Ecosyste.ms: Issues

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GitHub / hdmf-dev/hdmf issues and pull requests

#817 - [Bug]: AttributeError: 'NWBHDF5IO' object has no attribute '_HDF5IO__open_links'

Issue - State: closed - Opened by yarikoptic almost 2 years ago - 22 comments
Labels: category: bug, priority: critical

#816 - Update release.md

Pull Request - State: closed - Opened by mavaylon1 almost 2 years ago - 1 comment

#815 - Release 3.5.0

Pull Request - State: closed - Opened by mavaylon1 almost 2 years ago - 3 comments

#814 - Create project_action.yml

Pull Request - State: closed - Opened by mavaylon1 almost 2 years ago - 1 comment

#813 - Clarify documentation of DataChunkIterator

Pull Request - State: closed - Opened by oruebel almost 2 years ago - 1 comment
Labels: topic: docs, priority: low

#812 - Allow custom message as part of TestCase.assert... functions

Pull Request - State: closed - Opened by oruebel almost 2 years ago - 1 comment
Labels: category: enhancement, priority: low, topic: testing

#811 - Make sure that the file is closed on deletion

Pull Request - State: closed - Opened by oruebel almost 2 years ago - 4 comments
Labels: category: enhancement, priority: medium

#810 - [Bug]: Replace requires.io link - service has shut down

Issue - State: closed - Opened by rly almost 2 years ago

#809 - Add hdmf-zarr tests to HDMF test suite

Issue - State: open - Opened by oruebel over 2 years ago - 2 comments
Labels: priority: medium, topic: testing

#808 - Fix exporting new soft links

Pull Request - State: closed - Opened by rly almost 2 years ago - 1 comment

#806 - fix generic DCI tutorial

Pull Request - State: closed - Opened by bendichter almost 2 years ago - 1 comment

#805 - External Resources Tools and Validation

Pull Request - State: closed - Opened by mavaylon1 almost 2 years ago - 1 comment
Labels: category: enhancement, priority: high

#804 - Bump setuptools from 65.4.1 to 65.5.1

Pull Request - State: closed - Opened by dependabot[bot] almost 2 years ago - 1 comment
Labels: compatability: dependencies

#803 - Add Python 3.11 support

Pull Request - State: closed - Opened by rly almost 2 years ago - 7 comments
Labels: category: enhancement, priority: medium

#802 - Fix incompatibility with tox 4

Pull Request - State: closed - Opened by rly almost 2 years ago - 1 comment

#801 - [Bug]: Python 3.10 optional, upgraded, and prerelease tests failing

Issue - State: closed - Opened by rly almost 2 years ago
Labels: category: bug, priority: high

#800 - Set fixed values and column attrs on autogen class

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

#799 - Updated ExternalResources

Pull Request - State: closed - Opened by mavaylon1 almost 2 years ago - 7 comments

#798 - [Bug]: Handling of attributes with fixed value in get_class

Issue - State: closed - Opened by oruebel almost 2 years ago - 1 comment
Labels: category: bug, priority: high

#797 - [Feature]: checking data types of arrays on construction

Issue - State: open - Opened by bendichter almost 2 years ago - 5 comments
Labels: category: enhancement, priority: medium

#796 - Allow basic recursion in get_class

Pull Request - State: open - Opened by rly almost 2 years ago

#795 - [Feature]: Look into HDF5 SWMR support

Issue - State: open - Opened by rly about 2 years ago - 3 comments
Labels: category: proposal, priority: low

#794 - [Bug]: `get_class` can't work recursively

Issue - State: open - Opened by bendichter about 2 years ago - 4 comments
Labels: category: bug, priority: low, topic: extension

#793 - JSON IO

Pull Request - State: closed - Opened by mavaylon1 about 2 years ago - 2 comments

#792 - [Bug]: `default_value` for datasets is not supported

Issue - State: closed - Opened by rly about 2 years ago - 2 comments
Labels: category: enhancement, priority: low, topic: extension

