From 9cf4e1989c8ff4d7aac188d81dc10172921a539a Mon Sep 17 00:00:00 2001
From: Kevin Schaper <kevinschaper@gmail.com>
Date: Fri, 5 Sep 2025 13:55:01 -0700
Subject: [PATCH] use experimental monorepo of linkml + linkml_runtime in
 biolink

---
 poetry.lock    | 34 +++++++++++++++-------------------
 pyproject.toml |  2 +-
 2 files changed, 16 insertions(+), 20 deletions(-)

diff --git a/poetry.lock b/poetry.lock
index 42767ef109..2a9e9dffdd 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -1,4 +1,4 @@
-# This file is automatically @generated by Poetry 2.1.2 and should not be changed by hand.
+# This file is automatically @generated by Poetry 2.1.4 and should not be changed by hand.
 
 [[package]]
 name = "alabaster"
@@ -1070,26 +1070,24 @@ referencing = ">=0.31.0"
 
 [[package]]
 name = "linkml"
-version = "1.9.2"
+version = "1.9.4.post1262.dev0+d7af431f2"
 description = "Linked Open Data Modeling Language"
 optional = false
 python-versions = ">=3.9"
 groups = ["main", "dev"]
-files = [
-    {file = "linkml-1.9.2-py3-none-any.whl", hash = "sha256:4c9cf217948367df8a20cdf68e8f6da24ba23ab97a551f8ae32e9d4264e702cc"},
-    {file = "linkml-1.9.2.tar.gz", hash = "sha256:2f9141d2bc8a93bfe1d4b86a015ad0acbb94c2af099177f5687a50d3331d2b34"},
-]
+files = []
+develop = false
 
 [package.dependencies]
 antlr4-python3-runtime = ">=4.9.0,<4.10"
-click = ">=7.0"
+click = ">=8.0,<8.2"
 graphviz = ">=0.10.1"
 hbreader = "*"
 isodate = ">=0.6.0"
 jinja2 = ">=3.1.0"
 jsonasobj2 = ">=1.0.3,<2.0.0"
 jsonschema = {version = ">=4.0.0", extras = ["format"]}
-linkml-runtime = ">=1.9.2,<2.0.0"
+linkml-runtime = ">=1.9.5,<2.0.0"
 openpyxl = "*"
 parse = "*"
 prefixcommons = ">=0.1.7"
@@ -1107,24 +1105,22 @@ sqlalchemy = ">=1.4.31"
 typing-extensions = {version = ">=4.6.0", markers = "python_version < \"3.12\""}
 watchdog = ">=0.9.0"
 
-[package.extras]
-black = ["black (>=24.0.0)"]
-numpydantic = ["numpydantic (>=1.6.1)"]
-pandera = ["pandera (>=0.19.0)"]
-polars-lts-cpu = ["polars-lts-cpu (>=1.0.0)"]
-shacl = ["pyshacl (>=0.25.0)"]
-tests = ["black (>=24.0.0)", "numpydantic (>=1.6.1)", "pyshacl (>=0.25.0)"]
+[package.source]
+type = "git"
+url = "https://github.com/linkml/linkml.git"
+reference = "merge-linkml-runtime-into-linkml"
+resolved_reference = "d7af431f2c9b61c94cfd7eadbd1344346e1815ce"
 
 [[package]]
 name = "linkml-runtime"
-version = "1.9.3"
+version = "1.9.5"
 description = "Runtime environment for LinkML, the Linked open data modeling language"
 optional = false
 python-versions = ">=3.9"
 groups = ["main", "dev"]
 files = [
-    {file = "linkml_runtime-1.9.3-py3-none-any.whl", hash = "sha256:39a8aa51b40decd58fd04f4c02a213aad06b971df4c042aa7764f4b75cc09aa8"},
-    {file = "linkml_runtime-1.9.3.tar.gz", hash = "sha256:1b65358bf91868b7607675abb98c26597873bb45f73ab309b7d4c31a84e58e1b"},
+    {file = "linkml_runtime-1.9.5-py3-none-any.whl", hash = "sha256:fece3e8aa25a4246165c6528b6a7fe83a929b985d2ce1951cc8a0f4da1a30b90"},
+    {file = "linkml_runtime-1.9.5.tar.gz", hash = "sha256:78dc1383adf11ad5f20bb11b6adde56ed566fbd2429a292d57699ad4596c738a"},
 ]
 
 [package.dependencies]
@@ -3184,4 +3180,4 @@ docs = []
 [metadata]
 lock-version = "2.1"
 python-versions = "^3.9"
-content-hash = "fd1cd680472fb2b7d670c6065b087f914ecd29e17d58185f62966e3a50c09288"
+content-hash = "e0e4040b6df60e2a5f0a6c6658c49bf4cac839ed3d41ef18509f73fd9fffe1a4"
diff --git a/pyproject.toml b/pyproject.toml
index 8ad234b230..0d38d4e3a6 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -23,7 +23,7 @@ yamllint = "^1.35.1"
 path = "^17.0.0"
 linkml-runtime = "^1.8.3"
 requests = ">=2.32.3"
-linkml = "^1.9.1"
+linkml = {git = "https://github.com/linkml/linkml.git", rev = "merge-linkml-runtime-into-linkml"}
 click = ">8.0.0,<8.2.0"
 
 [tool.poetry-dynamic-versioning]