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Title: DataJoint 2.0 by dimitri-yatsenko · Pull Request #1311 · datajoint/datajoint-python · GitHub

Open Graph Title: DataJoint 2.0 by dimitri-yatsenko · Pull Request #1311 · datajoint/datajoint-python

X Title: DataJoint 2.0 by dimitri-yatsenko · Pull Request #1311 · datajoint/datajoint-python

Description: Summary DataJoint 2.0 is a major release that modernizes the entire codebase while maintaining backward compatibility for core functionality. This release focuses on extensibility, type safety, and...

Open Graph Description: Summary DataJoint 2.0 is a major release that modernizes the entire codebase while maintaining backward compatibility for core functionality. This release focuses on extensibility, type safety, and...

X Description: Summary DataJoint 2.0 is a major release that modernizes the entire codebase while maintaining backward compatibility for core functionality. This release focuses on extensibility, type safety, and...

Opengraph URL: https://github.com/datajoint/datajoint-python/pull/1311

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DataJoint 2.0 Planhttps://github.com/datajoint/datajoint-python/issues/1256
Milestone 2.0https://github.com/datajoint/datajoint-python/milestone/24
IMPR: Error specificity on empty insert for table with default values #1280https://github.com/datajoint/datajoint-python/issues/1280
#1307https://github.com/datajoint/datajoint-python/issues/1307
#1235https://github.com/datajoint/datajoint-python/discussions/1235
IMPR: Deprecate and Remove the ~log Table. #1298https://github.com/datajoint/datajoint-python/issues/1298
IMPR: Deprecate otumat support #1252https://github.com/datajoint/datajoint-python/issues/1252
datajoint-docshttps://github.com/datajoint/datajoint-docs
Diátaxis frameworkhttps://diataxis.fr/
IMPR: src layout #1267https://github.com/datajoint/datajoint-python/issues/1267
IMPR: Modernize pre-commit #1271https://github.com/datajoint/datajoint-python/issues/1271
IMPR: split unit/integration test #1211https://github.com/datajoint/datajoint-python/issues/1211
Modernize virtual schema infrastructure #1307https://github.com/datajoint/datajoint-python/issues/1307
IMPR: Deprecate and Remove the ~log Table. #1298https://github.com/datajoint/datajoint-python/issues/1298
IMPR: Error specificity on empty insert for table with default values #1280https://github.com/datajoint/datajoint-python/issues/1280
Can't pass super.delete kwargs to Part.delete #1276https://github.com/datajoint/datajoint-python/issues/1276
IMPR: Modernize pre-commit #1271https://github.com/datajoint/datajoint-python/issues/1271
IMPR: src layout #1267https://github.com/datajoint/datajoint-python/issues/1267
IMPR: Type annotations #1266https://github.com/datajoint/datajoint-python/issues/1266
IMPR: Deprecate otumat support #1252https://github.com/datajoint/datajoint-python/issues/1252
FEAT: dj.Top orders the preview with order_by #1242https://github.com/datajoint/datajoint-python/issues/1242
IMPR: split unit/integration test #1211https://github.com/datajoint/datajoint-python/issues/1211
Test fails in relational_operand due to test code, not functionality. #1205https://github.com/datajoint/datajoint-python/issues/1205
Bug: conda-forge Python 3.13 | ModuleNotFoundError: No module named 'pkg_resources' #1218https://github.com/datajoint/datajoint-python/issues/1218
DataJoint import error due to missing pyarrow (a pandas dependency) #1202https://github.com/datajoint/datajoint-python/issues/1202
ValueError in DataJoint-Python 0.14.3 when using numpy 2.2.* #1201https://github.com/datajoint/datajoint-python/issues/1201
Reserved MySQL keywords as field names result in syntax errors on string restriction #1196https://github.com/datajoint/datajoint-python/issues/1196
LostConnectionError during a long-duration make #1195https://github.com/datajoint/datajoint-python/issues/1195
DataJoint Diagram does not work with the latest version of pydot/networkx across Python 3.10-3.12; encapsulating double quotes needed #1175https://github.com/datajoint/datajoint-python/issues/1175
Long make calls lock table metadata #1170https://github.com/datajoint/datajoint-python/issues/1170
Error withdj.Diagram() and new release of pydot==3.0.* #1169https://github.com/datajoint/datajoint-python/issues/1169
Include support for Python 3.12 #1165https://github.com/datajoint/datajoint-python/issues/1165
IMPR: Documentation for populate generator #1246https://github.com/datajoint/datajoint-python/issues/1246
