feat(generators): add --exclude-external-imports flag

CITATION.cff

@@ -6,70 +6,100 @@ authors:
     orcid: https://orcid.org/0000-0002-8719-7760
   - family-names: Solbrig
     given-names: Harold
+    orcid: https://orcid.org/0000-0002-5928-3071
   - family-names: Harris
     given-names: Nomi L.
     orcid: https://orcid.org/0000-0001-6315-3707
   - family-names: Kalita
     given-names: Patrick
+    orcid: https://orcid.org/0000-0002-6150-307X
   - family-names: Miller
     given-names: Mark A.
   - family-names: Patil
     given-names: Sujay
+    orcid: https://orcid.org/0000-0001-6142-1106
   - family-names: Schaper
     given-names: Kevin
+    orcid: https://orcid.org/0000-0003-3311-7320
   - family-names: Bizon
     given-names: Chris
+    orcid: https://orcid.org/0000-0002-9491-7674
   - family-names: Caufield
     given-names: J. Harry
+    orcid: https://orcid.org/0000-0001-5705-7831
   - family-names: Cirujano Cuesta
     given-names: Silvano
   - family-names: Cox
     given-names: Corey
+    orcid: https://orcid.org/0000-0001-9042-5982
   - family-names: Dekervel
     given-names: Frank
+    orcid: https://orcid.org/0009-0008-4913-7127
   - family-names: Dooley
     given-names: Damion M.
+    orcid: https://orcid.org/0000-0002-8844-9165
   - family-names: Duncan
     given-names: William D.
+    orcid: https://orcid.org/0000-0001-9625-1899
   - family-names: Fliss
     given-names: Tim
+    orcid: https://orcid.org/0000-0003-3303-658X
   - family-names: Gehrke
     given-names: Sarah
+    orcid: https://orcid.org/0000-0003-3245-2880
   - family-names: Graefe
     given-names: Adam S.L.
+    orcid: https://orcid.org/0009-0004-8124-8864
   - family-names: Hegde
     given-names: Harshad
+    orcid: https://orcid.org/0000-0002-2411-565X
   - family-names: Ireland
     given-names: AJ
+    orcid: https://orcid.org/0000-0003-1982-9065
   - family-names: Jacobsen
     given-names: Julius O.B.
+    orcid: https://orcid.org/0000-0002-3265-1591
   - family-names: Krishnamurthy
     given-names: Madan
+    orcid: https://orcid.org/0000-0002-9767-3636
   - family-names: Kroll
     given-names: Carlo
+    orcid: https://orcid.org/0009-0008-4562-7399
   - family-names: Linke
     given-names: David
+    orcid: https://orcid.org/0000-0002-5898-1820
   - family-names: Ly
     given-names: Ryan
+    orcid: https://orcid.org/0000-0001-9238-0642
   - family-names: Matentzoglu
     given-names: Nicolas
+    orcid: https://orcid.org/0000-0002-7356-1779
   - family-names: Overton
     given-names: James A.
+    orcid: https://orcid.org/0000-0001-5139-5557
   - family-names: Saunders
     given-names: Jonny L.
+    orcid: https://orcid.org/0000-0003-0545-5066
   - family-names: Unni
     given-names: Deepak R.
+    orcid: https://orcid.org/0000-0002-3583-7340
   - family-names: Vaidya
     given-names: Gaurav
+    orcid: https://orcid.org/0000-0003-0587-0454
   - family-names: Vierdag
     given-names: Wouter-Michiel A.M.
-  - family-names: LinkML Community Contributors
+    orcid: https://orcid.org/0000-0003-1666-5421
+  - family-names: Putman
+    given-names: Tim
   - family-names: Ruebel
     given-names: Oliver
+    orcid: https://orcid.org/0000-0001-9902-1984
   - family-names: Chute
     given-names: Christopher G.
+    orcid: https://orcid.org/0000-0001-5437-2545
   - family-names: Brush
     given-names: Matthew H.
+    orcid: https://orcid.org/0000-0002-1048-5019
   - family-names: Haendel
     given-names: Melissa A.
     orcid: https://orcid.org/0000-0001-9114-8737
@@ -88,82 +118,109 @@ preferred-citation:
       orcid: https://orcid.org/0000-0002-8719-7760
     - family-names: Solbrig
       given-names: Harold
+      orcid: https://orcid.org/0000-0002-5928-3071
     - family-names: Harris
       given-names: Nomi L.
       orcid: https://orcid.org/0000-0001-6315-3707
     - family-names: Kalita
       given-names: Patrick
