From 4647c2010db9f5cb5d7f6be9c7eed3923969eec1 Mon Sep 17 00:00:00 2001
From: Michal Baumgartner <michal.baumgartner@deepnote.com>
Date: Fri, 7 Nov 2025 11:03:33 +0100
Subject: [PATCH 01/15] chore(ci): Combine code coverage in CI before uploading
 to codecov

---
 .github/workflows/ci.yml | 99 ++++++++++++++++++++++++++++++++++------
 1 file changed, 85 insertions(+), 14 deletions(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 81e283f..430ebf6 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -338,30 +338,22 @@ jobs:
         env:
           TOOLKIT_VERSION: ${{ steps.version.outputs.VERSION }}
           PYTHON_VERSION: ${{ matrix.python-version }}
-          COVERAGE_FILE: coverage/.coverage.${{ matrix.python-version }}
+          COVERAGE_FILE: .coverage.${{ matrix.python-version }}
         run: |
           set -euo pipefail
 
-          # Create coverage directory
-          mkdir -p coverage
-
-          # Run tests with coverage
           poetry run pytest tests/unit \
             --cov=deepnote_toolkit \
             --cov=installer \
             --cov=deepnote_core \
             --cov-branch \
             --cov-report=term-missing:skip-covered \
-            --cov-report=xml:coverage/coverage-${PYTHON_VERSION}.xml \
-            --cov-report=json:coverage/coverage-${PYTHON_VERSION}.json \
             --junitxml=junit.xml \
             -o junit_family=legacy
 
           # Check if coverage file was generated
-          if [ -f "coverage/.coverage.${PYTHON_VERSION}" ]; then
+          if [ -f ".coverage.${PYTHON_VERSION}" ]; then
             echo "coverage_generated=true" >> $GITHUB_OUTPUT
-            echo "Coverage files found:"
-            ls -la coverage/
           else
             echo "coverage_generated=false" >> $GITHUB_OUTPUT
             echo "Warning: No coverage file generated"
@@ -373,7 +365,7 @@ jobs:
           PYTHON_VERSION: ${{ matrix.python-version }}
         run: |
           echo "## Python ${PYTHON_VERSION} Coverage" >> $GITHUB_STEP_SUMMARY
-          poetry run coverage report --data-file=coverage/.coverage.${PYTHON_VERSION} --format=markdown >> $GITHUB_STEP_SUMMARY
+          poetry run coverage report --data-file=.coverage.${PYTHON_VERSION} --format=markdown >> $GITHUB_STEP_SUMMARY
 
       - name: Upload test results to Codecov (these are results not coverage reports)
         if: ${{ !cancelled() }}
@@ -382,14 +374,93 @@ jobs:
           token: ${{ secrets.CODECOV_TOKEN }}
           flags: python-${{ matrix.python-version }}
 
-      - name: Upload coverage to Codecov
+      - name: Upload coverage artifacts
+        if: steps.test-unit.outputs.coverage_generated == 'true'
+        uses: actions/upload-artifact@ea165f8d65b6e75b540449e92b4886f43607fa02 # v4
+        with:
+          name: coverage-${{ matrix.python-version }}
+          path: .coverage.${{ matrix.python-version }}
+          retention-days: 1
+
+  coverage-combine:
+    name: Combine and Upload Coverage
+    runs-on: ubuntu-latest
+    needs: tests-unit
+    if: always()
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@08eba0b27e820071cde6df949e0beb9ba4906955 # v4
+        with:
+          persist-credentials: false
+
+      - name: Set up Python
+        uses: actions/setup-python@a26af69be951a213d495a4c3e4e4022e16d87065 # v5
+        with:
+          python-version: '3.11'
+
+      - name: Install coverage
+        run: pip install coverage[toml]
+
+      - name: Download all coverage artifacts
+        uses: actions/download-artifact@fa0a91b85d4f404e444e00e005971372dc801d16 # v4
+        continue-on-error: true
+        with:
+          pattern: coverage-*
+          path: coverage-data/
+          merge-multiple: true
+
+      - name: Combine coverage files
+        id: combine
+        run: |
+          set -euo pipefail
+
+          if [ ! -d "coverage-data" ] || [ -z "$(ls -A coverage-data 2>/dev/null)" ]; then
+            echo "No coverage artifacts were downloaded. All tests may have failed before generating coverage."
+            echo "success=false" >> $GITHUB_OUTPUT
+            exit 0
+          fi
+
+          echo "Downloaded coverage files:"
+          ls -la coverage-data/
+
+          shopt -s nullglob
+          coverage_files=(coverage-data/.coverage.*)
+          if [ ${#coverage_files[@]} -eq 0 ]; then
+            echo "No .coverage.* files found to combine"
+            echo "success=false" >> $GITHUB_OUTPUT
+            exit 0
+          fi
+
+          echo "Found ${#coverage_files[@]} coverage file(s) to combine"
+
+          cd coverage-data
+          coverage combine
+          coverage xml -o coverage.xml
+          coverage report
+
+          echo "## Combined Coverage Report" >> $GITHUB_STEP_SUMMARY
+          coverage report --format=markdown >> $GITHUB_STEP_SUMMARY
+
+          echo "success=true" >> $GITHUB_OUTPUT
+
+      - name: Upload combined coverage to Codecov
+        if: steps.combine.outputs.success == 'true'
         uses: codecov/codecov-action@5a1091511ad55cbe89839c7260b706298ca349f7 # v5
         with:
           token: ${{ secrets.CODECOV_TOKEN }}
-          slug: deepnote/deepnote-toolkit
-          files: ./coverage/coverage-${{ matrix.python-version }}.xml
+          slug: ${{ github.repository }}
+          files: ./coverage-data/coverage.xml
+          flags: combined
           fail_ci_if_error: ${{ github.event.pull_request.head.repo.full_name == github.repository || github.event_name == 'push' }}
 
