Linkml Versions Save

Linked Open Data Modeling Language

v1.7.11rc1

1 week ago

What's Changed

[pydanticgen] Embed extra metadata in modules, classes, and fields by @sneakers-the-rat in https://github.com/linkml/linkml/pull/2036

Full Changelog: https://github.com/linkml/linkml/compare/v1.7.10...v1.7.11rc1

v1.7.10

1 week ago

What's Changed

[poetry] Update Lockfile by @linkml-pr-bot in https://github.com/linkml/linkml/pull/2098
Adding link to expr lang docs by @cmungall in https://github.com/linkml/linkml/pull/2086
Fix typo in docs (add missing closing parenthesis) by @eecavanna in https://github.com/linkml/linkml/pull/2097
Update slot cardinality meaning on main linkml docs site by @sujaypatil96 in https://github.com/linkml/linkml/pull/2100
genshacl: fix the propagation of types to SHACL sh:datatype and sh:nodeKind by @jsheunis in https://github.com/linkml/linkml/pull/2102
Autodetect pydantic version in gen-pydantic issue #2077 by @manulera in https://github.com/linkml/linkml/pull/2078

New Contributors

@jsheunis made their first contribution in https://github.com/linkml/linkml/pull/2102
@manulera made their first contribution in https://github.com/linkml/linkml/pull/2078

Full Changelog: https://github.com/linkml/linkml/compare/v1.7.9...v1.7.10

v1.7.9

2 weeks ago

What's Changed

Add --without-cache option to tests by @sneakers-the-rat in https://github.com/linkml/linkml/pull/2051
Add deprecations module and add deprecation warnings for pydantic v1 by @sneakers-the-rat in https://github.com/linkml/linkml/pull/1957
feat: add '--version' to linkml-run-examples by @Silvanoc in https://github.com/linkml/linkml/pull/2058
Pass strings rather than printing to stdout in generators by @sneakers-the-rat in https://github.com/linkml/linkml/pull/2061
[poetry] Update Lockfile by @github-actions in https://github.com/linkml/linkml/pull/2056
Use app installation token in poetry update workflow by @pkalita-lbl in https://github.com/linkml/linkml/pull/2062
[poetry] Update Lockfile by @linkml-pr-bot in https://github.com/linkml/linkml/pull/2066
Make class blocks in mermaid class diagrams clickable/hyperlinked by @sujaypatil96 in https://github.com/linkml/linkml/pull/2065
Display single/multi-valuedness (cardinality) on slot edges by @sujaypatil96 in https://github.com/linkml/linkml/pull/2071
[poetry] Update Lockfile by @linkml-pr-bot in https://github.com/linkml/linkml/pull/2075
Documentation: Recommend the official docker image in docs and improve structure of installation intro by @mkbrechtel in https://github.com/linkml/linkml/pull/2073
Improve Dockerfile: Update Baseimages, make build work with Buildah/Podman and install python packages globally in runner by @mkbrechtel in https://github.com/linkml/linkml/pull/2074
[poetry] Update Lockfile by @linkml-pr-bot in https://github.com/linkml/linkml/pull/2083
Ensure consistency of cardinality displayed on edges of Mermaid class diagram by @sujaypatil96 in https://github.com/linkml/linkml/pull/2080
Minor fixes and improvements to text by @nlharris in https://github.com/linkml/linkml/pull/2082
Add generator flag to include an import outside the normal import mechanism by @sierra-moxon in https://github.com/linkml/linkml/pull/2079
plantuml: hide circle and empty members, remove quotes by @VladimirAlexiev in https://github.com/linkml/linkml/pull/2060
Clarify use of slack channel in contribution docs by @matentzn in https://github.com/linkml/linkml/pull/2093
Allow control over which OWL types are used for enums. Fixes #2090 by @cmungall in https://github.com/linkml/linkml/pull/2095
validator: support including validator context when reporting errors by @paulmillar in https://github.com/linkml/linkml/pull/2089