+      orcid: https://orcid.org/0000-0002-6150-307X
     - family-names: Miller
       given-names: Mark A.
     - family-names: Patil
       given-names: Sujay
+      orcid: https://orcid.org/0000-0001-6142-1106
     - family-names: Schaper
       given-names: Kevin
+      orcid: https://orcid.org/0000-0003-3311-7320
     - family-names: Bizon
       given-names: Chris
+      orcid: https://orcid.org/0000-0002-9491-7674
     - family-names: Caufield
       given-names: J. Harry
+      orcid: https://orcid.org/0000-0001-5705-7831
     - family-names: Cirujano Cuesta
       given-names: Silvano
     - family-names: Cox
       given-names: Corey
+      orcid: https://orcid.org/0000-0001-9042-5982
     - family-names: Dekervel
       given-names: Frank
+      orcid: https://orcid.org/0009-0008-4913-7127
     - family-names: Dooley
       given-names: Damion M.
+      orcid: https://orcid.org/0000-0002-8844-9165
     - family-names: Duncan
       given-names: William D.
+      orcid: https://orcid.org/0000-0001-9625-1899
     - family-names: Fliss
       given-names: Tim
+      orcid: https://orcid.org/0000-0003-3303-658X
     - family-names: Gehrke
       given-names: Sarah
+      orcid: https://orcid.org/0000-0003-3245-2880
     - family-names: Graefe
       given-names: Adam S.L.
+      orcid: https://orcid.org/0009-0004-8124-8864
     - family-names: Hegde
       given-names: Harshad
+      orcid: https://orcid.org/0000-0002-2411-565X
     - family-names: Ireland
       given-names: AJ
+      orcid: https://orcid.org/0000-0003-1982-9065
     - family-names: Jacobsen
       given-names: Julius O.B.
+      orcid: https://orcid.org/0000-0002-3265-1591
     - family-names: Krishnamurthy
       given-names: Madan
+      orcid: https://orcid.org/0000-0002-9767-3636
     - family-names: Kroll
       given-names: Carlo
+      orcid: https://orcid.org/0009-0008-4562-7399
     - family-names: Linke
       given-names: David
+      orcid: https://orcid.org/0000-0002-5898-1820
     - family-names: Ly
       given-names: Ryan
+      orcid: https://orcid.org/0000-0001-9238-0642
     - family-names: Matentzoglu
       given-names: Nicolas
+      orcid: https://orcid.org/0000-0002-7356-1779
     - family-names: Overton
       given-names: James A.
+      orcid: https://orcid.org/0000-0001-5139-5557
     - family-names: Saunders
       given-names: Jonny L.
+      orcid: https://orcid.org/0000-0003-0545-5066
     - family-names: Unni
       given-names: Deepak R.
+      orcid: https://orcid.org/0000-0002-3583-7340
     - family-names: Vaidya
       given-names: Gaurav
+      orcid: https://orcid.org/0000-0003-0587-0454
     - family-names: Vierdag
       given-names: Wouter-Michiel A.M.
-    - family-names: Putman
-      given-names: Tim
-    - family-names: LinkML Community Contributors
+      orcid: https://orcid.org/0000-0003-1666-5421
     - family-names: Ruebel
       given-names: Oliver
+      orcid: https://orcid.org/0000-0001-9902-1984
     - family-names: Chute
       given-names: Christopher G.
+      orcid: https://orcid.org/0000-0001-5437-2545
     - family-names: Brush
       given-names: Matthew H.
+      orcid: https://orcid.org/0000-0002-1048-5019
     - family-names: Haendel
       given-names: Melissa A.
       orcid: https://orcid.org/0000-0001-9114-8737
     - family-names: Mungall
       given-names: Christopher J.
       orcid: https://orcid.org/0000-0002-6601-2165
+    - family-names: LinkML Community Contributors
   title: "LinkML: an open data modeling framework"
   journal: GigaScience
   volume: 15
   pages: giaf152
-  year: 2025
+  year: 2026
   url: https://doi.org/10.1093/gigascience/giaf152
   doi: 10.1093/gigascience/giaf152

docs/code/deprecation.rst

@@ -3,7 +3,7 @@
 Deprecation Log
 ---------------------
 
-See `Deprecation Guide <../maintainers/deprecation.md>`_
+See :ref:`deprecation-guide`
 