#790 - Er bug

Pull Request - State: closed - Opened by mavaylon1 about 2 years ago - 1 comment

#789 - in validation, add check for if a varlen datasets is empty

Pull Request - State: closed - Opened by bendichter about 2 years ago - 4 comments
Labels: category: bug, topic: validator

#788 - [Bug]: validation fails if file contains an empty dataset

Issue - State: closed - Opened by bendichter about 2 years ago - 1 comment
Labels: category: bug, topic: validator, priority: high

#787 - better shape error message

Pull Request - State: open - Opened by bendichter about 2 years ago - 2 comments

#776 - create more links to API, and fix a few typos

Pull Request - State: closed - Opened by bendichter about 2 years ago - 1 comment
Labels: topic: docs

#775 - [Bug]: Validation returns "IndexError: Index (0) out of range for empty dimension" for dataset with empty shape

Issue - State: open - Opened by rly about 2 years ago
Labels: category: bug, topic: validator, priority: low

#774 - [Feature]: Publish sources to Zenodo on release

Issue - State: closed - Opened by rly about 2 years ago - 2 comments
Labels: category: enhancement, help wanted: deep dive, priority: low

#766 - Prepare deprecations for HDMF 4.0

Issue - State: open - Opened by rly about 2 years ago - 1 comment
Labels: category: enhancement, priority: low, compatibility: breaking change

#760 - Miscellaneous minor infrastructure fixes

Pull Request - State: closed - Opened by rly about 2 years ago - 1 comment

#756 - [Bug]: Creating file that links to existing indexed column data is slow

Issue - State: open - Opened by rly over 2 years ago
Labels: category: bug, priority: medium

#755 - EnumData gives a warning

Issue - State: closed - Opened by cmungall over 2 years ago - 1 comment
Labels: priority: low

#745 - [Feature]: add more traceback or module/package info for FutureWarning

Issue - State: closed - Opened by yarikoptic over 2 years ago - 1 comment
Labels: category: enhancement, priority: low

#737 - [Feature]: Raise error when creating certain dataset specs without data type inc/def

Issue - State: open - Opened by rly over 2 years ago
Labels: category: enhancement, priority: low, topic: extension

#729 - [Feature]: Add official optional support for additional HDF5 filters

Issue - State: open - Opened by rly over 2 years ago - 8 comments
Labels: category: enhancement, priority: low

#719 - Added functionality to load plugins for HDMF

Pull Request - State: closed - Opened by oruebel over 2 years ago - 4 comments
Labels: category: proposal, priority: low

#716 - [Bug]: Cannot export cached namespace if loaded from file

Issue - State: closed - Opened by rly over 2 years ago

#706 - AbstractContainer & Container _fields_ / building new objects tutorial

Pull Request - State: closed - Opened by mavaylon1 over 2 years ago - 1 comment

#704 - Fix pre-release CI

Issue - State: closed - Opened by rly over 2 years ago - 1 comment
Labels: category: bug, priority: low

#702 - Raise errors on warnings in CI

Issue - State: open - Opened by rly over 2 years ago - 1 comment
Labels: category: enhancement, priority: low

#698 - Add more complete documentation for Container.reset_parent

Issue - State: open - Opened by rly almost 3 years ago - 1 comment
Labels: category: enhancement, topic: docs, priority: low

#691 - Cannot move containers or add/copy existing containers to another file

Issue - State: open - Opened by rly almost 3 years ago - 1 comment
Labels: category: proposal, priority: low

#688 - Adding MeasurementData Class

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

#686 - Er ontology

Pull Request - State: closed - Opened by mavaylon1 almost 3 years ago - 2 comments

#685 - Replace CircleCI scheduled workflows with scheduled pipelines

Issue - State: closed - Opened by rly almost 3 years ago - 1 comment
Labels: category: bug, priority: low, topic: testing