New Contributors

@github-actions made their first contribution in https://github.com/linkml/linkml/pull/2056
@linkml-pr-bot made their first contribution in https://github.com/linkml/linkml/pull/2066
@mkbrechtel made their first contribution in https://github.com/linkml/linkml/pull/2073
@VladimirAlexiev made their first contribution in https://github.com/linkml/linkml/pull/2060
@matentzn made their first contribution in https://github.com/linkml/linkml/pull/2093

Full Changelog: https://github.com/linkml/linkml/compare/v1.7.8...v1.7.9

v1.7.8

1 month ago

What's Changed

Ensure unique key constraints on foreign keys are mapped in SQL transform. by @cmungall in https://github.com/linkml/linkml/pull/2035
fix link to "inlining" documentation by @nlharris in https://github.com/linkml/linkml/pull/2039
Fix testing infrasucture for Pydantic 2 default by @pkalita-lbl in https://github.com/linkml/linkml/pull/2041
[perf] Finish putting file I/O behind --with-output flag in compliance tests (and other free perf) by @sneakers-the-rat in https://github.com/linkml/linkml/pull/2045
Issue 2037: extend shaclgen.py to add the suffix "Shape" to the generated SHACL shape by @robertschubert in https://github.com/linkml/linkml/pull/2038
Make docs dependencies optional and in a separate group by @sneakers-the-rat in https://github.com/linkml/linkml/pull/1991
Optimize logic in subset.md.jinja2 by @sujaypatil96 in https://github.com/linkml/linkml/pull/2046
[tests] Remove test outputs and GeneratorTestCase by @sneakers-the-rat in https://github.com/linkml/linkml/pull/1976
WIP: Tests remove testcase by @pkalita-lbl in https://github.com/linkml/linkml/pull/2048
Automatically PR to update poetry lockfile v3 by @sneakers-the-rat in https://github.com/linkml/linkml/pull/2044
convert test_data to pytest by @sneakers-the-rat in https://github.com/linkml/linkml/pull/2050
Run code quality checks only once in testing workflow by @pkalita-lbl in https://github.com/linkml/linkml/pull/2055
convert enhancements to pytest by @sneakers-the-rat in https://github.com/linkml/linkml/pull/2052

New Contributors

@robertschubert made their first contribution in https://github.com/linkml/linkml/pull/2038

Full Changelog: https://github.com/linkml/linkml/compare/v1.7.7...v1.7.8

v1.7.7

1 month ago

Highlights

[pydanticgen] Add list of lists array implementation by @rly @sneakers-the-rat in https://github.com/linkml/linkml/pull/1887

This release sees the first implementation of the array spec in pydanticgen.

An overview of arrays is present in the schema guide: https://linkml.io/linkml/schemas/arrays

With the introduction of the 1.7.0 it has been possible to represent N-dimensional arrays, e.g.

MyClass:
  attributes:
    data:
      range: integer
      array:
        minimum_number_dimensions: 3
        maximum_number_dimensions: 5

This release equips pydanticgen with the ability to translate these to nested lists, and lays the framework for representation using numpytyping.

This implementation is the result of heroic efforts by the @linkml/ndarray-wg, and in particular, @sneakers-the-rat and @rly