Proposal to Change DataJoint Python License #1235https://github.com/datajoint/datajoint-python/discussions/1235
Support more algebraic/graph operations on Diagram #1191https://github.com/datajoint/datajoint-python/issues/1191
Construct a Diagram from multiple schemas #1190https://github.com/datajoint/datajoint-python/issues/1190
datajoint-docs PR #97https://github.com/datajoint/datajoint-docs/pull/97
datajoint-docs PR #98https://github.com/datajoint/datajoint-docs/pull/98
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December 20, 2025 23:16https://patch-diff.githubusercontent.com/datajoint/datajoint-python/pull/1311#commits-pushed-997d992
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Finalize staged_insert1 API for direct object storage writeshttps://patch-diff.githubusercontent.com/datajoint/datajoint-python/pull/1311/commits/997d992e38eaa6486d2184a43a54a5150e352f69
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Simplify object naming: field name as base, extension from sourcehttps://patch-diff.githubusercontent.com/datajoint/datajoint-python/pull/1311/commits/36806cccdca2616a6f2af247963c7e2bda2d090a
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Restructure store paths: objects/ after table, rename store confighttps://patch-diff.githubusercontent.com/datajoint/datajoint-python/pull/1311/commits/6c6349b96e2093627e290324f8653b1729be525c
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Make content hashing optional, add folder manifestshttps://patch-diff.githubusercontent.com/datajoint/datajoint-python/pull/1311/commits/0ea880ae1f13e1a3ad1291c7f385b97dac2b8043
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Highlight no hidden tables - key architectural differencehttps://patch-diff.githubusercontent.com/datajoint/datajoint-python/pull/1311/commits/38844f12ddca9d67f199e8390203e4ef55de72bf
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Refactor external storage to use fsspec for unified backendhttps://patch-diff.githubusercontent.com/datajoint/datajoint-python/pull/1311/commits/d65ece72efc4a2137edf30d43467540018cd5f9f
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Fix unused imports (ruff lint)https://patch-diff.githubusercontent.com/datajoint/datajoint-python/pull/1311/commits/4b7e7bd75303bbf2f65457bb013a93257e117001
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Fix ruff-format: add blank lines after local importshttps://patch-diff.githubusercontent.com/datajoint/datajoint-python/pull/1311/commits/949b8a6f09a8439cfe9e59901cdec3647b4c1978
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Implement object column type for managed file storagehttps://patch-diff.githubusercontent.com/datajoint/datajoint-python/pull/1311/commits/0019109475d3ce57baf7ffbbec1fe5a45aabafab
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Fix ruff lint: line length and unused importshttps://patch-diff.githubusercontent.com/datajoint/datajoint-python/pull/1311/commits/b45df2c1cd9905e94aacb4cfbe036875e769d31d
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Fix ruff-format: add blank lines after local importshttps://patch-diff.githubusercontent.com/datajoint/datajoint-python/pull/1311/commits/7ef4e61e70d4e432580b6c903d97c88da632c180
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"strongly-typed" -> "type-checked" Json in documentation.https://patch-diff.githubusercontent.com/datajoint/datajoint-python/pull/1311/commits/f9e749674d45c084495aca6d8d8997fab7258858
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feat: add bool/boolean type aliashttps://patch-diff.githubusercontent.com/datajoint/datajoint-python/pull/1311/commits/d68ea68832c6f4911732d6eb429ac0c7479cf756
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refactor: simplify bool type alias to only support 'bool'https://patch-diff.githubusercontent.com/datajoint/datajoint-python/pull/1311/commits/e20281856521a401b621af9a27981f5dbfef0a9b
e202818https://patch-diff.githubusercontent.com/datajoint/datajoint-python/pull/1311/commits/e20281856521a401b621af9a27981f5dbfef0a9b
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Address Zarr reviewer feedback: optional metadata fieldshttps://patch-diff.githubusercontent.com/datajoint/datajoint-python/pull/1311/commits/15418c339cde649adf85bf819869440c512ec1d4
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Add Augmented Schema vs External References sectionhttps://patch-diff.githubusercontent.com/datajoint/datajoint-python/pull/1311/commits/fb8c0cba6f02a5aee4223c8b949ca0cb874fda0f
