From e126b47764a0e0fd3e7e92f8cfe2eb455d589106 Mon Sep 17 00:00:00 2001
From: Jordan Dialpuri <44945647+Dialpuri@users.noreply.github.com>
Date: Tue, 24 Mar 2026 18:16:19 +0000
Subject: [PATCH 1/5] Update test workflows to use `uv` for package management

---
 .github/workflows/test-python.yml | 40 ++++++++++++++++++-------------
 1 file changed, 23 insertions(+), 17 deletions(-)

diff --git a/.github/workflows/test-python.yml b/.github/workflows/test-python.yml
index b1f2f71..4f2c312 100644
--- a/.github/workflows/test-python.yml
+++ b/.github/workflows/test-python.yml
@@ -41,12 +41,15 @@ jobs:
           ./get_sources
         working-directory: ./package
 
+      - name: Install uv
+        uses: astral-sh/setup-uv@v7
+
       - name: Install NucleoFind
-        run: pip install .
+        run: uv pip install .
         working-directory: ./package
 
       - name: Install pytest
-        run: pip install pytest
+        run: uv pip install pytest
 
       - name: Install NucleoFind models
         run: |
@@ -54,7 +57,7 @@ jobs:
           nucleofind-install -m nano
 
       - name: Run tests
-        run : pytest tests
+        run: pytest tests
         working-directory: ./package
 
   run_windows_tests:
@@ -76,31 +79,34 @@ jobs:
           sh get_sources
         working-directory: ./package
 
+      - name: Install uv
+        uses: astral-sh/setup-uv@v7
+
       - name: Install NucleoFind
-        run: pip install .
+        run: uv pip install .
         working-directory: ./package
 
       - name: Install pytest
-        run: pip install pytest
+        run: uv pip install pytest
 
       - name: Install NucleoFind models
-        run:  |
+        run: |
           nucleofind-install -m nano
           nucleofind-install -m core
 
       - name: Run tests
-        run : pytest tests
+        run: pytest tests
         working-directory: ./package
 
 
   debug:
-      needs: [run_unix_tests, run_windows_tests]
-      runs-on: ubuntu-latest
-      if: ${{ failure() }}
-      steps:
-        - uses: actions/checkout@v3
-        - name: Notify chat
-          uses: teknatha136/actions-google-chat-text-message@main
-          with:
-            google-chat-webhook: ${{ secrets.WEBHOOK_URL }}
-            text-message: ${{ github.actor }} attempted to merge a change into NucleoFind, but this PR failed testing. Link ${{ github.server_url }}/${{ github.repository }}/actions/runs/${{ github.run_id }} \n
\ No newline at end of file
+    needs: [ run_unix_tests, run_windows_tests ]
+    runs-on: ubuntu-latest
+    if: ${{ failure() }}
+    steps:
+      - uses: actions/checkout@v3
+      - name: Notify chat
+        uses: teknatha136/actions-google-chat-text-message@main
+        with:
+          google-chat-webhook: ${{ secrets.WEBHOOK_URL }}
+          text-message: ${{ github.actor }} attempted to merge a change into NucleoFind, but this PR failed testing. Link ${{ github.server_url }}/${{ github.repository }}/actions/runs/${{ github.run_id }} \n
\ No newline at end of file

From 3852bf6b5217cf4386de9ba2f695c038d424e46a Mon Sep 17 00:00:00 2001
From: Jordan Dialpuri <44945647+Dialpuri@users.noreply.github.com>
Date: Tue, 24 Mar 2026 18:20:45 +0000
Subject: [PATCH 2/5] Update test workflows to replace `setup-python` with `uv`
 for Python management and test execution

---
 .github/workflows/test-python.yml | 20 ++++++++++++--------
 1 file changed, 12 insertions(+), 8 deletions(-)

diff --git a/.github/workflows/test-python.yml b/.github/workflows/test-python.yml
index 4f2c312..a5d386d 100644
--- a/.github/workflows/test-python.yml
+++ b/.github/workflows/test-python.yml
@@ -16,9 +16,6 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v4
-      - uses: actions/setup-python@v5
-        with:
-          python-version: '3.9'
 
       - name: Install Clang
         run: |
@@ -44,6 +41,11 @@ jobs:
       - name: Install uv
         uses: astral-sh/setup-uv@v7
 
+      - name: Set up Python
+        run: uv python install
+        with:
+          python-version: '3.9'
+
       - name: Install NucleoFind
         run: uv pip install .
         working-directory: ./package
@@ -57,7 +59,7 @@ jobs:
           nucleofind-install -m nano
 
       - name: Run tests
-        run: pytest tests
+        run: uv run pytest tests
         working-directory: ./package
 
   run_windows_tests:
@@ -65,9 +67,6 @@ jobs:
     runs-on: windows-latest
     steps:
       - uses: actions/checkout@v4
-      - uses: actions/setup-python@v4
-        with:
-          python-version: '3.9'
 