#680 - Include `data_types` key in cached schema

Issue - State: open - Opened by rly about 3 years ago - 1 comment
Labels: category: bug, priority: medium, topic: extension

#677 - Modify dset/attr builders based on sidecar JSON

Pull Request - State: open - Opened by rly about 3 years ago - 31 comments

#676 - Support modifications of a read file in an external overlay

Issue - State: open - Opened by rly about 3 years ago - 2 comments
Labels: category: proposal, priority: medium

#670 - Add Edge Case Test to ER

Pull Request - State: closed - Opened by mavaylon1 about 3 years ago
Labels: category: enhancement, priority: medium

#656 - Improve access of DynamicTable and DynamicTableRegion subset IDs

Issue - State: open - Opened by rly over 3 years ago - 1 comment
Labels: category: enhancement, priority: low

#655 - Cannot write DynamicTable with compound data type column

Issue - State: open - Opened by rly over 3 years ago - 1 comment
Labels: category: bug, priority: low

#654 - Setup sphinx.ext.autosummary for the API-docs

Pull Request - State: open - Opened by oruebel over 3 years ago - 5 comments

#653 - Use sphinx.ext.autosummary to create better index for API docs

Issue - State: open - Opened by oruebel over 3 years ago - 3 comments
Labels: category: enhancement, help wanted: good first issue, topic: docs, priority: low

#649 - Support multiple DynamicTableRegion when converting to a hierarchical dataframe

Issue - State: open - Opened by oruebel over 3 years ago - 3 comments
Labels: category: enhancement, help wanted: good first issue, priority: low

#648 - Add tutorial for DynamicTableRegion and Linked Tables

Issue - State: closed - Opened by oruebel over 3 years ago - 1 comment
Labels: category: enhancement, help wanted: good first issue, topic: docs

#647 - Include default value in docval docstrings

Issue - State: open - Opened by oruebel over 3 years ago
Labels: category: enhancement, help wanted: good first issue, topic: docs, priority: low

#644 - Enhance support for modular storage of large datasets

Issue - State: closed - Opened by oruebel over 3 years ago - 2 comments
Labels: category: enhancement

#637 - With h5py 3, dsets with compound dtype that includes str returned as bytes

Issue - State: open - Opened by rly over 3 years ago - 1 comment
Labels: category: bug, priority: low

#635 - Support append of ExternalResources

Issue - State: closed - Opened by oruebel over 3 years ago - 4 comments
Labels: category: enhancement

#634 - Raise warning if a sub-group/dataset with required name is missing on write

Issue - State: closed - Opened by rly over 3 years ago - 1 comment
Labels: category: enhancement, priority: wontfix

#632 - Support validation of dataset references

Issue - State: open - Opened by dsleiter over 3 years ago - 2 comments
Labels: category: enhancement, topic: validator

#632 - Support validation of dataset references

Issue - State: open - Opened by dsleiter over 3 years ago - 1 comment
Labels: category: enhancement, topic: validator

#628 - Create short tutorial on using HDF5 drivers, e.g., ros3

Issue - State: open - Opened by oruebel over 3 years ago
Labels: category: enhancement, topic: docs

#628 - Create short tutorial on using HDF5 drivers, e.g., ros3

Issue - State: open - Opened by oruebel over 3 years ago
Labels: category: enhancement, topic: docs

#624 - Create validation warnings on extra fields

Issue - State: open - Opened by dsleiter over 3 years ago
Labels: category: enhancement, topic: validator

#624 - Create validation warnings on extra fields

Issue - State: open - Opened by dsleiter over 3 years ago
Labels: category: enhancement, topic: validator

#623 - DataChunkIterator clarify iteration behavior

Issue - State: closed - Opened by oruebel over 3 years ago
Labels: topic: docs

#616 - duecredit results in internal error

Issue - State: closed - Opened by rly over 3 years ago - 3 comments
Labels: category: bug

