hdmf-dev/hdmf issues and pull requests

#1116 - Fix warning

Pull Request - State: closed - Opened by mavaylon1 7 months ago - 5 comments

#1115 - Update pyproject.toml to use only Numpy <2.0

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

#1114 - [Bug]: Test collection fails for three tests with pytest 8.2.0

Issue - State: open - Opened by penguinpee 7 months ago - 6 comments
Labels: category: bug, category: enhancement

#1113 - [Feature]: Running NeuroConv tests on dev branches

Issue - State: open - Opened by CodyCBakerPhD 7 months ago - 3 comments
Labels: category: enhancement, priority: medium

#1112 - Update run_pynwb_tests.yml

Pull Request - State: closed - Opened by mavaylon1 7 months ago - 1 comment

#1111 - [Bug]: NeuroConv dev tests - Last axis of data shapes is None

Issue - State: open - Opened by CodyCBakerPhD 7 months ago - 12 comments
Labels: category: bug, priority: medium

#1110 - Expose progress bar class control

Pull Request - State: closed - Opened by CodyCBakerPhD 7 months ago - 3 comments

#1109 - Bump tqdm from 4.41.0 to 4.66.3

Pull Request - State: closed - Opened by dependabot[bot] 7 months ago - 1 comment
Labels: compatability: dependencies, python

#1108 - [Feature]: Add an object path as a way to uniquely identify an object in the API

Issue - State: open - Opened by h-mayorquin 7 months ago - 8 comments
Labels: category: enhancement, priority: low, topic: PyNWB

#1107 - Update coverage call, don't install in editable mode in testing

Pull Request - State: closed - Opened by rly 7 months ago - 1 comment
Labels: category: enhancement, topic: testing

#1106 - [Bug]: Numpy 2.0

Issue - State: closed - Opened by mavaylon1 7 months ago
Labels: category: bug

#1105 - Ignore config cache warnings in sphinx

Pull Request - State: closed - Opened by stephprince 7 months ago - 1 comment

#1104 - Workflows to support python 3.9 and 3.8 with Mac OS 13

Pull Request - State: closed - Opened by mavaylon1 7 months ago - 1 comment

#1103 - speed up loading of namespaces: return shallow copy in build_const_args

Pull Request - State: closed - Opened by magland 7 months ago - 5 comments
Labels: category: enhancement, topic: performance

#1102 - speed up loading of namespaces: skip register type when already registered when loading namespace

Pull Request - State: closed - Opened by magland 7 months ago - 2 comments
Labels: category: enhancement, topic: performance

#1101 - [Bug]: Custom class generator does not account for fields refined from parent type

Issue - State: open - Opened by rly 7 months ago - 1 comment
Labels: category: bug, priority: low, topic: extension

#1100 - improve html representation of datasets

Pull Request - State: closed - Opened by h-mayorquin 7 months ago - 14 comments
Labels: category: enhancement

#1099 - [Bug]: Compound dtype attributes are not supported

Issue - State: open - Opened by rly 7 months ago - 2 comments
Labels: category: bug

#1098 - [Bug]: When appending to file with newer schema, the older schema is not deleted

Issue - State: open - Opened by rly 8 months ago - 11 comments
Labels: category: bug, category: enhancement, priority: low

#1097 - Bump actions/add-to-project from 0.6.1 to 1.0.1

Pull Request - State: closed - Opened by dependabot[bot] 8 months ago - 2 comments
Labels: compatability: dependencies, github_actions

#1096 - [Bug]: Support writing multidimensional string datasets and attributes

Issue - State: closed - Opened by rly 8 months ago - 1 comment
Labels: category: bug, priority: medium

#1095 - [Feature]: Refactor to reduce code complexity

Issue - State: open - Opened by rly 8 months ago - 1 comment
Labels: category: enhancement, priority: low, topic: maintenance

