Changed CI naming; added codecov; added readthedocs deps

Author: lukaswittmann

.github/workflows/ci.yml .github/workflows/ci_build.yml.github/workflows/ci.yml renamed to .github/workflows/ci_build.yml

@@ -1,4 +1,4 @@
-name: CI
+name: Build
 
 on:
   push:

.github/workflows/ci_cov.yml

@@ -0,0 +1,54 @@
+name: Coverage
+
+on:
+  push:
+  pull_request:
+
+jobs:
+  coverage:
+    name: coverage (gnu14)
+    runs-on: ubuntu-24.04
+    steps:
+      - uses: actions/checkout@v5
+
+      - name: Install compiler
+        uses: fortran-lang/setup-fortran@v1
+        with:
+          compiler: gcc
+          version: '14'
+
+      - name: Install dependencies (Linux)
+        run: |
+          sudo apt-get update
+          sudo apt-get install -y meson ninja-build liblapack-dev libunwind-dev gcovr
+
+      - name: Set compiler environment
+        run: |
+          echo "FC=gfortran" >> "$GITHUB_ENV"
+          echo "CC=gcc" >> "$GITHUB_ENV"
+
+      - name: Point gcov at the gcc 14 toolchain
+        # gcovr calls the bare `gcov`, which on ubuntu-24.04 is the gcc 13 build
+        # and cannot read gcc 14 .gcno files. Shim it to the matching version.
+        run: |
+          sudo ln -sf "$(command -v gcov-14)" /usr/local/bin/gcov
+          gcov --version | head -n1
+
+      - name: Build with coverage instrumentation
+        run: |
+          meson setup build -Db_coverage=true
+          meson compile -C build
+
+      - name: Run tests
+        run: meson test -C build --suite moist --print-errorlogs
+
+      - name: Generate Cobertura XML coverage report
+        run: ninja -C build coverage-xml
+
+      - name: Upload coverage to Codecov
+        uses: codecov/codecov-action@v5
+        with:
+          files: build/meson-logs/coverage.xml
+          flags: fortran
+          token: ${{ secrets.CODECOV_TOKEN }}
+          fail_ci_if_error: false

.github/workflows/lint.yml .github/workflows/ci_lint.yml.github/workflows/lint.yml renamed to .github/workflows/ci_lint.yml

@@ -36,6 +36,12 @@
 /install*/
 /_*/
 
+# Coverage artifacts
+*.gcda
+*.gcno
+*.gcov
+coverage.xml
+
 # Meson subproject artifacts (transitive wraps + lock are auto-generated)
 subprojects/toml-f.wrap
 .wraplock

.gitignore

@@ -14,9 +14,7 @@ build:
 sphinx:
    configuration: docs/conf.py
 
-# Optionally, but recommended,
-# declare the Python requirements required to build your documentation
-# See https://docs.readthedocs.io/en/stable/guides/reproducible-builds.html
-# python:
-#    install:
-#    - requirements: docs/requirements.txt
+# Declare the Python requirements required to build your docs
+python:
+  install:
+    - requirements: docs/requirements.txt

.readthedocs.yaml

@@ -1,6 +1,8 @@
 MOIST: Modular and Open-source Implicit Solvation Toolkit
 ==============
 
+[![Coverage](https://codecov.io/gh/lukaswittmann/moist/graph/badge.svg)](https://codecov.io/gh/lukaswittmann/moist)
+
 > [!Note]
 >  MOIST is currently in a pre-release state.
 > This version only includes the cavity construction capabilities of the Modular and Open-source Implicit Solvation Toolkit.

README.md

@@ -0,0 +1,23 @@
+# Codecov configuration for MOIST.
+# Coverage is reported for the core Fortran library (src/) only and is purely
+# informational — it never blocks a merge.
+# Reference: https://docs.codecov.com/docs/codecovyml-reference
+
+coverage:
+  status:
+    project:
+      default:
+        informational: true
+    patch:
+      default:
+        informational: true
+
+# Vendored subprojects, the test suite, the CLI driver and the Python wrapper
+# are not part of the core library coverage.
+ignore:
+  - "subprojects"
+  - "test"
+  - "app"
+  - "python"
+  - "config"
+  - "build"