#616 - duecredit results in internal error

Issue - State: closed - Opened by rly over 3 years ago - 3 comments
Labels: category: bug

#610 - Make validation errors immutable

Issue - State: open - Opened by dsleiter over 3 years ago
Labels: category: enhancement, topic: validator

#610 - Make validation errors immutable

Issue - State: open - Opened by dsleiter over 3 years ago
Labels: category: enhancement, topic: validator

#608 - Account for all loaded namespaces during validation

Issue - State: open - Opened by rly over 3 years ago
Labels: category: bug, topic: validator

#604 - Cannot create multi-indexed column using __init__ or from_dataframe

Issue - State: open - Opened by rly over 3 years ago
Labels: category: bug, priority: low

#597 - Exporting from file with cached extension does not write extension

Issue - State: closed - Opened by rly over 3 years ago - 2 comments
Labels: category: bug

#597 - Exporting from file with cached extension does not write extension

Issue - State: closed - Opened by rly over 3 years ago - 2 comments
Labels: category: bug

#595 - Cannot access all EnumData contents on read

Issue - State: open - Opened by rly over 3 years ago
Labels: category: bug, priority: medium

#594 - Cannot read DynamicTable with EnumData with only one row

Issue - State: open - Opened by rly over 3 years ago
Labels: category: bug, priority: medium

#592 - Test all extensions in NDX Catalog in CI

Issue - State: open - Opened by rly over 3 years ago - 1 comment
Labels: category: proposal, priority: medium, topic: testing

#582 - Mismatched fixed name and included name causes errors on read/validate

Issue - State: closed - Opened by rly over 3 years ago - 6 comments
Labels: category: bug

#559 - Error when namespace includes same source extension twice

Issue - State: open - Opened by rly over 3 years ago
Labels: category: bug, priority: low, topic: extension

#559 - Error when namespace includes same source extension twice

Issue - State: open - Opened by rly over 3 years ago
Labels: category: bug, priority: low, topic: extension

#554 - Autogmatic class generation for AlignedDynamicTable fails

Issue - State: open - Opened by oruebel over 3 years ago
Labels: category: bug, priority: low, topic: extension

#554 - Autogmatic class generation for AlignedDynamicTable fails

Issue - State: open - Opened by oruebel over 3 years ago
Labels: category: bug, priority: low, topic: extension

#546 - Save schema SHA

Pull Request - State: open - Opened by ajtritt over 3 years ago - 1 comment

#539 - External resources doc

Pull Request - State: closed - Opened by mavaylon1 over 3 years ago - 2 comments

#538 - Decorator to mark experimental features

Issue - State: open - Opened by oruebel over 3 years ago - 3 comments
Labels: category: enhancement, topic: docs, priority: low

#538 - Decorator to mark experimental features

Issue - State: open - Opened by oruebel over 3 years ago - 3 comments
Labels: category: enhancement, topic: docs, priority: low

#534 - [WIP] Extract class generation code out of TypeMap

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

#531 - Disallow or explicitly allow spec quantity to be specified with a numeric string

Issue - State: open - Opened by dsleiter over 3 years ago
Labels: category: enhancement, priority: low

#530 - Matching of GroupSpec children against builders does not consider max quantity

Issue - State: open - Opened by dsleiter over 3 years ago
Labels: category: bug, topic: validator

#530 - Matching of GroupSpec children against builders does not consider max quantity

Issue - State: open - Opened by dsleiter over 3 years ago
Labels: category: bug, topic: validator

#529 - Difference in validation errors depending on order of GroupBuilder children

Issue - State: open - Opened by dsleiter over 3 years ago
Labels: category: bug, topic: validator

#529 - Difference in validation errors depending on order of GroupBuilder children

Issue - State: open - Opened by dsleiter over 3 years ago
Labels: category: bug, topic: validator