       - uses: TheMrMilchmann/setup-msvc-dev@v3
         with:
@@ -82,6 +81,11 @@ jobs:
       - name: Install uv
         uses: astral-sh/setup-uv@v7
 
+      - name: Set up Python
+        run: uv python install
+        with:
+          python-version: '3.9'
+
       - name: Install NucleoFind
         run: uv pip install .
         working-directory: ./package
@@ -95,7 +99,7 @@ jobs:
           nucleofind-install -m core
 
       - name: Run tests
-        run: pytest tests
+        run: uv run pytest tests
         working-directory: ./package
 
 

From d4088497bc2ddfc53b61121aacdd4c0898797343 Mon Sep 17 00:00:00 2001
From: Jordan Dialpuri <44945647+Dialpuri@users.noreply.github.com>
Date: Tue, 24 Mar 2026 18:21:35 +0000
Subject: [PATCH 3/5] Clean up workflow: fix formatting and adjust step spacing
 in `test-python.yml`.

---
 .github/workflows/test-python.yml | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/.github/workflows/test-python.yml b/.github/workflows/test-python.yml
index a5d386d..b3cb986 100644
--- a/.github/workflows/test-python.yml
+++ b/.github/workflows/test-python.yml
@@ -40,11 +40,11 @@ jobs:
 
       - name: Install uv
         uses: astral-sh/setup-uv@v7
+        with:
+          python-version: '3.9'
 
       - name: Set up Python
         run: uv python install
-        with:
-          python-version: '3.9'
 
       - name: Install NucleoFind
         run: uv pip install .
@@ -80,11 +80,11 @@ jobs:
 
       - name: Install uv
         uses: astral-sh/setup-uv@v7
+        with:
+          python-version: '3.9'
 
       - name: Set up Python
         run: uv python install
-        with:
-          python-version: '3.9'
 
       - name: Install NucleoFind
         run: uv pip install .

From 69b0cb517eb26466d9a5701ec317c5a19da8b662 Mon Sep 17 00:00:00 2001
From: Jordan Dialpuri <44945647+Dialpuri@users.noreply.github.com>
Date: Tue, 24 Mar 2026 18:22:55 +0000
Subject: [PATCH 4/5] Set `UV_SYSTEM_PYTHON` environment variable for all test
 workflows

---
 .github/workflows/test-python.yml | 6 ++++++
 1 file changed, 6 insertions(+)

diff --git a/.github/workflows/test-python.yml b/.github/workflows/test-python.yml
index b3cb986..e80a2db 100644
--- a/.github/workflows/test-python.yml
+++ b/.github/workflows/test-python.yml
@@ -12,6 +12,9 @@ on:
 
 jobs:
   run_unix_tests:
+    env:
+      UV_SYSTEM_PYTHON: 1
+
     name: Run Python tests on Ubuntu
     runs-on: ubuntu-latest
     steps:
@@ -65,6 +68,9 @@ jobs:
   run_windows_tests:
     name: Run Python tests on Windows
     runs-on: windows-latest
+    env:
+      UV_SYSTEM_PYTHON: 1
+
     steps:
       - uses: actions/checkout@v4
 

From f3b6677a550801230ad0c82e809f6ca3ebdd6d10 Mon Sep 17 00:00:00 2001
From: Jordan Dialpuri <44945647+Dialpuri@users.noreply.github.com>
Date: Tue, 24 Mar 2026 18:26:36 +0000
Subject: [PATCH 5/5] Update `test-python.yml` to add `--break-system-packages`
 flag for pip commands

---
 .github/workflows/test-python.yml | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/.github/workflows/test-python.yml b/.github/workflows/test-python.yml
index e80a2db..083ab1a 100644
--- a/.github/workflows/test-python.yml
+++ b/.github/workflows/test-python.yml
@@ -50,11 +50,11 @@ jobs:
         run: uv python install
 
       - name: Install NucleoFind
-        run: uv pip install .
+        run: uv pip install . --break-system-packages
         working-directory: ./package
 
       - name: Install pytest
-        run: uv pip install pytest
+        run: uv pip install pytest --break-system-packages
 
       - name: Install NucleoFind models
         run: |
@@ -93,7 +93,7 @@ jobs:
         run: uv python install
 
       - name: Install NucleoFind
-        run: uv pip install .
+        run: uv pip install . --break-system-packages
         working-directory: ./package
 
       - name: Install pytest
@@ -105,7 +105,7 @@ jobs:
           nucleofind-install -m core
 
       - name: Run tests
-        run: uv run pytest tests
+        run: uv run pytest tests --break-system-packages
         working-directory: ./package