[pydanticgen] Embed extra metadata in modules, classes, and fields (l…

…inkml#2036)

* embed extra metadata in pydantic objects

* black formatting

* lint

* oop wrong import location, that's just in my fork

* different modes for metadata generation

* correctly exclude children when in dict and lists

* lint, fix docs

* fix pydantic 1 compatibility with __root__ assignment, generalize compliance tests to not close expected python annotations. make arraytypes a string enum

* fix string comparisons in pydanticgen tests!

* Accept Nones and strs in metadata mode

* a single comma

autodetect pydantic in pydanticgen cli (linkml#2078)

validator: support including validator context when reporting errors (l…

…inkml#2089)

* validator: support including validator context when reporting errors

Motivation:

When validating JSON, the `linkml-validate` command builds a JSON Schema
against which the JSON input is checked.  If there are validation
problems, the command prints a single line for each such problem.

In some cases, the failing node is a composition (`allOf`, `anyOf`,
`oneOf`) and the resulting error message is currently rather vague.

Modification:

Update the `ValidationResult` class to include a List of strings.  These
are the validation errors that led to the composition failing.

Note, these contextual failures could (themselves) have further
contextual failures, forming a tree.  In the interests of keeping the
patch small, this change records only the next level; however, a future
patch may address this issue.

The error output is updated to support providing the validation error's
context as lines starting `[CONTEXT]`.

The command-line arguments are updated to support the `-v`/`--verbose`
flag.  Specifying this flag results in the validator printing any
validation error context.

Note, support for the `-v` flag was included for backwards
compatibility; however, it may be acceptable to print the validation
error's context unconditionally.  If so, a future patch could remove
this flag.

Result:

`linkml-validate` now supports the `-v`/`--verbose` option.  Specifying
this option will result in certain validation error reports containing
more information.

Closes: linkml#2088

* Update cli.py

* Update cli.py

---------

Co-authored-by: Chris Mungall <[email protected]>

convert enhancements to pytest (linkml#2052)

* convert enhancements to pytest

* catch `None` log_level that somehow happens

optimize rendering of Applicable classes section on slot documentatio…

…n pages (linkml#2009)

* optimize use of get_classes_by_slot() in slot.md.jinja2

* updating pyproject.toml to use linkml-runtime v1.7.4

include python version in cache key (linkml#1990)

additional tests for patterns, mixins, and abstract classes. (linkml#…

…1947)

Ensure owlgen doesn't pun when literal constraints are applied
to slots that are translated to ObjectProperties. Fixes linkml#1841

[wip] fixing context generator for `any_of` with `range` (linkml#1898)

Pydantic generated models require importing Decimal (linkml#1911)

* Decimal is a required type for Pydantic generation

* Add a decimal slot to ensure Pydantic dependency issue is resolved

---------

Co-authored-by: Noah Lorang <[email protected]>

restore auto-versioning (linkml#1886)