+      - name: Upload combined coverage report
+        if: steps.combine.outputs.success == 'true'
+        uses: actions/upload-artifact@ea165f8d65b6e75b540449e92b4886f43607fa02 # v4
+        with:
+          name: coverage-combined-report
+          path: coverage-data/coverage.xml
+          retention-days: 30
+
   audit-prod:
     name: Audit - Production
     runs-on: ubuntu-latest

From 1bea06f3443b87347469e4cf5d10c42e8404f4c8 Mon Sep 17 00:00:00 2001
From: Michal Baumgartner <michal.baumgartner@deepnote.com>
Date: Fri, 7 Nov 2025 11:18:44 +0100
Subject: [PATCH 02/15] fix(ci): Account for parallel mode creating multiple
 coverage files

---
 .github/workflows/ci.yml | 35 ++++++++++++++++-------------------
 1 file changed, 16 insertions(+), 19 deletions(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 430ebf6..8de8e0b 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -338,7 +338,6 @@ jobs:
         env:
           TOOLKIT_VERSION: ${{ steps.version.outputs.VERSION }}
           PYTHON_VERSION: ${{ matrix.python-version }}
-          COVERAGE_FILE: .coverage.${{ matrix.python-version }}
         run: |
           set -euo pipefail
 
@@ -351,14 +350,21 @@ jobs:
             --junitxml=junit.xml \
             -o junit_family=legacy
 
-          # Check if coverage file was generated
-          if [ -f ".coverage.${PYTHON_VERSION}" ]; then
-            echo "coverage_generated=true" >> $GITHUB_OUTPUT
-          else
+          # Coverage parallel mode creates multiple .coverage.* files, combine them
+          shopt -s nullglob
+          coverage_files=(.coverage.*)
+          
+          if [ ${#coverage_files[@]} -eq 0 ]; then
+            echo "Error: No coverage data generated"
             echo "coverage_generated=false" >> $GITHUB_OUTPUT
-            echo "Warning: No coverage file generated"
+            exit 1
           fi
 
+          poetry run coverage combine
+          mv .coverage .coverage.${PYTHON_VERSION}
+          echo "Coverage saved as .coverage.${PYTHON_VERSION}"
+          echo "coverage_generated=true" >> $GITHUB_OUTPUT
+
       - name: Per-version coverage summary
         if: steps.test-unit.outputs.coverage_generated == 'true'
         env:
@@ -414,33 +420,24 @@ jobs:
         run: |
           set -euo pipefail
 
-          if [ ! -d "coverage-data" ] || [ -z "$(ls -A coverage-data 2>/dev/null)" ]; then
-            echo "No coverage artifacts were downloaded. All tests may have failed before generating coverage."
-            echo "success=false" >> $GITHUB_OUTPUT
-            exit 0
-          fi
-
-          echo "Downloaded coverage files:"
-          ls -la coverage-data/
-
           shopt -s nullglob
           coverage_files=(coverage-data/.coverage.*)
+          
           if [ ${#coverage_files[@]} -eq 0 ]; then
-            echo "No .coverage.* files found to combine"
+            echo "No coverage files to combine (tests may have failed)"
             echo "success=false" >> $GITHUB_OUTPUT
             exit 0
           fi
 
-          echo "Found ${#coverage_files[@]} coverage file(s) to combine"
-
+          echo "Combining ${#coverage_files[@]} coverage file(s)"
           cd coverage-data
+          
           coverage combine
           coverage xml -o coverage.xml
           coverage report
 
           echo "## Combined Coverage Report" >> $GITHUB_STEP_SUMMARY
           coverage report --format=markdown >> $GITHUB_STEP_SUMMARY
-
           echo "success=true" >> $GITHUB_OUTPUT
 