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Rename file-type-spec.md to object-type-spec.mdhttps://patch-diff.githubusercontent.com/datajoint/datajoint-python/pull/1311/commits/a9447e73a628bf10046d324b1773cbc764984df6
a9447e7https://patch-diff.githubusercontent.com/datajoint/datajoint-python/pull/1311/commits/a9447e73a628bf10046d324b1773cbc764984df6
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Fix ruff-format: single line error messagehttps://patch-diff.githubusercontent.com/datajoint/datajoint-python/pull/1311/commits/5170ab14f96613dfe2b07badd8a402f7ec3c28ed
5170ab1https://patch-diff.githubusercontent.com/datajoint/datajoint-python/pull/1311/commits/5170ab14f96613dfe2b07badd8a402f7ec3c28ed
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Simplify ExternalTable storage initializationhttps://patch-diff.githubusercontent.com/datajoint/datajoint-python/pull/1311/commits/3e321881d726ddd056e62eea6bd02422ef2dbc68
3e32188https://patch-diff.githubusercontent.com/datajoint/datajoint-python/pull/1311/commits/3e321881d726ddd056e62eea6bd02422ef2dbc68
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Clarify staged insert compatibility: Zarr/TileDB yes, HDF5 nohttps://patch-diff.githubusercontent.com/datajoint/datajoint-python/pull/1311/commits/4e90c1e83dedef767d7eecb53a563199d1bbd6c1
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Add remote URL support for copy inserthttps://patch-diff.githubusercontent.com/datajoint/datajoint-python/pull/1311/commits/5a727d2877f783f349f7cb0364c9937ad44ae58f
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Remove redundant self.spec attribute from ExternalTablehttps://patch-diff.githubusercontent.com/datajoint/datajoint-python/pull/1311/commits/4bdc8827520cc6b761c8c7b11cf854e7398aa130
4bdc882https://patch-diff.githubusercontent.com/datajoint/datajoint-python/pull/1311/commits/4bdc8827520cc6b761c8c7b11cf854e7398aa130
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fix: create storage directories in test fixtures for StorageBackend v…https://patch-diff.githubusercontent.com/datajoint/datajoint-python/pull/1311/commits/4cd99f68e90483544fe4eeb37f08a3a135d5ce35
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test: update summary - all 520 integration tests passing ✓https://patch-diff.githubusercontent.com/datajoint/datajoint-python/pull/1311/commits/6487ae4f42b96ad5855e129caaeb37692c08edb1
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style: apply ruff-format to conftest.pyhttps://patch-diff.githubusercontent.com/datajoint/datajoint-python/pull/1311/commits/35a2c60c1c6cc68010026deb278557d715a4d178
35a2c60https://patch-diff.githubusercontent.com/datajoint/datajoint-python/pull/1311/commits/35a2c60c1c6cc68010026deb278557d715a4d178
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Remove 'objects' literal from schema-addressed storage pathshttps://patch-diff.githubusercontent.com/datajoint/datajoint-python/pull/1311/commits/5512659d3ad93f546a32c96178b74ee08898bf3e
5512659https://patch-diff.githubusercontent.com/datajoint/datajoint-python/pull/1311/commits/5512659d3ad93f546a32c96178b74ee08898bf3e
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Support partition_pattern in schema-addressed storagehttps://patch-diff.githubusercontent.com/datajoint/datajoint-python/pull/1311/commits/c3e01639b97a341317385915ec1a6882572792c4
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docs: fix partition_pattern order preservationhttps://patch-diff.githubusercontent.com/datajoint/datajoint-python/pull/1311/commits/cd7c89fed2dfecdef4581ee1d14e8561c5947d59
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feat: add parallel schema migration helpers to migrate modulehttps://patch-diff.githubusercontent.com/datajoint/datajoint-python/pull/1311/commits/119eb9bcd74c8e9ea1a22fcee712930eb8f8463b
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feat: add migrate_external_pointers_v2 helperhttps://patch-diff.githubusercontent.com/datajoint/datajoint-python/pull/1311/commits/93cf0efe36cdb2610f56341aed84da9cd04fbdc3
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style: fix linting issues in migrate.pyhttps://patch-diff.githubusercontent.com/datajoint/datajoint-python/pull/1311/commits/4b0e9a8be56bfcb0c26d1c5793c16c7fbdf39cb9
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style: apply ruff-format to builtin_codecs.pyhttps://patch-diff.githubusercontent.com/datajoint/datajoint-python/pull/1311/commits/63ecba9b1a6d7b8c58963de402ff3bc8f66cc37e