🙏 🙏 🙏

What's Changed

Fix Node Kind for Custom Class Ranges by @vincentkelleher in https://github.com/linkml/linkml/pull/2003
Adding documentation for linkml expression language by @turbomam in https://github.com/linkml/linkml/pull/2011
owlgen - skip nested annotations by @cmungall in https://github.com/linkml/linkml/pull/2013
Adding compliance tests for importing and subsetting metamodel, fixes #2015 by @cmungall in https://github.com/linkml/linkml/pull/2016
Update lockfile by @sneakers-the-rat in https://github.com/linkml/linkml/pull/2002
Use fetch-depth: 0 in docker-build workflow by @pkalita-lbl in https://github.com/linkml/linkml/pull/2022
JSON-LD Context Generator Fixes by @vincentkelleher in https://github.com/linkml/linkml/pull/1981
Automatically PR to update poetry lockfile by @sneakers-the-rat in https://github.com/linkml/linkml/pull/2023
Add support for Python 3.12 by @Silvanoc in https://github.com/linkml/linkml/pull/1704
[pydanticgen] Add list of lists array implementation by @rly @sneakers-the-rat in https://github.com/linkml/linkml/pull/1887
Adding ifabsent tests. by @cmungall in https://github.com/linkml/linkml/pull/2014
Automatically PR to update poetry lockfile v2 by @sneakers-the-rat in https://github.com/linkml/linkml/pull/2028
optimize rendering of Applicable classes section on slot documentation pages by @sujaypatil96 in https://github.com/linkml/linkml/pull/2009

Full Changelog: https://github.com/linkml/linkml/compare/v1.7.6...v1.7.7

v1.7.6

1 month ago

What's Changed

Cache network requests during tests by @sneakers-the-rat in https://github.com/linkml/linkml/pull/1949
Pydanticgen - Modularize template by @sneakers-the-rat in https://github.com/linkml/linkml/pull/1927
Account for any_of ranges in documentation pages by @sujaypatil96 in https://github.com/linkml/linkml/pull/1856
Unbreak the docs & test them by @sneakers-the-rat in https://github.com/linkml/linkml/pull/1954
[pydanticgen] Replace classmethod-property chain with init subclass by @sneakers-the-rat in https://github.com/linkml/linkml/pull/1959
Add any_of implementation to shaclgen.py by @anjastrunk in https://github.com/linkml/linkml/pull/1601
Support ifabsent in the Shacl generator by @vincentkelleher in https://github.com/linkml/linkml/pull/1964
remove tab in biolink model by @sneakers-the-rat in https://github.com/linkml/linkml/pull/1971
Replace metamodel with kitchen sink in script tests by @sneakers-the-rat in https://github.com/linkml/linkml/pull/1969
[docker] Fix error from COPY .git directory by using ADD by @sneakers-the-rat in https://github.com/linkml/linkml/pull/1980
Add debug logs to doc-gen by @timothy-trinidad-ps in https://github.com/linkml/linkml/pull/1974
Allow multiple files to be passed to linkml-sqldb dump by @cmungall in https://github.com/linkml/linkml/pull/1985
Cast rdflib Namespace instances to strings when used as base for contextgen by @sneakers-the-rat in https://github.com/linkml/linkml/pull/1982
Adding imports tests to compliance test suite. by @cmungall in https://github.com/linkml/linkml/pull/1987
use typing version of Tuple, not class for 3.8 compat by @sneakers-the-rat in https://github.com/linkml/linkml/pull/1989
Linter: add patterns in config for classes and slots by @linupi in https://github.com/linkml/linkml/pull/1979
Fixing test for #25 by explicitly invoking jsonld1.1. by @cmungall in https://github.com/linkml/linkml/pull/1995
Make pyshacl an extra by @sneakers-the-rat in https://github.com/linkml/linkml/pull/1992
Include python version in CI cache key by @sneakers-the-rat in https://github.com/linkml/linkml/pull/1990

New Contributors

@vincentkelleher made their first contribution in https://github.com/linkml/linkml/pull/1964
@timothy-trinidad-ps made their first contribution in https://github.com/linkml/linkml/pull/1974
@linupi made their first contribution in https://github.com/linkml/linkml/pull/1979