       - name: Upload combined coverage to Codecov

From 2fae2c93f841910183468c82925d552eb6046cef Mon Sep 17 00:00:00 2001
From: Michal Baumgartner <michal.baumgartner@deepnote.com>
Date: Fri, 7 Nov 2025 11:22:45 +0100
Subject: [PATCH 03/15] test: Debug coverage files

---
 .github/workflows/ci.yml | 39 +++++++++++++++++++++++++++------------
 1 file changed, 27 insertions(+), 12 deletions(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 8de8e0b..e46d749 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -350,21 +350,36 @@ jobs:
             --junitxml=junit.xml \
             -o junit_family=legacy
 
-          # Coverage parallel mode creates multiple .coverage.* files, combine them
-          shopt -s nullglob
-          coverage_files=(.coverage.*)
+          # Debug: Check what coverage files exist
+          echo "=== Coverage files after pytest ==="
+          ls -la .coverage* 2>/dev/null || echo "No .coverage* files found"
+          ls -la .coverage.* 2>/dev/null || echo "No .coverage.* files found"
           
-          if [ ${#coverage_files[@]} -eq 0 ]; then
-            echo "Error: No coverage data generated"
-            echo "coverage_generated=false" >> $GITHUB_OUTPUT
-            exit 1
+          # Coverage parallel mode may create .coverage.machine.pid files
+          # Check for both .coverage and .coverage.* patterns
+          if [ -f ".coverage" ]; then
+            # Single .coverage file exists (parallel mode auto-combined or not used)
+            mv .coverage .coverage.${PYTHON_VERSION}
+            echo "Renamed .coverage to .coverage.${PYTHON_VERSION}"
+            echo "coverage_generated=true" >> $GITHUB_OUTPUT
+          else
+            # Check for parallel coverage files
+            shopt -s nullglob
+            coverage_files=(.coverage.*)
+            
+            if [ ${#coverage_files[@]} -gt 0 ]; then
+              echo "Found ${#coverage_files[@]} parallel coverage files, combining..."
+              poetry run coverage combine
+              mv .coverage .coverage.${PYTHON_VERSION}
+              echo "Combined and saved as .coverage.${PYTHON_VERSION}"
+              echo "coverage_generated=true" >> $GITHUB_OUTPUT
+            else
+              echo "Error: No coverage data files found"
+              echo "coverage_generated=false" >> $GITHUB_OUTPUT
+              exit 1
+            fi
           fi
 
-          poetry run coverage combine
-          mv .coverage .coverage.${PYTHON_VERSION}
-          echo "Coverage saved as .coverage.${PYTHON_VERSION}"
-          echo "coverage_generated=true" >> $GITHUB_OUTPUT
-
       - name: Per-version coverage summary
         if: steps.test-unit.outputs.coverage_generated == 'true'
         env:

From e7a4fe548eb09283d4ee41e7a1600149162e52d7 Mon Sep 17 00:00:00 2001
From: Michal Baumgartner <michal.baumgartner@deepnote.com>
Date: Fri, 7 Nov 2025 11:29:39 +0100
Subject: [PATCH 04/15] fix: Debug coverage artifacts

---
 .github/workflows/ci.yml | 21 +++++++++++++++------
 1 file changed, 15 insertions(+), 6 deletions(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index e46d749..f9b5ee0 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -424,19 +424,22 @@ jobs:
 
       - name: Download all coverage artifacts
         uses: actions/download-artifact@fa0a91b85d4f404e444e00e005971372dc801d16 # v4
-        continue-on-error: true
         with:
           pattern: coverage-*
-          path: coverage-data/
-          merge-multiple: true
+          path: coverage-artifacts/
 
       - name: Combine coverage files
         id: combine
         run: |
           set -euo pipefail
 
+          # List downloaded artifacts structure
+          echo "=== Downloaded artifacts structure ==="
+          find coverage-artifacts -type f -name ".coverage.*" || echo "No .coverage.* files found"
+          
+          # Collect all coverage files from artifact subdirectories
           shopt -s nullglob
-          coverage_files=(coverage-data/.coverage.*)
+          coverage_files=(coverage-artifacts/*/.coverage.*)
           
           if [ ${#coverage_files[@]} -eq 0 ]; then
             echo "No coverage files to combine (tests may have failed)"
@@ -444,9 +447,15 @@ jobs:
             exit 0
           fi
 
-          echo "Combining ${#coverage_files[@]} coverage file(s)"
-          cd coverage-data
+          echo "Found ${#coverage_files[@]} coverage file(s) to combine"
           
+          # Copy all coverage files to a single directory for combining
+          mkdir -p coverage-data
+          for file in "${coverage_files[@]}"; do
+            cp "$file" coverage-data/
+          done
+          
+          cd coverage-data
           coverage combine
           coverage xml -o coverage.xml
           coverage report