#1094 - Field_config refactored

Pull Request - State: closed - Opened by mavaylon1 8 months ago - 1 comment

#1093 - VectorData Expand by Default via write_dataset

Pull Request - State: closed - Opened by mavaylon1 8 months ago - 18 comments

#1092 - [Feature]: Support annotation of substrings with HERD or another system

Issue - State: open - Opened by rly 8 months ago - 3 comments
Labels: category: proposal, priority: low

#1091 - Don't override col_cls in DynamicTable.add_column

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

#1090 - [Feature]: Raise warning when a container is not written because it does not map to a spec

Issue - State: open - Opened by rly 8 months ago - 1 comment
Labels: category: enhancement, priority: low

#1089 - Post init option for class generator

Pull Request - State: closed - Opened by mavaylon1 8 months ago - 20 comments

#1088 - Bump actions/add-to-project from 0.6.1 to 1.0.0

Pull Request - State: closed - Opened by dependabot[bot] 8 months ago - 1 comment
Labels: compatability: dependencies, github_actions

#1087 - [Feature]: Global or IO-specific TypeConfigurator?

Issue - State: closed - Opened by rly 8 months ago - 1 comment
Labels: category: enhancement, priority: wontfix

#1086 - [Bug]: Extensions are not robust to order

Issue - State: open - Opened by rly 8 months ago - 6 comments
Labels: category: bug, priority: low

#1085 - [Documentation]: Add Documentation/Tutorial for TypeConfigurator

Issue - State: closed - Opened by mavaylon1 8 months ago - 1 comment
Labels: category: enhancement

#1084 - Trimming HDMF

Issue - State: open - Opened by mavaylon1 8 months ago
Labels: category: enhancement

#1083 - HDMF Test Coverage Tracker

Issue - State: open - Opened by mavaylon1 8 months ago
Labels: category: enhancement

#1082 - [pre-commit.ci] pre-commit autoupdate

Pull Request - State: closed - Opened by pre-commit-ci[bot] 8 months ago - 1 comment

#1081 - Write dimension labels to DatasetBuilder on build

Pull Request - State: closed - Opened by rly 8 months ago - 4 comments

#1080 - Update GitHub release checklist

Pull Request - State: closed - Opened by rly 8 months ago - 1 comment

#1079 - [Bug]: Tests with optional requirements failing

Issue - State: open - Opened by rly 8 months ago - 3 comments
Labels: category: bug, priority: low, topic: testing

#1078 - Bump actions/add-to-project from 0.6.0 to 0.6.1

Pull Request - State: closed - Opened by dependabot[bot] 8 months ago
Labels: compatability: dependencies, github_actions

#1077 - [Feature]: Store dimension labels in DatasetBuilder for backends to write

Issue - State: closed - Opened by rly 8 months ago
Labels: category: enhancement, priority: medium

#1076 - Remove outdated comment in requirements-opt.txt

Pull Request - State: closed - Opened by rly 8 months ago - 1 comment

#1075 - Bump black from 23.10.1 to 24.3.0

Pull Request - State: closed - Opened by dependabot[bot] 8 months ago
Labels: compatability: dependencies, python

#1074 - Release 3.13

Pull Request - State: closed - Opened by mavaylon1 8 months ago - 2 comments

#1073 - Release 3.13

Pull Request - State: closed - Opened by mavaylon1 8 months ago - 1 comment

#1072 - [Feature]: Add a `post_init` method to `get_class`

Issue - State: closed - Opened by h-mayorquin 8 months ago - 1 comment
Labels: category: enhancement, priority: low

#1071 - [pre-commit.ci] pre-commit autoupdate

Pull Request - State: closed - Opened by pre-commit-ci[bot] 8 months ago - 1 comment