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Merge pull requesthttps://patch-diff.githubusercontent.com/datajoint/datajoint-python/pull/1311/commits/bf62620697cbc76542c3ba1237a0a0f9075c36c5
#1333https://github.com/datajoint/datajoint-python/pull/1333
from datajoint/feature/unified-stores-confighttps://patch-diff.githubusercontent.com/datajoint/datajoint-python/pull/1311/commits/bf62620697cbc76542c3ba1237a0a0f9075c36c5
bf62620https://patch-diff.githubusercontent.com/datajoint/datajoint-python/pull/1311/commits/bf62620697cbc76542c3ba1237a0a0f9075c36c5
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docs: harmonize terminology from 'external storage' to 'object storage'https://patch-diff.githubusercontent.com/datajoint/datajoint-python/pull/1311/commits/fa6957a8144ac6e6ac557ce051711626c451e0ad
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term: eliminate 'semijoin' and 'antijoin' terminologyhttps://patch-diff.githubusercontent.com/datajoint/datajoint-python/pull/1311/commits/f3e5aaebb65fb1b063aa57d61a5d823803d669c3
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docs: clarify dual-mode codecs in builtin_codecs docstringhttps://patch-diff.githubusercontent.com/datajoint/datajoint-python/pull/1311/commits/75b6f29038313671535df99d1171bedd7b5789d4
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Merge pull requesthttps://patch-diff.githubusercontent.com/datajoint/datajoint-python/pull/1311/commits/984a9be1f455a008ce5ed7d9c8a147a853adb44e
#1334https://github.com/datajoint/datajoint-python/pull/1334
from datajoint/feature/unified-stores-confighttps://patch-diff.githubusercontent.com/datajoint/datajoint-python/pull/1311/commits/984a9be1f455a008ce5ed7d9c8a147a853adb44e
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feat: Remove unsigned integer types from core typeshttps://patch-diff.githubusercontent.com/datajoint/datajoint-python/pull/1311/commits/1d6fd3b646a4085a52baf5b3d035a8712ccd22b7
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test: Replace unsigned integer types with signed equivalentshttps://patch-diff.githubusercontent.com/datajoint/datajoint-python/pull/1311/commits/b94896d0c538d4561c525b90c11dce83f0a44ca8
b94896dhttps://patch-diff.githubusercontent.com/datajoint/datajoint-python/pull/1311/commits/b94896d0c538d4561c525b90c11dce83f0a44ca8
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fix: Replace unsigned types in job queue definitionhttps://patch-diff.githubusercontent.com/datajoint/datajoint-python/pull/1311/commits/825d75ef2a46ac1297ef457136e61968c612a154
825d75ehttps://patch-diff.githubusercontent.com/datajoint/datajoint-python/pull/1311/commits/825d75ef2a46ac1297ef457136e61968c612a154
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test: Add test for native MySQL unsigned types pass-throughhttps://patch-diff.githubusercontent.com/datajoint/datajoint-python/pull/1311/commits/7688fddee4b590d572a8d2029f164fe551ada48d
7688fddhttps://patch-diff.githubusercontent.com/datajoint/datajoint-python/pull/1311/commits/7688fddee4b590d572a8d2029f164fe551ada48d
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Merge pull requesthttps://patch-diff.githubusercontent.com/datajoint/datajoint-python/pull/1311/commits/ac98154657d146091084385c9c23016eb2dca733
#1335https://github.com/datajoint/datajoint-python/pull/1335
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fix: Replace NOW() with CURRENT_TIMESTAMP for PostgreSQL compatibilityhttps://patch-diff.githubusercontent.com/datajoint/datajoint-python/pull/1311/commits/c1d109eaa3c2124ab0a56af38c536bb71abe4266
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Merge pull requesthttps://patch-diff.githubusercontent.com/datajoint/datajoint-python/pull/1311/commits/2ea5a17e1d879553b866ec41d15b4edcadf3abfb
#1336https://github.com/datajoint/datajoint-python/pull/1336
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chore: Remove obsolete files and improve PostgreSQL compatibility (https://patch-diff.githubusercontent.com/datajoint/datajoint-python/pull/1311/commits/f4b02583251c5a7ca47ba39a00a269f167ef636e
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fix: Handle nested parentheses in index parsing for JSON path indexeshttps://patch-diff.githubusercontent.com/datajoint/datajoint-python/pull/1311/commits/bf12aba3a9d63e40a84164d08bb589815f840066
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