Full Changelog: https://github.com/linkml/linkml/compare/v1.7.5...v1.7.6

v1.7.5

2 months ago

What's Changed

Fix docstrings by @bendichter in https://github.com/linkml/linkml/pull/1929
Update sqlalchemygen.py style by @bendichter in https://github.com/linkml/linkml/pull/1904
Perf: Mark shex generator as slow, skip except for gh actions runner by @sneakers-the-rat in https://github.com/linkml/linkml/pull/1921
change methods to static where appropriate by @bendichter in https://github.com/linkml/linkml/pull/1908
Add suggestions of permissive licenses by @nlharris in https://github.com/linkml/linkml/pull/1928
Update gen-json-schema command in tutorial to use --top-class option by @pkalita-lbl in https://github.com/linkml/linkml/pull/1931
[QoL] Make generating output optional in compliance tests by @sneakers-the-rat in https://github.com/linkml/linkml/pull/1941
[QoL] Quiet warnings by @sneakers-the-rat in https://github.com/linkml/linkml/pull/1939
Deprecate SQLDDLGenerator and change references to SQLTableGenerator by @sneakers-the-rat in https://github.com/linkml/linkml/pull/1940
additional tests for patterns, mixins, and abstract classes. by @cmungall in https://github.com/linkml/linkml/pull/1947

Full Changelog: https://github.com/linkml/linkml/compare/v1.7.4...v1.7.5

v1.7.4

3 months ago

What's Changed

fix some grammatical errors by @bendichter in https://github.com/linkml/linkml/pull/1913
Pydanticgen: Inject imports, slots, and classes by @sneakers-the-rat in https://github.com/linkml/linkml/pull/1916
remove mutables as default arguments by @bendichter in https://github.com/linkml/linkml/pull/1912
Adding tests for empty preconditions in rules. by @cmungall in https://github.com/linkml/linkml/pull/1926
Add timeout to requests by @sneakers-the-rat in https://github.com/linkml/linkml/pull/1918
fixing context generator for any_of with range by @djarecka in https://github.com/linkml/linkml/pull/1898

New Contributors

@djarecka made their first contribution in https://github.com/linkml/linkml/pull/1898

Full Changelog: https://github.com/linkml/linkml/compare/v1.7.3...v1.7.4

v1.7.3

3 months ago

What's Changed

Add blurb about dev environment setup to contributing guide by @pkalita-lbl in https://github.com/linkml/linkml/pull/1892
pydanticgen enum titles (issue 1810) by @kevinschaper in https://github.com/linkml/linkml/pull/1891
Updating the docs on NDArrays to reflect 1.7 changes by @cmungall in https://github.com/linkml/linkml/pull/1893
Correct import for sqlalchemy.pool.StaticPool by @bendichter in https://github.com/linkml/linkml/pull/1895
Adding support for serializing inlined tuples as simple dicts in pydantic. by @cmungall in https://github.com/linkml/linkml/pull/1869
Additional owlgen compliance tests. by @cmungall in https://github.com/linkml/linkml/pull/1894
add database files to .gitignore by @bendichter in https://github.com/linkml/linkml/pull/1906
Fix tutorial09.md typos by @bendichter in https://github.com/linkml/linkml/pull/1903
Poetry extras removal by @dalito in https://github.com/linkml/linkml/pull/1900
rmv unnecessary default_factories by @bendichter in https://github.com/linkml/linkml/pull/1905
Update doc build instructions and add makefile command to build docs by @dalito in https://github.com/linkml/linkml/pull/1899
Foreign keys should be of same type as the primary key they reference by @noahhl in https://github.com/linkml/linkml/pull/1907
Pydantic generated models require importing Decimal by @noahhl in https://github.com/linkml/linkml/pull/1911

New Contributors

@noahhl made their first contribution in https://github.com/linkml/linkml/pull/1907

Full Changelog: https://github.com/linkml/linkml/compare/v1.7.2...v1.7.3

v1.7.2

3 months ago

What's Changed

restore auto-versioning by @cmungall in https://github.com/linkml/linkml/pull/1886

Full Changelog: https://github.com/linkml/linkml/compare/v1.7.0...v1.7.2