hdmf-dev/hdmf issues and pull requests

#948 - [Bug]: Inheriting from subclass of DynamicTable triggers attribute error

Issue - State: closed - Opened by dysprague over 1 year ago - 24 comments

#947 - Release 3.9.0

Pull Request - State: closed - Opened by mavaylon1 over 1 year ago - 2 comments

#946 - add RemFile as a supported format

Pull Request - State: closed - Opened by bendichter over 1 year ago - 1 comment

#945 - [Feature]: preview of docs changes in PRs

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

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

Pull Request - State: closed - Opened by pre-commit-ci[bot] over 1 year ago - 1 comment

#943 - Fix termset reqs, rename deps tag

Pull Request - State: closed - Opened by rly over 1 year ago - 1 comment

#942 - [Bug]: Refactor some changes regarding TermSet

Issue - State: closed - Opened by rly over 1 year ago

#941 - Update HERD for user defined zip file

Pull Request - State: closed - Opened by mavaylon1 over 1 year ago - 3 comments

#940 - [Bug]: Dev branches import failure from daily CI

Issue - State: closed - Opened by CodyCBakerPhD over 1 year ago - 3 comments

#939 - improve links to DynamicTable API docs

Pull Request - State: closed - Opened by bendichter over 1 year ago - 3 comments

#938 - [Feature]: TermSet Restructure (Stage 5): Compound Data

Issue - State: closed - Opened by mavaylon1 over 1 year ago
Labels: category: enhancement, priority: low

#937 - [Bug]: Rename "latest" wheels

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

#936 - Update CHANGELOG.md for #925

Pull Request - State: closed - Opened by rly over 1 year ago - 2 comments

#935 - TermSet Update #1

Pull Request - State: closed - Opened by mavaylon1 over 1 year ago - 3 comments

#934 - set_data_io method and associated test

Pull Request - State: closed - Opened by bendichter over 1 year ago - 4 comments

#933 - HERD name change

Pull Request - State: closed - Opened by mavaylon1 over 1 year ago - 5 comments

#932 - [Feature]: Change ExternalResources to HERD

Issue - State: closed - Opened by mavaylon1 over 1 year ago
Labels: category: enhancement

#931 - [Documentation]: Integrate Github Codespace

Issue - State: open - Opened by mavaylon1 over 1 year ago
Labels: category: enhancement, priority: low

#930 - [Feature]: TermSet Restructure (Stage 4): Iterative Write

Issue - State: closed - Opened by mavaylon1 over 1 year ago - 2 comments
Labels: category: enhancement, priority: wontfix

#929 - [Feature]: TermSet Restructure Part 3

Issue - State: closed - Opened by mavaylon1 over 1 year ago - 1 comment
Labels: category: enhancement, priority: medium

#928 - [Feature]: TermSet Restructure (Stage 2 & 3): Wrapper class and "write" compatibility

Issue - State: closed - Opened by mavaylon1 over 1 year ago
Labels: category: enhancement, priority: high

#927 - [Feature]: TermSet Restructure (Stage 1): add from root_container

Issue - State: closed - Opened by mavaylon1 over 1 year ago - 1 comment
Labels: category: enhancement, category: proposal, priority: high

#926 - rmv warning from load_namespaces

Pull Request - State: closed - Opened by bendichter over 1 year ago - 2 comments

#925 - change chunk default size to 10MB

Pull Request - State: closed - Opened by bendichter over 1 year ago - 7 comments

#924 - Add base methods for iterator serialization

Pull Request - State: closed - Opened by CodyCBakerPhD over 1 year ago - 2 comments

#923 - DynamicEnums and Schemasheets integration

Pull Request - State: closed - Opened by mavaylon1 over 1 year ago - 4 comments

#922 - [Feature]: Make creating extensions of DynamicTable easier

Issue - State: open - Opened by oruebel over 1 year ago - 3 comments
Labels: help wanted: good first issue, category: proposal, priority: low, topic: extension

#921 - [Feature]: Allow initializing DynamicTable with req/opt cols more directly

Issue - State: open - Opened by rly over 1 year ago - 1 comment
Labels: category: enhancement, priority: medium

#920 - [Feature]: Read linked files with only warnings rather than errors

Issue - State: open - Opened by oruebel over 1 year ago
Labels: category: enhancement, help wanted: deep dive, priority: medium