 .. plot:: plots/deprecation_plot.py
 

docs/developers/schemabuilder.rst

@@ -1,10 +1,14 @@
 SchemaBuilder
 -------------
 
-The SchemaBuilder class in the linkml package provides a way of programmatically constructing
+The SchemaBuilder class in the linkml_runtime package provides a way of programmatically constructing
 schemas following a `Builder pattern <https://en.wikipedia.org/wiki/Builder_pattern>`_.
 
-.. currentmodule:: linkml.utils.schema_builder
+.. deprecated::
+   Importing ``SchemaBuilder`` from ``linkml.utils.schema_builder`` is deprecated.
+   Use ``from linkml_runtime.utils.schema_builder import SchemaBuilder`` instead.
+
+.. currentmodule:: linkml_runtime.utils.schema_builder
 
 .. autoclass:: SchemaBuilder
     :members:

docs/generators/dashboard.md

@@ -25,7 +25,7 @@ Each cell shows the aggregate result across all tests in that category. Scroll d
 | <a href="#arrays">Arrays</a> | ✅ | ❓ | ⚠️ | ⚠️ | ❓ | ⚠️ | ❓ | ⚠️ | ❓ | ⚠️ | ⚠️ | ⚠️ |
 | <a href="#boolean-expressions">Boolean Expressions</a> | ⚠️ | ⚠️ | ⚠️ | ⚠️ | ⚠️ | ⚠️ | ⚠️ | ⚠️ | ⚠️ | ⚠️ | ⚠️ | ⚠️ |
 | <a href="#cardinality-presence">Cardinality & Presence</a> | ⚠️ | ⚠️ | ✅ | ⚠️ | ⚠️ | ⚠️ | ⚠️ | ⚠️ | ⚠️ | ⚠️ | ⚠️ | ⚠️ |
-| <a href="#core-structure">Core Structure</a> | ⚠️ | ⚠️ | ✅ | ⚠️ | ⚠️ | ⚠️ | ⚠️ | ⚠️ | ⚠️ | ⚠️ | ⚠️ | ⚠️ |
+| <a href="#core-structure">Core Structure</a> | ⚠️ | ⚠️ | ⚠️ | ❓ | ⚠️ | ❓ | ⚠️ | ✅ | ⚠️ | ❓ | ⚠️ | ✅ |
 | <a href="#defaults-computed">Defaults & Computed</a> | ✅ | ✅ | ⚠️ | ❓ | ✅ | ❓ | ❓ | ✅ | ⚠️ | ❓ | ✅ | ✅ |
 | <a href="#enumerations">Enumerations</a> | ⚠️ | ⚠️ | ✅ | ⚠️ | ⚠️ | ⚠️ | ⚠️ | ⚠️ | ⚠️ | ⚠️ | ⚠️ | ⚠️ |
 | <a href="#identity-keys">Identity & Keys</a> | ⚠️ | ⚠️ | ⚠️ | ⚠️ | ⚠️ | ⚠️ | ⚠️ | ⚠️ | ⚠️ | ⚠️ | ❓ | ⚠️ |
@@ -37,25 +37,26 @@ Each cell shows the aggregate result across all tests in that category. Scroll d
 | <a href="#schema-level">Schema-Level</a> | ✅ | ✅ | ✅ | ❓ | ⚠️ | ❓ | ❓ | ✅ | ✅ | ❓ | ⚠️ | ✅ |
 | <a href="#slot-typing-ranges">Slot Typing & Ranges</a> | ⚠️ | ⚠️ | ⚠️ | ❓ | ⚠️ | ⚠️ | ⚠️ | ✅ | ⚠️ | ❓ | ⚠️ | ⚠️ |
 | <a href="#value-constraints">Value Constraints</a> | ⚠️ | ⚠️ | ⚠️ | ⚠️ | ⚠️ | ⚠️ | ⚠️ | ⚠️ | ⚠️ | ⚠️ | ⚠️ | ⚠️ |
+| <a href="#uncategorized">Uncategorized</a> | ⚠️ | ⚠️ | ✅ | ⚠️ | ⚠️ | ⚠️ | ❓ | ⚠️ | ⚠️ | ⚠️ | ❓ | ⚠️ |
 