From 2f1a731a1c404ed0bc6ed7351742e7f93bd10757 Mon Sep 17 00:00:00 2001
From: Michal Baumgartner <michal.baumgartner@deepnote.com>
Date: Fri, 7 Nov 2025 11:37:21 +0100
Subject: [PATCH 05/15] test: Simplify code coverage artifact paths

---
 .github/workflows/ci.yml | 58 ++++++++++++----------------------------
 1 file changed, 17 insertions(+), 41 deletions(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index f9b5ee0..9c13977 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -350,43 +350,21 @@ jobs:
             --junitxml=junit.xml \
             -o junit_family=legacy
 
-          # Debug: Check what coverage files exist
-          echo "=== Coverage files after pytest ==="
-          ls -la .coverage* 2>/dev/null || echo "No .coverage* files found"
-          ls -la .coverage.* 2>/dev/null || echo "No .coverage.* files found"
-          
-          # Coverage parallel mode may create .coverage.machine.pid files
-          # Check for both .coverage and .coverage.* patterns
-          if [ -f ".coverage" ]; then
-            # Single .coverage file exists (parallel mode auto-combined or not used)
-            mv .coverage .coverage.${PYTHON_VERSION}
-            echo "Renamed .coverage to .coverage.${PYTHON_VERSION}"
-            echo "coverage_generated=true" >> $GITHUB_OUTPUT
-          else
-            # Check for parallel coverage files
-            shopt -s nullglob
-            coverage_files=(.coverage.*)
-            
-            if [ ${#coverage_files[@]} -gt 0 ]; then
-              echo "Found ${#coverage_files[@]} parallel coverage files, combining..."
-              poetry run coverage combine
-              mv .coverage .coverage.${PYTHON_VERSION}
-              echo "Combined and saved as .coverage.${PYTHON_VERSION}"
-              echo "coverage_generated=true" >> $GITHUB_OUTPUT
-            else
-              echo "Error: No coverage data files found"
-              echo "coverage_generated=false" >> $GITHUB_OUTPUT
-              exit 1
-            fi
+          # Check if coverage data was generated
+          if [ ! -f ".coverage" ]; then
+            echo "Error: No coverage data file generated"
+            echo "coverage_generated=false" >> $GITHUB_OUTPUT
+            exit 1
           fi
+          
+          echo "Coverage data generated successfully"
+          echo "coverage_generated=true" >> $GITHUB_OUTPUT
 
       - name: Per-version coverage summary
         if: steps.test-unit.outputs.coverage_generated == 'true'
-        env:
-          PYTHON_VERSION: ${{ matrix.python-version }}
         run: |
-          echo "## Python ${PYTHON_VERSION} Coverage" >> $GITHUB_STEP_SUMMARY
-          poetry run coverage report --data-file=.coverage.${PYTHON_VERSION} --format=markdown >> $GITHUB_STEP_SUMMARY
+          echo "## Python ${{ matrix.python-version }} Coverage" >> $GITHUB_STEP_SUMMARY
+          poetry run coverage report --format=markdown >> $GITHUB_STEP_SUMMARY
 
       - name: Upload test results to Codecov (these are results not coverage reports)
         if: ${{ !cancelled() }}
@@ -400,7 +378,7 @@ jobs:
         uses: actions/upload-artifact@ea165f8d65b6e75b540449e92b4886f43607fa02 # v4
         with:
           name: coverage-${{ matrix.python-version }}
-          path: .coverage.${{ matrix.python-version }}
+          path: .coverage
           retention-days: 1
 
   coverage-combine:
@@ -433,13 +411,9 @@ jobs:
         run: |
           set -euo pipefail
 
-          # List downloaded artifacts structure
-          echo "=== Downloaded artifacts structure ==="
-          find coverage-artifacts -type f -name ".coverage.*" || echo "No .coverage.* files found"
-          
-          # Collect all coverage files from artifact subdirectories
+          # Collect all .coverage files from artifact subdirectories
           shopt -s nullglob
-          coverage_files=(coverage-artifacts/*/.coverage.*)
+          coverage_files=(coverage-artifacts/*/.coverage)
           
           if [ ${#coverage_files[@]} -eq 0 ]; then
             echo "No coverage files to combine (tests may have failed)"
@@ -449,10 +423,12 @@ jobs:
 
           echo "Found ${#coverage_files[@]} coverage file(s) to combine"
           
-          # Copy all coverage files to a single directory for combining
+          # Rename each file to include a unique suffix for coverage combine
           mkdir -p coverage-data
+          i=0
           for file in "${coverage_files[@]}"; do
-            cp "$file" coverage-data/
+            cp "$file" "coverage-data/.coverage.$i"
+            ((i++))
           done
           
           cd coverage-data

From d4dedac8a13416cc70c22287703d902432d69c55 Mon Sep 17 00:00:00 2001
From: Michal Baumgartner <michal.baumgartner@deepnote.com>
Date: Fri, 7 Nov 2025 11:42:07 +0100
Subject: [PATCH 06/15] test: Inspect generated coverage files as they are
 missing before upload