#1070 - Unwrap TermSetWrapper in ObjectMapper and not the IO

Pull Request - State: closed - Opened by mavaylon1 9 months ago - 6 comments

#1069 - Add docs on spec language support

Pull Request - State: closed - Opened by rly 9 months ago - 1 comment

#1068 - Documents parts of hdmf-schema-language that are not yet supported

Issue - State: closed - Opened by rly 9 months ago

#1067 - Unwrap TermSetWrapper for the IO

Pull Request - State: closed - Opened by mavaylon1 9 months ago - 1 comment

#1066 - Warn when adding ragged arrays to DynamicTable without index argument

Pull Request - State: closed - Opened by stephprince 9 months ago - 4 comments

#1065 - [Feature]: Warn to use index argument on call to add_row or add_column

Issue - State: closed - Opened by stephprince 9 months ago

#1064 - Have VectorData expandable by default

Pull Request - State: closed - Opened by mavaylon1 9 months ago - 2 comments
Labels: category: enhancement, priority: medium

#1063 - Bump actions/add-to-project from 0.5.0 to 0.6.0

Pull Request - State: closed - Opened by dependabot[bot] 9 months ago - 1 comment
Labels: compatability: dependencies

#1062 - [Feature]: Generalize unwrapping the TermSetWrapper to support different storage backends

Issue - State: closed - Opened by mavaylon1 9 months ago
Labels: category: enhancement, priority: high

#1061 - Compound Dataset Support for TermSetWrapper

Pull Request - State: closed - Opened by mavaylon1 9 months ago - 5 comments
Labels: category: enhancement, priority: medium

#1060 - Fix link checker badge in the README

Pull Request - State: closed - Opened by oruebel 9 months ago - 1 comment

#1059 - Update release.md

Pull Request - State: closed - Opened by mavaylon1 9 months ago - 4 comments

#1058 - fix circular reference for html repr

Pull Request - State: open - Opened by bendichter 9 months ago - 1 comment

#1057 - [Bug]: HTML rendering of objects with links

Issue - State: closed - Opened by bendichter 9 months ago - 4 comments

#1056 - [pre-commit.ci] pre-commit autoupdate

Pull Request - State: closed - Opened by pre-commit-ci[bot] 10 months ago - 1 comment

#1055 - [Bug]: Error when initializing DtypeError

Issue - State: closed - Opened by rly 10 months ago
Labels: category: bug, priority: low

#1054 - [pre-commit.ci] pre-commit autoupdate

Pull Request - State: closed - Opened by pre-commit-ci[bot] 10 months ago - 1 comment

#1053 - Prepare for release of HDMF 3.12.1

Pull Request - State: closed - Opened by rly 10 months ago - 1 comment

#1052 - Bump codecov/codecov-action from 3 to 4

Pull Request - State: closed - Opened by dependabot[bot] 10 months ago - 1 comment
Labels: compatability: dependencies

#1051 - [Bug]: Error not raised on write if container fields do not match required names in spec

Issue - State: open - Opened by rly 10 months ago
Labels: category: bug, topic: validator, priority: medium

#1050 - Fix validator not validating on spec of builder data type

Pull Request - State: closed - Opened by rly 10 months ago - 4 comments

#1049 - [Bug]: Invalid object passing validation

Issue - State: closed - Opened by bendichter 10 months ago - 11 comments
Labels: category: bug, topic: validator, priority: high

#1048 - Testing CI (ignore)

Pull Request - State: closed - Opened by mavaylon1 10 months ago

#1047 - Fix to_dataframe for TermSetWrapper

Pull Request - State: closed - Opened by mavaylon1 10 months ago

#1046 - Fix the path for finding the herd zip file.

Pull Request - State: closed - Opened by mavaylon1 10 months ago - 1 comment

#1045 - [Bug]: HERD does not generate the paths properly when reading a zip

Issue - State: closed - Opened by mavaylon1 10 months ago
Labels: category: bug, priority: high

#1044 - [Bug]: Pandas does not know what a TermSetWrapper is

Issue - State: closed - Opened by mavaylon1 10 months ago - 1 comment
Labels: category: bug, priority: high

#1043 - [Feature]: In `Container._repr_html_`, indicate which fields are links

Issue - State: open - Opened by rly 10 months ago
Labels: category: enhancement, priority: low