#919 - Fix/read bad icephys table

Pull Request - State: closed - Opened by oruebel over 1 year ago - 2 comments

#918 - [Bug]: Reading AlignedDynamicTable from disk causes hdf5 error

Issue - State: closed - Opened by rly over 1 year ago - 4 comments
Labels: category: bug, priority: medium

#917 - Refactor DTR warning

Pull Request - State: closed - Opened by rly over 1 year ago - 2 comments

#916 - Fix pytest UnraisableExceptionWarning

Pull Request - State: closed - Opened by rly over 1 year ago - 2 comments

#915 - Fix error with setting read_io to same obj twice

Pull Request - State: closed - Opened by rly over 1 year ago - 1 comment

#914 - [Bug]: Calling io.read() more than once results in error

Issue - State: closed - Opened by rly over 1 year ago

#913 - [Bug]: Container.__read_io not found if ContainerSubclass.init raises error

Issue - State: closed - Opened by rly over 1 year ago - 4 comments
Labels: category: bug, priority: low

#912 - Release 3.8.0

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

#911 - [Feature]: Change the external resources file name

Issue - State: closed - Opened by rly over 1 year ago - 9 comments

#910 - Add ER write capability to IO backend

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

#909 - TermSet get attribute replacement

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

#908 - [Feature]: Allow classes to define their own _generate_html_repr

Issue - State: open - Opened by bendichter over 1 year ago
Labels: category: enhancement, priority: medium

#907 - assign a filler to version if it cannot be imported

Pull Request - State: closed - Opened by bendichter over 1 year ago - 2 comments
Labels: priority: critical

#906 - Update bug_report.yml

Pull Request - State: closed - Opened by bendichter over 1 year ago - 1 comment

#905 - [Bug]: Import error in dev mode

Issue - State: closed - Opened by bendichter over 1 year ago - 2 comments

#904 - [Feature]: Add tests for Python 3.12

Issue - State: closed - Opened by rly over 1 year ago - 1 comment
Labels: category: enhancement, priority: low

#903 - Fix GenericDataChunkIteratorTests.test_abstract_assertions for Python 3.12

Pull Request - State: closed - Opened by musicinmybrain over 1 year ago - 3 comments

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

Pull Request - State: closed - Opened by pre-commit-ci[bot] over 1 year ago - 1 comment

#901 - Release 3.7.0

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

#900 - Update software_process.rst

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

#899 - [Bug]: Can't write

Issue - State: closed - Opened by CodyCBakerPhD over 1 year ago - 1 comment

#898 - [Bug]: Address upcoming NumPy deprecations

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

#897 - Drop Python 3.7 support

Pull Request - State: closed - Opened by rly over 1 year ago - 1 comment

#896 - Update make_a_release.rst to fix broken sphinx links

Pull Request - State: closed - Opened by rly over 1 year ago - 1 comment

#895 - ExternalResources I/O

Pull Request - State: closed - Opened by mavaylon1 over 1 year ago - 6 comments

#894 - Remove broken conda install line in developer docs

Pull Request - State: closed - Opened by oruebel over 1 year ago - 1 comment

#893 - [Feature]: Enhance TermSet

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

#892 - Bump scipy from 1.1 to 1.10.0

Pull Request - State: closed - Opened by dependabot[bot] over 1 year ago - 3 comments
Labels: compatability: dependencies

#891 - Warning for links

Pull Request - State: closed - Opened by mavaylon1 over 1 year ago - 3 comments

#890 - Use hatch versioning, drop setuptools

Pull Request - State: closed - Opened by rly over 1 year ago - 2 comments

#889 - [Bug]: HDMF is not reporting correct version in conda.

Issue - State: closed - Opened by rly over 1 year ago - 1 comment
Labels: category: bug, priority: medium

#888 - [Feature]: html rendering for Data objects

Issue - State: open - Opened by bendichter over 1 year ago

#887 - include count in html

Pull Request - State: closed - Opened by bendichter over 1 year ago - 5 comments

#886 - improve html output

Pull Request - State: closed - Opened by bendichter over 1 year ago - 7 comments

#885 - [Feature]: Create a warning if linked objects are not already present in an NWBfile.