 ## Coverage Scores
 
 Percentage of tests where the generator fully implements the feature (excluding not-applicable).
 
 | Generator | Implements | Partial | Ignores | N/A | Total | Score |
 |-----------|:----------:|:-------:|:-------:|:---:|:-----:|:-----:|
-| Pydantic | 29 | 31 | 1 | 0 | 61 | 48% |
-| Python DC | 16 | 36 | 9 | 0 | 61 | 26% |
-| JSON Schema | 39 | 20 | 2 | 0 | 61 | 64% |
-| Java | 0 | 22 | 39 | 0 | 61 | 0% |
-| SHACL | 19 | 23 | 19 | 0 | 61 | 31% |
-| ShEx | 0 | 23 | 38 | 0 | 61 | 0% |
-| OWL | 0 | 25 | 36 | 0 | 61 | 0% |
-| JSON-LD Ctx | 33 | 22 | 6 | 0 | 61 | 54% |
-| SQLite DDL | 12 | 38 | 11 | 0 | 61 | 20% |
-| Postgres DDL | 0 | 22 | 39 | 0 | 61 | 0% |
-| Pandera | 14 | 27 | 20 | 0 | 61 | 23% |
-| Polars Schema | 27 | 21 | 13 | 0 | 61 | 44% |
+| Pydantic | 29 | 33 | 1 | 0 | 63 | 46% |
+| Python DC | 16 | 37 | 10 | 0 | 63 | 25% |
+| JSON Schema | 38 | 23 | 2 | 0 | 63 | 60% |
+| Java | 0 | 23 | 40 | 0 | 63 | 0% |
+| SHACL | 19 | 24 | 20 | 0 | 63 | 30% |
+| ShEx | 0 | 23 | 40 | 0 | 63 | 0% |
+| OWL | 0 | 25 | 38 | 0 | 63 | 0% |
+| JSON-LD Ctx | 34 | 23 | 6 | 0 | 63 | 54% |
+| SQLite DDL | 12 | 39 | 12 | 0 | 63 | 19% |
+| Postgres DDL | 0 | 22 | 41 | 0 | 63 | 0% |
+| Pandera | 14 | 27 | 22 | 0 | 63 | 22% |
+| Polars Schema | 28 | 22 | 13 | 0 | 63 | 44% |
 
 ## Details by Category
 
@@ -91,11 +92,11 @@ Percentage of tests where the generator fully implements the feature (excluding
 
 | Test | Pydantic | Python DC | JSON Schema | Java | SHACL | ShEx | OWL | JSON-LD Ctx | SQLite DDL | Postgres DDL | Pandera | Polars Schema |
 |------| :-: | :-: | :-: | :-: | :-: | :-: | :-: | :-: | :-: | :-: | :-: | :-: |
-| Abstract classes | ⚠️ | ⚠️ | ✅ | ⚠️ | ⚠️ | ⚠️ | ⚠️ | ⚠️ | ⚠️ | ⚠️ | ⚠️ | ⚠️ |
+| Abstract classes | ⚠️ | ⚠️ | ⚠️ | ❓ | ⚠️ | ❓ | ⚠️ | ✅ | ⚠️ | ❓ | ⚠️ | ✅ |
 | Attribute refinement | ✅ | ✅ | ✅ | ❓ | ✅ | ❓ | ❓ | ✅ | ✅ | ❓ | ⚠️ | ✅ |
 | Attributes | ✅ | ✅ | ✅ | ❓ | ✅ | ❓ | ❓ | ✅ | ✅ | ❓ | ✅ | ✅ |
-| Class inheritance (is_a) | ⚠️ | ⚠️ | ✅ | ❓ | ⚠️ | ❓ | ⚠️ | ✅ | ⚠️ | ❓ | ⚠️ | ✅ |
-| Mixins | ⚠️ | ⚠️ | ✅ | ❓ | ⚠️ | ❓ | ⚠️ | ✅ | ⚠️ | ❓ | ⚠️ | ✅ |
+| Class inheritance (is_a) | ⚠️ | ⚠️ | ⚠️ | ❓ | ⚠️ | ❓ | ⚠️ | ✅ | ⚠️ | ❓ | ⚠️ | ✅ |
+| Mixins | ⚠️ | ⚠️ | ⚠️ | ❓ | ⚠️ | ❓ | ⚠️ | ✅ | ⚠️ | ❓ | ⚠️ | ✅ |
 | Slot inheritance | ✅ | ⚠️ | ✅ | ❓ | ⚠️ | ❓ | ❓ | ✅ | ⚠️ | ❓ | ⚠️ | ✅ |
 | Slot usage | ✅ | ⚠️ | ✅ | ❓ | ⚠️ | ❓ | ❓ | ✅ | ⚠️ | ❓ | ⚠️ | ✅ |
 
