[INFRA] Codecov: Use stable/experimental flags

Author: eseiler

.codecov.yml

@@ -16,26 +16,23 @@ coverage:
         if_ci_failed: success # per default, codecov would fail if any CI fails
         informational: true   # the codecov/patch status is never "fail"
         flags:
-          - current
+          - stable
     patch:  # patch is the code-coverage of the changed lines in the PR and often reports false positives
       default:
         if_ci_failed: success # per default, codecov would fail if any CI fails
         informational: true   # the codecov/patch status is never "fail"
         only_pulls: true      # only post codecov/patch status on PRs
         flags:
-          - current
+          - stable
 
 parsers:
   cobertura:
     partials_as_hits: true
 
 flags:
+  stable:
+    carryforward: false
+    joined: true
   experimental:
     carryforward: false
     joined: false
-    paths:
-      - include/raptor/argument_parsing/update_arguments.hpp
-      - include/raptor/argument_parsing/update_parsing.hpp
-      - include/raptor/update
-      - src/argument_parsing/update_parsing.cpp
-      - src/update

.github/workflows/ci_coverage.yml

@@ -41,8 +41,6 @@ jobs:
     steps:
       - name: Checkout
         uses: actions/checkout@v4
-        with:
-          fetch-depth: 0
 
       - name: Load ccache
         uses: actions/cache@v4
@@ -74,6 +72,37 @@ jobs:
                 ${GITHUB_WORKSPACE}/build \
                 --filter ${GITHUB_WORKSPACE}/include \
                 --filter ${GITHUB_WORKSPACE}/src \
+                --exclude ${GITHUB_WORKSPACE}/include/raptor/argument_parsing/update_arguments.hpp \
+                --exclude ${GITHUB_WORKSPACE}/include/raptor/argument_parsing/update_parsing.hpp \
+                --exclude ${GITHUB_WORKSPACE}/include/raptor/update \
+                --exclude ${GITHUB_WORKSPACE}/src/argument_parsing/update_parsing.cpp \
+                --exclude ${GITHUB_WORKSPACE}/src/update \
+                --exclude-lines-by-pattern '^\s*}|^\s*};|^\s*HIBF_UNREACHABLE;|^\s*\.[^\s]+ = \".*\"' \
+                --exclude-noncode-lines \
+                --exclude-throw-branches \
+                --exclude-unreachable-branches \
+                --merge-mode-functions separate \
+                -j \
+                --cobertura \
+                --output ${GITHUB_WORKSPACE}/build/coverage_report.xml
+
+      - name: Submit coverage report
+        uses: codecov/codecov-action@v3.1.5
+        with:
+          files: build/coverage_report.xml
+          fail_ci_if_error: false
+          flags: stable
+
+      - name: Generate coverage report
+        run: |
+          rm ${GITHUB_WORKSPACE}/build/coverage_report.xml
+          gcovr --root ${GITHUB_WORKSPACE}/test/coverage \
+                ${GITHUB_WORKSPACE}/build \
+                --filter ${GITHUB_WORKSPACE}/include/raptor/argument_parsing/update_arguments.hpp \
+                --filter ${GITHUB_WORKSPACE}/include/raptor/argument_parsing/update_parsing.hpp \
+                --filter ${GITHUB_WORKSPACE}/include/raptor/update \
+                --filter ${GITHUB_WORKSPACE}/src/argument_parsing/update_parsing.cpp \
+                --filter ${GITHUB_WORKSPACE}/src/update \
                 --exclude-lines-by-pattern '^\s*}|^\s*};|^\s*HIBF_UNREACHABLE;|^\s*\.[^\s]+ = \".*\"' \
                 --exclude-noncode-lines \
                 --exclude-throw-branches \
@@ -88,4 +117,4 @@ jobs:
         with:
           files: build/coverage_report.xml
           fail_ci_if_error: false
-          flags: current
+          flags: experimental

README.md

@@ -8,7 +8,7 @@ SPDX-License-Identifier: CC-BY-4.0
 
 [1]: https://img.shields.io/github/actions/workflow/status/seqan/raptor/ci_linux.yml?branch=main&style=flat&logo=github&label=Raptor%20CI
 [2]: https://github.com/seqan/raptor/actions?query=branch%3Amain
-[3]: https://codecov.io/gh/seqan/raptor/branch/main/graph/badge.svg?token=SJVMYRUKW2
+[3]: https://codecov.io/gh/seqan/raptor/branch/main/graph/badge.svg?token=SJVMYRUKW2&flag=stable
 [4]: https://codecov.io/gh/seqan/raptor
 [5]: https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat
 [6]: #install-with-bioconda-linux