From 9341c5766505338ac3a77bb33fedf30107ce4869 Mon Sep 17 00:00:00 2001
From: Chris Markiewicz <effigies@gmail.com>
Date: Mon, 17 Apr 2023 08:54:32 -0400
Subject: [PATCH] CI: Switch to codecov action

---
 .github/workflows/misc.yml        |  3 ---
 .github/workflows/pre-release.yml |  5 +++--
 .github/workflows/stable.yml      |  5 +++--
 tools/ci/check.sh                 |  2 +-
 tools/ci/submit_coverage.sh       | 21 ---------------------
 5 files changed, 7 insertions(+), 29 deletions(-)
 delete mode 100755 tools/ci/submit_coverage.sh

diff --git a/.github/workflows/misc.yml b/.github/workflows/misc.yml
index ade350aaa7..90645b40eb 100644
--- a/.github/workflows/misc.yml
+++ b/.github/workflows/misc.yml
@@ -59,9 +59,6 @@ jobs:
       - name: Run tests
         run: tools/ci/check.sh
         if: ${{ matrix.check != 'skiptests' }}
-      - name: Submit coverage
-        run: tools/ci/submit_coverage.sh
-        if: ${{ always() }}
       - name: Upload pytest test results
         uses: actions/upload-artifact@v3
         with:
diff --git a/.github/workflows/pre-release.yml b/.github/workflows/pre-release.yml
index 9ceb4033ae..630f09d99b 100644
--- a/.github/workflows/pre-release.yml
+++ b/.github/workflows/pre-release.yml
@@ -87,9 +87,10 @@ jobs:
       - name: Run tests
         run: tools/ci/check.sh
         if: ${{ matrix.check != 'skiptests' }}
-      - name: Submit coverage
-        run: tools/ci/submit_coverage.sh
+      - uses: codecov/codecov-action@v3
         if: ${{ always() }}
+        with:
+          files: cov.xml
       - name: Upload pytest test results
         uses: actions/upload-artifact@v3
         with:
diff --git a/.github/workflows/stable.yml b/.github/workflows/stable.yml
index 315534107f..18a30d6d07 100644
--- a/.github/workflows/stable.yml
+++ b/.github/workflows/stable.yml
@@ -181,9 +181,10 @@ jobs:
       - name: Run tests
         if: ${{ matrix.check != 'skiptests' }}
         run: tools/ci/check.sh
-      - name: Submit coverage
+      - uses: codecov/codecov-action@v3
         if: ${{ always() }}
-        run: tools/ci/submit_coverage.sh
+        with:
+          files: cov.xml
       - name: Upload pytest test results
         if: ${{ always() && matrix.check == 'test' }}
         uses: actions/upload-artifact@v3
diff --git a/tools/ci/check.sh b/tools/ci/check.sh
index bcb1a934e2..cd90650722 100755
--- a/tools/ci/check.sh
+++ b/tools/ci/check.sh
@@ -23,7 +23,7 @@ elif [ "${CHECK_TYPE}" == "test" ]; then
     mkdir for_testing
     cd for_testing
     cp ../.coveragerc .
-    pytest --doctest-modules --doctest-plus --cov nibabel --cov-report xml \
+    pytest --doctest-modules --doctest-plus --cov nibabel --cov-report xml:../cov.xml \
         --junitxml=test-results.xml -v --pyargs nibabel -n auto
 elif [ "${CHECK_TYPE}" == "typing" ]; then
     mypy nibabel
diff --git a/tools/ci/submit_coverage.sh b/tools/ci/submit_coverage.sh
deleted file mode 100755
index 17bfe3933b..0000000000
--- a/tools/ci/submit_coverage.sh
+++ /dev/null
@@ -1,21 +0,0 @@
-#!/bin/bash
-
-echo Submitting coverage
-
-source tools/ci/activate.sh
-
-set -eu
-
-set -x
-
-COVERAGE_FILE="for_testing/coverage.xml"
-
-if [ -e "$COVERAGE_FILE" ]; then
-    # Pin codecov version to reduce scope for malicious updates
-    python -m pip install "codecov==2.1.11"
-    python -m codecov --file for_testing/coverage.xml
-fi
-
-set +eux
-
-echo Done submitting coverage