test `add_two_photon_series` in the `roiextractors.py` module

Pull Request - State: closed - Opened by h-mayorquin over 2 years ago - 1 comment
Labels: high priority, testing

#544 - [Bug] source data validation fails when using new numpy typing

Pull Request - State: closed - Opened by h-mayorquin over 2 years ago - 2 comments
Labels: testing, schema

#543 - Unit test `roiextractors.py` module `add device`

Pull Request - State: closed - Opened by h-mayorquin over 2 years ago - 2 comments
Labels: high priority, testing, refactoring

#542 - [Refactoring/Enhancement] Pad buffering in GenericDataChunkIterator

Pull Request - State: closed - Opened by CodyCBakerPhD over 2 years ago - 6 comments
Labels: enhancement

#541 - Added check to avoid adding roi response series with only 0 values

Pull Request - State: closed - Opened by h-mayorquin over 2 years ago - 1 comment
Labels: high priority

#540 - Refactor of add_two_photon_series II

Pull Request - State: closed - Opened by h-mayorquin over 2 years ago - 1 comment

#539 - `Device` and `ImagingPlane` should not be top properties of the `Ophys` schema.

Issue - State: closed - Opened by h-mayorquin over 2 years ago - 10 comments
Labels: discussion, organization, schema

#538 - Fix metadata combination of imaging and segmentation interfaces

Pull Request - State: closed - Opened by h-mayorquin over 2 years ago - 2 comments
Labels: bug, high priority, testing

#537 - [Bug] metadata of segmentation extractor and imaging extractor interfaces are incompatible

Issue - State: closed - Opened by h-mayorquin over 2 years ago - 2 comments
Labels: bug

#536 - Refactor of `add_two_photon_series`

Pull Request - State: closed - Opened by h-mayorquin over 2 years ago - 5 comments
Labels: refactoring

#535 - Update default parameters for ophys

Pull Request - State: closed - Opened by h-mayorquin over 2 years ago - 8 comments
Labels: high priority

#534 - Fix order of TwoPhotonSeries metadata update

Pull Request - State: closed - Opened by weiglszonja over 2 years ago - 2 comments

#533 - Add scanimage

Pull Request - State: closed - Opened by bendichter over 2 years ago - 2 comments

#532 - Small refactor of `test_gin_behavior` to pin new CI error

Pull Request - State: closed - Opened by h-mayorquin over 2 years ago - 6 comments
Labels: bug, testing

#531 - Add `.yaml` to accepted yaml extensions in `load_dict_from_file` function

Pull Request - State: closed - Opened by h-mayorquin over 2 years ago - 8 comments
Labels: enhancement, low priority

#530 - [Feature]: propagate roiextractor stubbing

Issue - State: closed - Opened by CodyCBakerPhD over 2 years ago
Labels: enhancement

#529 - [CI] swap to pre commit bot instead of actions

Pull Request - State: closed - Opened by CodyCBakerPhD over 2 years ago - 2 comments
Labels: testing

#528 - fixup for TestMovieInterface

Pull Request - State: closed - Opened by weiglszonja over 2 years ago

#527 - Add timestamps for MovieDataInterface

Pull Request - State: closed - Opened by weiglszonja over 2 years ago - 3 comments
Labels: enhancement, high priority

#526 - [Refactor] standardize LFP conversion kwargs

Pull Request - State: closed - Opened by CodyCBakerPhD over 2 years ago - 2 comments
Labels: code reduction, refactoring

#525 - [Refactor] standardize sorting interface kwargs

Pull Request - State: closed - Opened by CodyCBakerPhD over 2 years ago - 5 comments
Labels: code reduction, refactoring

#524 - [Refactor] Standardize conversion kwargs ophys

Pull Request - State: closed - Opened by CodyCBakerPhD over 2 years ago - 2 comments
Labels: code reduction, refactoring

#518 - [Feature]: create RoiextractorsDataChunkIterator

Issue - State: closed - Opened by CodyCBakerPhD over 2 years ago - 2 comments
Labels: enhancement

#508 - [Feature]: TIFF interface should take a list of files

Issue - State: open - Opened by CodyCBakerPhD over 2 years ago - 4 comments
Labels: enhancement

#507 - [Feature]: read metadata for intan

Issue - State: closed - Opened by bendichter over 2 years ago - 6 comments
Labels: enhancement

#499 - Bug in the movie data interface only appearing on CI

Issue - State: closed - Opened by h-mayorquin over 2 years ago - 2 comments
Labels: bug

#486 - Reduce the number of warnings in the CI

Issue - State: closed - Opened by h-mayorquin over 2 years ago - 2 comments
Labels: low priority, warnings

#479 - Stubbing conversions

Issue - State: closed - Opened by h-mayorquin over 2 years ago - 8 comments
Labels: question, discussion

#475 - [Feature]: add verbosity control to main converter

Pull Request - State: closed - Opened by CodyCBakerPhD over 2 years ago - 8 comments
Labels: enhancement

#461 - [Testing]: add NeuroscopeLFP

Pull Request - State: closed - Opened by CodyCBakerPhD over 2 years ago - 18 comments
Labels: bug, high priority, coverage

#450 - [DO NOT MERGE] refactor of `add_units` function

Pull Request - State: closed - Opened by h-mayorquin over 2 years ago - 9 comments
Labels: enhancement, medium priority

#449 - [Feature]: tests take a long time to run locally

Issue - State: open - Opened by bendichter over 2 years ago - 2 comments
Labels: enhancement, low priority

#443 - [Feature]: stream_id argument not propagating down into write_electrical_series

Issue - State: closed - Opened by Saksham20 over 2 years ago - 2 comments
Labels: enhancement, low priority

#442 - [Documentation]: Provide example conversion code in the docstring of each non-abstract DataInterface

Issue - State: closed - Opened by bendichter over 2 years ago - 2 comments
Labels: documentation, high priority

#414 - Interface for DLC data

Pull Request - State: closed - Opened by Saksham20 over 2 years ago - 11 comments
Labels: enhancement, medium priority

#362 - Icephys and Neo interfaces

Pull Request - State: closed - Opened by luiztauffer almost 3 years ago - 15 comments
Labels: enhancement, high priority

#289 - Add 'exclude' argument to get_schema_from_hdmf

Issue - State: closed - Opened by CodyCBakerPhD about 3 years ago - 2 comments
Labels: enhancement, low priority, code reduction

#287 - Convert many tests to unittest.TestCases

Issue - State: closed - Opened by CodyCBakerPhD about 3 years ago - 1 comment
Labels: low priority, coverage, code reduction

#277 - increase test coverage

Issue - State: closed - Opened by bendichter about 3 years ago - 9 comments
Labels: enhancement

#255 - Icephys and Neo interfaces

Pull Request - State: closed - Opened by luiztauffer about 3 years ago - 3 comments
Labels: documentation, enhancement, coverage

#110 - add dynamic_nwb_converter and test

Pull Request - State: closed - Opened by bendichter almost 4 years ago - 2 comments

#56 - Use click for command line interface

Issue - State: closed - Opened by alejoe91 over 4 years ago
Labels: enhancement, medium priority

#41 - Write SpikeExtractor for Bonsai

Issue - State: closed - Opened by nicolocin over 4 years ago - 1 comment
Labels: enhancement, low priority

#12 - GUI flexibly handling times in TimeSeries

Issue - State: closed - Opened by bendichter almost 5 years ago - 4 comments
Labels: enhancement

GitHub / catalystneuro/nwb-conversion-tools issues and pull requests