---
 .github/workflows/ci.yml | 8 ++++++++
 1 file changed, 8 insertions(+)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 9c13977..d62803f 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -373,6 +373,14 @@ jobs:
           token: ${{ secrets.CODECOV_TOKEN }}
           flags: python-${{ matrix.python-version }}
 
+      - name: Debug - Check file before upload
+        if: steps.test-unit.outputs.coverage_generated == 'true'
+        run: |
+          echo "PWD: $(pwd)"
+          echo "Looking for .coverage file:"
+          ls -la .coverage || echo ".coverage not found"
+          find . -name ".coverage" -type f || echo "No .coverage found anywhere"
+
       - name: Upload coverage artifacts
         if: steps.test-unit.outputs.coverage_generated == 'true'
         uses: actions/upload-artifact@ea165f8d65b6e75b540449e92b4886f43607fa02 # v4

From 88a9cc81c0454d006ca1a406f40e9bfbb117b68a Mon Sep 17 00:00:00 2001
From: Michal Baumgartner <michal.baumgartner@deepnote.com>
Date: Fri, 7 Nov 2025 11:45:18 +0100
Subject: [PATCH 07/15] fix: Ensure upload-artifact action includes gitignored
 `.coverage` file

---
 .github/workflows/ci.yml | 9 +--------
 1 file changed, 1 insertion(+), 8 deletions(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index d62803f..d0ad828 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -373,14 +373,6 @@ jobs:
           token: ${{ secrets.CODECOV_TOKEN }}
           flags: python-${{ matrix.python-version }}
 
-      - name: Debug - Check file before upload
-        if: steps.test-unit.outputs.coverage_generated == 'true'
-        run: |
-          echo "PWD: $(pwd)"
-          echo "Looking for .coverage file:"
-          ls -la .coverage || echo ".coverage not found"
-          find . -name ".coverage" -type f || echo "No .coverage found anywhere"
-
       - name: Upload coverage artifacts
         if: steps.test-unit.outputs.coverage_generated == 'true'
         uses: actions/upload-artifact@ea165f8d65b6e75b540449e92b4886f43607fa02 # v4
@@ -388,6 +380,7 @@ jobs:
           name: coverage-${{ matrix.python-version }}
           path: .coverage
           retention-days: 1
+          include-hidden-files: true
 
   coverage-combine:
     name: Combine and Upload Coverage

From f0e982f2d443f561ee743581f43bdbdfb9d368e3 Mon Sep 17 00:00:00 2001
From: Michal Baumgartner <michal.baumgartner@deepnote.com>
Date: Fri, 7 Nov 2025 11:50:13 +0100
Subject: [PATCH 08/15] test: Debug coverage combining step

---
 .github/workflows/ci.yml | 16 +++++++++++++---
 1 file changed, 13 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index d0ad828..d94c8d5 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -413,6 +413,7 @@ jobs:
           set -euo pipefail
 
           # Collect all .coverage files from artifact subdirectories
+          echo "Collecting coverage files from artifact subdirectories"
           shopt -s nullglob
           coverage_files=(coverage-artifacts/*/.coverage)
           
@@ -428,14 +429,23 @@ jobs:
           mkdir -p coverage-data
           i=0
           for file in "${coverage_files[@]}"; do
+            echo "Copying $file to coverage-data/.coverage.$i"
             cp "$file" "coverage-data/.coverage.$i"
             ((i++))
           done
           
           cd coverage-data
-          coverage combine
-          coverage xml -o coverage.xml
-          coverage report
+          echo "Files in coverage-data:"
+          ls -la
+          
+          echo "Running coverage combine..."
+          coverage combine || { echo "coverage combine failed"; exit 1; }
+          
+          echo "Generating XML report..."
+          coverage xml -o coverage.xml || { echo "coverage xml failed"; exit 1; }
+          
+          echo "Generating text report..."
+          coverage report || { echo "coverage report failed"; exit 1; }
 
           echo "## Combined Coverage Report" >> $GITHUB_STEP_SUMMARY
           coverage report --format=markdown >> $GITHUB_STEP_SUMMARY

From 7d17871621006b6eccd58d528a7d009faa7b9cb1 Mon Sep 17 00:00:00 2001
From: Michal Baumgartner <michal.baumgartner@deepnote.com>
Date: Fri, 7 Nov 2025 11:55:22 +0100
Subject: [PATCH 09/15] fix: Coverage artifact ID incrementing