@@ -195,6 +196,13 @@ Percentage of tests where the generator fully implements the feature (excluding
 | Min/max value | ✅ | ⚠️ | ✅ | ❓ | ✅ | ❓ | ❓ | ✅ | ⚠️ | ❓ | ✅ | ✅ |
 | Regex pattern | ⚠️ | ⚠️ | ⚠️ | ❓ | ✅ | ❓ | ❓ | ✅ | ⚠️ | ❓ | ⚠️ | ✅ |
 
+### Uncategorized
+
+| Test | Pydantic | Python DC | JSON Schema | Java | SHACL | ShEx | OWL | JSON-LD Ctx | SQLite DDL | Postgres DDL | Pandera | Polars Schema |
+|------| :-: | :-: | :-: | :-: | :-: | :-: | :-: | :-: | :-: | :-: | :-: | :-: |
+| range expression booleans | ⚠️ | ❓ | ✅ | ⚠️ | ❓ | ❓ | ❓ | ⚠️ | ❓ | ❓ | ❓ | ⚠️ |
+| range expression nesting | ⚠️ | ⚠️ | ✅ | ⚠️ | ⚠️ | ⚠️ | ❓ | ⚠️ | ⚠️ | ⚠️ | ❓ | ⚠️ |
+
 ---
 
 *This dashboard is auto-generated from compliance test results. To update: run the compliance tests with `--with-output`, then run `uv run python scripts/generate_dashboard.py`. To add features, write a new compliance test and decorate it with `@feature_category("Category Name", "Display Name")`.*

docs/get-involved/Community-Meetings.md

@@ -10,7 +10,7 @@ Join the LinkML community for regular sessions featuring presentations on LinkML
 [Sarah Gehrke](https://tislab.org/members/sarah-gehrke.html), University of North Carolina at Chapel Hill <br>
 
 ## What to present at a Community meeting?
-Contact Sarah Gehrke on [Slack](https://join.slack.com/t/obo-communitygroup/shared_invite/zt-1oq48ttk7-kKo0i6TwntYtAq~Jcjjg4g) and they can help get you on the schedule!
+Contact Sarah Gehrke on Slack and they can help get you on the schedule!
 
 ## Helpful links
 - [Community Meeting Agenda](https://docs.google.com/document/d/1MStpDyh9LOZYJTjLtnpOsNYc3HaeU-bz0CHAI9xOjfQ/edit?tab=t.0#heading=h.6sqkx1xhumse): In this document you can find the zoom link to join the monthly call as well as recordings of previous sessions.
@@ -20,8 +20,8 @@ Contact Sarah Gehrke on [Slack](https://join.slack.com/t/obo-communitygroup/shar
 