Issue - State: closed - Opened by mavaylon1 over 1 year ago - 2 comments
Labels: category: enhancement

#884 - [Feature]: Create NWBDatasetIncSpec and NWBGroupIncSpec

Issue - State: open - Opened by rly over 1 year ago - 4 comments
Labels: topic: docs, category: proposal, priority: medium, topic: extension

#883 - Add html repr

Pull Request - State: closed - Opened by edeno over 1 year ago - 26 comments
Labels: topic: docs, category: proposal, priority: medium, topic: PyNWB

#882 - add io attr

Pull Request - State: closed - Opened by bendichter over 1 year ago - 18 comments
Labels: category: proposal, priority: medium, topic: PyNWB

#881 - [Feature]: Move shape, type, and is-required-field validation to outside of constructor docval

Issue - State: open - Opened by rly over 1 year ago

#880 - TermSet Integration with up-to-date HDMF

Pull Request - State: closed - Opened by mavaylon1 over 1 year ago - 18 comments

#879 - TermSet Integration

Pull Request - State: closed - Opened by mavaylon1 over 1 year ago

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

Pull Request - State: closed - Opened by pre-commit-ci[bot] over 1 year ago - 1 comment

#877 - Fix testing of min requirements

Pull Request - State: closed - Opened by rly over 1 year ago - 3 comments

#876 - [Bug]: requirements-min.txt ignored in CI

Issue - State: closed - Opened by rly over 1 year ago
Labels: category: bug, priority: low, topic: testing

#875 - add can_read method to HDMFIO and HDF5IO

Pull Request - State: closed - Opened by bendichter over 1 year ago - 1 comment

#874 - allow a `datetime.date` object to be used instead of `datetime.datetime` for isodatetime data

Pull Request - State: closed - Opened by bendichter over 1 year ago - 1 comment
Labels: category: enhancement, priority: medium

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

Pull Request - State: closed - Opened by pre-commit-ci[bot] over 1 year ago - 1 comment

#872 - Addition of ER EntityKeyTable and bug fixes

Pull Request - State: closed - Opened by mavaylon1 over 1 year ago - 2 comments

#871 - [Feature]: ExternalResources write multiple tables to zip

Issue - State: closed - Opened by mavaylon1 over 1 year ago - 1 comment

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

Pull Request - State: closed - Opened by pre-commit-ci[bot] over 1 year ago - 1 comment

#869 - Release 3.6.1

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

#868 - Allow reassigning and resetting AbstractContainer attributes/fields

Pull Request - State: open - Opened by rly almost 2 years ago - 8 comments

#867 - [Feature]: Avoid clearing builder cache if possible

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

#866 - Convert object arrays to string dtype by default

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

#865 - [Feature]: allow modification of fields of unbound containers

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

#864 - [Feature]: Warn when creating an extension that adds attrs/datasets/groups to VectorData without data_type_def

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

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

Pull Request - State: closed - Opened by pre-commit-ci[bot] almost 2 years ago - 1 comment

#862 - TermSet Integration

Pull Request - State: closed - Opened by mavaylon1 almost 2 years ago - 5 comments

#861 - Release 3.6.0

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

#860 - Use and apply black formatting

Pull Request - State: open - Opened by rly almost 2 years ago - 4 comments
Labels: category: enhancement, priority: low

#859 - Run HDMF-Zarr tests on PR and nightly

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

#858 - Update CHANGELOG to fix link to PR

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

#857 - [Bug]: ExternalResources children lost on read/write on roundtrip tests

Issue - State: closed - Opened by mavaylon1 almost 2 years ago - 1 comment
Labels: category: bug, priority: high

#856 - [Feature]: Allow set_dataio on containers for a dataset within

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

#855 - Export cached specs that are loaded in source IO manager but not in export IO manager

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

#854 - Fix broken link to requires.io and update docs

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

#853 - Fix streaming

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

#852 - [Feature]: Test streaming with ROS3 and fsspec

Issue - State: open - Opened by rly almost 2 years ago
Labels: category: enhancement, priority: medium, topic: testing

#851 - [Bug]: Using S3 URLs as source in HDMFIO causes error

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

#850 - ER Release (without TermSet)

Pull Request - State: closed - Opened by mavaylon1 almost 2 years ago - 13 comments

#849 - Remove unused codecov dep

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

GitHub / hdmf-dev/hdmf issues and pull requests