From 435aa3bd27857d8f99f33f380f970eaad8a9fea7 Mon Sep 17 00:00:00 2001
From: "github-actions[bot]" <github-actions[bot]@users.noreply.github.com>
Date: Wed, 27 May 2026 13:18:03 +0100
Subject: [PATCH 1/3] fix(medcat): CU-869ddh1jv: Fix lock file issue.

Issue was introduced in #503. Looks like because I didn't update uv.lock the entire dependency resolution was redone and broke.
This PR should - hopefully - fix it.
---
 medcat-v2/uv.lock | 35 ++++++++++++++++++++++++++++++++++-
 1 file changed, 34 insertions(+), 1 deletion(-)

diff --git a/medcat-v2/uv.lock b/medcat-v2/uv.lock
index e3e671daa..47159573c 100644
--- a/medcat-v2/uv.lock
+++ b/medcat-v2/uv.lock
@@ -1,6 +1,6 @@
 version = 1
 revision = 3
-requires-python = ">=3.9"
+requires-python = ">=3.10"
 resolution-markers = [
     "python_full_version >= '3.13'",
     "python_full_version == '3.12.*'",
@@ -873,6 +873,7 @@ deid = [
 ]
 dev = [
     { name = "mypy" },
+    { name = "pooch" },
     { name = "ruff" },
     { name = "types-pyyaml" },
     { name = "types-setuptools" },
@@ -898,6 +899,11 @@ spacy = [
     { name = "spacy" },
 ]
 
+[package.dev-dependencies]
+dev = [
+    { name = "pooch" },
+]
+
 [package.metadata]
 requires-dist = [
     { name = "datasets", marker = "extra == 'deid'", specifier = ">=2.2.2,<3.0.0" },
@@ -908,6 +914,7 @@ requires-dist = [
     { name = "packaging" },
     { name = "pandas", specifier = ">=2.2,<3.0" },
     { name = "peft", marker = "extra == 'meta-cat'", specifier = ">0.8.2,<1.0" },
+    { name = "pooch", marker = "extra == 'dev'" },
     { name = "pyahocorasick", marker = "extra == 'dict-ner'", specifier = ">=2.1.0,<3.0" },
     { name = "pydantic", specifier = ">2.0" },
     { name = "pyyaml" },
@@ -936,6 +943,9 @@ requires-dist = [
 ]
 provides-extras = ["dev", "spacy", "meta-cat", "dict-ner", "deid", "rel-cat", "test"]
 
+[package.metadata.requires-dev]
+dev = [{ name = "pooch", specifier = ">=1.9.0" }]
+
 [[package]]
 name = "mpmath"
 version = "1.3.0"
@@ -1553,6 +1563,29 @@ wheels = [
     { url = "https://files.pythonhosted.org/packages/49/fe/a2da1627aa9cb6310b6034598363bd26ac301c4a99d21f415b1b2855891e/peft-0.17.1-py3-none-any.whl", hash = "sha256:3d129d64def3d74779c32a080d2567e5f7b674e77d546e3585138216d903f99e", size = 504896, upload-time = "2025-08-21T09:25:18.974Z" },
 ]
 
+[[package]]
+name = "platformdirs"
+version = "4.9.6"
+source = { registry = "https://pypi.org/simple" }
+sdist = { url = "https://files.pythonhosted.org/packages/9f/4a/0883b8e3802965322523f0b200ecf33d31f10991d0401162f4b23c698b42/platformdirs-4.9.6.tar.gz", hash = "sha256:3bfa75b0ad0db84096ae777218481852c0ebc6c727b3168c1b9e0118e458cf0a", size = 29400, upload-time = "2026-04-09T00:04:10.812Z" }
+wheels = [
+    { url = "https://files.pythonhosted.org/packages/75/a6/a0a304dc33b49145b21f4808d763822111e67d1c3a32b524a1baf947b6e1/platformdirs-4.9.6-py3-none-any.whl", hash = "sha256:e61adb1d5e5cb3441b4b7710bea7e4c12250ca49439228cc1021c00dcfac0917", size = 21348, upload-time = "2026-04-09T00:04:09.463Z" },
+]
+
+[[package]]
+name = "pooch"
+version = "1.9.0"
+source = { registry = "https://pypi.org/simple" }
+dependencies = [
+    { name = "packaging" },
+    { name = "platformdirs" },
+    { name = "requests" },
+]
+sdist = { url = "https://files.pythonhosted.org/packages/83/43/85ef45e8b36c6a48546af7b266592dc32d7f67837a6514d111bced6d7d75/pooch-1.9.0.tar.gz", hash = "sha256:de46729579b9857ffd3e741987a2f6d5e0e03219892c167c6578c0091fb511ed", size = 61788, upload-time = "2026-01-30T19:15:09.649Z" }
+wheels = [
+    { url = "https://files.pythonhosted.org/packages/2a/2d/d4bf65e47cea8ff2c794a600c4fd1273a7902f268757c531e0ee9f18aa58/pooch-1.9.0-py3-none-any.whl", hash = "sha256:f265597baa9f760d25ceb29d0beb8186c243d6607b0f60b83ecf14078dbc703b", size = 67175, upload-time = "2026-01-30T19:15:08.36Z" },
+]
+
 [[package]]
 name = "preshed"
 version = "3.0.10"

From 4dfb3bf039196eb5a162dfb63cc595e1e98e5deb Mon Sep 17 00:00:00 2001
From: "github-actions[bot]" <github-actions[bot]@users.noreply.github.com>
Date: Wed, 27 May 2026 14:18:21 +0100
Subject: [PATCH 2/3] CU-869ddh1jv: Disallow latest typer version

---
 medcat-v2/pyproject.toml | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/medcat-v2/pyproject.toml b/medcat-v2/pyproject.toml
index 9dd28f816..6414a68e1 100644
--- a/medcat-v2/pyproject.toml
+++ b/medcat-v2/pyproject.toml
@@ -69,6 +69,9 @@ dependencies = [ # Optional
   "pyyaml",
   "requests",
   # TODO - others
+  # NOTE: transitive dependency that breaks other deps
+  #       e.g `spacy`'s dependency `click` isn't installed
+  "typer!=0.26.2",
 ]
 
 # List additional groups of dependencies here (e.g. development

From 30541ccffc769eaca6991b76d1942a458902120e Mon Sep 17 00:00:00 2001
From: "github-actions[bot]" <github-actions[bot]@users.noreply.github.com>
Date: Wed, 27 May 2026 14:31:54 +0100
Subject: [PATCH 3/3] CU-869ddh1jv: Disallow all recent typer versions

---
 medcat-v2/pyproject.toml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/medcat-v2/pyproject.toml b/medcat-v2/pyproject.toml
index 6414a68e1..551695582 100644
--- a/medcat-v2/pyproject.toml
+++ b/medcat-v2/pyproject.toml
@@ -71,7 +71,7 @@ dependencies = [ # Optional
   # TODO - others
   # NOTE: transitive dependency that breaks other deps
   #       e.g `spacy`'s dependency `click` isn't installed
-  "typer!=0.26.2",
+  "typer!=0.26.0,!=0.26.1,!=0.26.2",
 ]
 
 # List additional groups of dependencies here (e.g. development