---
 .github/workflows/ci.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index d94c8d5..64203e1 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -431,7 +431,7 @@ jobs:
           for file in "${coverage_files[@]}"; do
             echo "Copying $file to coverage-data/.coverage.$i"
             cp "$file" "coverage-data/.coverage.$i"
-            ((i++))
+            i=$((i + 1))
           done
           
           cd coverage-data

From dcaa0df755961c0d00cdc9ca88e52d2cb4cfaa1f Mon Sep 17 00:00:00 2001
From: Michal Baumgartner <michal.baumgartner@deepnote.com>
Date: Fri, 7 Nov 2025 11:59:56 +0100
Subject: [PATCH 10/15] fix: Fail fast and use correct directory when combining
 coverage files

---
 .github/workflows/ci.yml | 12 ++++--------
 1 file changed, 4 insertions(+), 8 deletions(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 64203e1..db8ab83 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -381,6 +381,7 @@ jobs:
           path: .coverage
           retention-days: 1
           include-hidden-files: true
+          if-no-files-found: error
 
   coverage-combine:
     name: Combine and Upload Coverage
@@ -429,20 +430,15 @@ jobs:
           mkdir -p coverage-data
           i=0
           for file in "${coverage_files[@]}"; do
-            echo "Copying $file to coverage-data/.coverage.$i"
             cp "$file" "coverage-data/.coverage.$i"
             i=$((i + 1))
           done
           
-          cd coverage-data
-          echo "Files in coverage-data:"
-          ls -la
-          
-          echo "Running coverage combine..."
-          coverage combine || { echo "coverage combine failed"; exit 1; }
+          echo "Running coverage combine from workspace root..."
+          coverage combine coverage-data/ || { echo "coverage combine failed"; exit 1; }
           
           echo "Generating XML report..."
-          coverage xml -o coverage.xml || { echo "coverage xml failed"; exit 1; }
+          coverage xml -o coverage-data/coverage.xml || { echo "coverage xml failed"; exit 1; }
           
           echo "Generating text report..."
           coverage report || { echo "coverage report failed"; exit 1; }

From 919d72d27ce0f8f6cfc83605d007ea2d50a501f5 Mon Sep 17 00:00:00 2001
From: Michal Baumgartner <michal.baumgartner@deepnote.com>
Date: Fri, 7 Nov 2025 12:05:43 +0100
Subject: [PATCH 11/15] fix: Only upload the provided combined coverage file to
 codecov

---
 .github/workflows/ci.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index db8ab83..2b5feb9 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -455,6 +455,7 @@ jobs:
           slug: ${{ github.repository }}
           files: ./coverage-data/coverage.xml
           flags: combined
+          disable_search: true
           fail_ci_if_error: ${{ github.event.pull_request.head.repo.full_name == github.repository || github.event_name == 'push' }}
 
       - name: Upload combined coverage report

From a1a69d3668d679c33746a289a43211a569b49c34 Mon Sep 17 00:00:00 2001
From: Michal Baumgartner <michal.baumgartner@deepnote.com>
Date: Fri, 7 Nov 2025 12:12:30 +0100
Subject: [PATCH 12/15] chore(ci): Simplify the logic and error handling for
 combining coverage

---
 .github/workflows/ci.yml | 51 +++++-----------------------------------
 1 file changed, 6 insertions(+), 45 deletions(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 2b5feb9..9196dda 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -334,13 +334,9 @@ jobs:
         run: poetry install --no-interaction --only-root
 
       - name: Run unit tests
-        id: test-unit
         env:
           TOOLKIT_VERSION: ${{ steps.version.outputs.VERSION }}
-          PYTHON_VERSION: ${{ matrix.python-version }}
         run: |
-          set -euo pipefail
-
           poetry run pytest tests/unit \
             --cov=deepnote_toolkit \
             --cov=installer \
@@ -350,23 +346,12 @@ jobs:
             --junitxml=junit.xml \
             -o junit_family=legacy
 
-          # Check if coverage data was generated
-          if [ ! -f ".coverage" ]; then
-            echo "Error: No coverage data file generated"
-            echo "coverage_generated=false" >> $GITHUB_OUTPUT
-            exit 1
-          fi
-          
-          echo "Coverage data generated successfully"
-          echo "coverage_generated=true" >> $GITHUB_OUTPUT
-
       - name: Per-version coverage summary
-        if: steps.test-unit.outputs.coverage_generated == 'true'
         run: |
           echo "## Python ${{ matrix.python-version }} Coverage" >> $GITHUB_STEP_SUMMARY
           poetry run coverage report --format=markdown >> $GITHUB_STEP_SUMMARY
 
-      - name: Upload test results to Codecov (these are results not coverage reports)
+      - name: Upload test results to Codecov
         if: ${{ !cancelled() }}
         uses: codecov/test-results-action@47f89e9acb64b76debcd5ea40642d25a4adced9f # v1
         with:
@@ -374,7 +359,6 @@ jobs:
           flags: python-${{ matrix.python-version }}
 
       - name: Upload coverage artifacts
-        if: steps.test-unit.outputs.coverage_generated == 'true'
         uses: actions/upload-artifact@ea165f8d65b6e75b540449e92b4886f43607fa02 # v4
         with:
           name: coverage-${{ matrix.python-version }}
@@ -409,46 +393,24 @@ jobs:
           path: coverage-artifacts/
 
