LinkML

What's Changed

• restore auto-versioning by @cmungall in https://github.com/linkml/linkml/pull/1886
• 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
• 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
• [wip] fixing context generator for any_of with range by @djarecka in https://github.com/linkml/linkml/pull/1898
• 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
• 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
• 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 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
• 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
• 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
• [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
• [pydanticgen] Embed extra metadata in modules, classes, and fields by @sneakers-the-rat in https://github.com/linkml/linkml/pull/2036
• [poetry] Update Lockfile by @linkml-pr-bot in https://github.com/linkml/linkml/pull/2106
• Adding documentation on monotonicity. by @cmungall in https://github.com/linkml/linkml/pull/2108
• [poetry] Update Lockfile by @linkml-pr-bot in https://github.com/linkml/linkml/pull/2120
• Re-enable tests/test_notebooks/test_examples.py test_distributed_models by @pkalita-lbl in https://github.com/linkml/linkml/pull/2119
• Make quality checks happy by @vladistan in https://github.com/linkml/linkml/pull/2136
• [poetry] Update Lockfile by @linkml-pr-bot in https://github.com/linkml/linkml/pull/2137
• hotwo on deprecation by @sierra-moxon in https://github.com/linkml/linkml/pull/2127
• shaclgen: Add --include-annotations option to let annotations be part of shacl shapes by @jsheunis in https://github.com/linkml/linkml/pull/2111
• Erdiagram include upstream by @vladistan in https://github.com/linkml/linkml/pull/2139
• [poetry] Update Lockfile by @linkml-pr-bot in https://github.com/linkml/linkml/pull/2143
• Adding tests for min/max as floats. by @cmungall in https://github.com/linkml/linkml/pull/2145
• Implement equals_string and equals_string_in; take 2 by @pkalita-lbl in https://github.com/linkml/linkml/pull/2150
• [poetry] Update Lockfile by @linkml-pr-bot in https://github.com/linkml/linkml/pull/2151
• [poetry] Update Lockfile by @linkml-pr-bot in https://github.com/linkml/linkml/pull/2173
• Mappings section should show on individual element pages and not just classes by @sujaypatil96 in https://github.com/linkml/linkml/pull/2172

New Contributors

• @noahhl made their first contribution in https://github.com/linkml/linkml/pull/1907
• @djarecka made their first contribution in https://github.com/linkml/linkml/pull/1898
• @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
• @robertschubert made their first contribution in https://github.com/linkml/linkml/pull/2038
• @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
• @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
• @vladistan made their first contribution in https://github.com/linkml/linkml/pull/2136

Full Changelog: https://github.com/linkml/linkml/compare/v1.7.0...v1.8.0rc2