 | Date | Presenter 1	| Topic 1	| Presenter 2	| Topic 2 |
 | :---: | :---: | :---: | :----: | :---: |
-| May 21, 2026 | | Open slot! Contact Sarah if you'd like to present.| |Open slot! Contact Sarah if you'd like to present.| |
-| April 19, 2026 | Daniel Kapitan| [LinkML in Hospital ETL pipelines](https://github.com/linkml/linkml/pull/3257#issuecomment-4055029669)| | Open slot! Contact Sarah if you'd like to present.| |
+| May 21, 2026 | Inge Vejsbjerg | [LinkML for AI Governance at IBM](https://ibm.github.io/ai-atlas-nexus/) |Sierra Moxon|LinkML Microschemas| |
+| April 19, 2026 | Daniel Kapitan| [LinkML in Hospital ETL pipelines](https://github.com/linkml/linkml/pull/3257#issuecomment-4055029669)| Community Discussion Topics| | |
 | [March 19, 2026](https://docs.google.com/presentation/d/13gQtrlTJcF3V8XzW4ruva9_D1tzyp8ZzDLATp2TuuMY/edit?slide=id.g36e69bd970c_1_50#slide=id.g36e69bd970c_1_50)| Damien Goutte-Gattat | [linkml-java](https://github.com/gouttegd/linkml-java): a LinkML runtime library for the Java language ([Slides](https://drive.google.com/file/d/1-hXJo9FFmIvpERrKNJjb_-tTO_6354cM/view?usp=sharing))| Chris Mungall| Validating dynamic value sets with [linkml-term-validator](https://github.com/linkml/linkml-term-validator) ([Slides](https://docs.google.com/presentation/d/1lhdDImxBQDaj8yFgpRYF_pnCTNDVn3Ilkb_pHfoR7Po/edit?slide=id.p#slide=id.p))|
 | [February 19, 2026](https://docs.google.com/presentation/d/1Wa_vX8JhLeA_5b7dsRDDoWAA7uTG9fsiH0nMYjxjSz0/edit?slide=id.g36e69bd970c_1_50#slide=id.g36e69bd970c_1_50) | David Linke | [The new LinkML project template based on copier and why we built it](https://zenodo.org/records/18704589) <br> Repo: [linkml-project-copier](https://github.com/linkml/linkml-project-copier) | Nico Matentzoglu | [The LinkML Community Governance & Community Discussion](https://drive.google.com/file/d/1s2Fslc2pN6ig2-TDkdtzjtBKa5z1oFqC/view?usp=sharing) |
 | [January 15, 2026](https://docs.google.com/presentation/d/1ed5P1BsAylCiifEw6ATHmnNY24j91mViK62oZKcVYyo/edit?slide=id.g36e69bd970c_1_50#slide=id.g36e69bd970c_1_50) | Adam Graefe | [LinkML in Rare Diseases: Ontology-Based Interoperability for Clinical Registries and Analysis](https://docs.google.com/presentation/d/1Zeme_WzQOMyyMjHkx5UIkvZMyTIzDVHy/edit?usp=sharing&ouid=113016219988110049925&rtpof=true&sd=true) | Community Discussion Topics | Markdown-data-dictionary generator with Vlad Korolev |

packages/linkml/src/linkml/generators/docgen/class.md.jinja2

@@ -1,3 +1,8 @@
+---
+search:
+  boost: {% if element.deprecated %}0.5{% else %}10.0{% endif %}
+---
+
 {%- if element.title %}
     {%- set title = element.title ~ ' (' ~ element.name ~ ')' -%}
 {%- else %}
@@ -34,6 +39,8 @@ _{{ element_description_line }}_
 {% endfor %}
 {% endif %}
 
+<div data-search-exclude markdown="1">
+
 {% if element.abstract %}
 * __NOTE__: this is an abstract class and should not be instantiated directly
 {% endif %}
@@ -279,3 +286,5 @@ The class must not satisfy any of:
 {%- if footer -%}
 {{ footer }}
 {%- endif -%}
+
+</div>

packages/linkml/src/linkml/generators/docgen/enum.md.jinja2

@@ -1,3 +1,8 @@
+---
+search:
+  boost: {% if element.deprecated %}0.5{% else %}2.0{% endif %}
+---
+
 {%- if element.title and element.title != element.name %}
     {%- set title = element.title ~ ' (' ~ element.name ~ ')' -%}
 {%- else %}
@@ -13,6 +18,8 @@ _{{ element_description_line }}_
 {% endfor %}
 {% endif %}
 
+<div data-search-exclude markdown="1">
+
 URI: {{ gen.uri_link(element) }}
 
 {%- if element.enum_uri %}
@@ -137,3 +144,5 @@ _This is a dynamic enum_
 {{ gen.yaml(element) }}
 ```
 </details>
+
+</div>