       - name: Combine coverage files
-        id: combine
         run: |
-          set -euo pipefail
-
-          # Collect all .coverage files from artifact subdirectories
-          echo "Collecting coverage files from artifact subdirectories"
           shopt -s nullglob
-          coverage_files=(coverage-artifacts/*/.coverage)
-          
-          if [ ${#coverage_files[@]} -eq 0 ]; then
-            echo "No coverage files to combine (tests may have failed)"
-            echo "success=false" >> $GITHUB_OUTPUT
-            exit 0
-          fi
-
-          echo "Found ${#coverage_files[@]} coverage file(s) to combine"
-          
-          # Rename each file to include a unique suffix for coverage combine
           mkdir -p coverage-data
+          
           i=0
-          for file in "${coverage_files[@]}"; do
+          for file in coverage-artifacts/*/.coverage; do
             cp "$file" "coverage-data/.coverage.$i"
             i=$((i + 1))
           done
           
-          echo "Running coverage combine from workspace root..."
-          coverage combine coverage-data/ || { echo "coverage combine failed"; exit 1; }
-          
-          echo "Generating XML report..."
-          coverage xml -o coverage-data/coverage.xml || { echo "coverage xml failed"; exit 1; }
-          
-          echo "Generating text report..."
-          coverage report || { echo "coverage report failed"; exit 1; }
+          coverage combine coverage-data/
+          coverage xml -o coverage-data/coverage.xml
+          coverage report
 
           echo "## Combined Coverage Report" >> $GITHUB_STEP_SUMMARY
           coverage report --format=markdown >> $GITHUB_STEP_SUMMARY
-          echo "success=true" >> $GITHUB_OUTPUT
 
       - name: Upload combined coverage to Codecov
-        if: steps.combine.outputs.success == 'true'
         uses: codecov/codecov-action@5a1091511ad55cbe89839c7260b706298ca349f7 # v5
         with:
           token: ${{ secrets.CODECOV_TOKEN }}
@@ -459,7 +421,6 @@ jobs:
           fail_ci_if_error: ${{ github.event.pull_request.head.repo.full_name == github.repository || github.event_name == 'push' }}
 
       - name: Upload combined coverage report
-        if: steps.combine.outputs.success == 'true'
         uses: actions/upload-artifact@ea165f8d65b6e75b540449e92b4886f43607fa02 # v4
         with:
           name: coverage-combined-report

From 91f6905e28c43f32ac17163071dc07409980be9b Mon Sep 17 00:00:00 2001
From: Michal Baumgartner <michal.baumgartner@deepnote.com>
Date: Fri, 7 Nov 2025 13:08:56 +0100
Subject: [PATCH 13/15] fix: Debug coverage using nox target

---
 noxfile.py | 33 ++++++++++++++++++++++-----------
 1 file changed, 22 insertions(+), 11 deletions(-)

diff --git a/noxfile.py b/noxfile.py
index 32b0c49..9c58eda 100644
--- a/noxfile.py
+++ b/noxfile.py
@@ -146,17 +146,28 @@ def coverage_report(session):
 
     import pathlib
 
-    coverage_dir = pathlib.Path("coverage")
+    # Use absolute path relative to session.invoked_from
+    project_root = pathlib.Path(session.invoked_from)
+    coverage_dir = project_root / "coverage"
+    
     if not coverage_dir.exists():
-        session.error("No coverage directory found. Run tests with --coverage first.")
-
-    # Combine all coverage files from coverage directory
-    session.run(
-        "coverage", "combine", "--data-file=coverage/.coverage", "coverage/.coverage.*"
-    )
+        session.error("No coverage directory found. Run tests with nox -s unit first.")
+
+    # Check if we have a combined coverage file or individual files
+    combined_file = coverage_dir / ".coverage"
+    coverage_files = sorted(coverage_dir.glob(".coverage.*"))
+
+    if not combined_file.exists() and not coverage_files:
+        session.error("No coverage files found. Run tests with nox -s unit first.")
+    
+    if coverage_files:
+        session.log(f"Combining {len(coverage_files)} coverage files")
+        session.run("coverage", "combine", "--data-file=coverage/.coverage", *[str(f) for f in coverage_files])
+    else:
+        session.log("Using existing combined coverage file")
 
     # Generate reports in coverage directory
-    session.run("coverage", "report", "--format=markdown")
-    session.run("coverage", "html", "-d", "coverage/htmlcov")
-    session.run("coverage", "xml", "-o", "coverage/coverage.xml", "-i")
-    session.run("coverage", "json", "-o", "coverage/coverage.json")
+    session.run("coverage", "report", "--data-file=coverage/.coverage", "--format=markdown")
+    session.run("coverage", "html", "--data-file=coverage/.coverage", "-d", "coverage/htmlcov")
+    session.run("coverage", "xml", "--data-file=coverage/.coverage", "-o", "coverage/coverage.xml", "-i")
+    session.run("coverage", "json", "--data-file=coverage/.coverage", "-o", "coverage/coverage.json")