#1042 - [Feature]: Config Future Development Ideas

Issue - State: closed - Opened by mavaylon1 10 months ago - 1 comment

#1041 - [Feature]: VectorData should use H5DataIO to be expandable (after write) by default

Issue - State: open - Opened by mavaylon1 10 months ago
Labels: category: enhancement, priority: low

#1040 - Expose AWS Region to HDF5IO

Pull Request - State: closed - Opened by CodyCBakerPhD 10 months ago - 6 comments

#1039 - [Bug]: Expose aws_region to HDF5IO

Issue - State: closed - Opened by CodyCBakerPhD 10 months ago - 1 comment
Labels: category: enhancement, priority: low

#1038 - add option to use a custom html field generation method

Pull Request - State: closed - Opened by stephprince 10 months ago - 1 comment

#1037 - [Bug]: VectorData with fixed name in spec

Issue - State: open - Opened by oruebel 10 months ago
Labels: category: bug, priority: low

#1036 - Update docval to accept fully qualified class names

Pull Request - State: closed - Opened by rly 10 months ago - 2 comments

#1035 - Update deploy_release.yml

Pull Request - State: closed - Opened by mavaylon1 10 months ago - 2 comments

#1034 - [pre-commit.ci] pre-commit autoupdate

Pull Request - State: closed - Opened by pre-commit-ci[bot] 10 months ago - 1 comment

#1033 - [Feature]: Move schema-specific typemap-related functions into configuration module/class

Issue - State: open - Opened by rly 10 months ago
Labels: category: proposal, priority: low

#1032 - Update CHANGELOG.md

Pull Request - State: closed - Opened by mavaylon1 11 months ago - 1 comment

#1031 - Fix internal links in docs

Pull Request - State: closed - Opened by stephprince 11 months ago - 12 comments

#1030 - Update deploy_release.yml

Pull Request - State: closed - Opened by mavaylon1 11 months ago - 1 comment

#1029 - [Feature]: Add function to reset a field to None

Issue - State: open - Opened by rly 11 months ago
Labels: category: enhancement, priority: low

#1028 - [pre-commit.ci] pre-commit autoupdate

Pull Request - State: closed - Opened by pre-commit-ci[bot] 11 months ago - 1 comment

#1027 - Use stacklevel to give better warning messages

Pull Request - State: closed - Opened by rly 11 months ago - 1 comment

#1026 - Fix validation of datetime-formatted strings

Pull Request - State: closed - Opened by rly 11 months ago - 1 comment

#1025 - Release 3.12

Pull Request - State: closed - Opened by mavaylon1 11 months ago - 1 comment

#1024 - Render code snippet in issue ticket as python

Pull Request - State: closed - Opened by rly 11 months ago - 1 comment

#1023 - [Bug]: Validator incorrectly reads datetime-formatted string as isodatetime when spec dtype is string

Issue - State: closed - Opened by rly 11 months ago
Labels: category: bug, topic: validator, priority: medium

#1022 - Fix broken sphinx link in software_process.rst

Pull Request - State: closed - Opened by rly 11 months ago - 1 comment

#1021 - fix typo

Pull Request - State: closed - Opened by bendichter 11 months ago - 1 comment

#1020 - Bump actions/download-artifact from 3 to 4

Pull Request - State: closed - Opened by dependabot[bot] 12 months ago - 1 comment
Labels: compatability: dependencies

#1019 - Bump actions/upload-artifact from 3 to 4

Pull Request - State: closed - Opened by dependabot[bot] 12 months ago - 1 comment
Labels: compatability: dependencies

#1018 - [Feature]: Remove or enchance the warning about ignoring cached name spaces

Issue - State: open - Opened by h-mayorquin 12 months ago - 3 comments
Labels: category: enhancement, priority: low, topic: PyNWB

#1017 - Make dyntab expandable

Pull Request - State: open - Opened by bendichter 12 months ago - 1 comment

GitHub / hdmf-dev/hdmf issues and pull requests