From c3ceab542342d15d57df4213fda96daa9631ce6f Mon Sep 17 00:00:00 2001
From: Kimberly Meechan <24316371+K-Meech@users.noreply.github.com>
Date: Tue, 16 Apr 2024 10:54:44 +0100
Subject: [PATCH 1/3] add codecov token

---
 .github/workflows/test_and_deploy.yml | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/.github/workflows/test_and_deploy.yml b/.github/workflows/test_and_deploy.yml
index 1ae8ae98..2ff3a525 100644
--- a/.github/workflows/test_and_deploy.yml
+++ b/.github/workflows/test_and_deploy.yml
@@ -65,6 +65,7 @@ jobs:
       - uses: neuroinformatics-unit/actions/test@v2
         with:
           python-version: ${{ matrix.python-version }}
+          secret-codecov-token: ${{ secrets.CODECOV_TOKEN }}
           use-xvfb: true
 
   test_numba_disabled:
@@ -89,6 +90,7 @@ jobs:
       - uses: neuroinformatics-unit/actions/test@v2
         with:
           python-version: "3.10"
+          secret-codecov-token: ${{ secrets.CODECOV_TOKEN }}
           codecov-flags: "numba"
 
   # Run brainglobe-workflows brainmapper-CLI tests to check for

From ab261f2f8fe4d1a296cd52f316cf443077d04508 Mon Sep 17 00:00:00 2001
From: Kimberly Meechan <24316371+K-Meech@users.noreply.github.com>
Date: Tue, 16 Apr 2024 13:53:31 +0100
Subject: [PATCH 2/3] generate xml coverage report

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

diff --git a/pyproject.toml b/pyproject.toml
index 6e5ac59d..2eeeb61e 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -120,7 +120,7 @@ python =
     3.10: py310
 
 [testenv]
-commands = python -m pytest -v --color=yes
+commands = python -m pytest -v --color=yes --cov=cellfinder --cov-report=xml
 deps =
     pytest
     pytest-cov

From b91a36af2221260f482af805296cae8047ec7255 Mon Sep 17 00:00:00 2001
From: Kimberly Meechan <24316371+K-Meech@users.noreply.github.com>
Date: Thu, 18 Apr 2024 10:04:07 +0100
Subject: [PATCH 3/3] add timeout to testing jobs

---
 .github/workflows/test_and_deploy.yml | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/.github/workflows/test_and_deploy.yml b/.github/workflows/test_and_deploy.yml
index 2ff3a525..2bf9e976 100644
--- a/.github/workflows/test_and_deploy.yml
+++ b/.github/workflows/test_and_deploy.yml
@@ -71,6 +71,7 @@ jobs:
   test_numba_disabled:
     needs: [linting, manifest]
     name: Run tests with numba disabled
+    timeout-minutes: 60
     runs-on: ubuntu-latest
     env:
        NUMBA_DISABLE_JIT: "1"
@@ -98,6 +99,7 @@ jobs:
   test_brainmapper_cli:
     needs: [linting, manifest]
     name: Run brainmapper tests to check for breakages
+    timeout-minutes: 60
     runs-on: ubuntu-latest
     steps:
       - name: Cache tensorflow model