From d058de1406af238973b8e62cff75bb7f38fafc06 Mon Sep 17 00:00:00 2001
From: Michal Baumgartner <michal.baumgartner@deepnote.com>
Date: Fri, 7 Nov 2025 13:11:44 +0100
Subject: [PATCH 14/15] fix: Lint

---
 noxfile.py | 36 +++++++++++++++++++++++++++++-------
 1 file changed, 29 insertions(+), 7 deletions(-)

diff --git a/noxfile.py b/noxfile.py
index 9c58eda..3cdb98f 100644
--- a/noxfile.py
+++ b/noxfile.py
@@ -149,7 +149,7 @@ def coverage_report(session):
     # Use absolute path relative to session.invoked_from
     project_root = pathlib.Path(session.invoked_from)
     coverage_dir = project_root / "coverage"
-    
+
     if not coverage_dir.exists():
         session.error("No coverage directory found. Run tests with nox -s unit first.")
 
@@ -159,15 +159,37 @@ def coverage_report(session):
 
     if not combined_file.exists() and not coverage_files:
         session.error("No coverage files found. Run tests with nox -s unit first.")
-    
+
     if coverage_files:
         session.log(f"Combining {len(coverage_files)} coverage files")
-        session.run("coverage", "combine", "--data-file=coverage/.coverage", *[str(f) for f in coverage_files])
+        session.run(
+            "coverage",
+            "combine",
+            "--data-file=coverage/.coverage",
+            *[str(f) for f in coverage_files],
+        )
     else:
         session.log("Using existing combined coverage file")
 
     # Generate reports in coverage directory
-    session.run("coverage", "report", "--data-file=coverage/.coverage", "--format=markdown")
-    session.run("coverage", "html", "--data-file=coverage/.coverage", "-d", "coverage/htmlcov")
-    session.run("coverage", "xml", "--data-file=coverage/.coverage", "-o", "coverage/coverage.xml", "-i")
-    session.run("coverage", "json", "--data-file=coverage/.coverage", "-o", "coverage/coverage.json")
+    session.run(
+        "coverage", "report", "--data-file=coverage/.coverage", "--format=markdown"
+    )
+    session.run(
+        "coverage", "html", "--data-file=coverage/.coverage", "-d", "coverage/htmlcov"
+    )
+    session.run(
+        "coverage",
+        "xml",
+        "--data-file=coverage/.coverage",
+        "-o",
+        "coverage/coverage.xml",
+        "-i",
+    )
+    session.run(
+        "coverage",
+        "json",
+        "--data-file=coverage/.coverage",
+        "-o",
+        "coverage/coverage.json",
+    )

From a3dc7359fbb2e103d1b5d2d62934ce093670f247 Mon Sep 17 00:00:00 2001
From: Michal Baumgartner <michal.baumgartner@deepnote.com>
Date: Fri, 7 Nov 2025 16:29:13 +0100
Subject: [PATCH 15/15] chore: Incorporate PR review suggestions

---
 noxfile.py | 18 +++++++++++-------
 1 file changed, 11 insertions(+), 7 deletions(-)

diff --git a/noxfile.py b/noxfile.py
index 3cdb98f..e976c1d 100644
--- a/noxfile.py
+++ b/noxfile.py
@@ -165,7 +165,7 @@ def coverage_report(session):
         session.run(
             "coverage",
             "combine",
-            "--data-file=coverage/.coverage",
+            f"--data-file={combined_file}",
             *[str(f) for f in coverage_files],
         )
     else:
@@ -173,23 +173,27 @@ def coverage_report(session):
 
     # Generate reports in coverage directory
     session.run(
-        "coverage", "report", "--data-file=coverage/.coverage", "--format=markdown"
+        "coverage", "report", f"--data-file={combined_file}", "--format=markdown"
     )
     session.run(
-        "coverage", "html", "--data-file=coverage/.coverage", "-d", "coverage/htmlcov"
+        "coverage",
+        "html",
+        f"--data-file={combined_file}",
+        "-d",
+        str(coverage_dir / "htmlcov"),
     )
     session.run(
         "coverage",
         "xml",
-        "--data-file=coverage/.coverage",
+        f"--data-file={combined_file}",
         "-o",
-        "coverage/coverage.xml",
+        str(coverage_dir / "coverage.xml"),
         "-i",
     )
     session.run(
         "coverage",
         "json",
-        "--data-file=coverage/.coverage",
+        f"--data-file={combined_file}",
         "-o",
-        "coverage/coverage.json",
+        str(coverage_dir / "coverage.json"),
     )