Try adding the variables under env.

This looks like a known issue with containers...

actions/upload-artifact#216 (comment)

.github/workflows/tests_run.yml

@@ -8,6 +8,12 @@ on:
     branches:
       - main
 
+env:
+  CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
+  GITHUB_REPOSITORY: ${{ github.repository }}
+  GITHUB_REF: ${{ github.ref }}
+  GITHUB_SHA: ${{ github.sha }}
+
 jobs:
   build-linux:
     runs-on: iris-gpu
@@ -23,9 +29,6 @@ jobs:
     steps:
       - name: Checkout repository code
         uses: actions/checkout@v4
-        with:
-          ref: "main"
-          fetch-depth: 0
 
       - name: Create conda environment
         uses: mamba-org/setup-micromamba@v1
@@ -54,7 +57,6 @@ jobs:
       - name: Upload coverage to Codecov
         uses: codecov/codecov-action@v3
         with:
-          working-directory: /__w/httomolibgpu/httomolibgpu
           token: ${{ secrets.CODECOV_TOKEN }}
           files: /home/runner/coverage.xml
           fail_ci_if_error: true