Toolchain/CMake: Improve dependency handling

.github/workflows/ase_plugin_test.yml

@@ -3,6 +3,10 @@ name: Atomic Simulation Environment (ASE) Plugin Test
 on:
   pull_request:
 
+defaults:
+  run:
+    shell: bash
+
 jobs:
   test:
     name: abacuslite
@@ -33,15 +37,24 @@ jobs:
           cd interfaces/ASE_interface
           pip install .
 
+      - name: Install external tools from toolchain
+        run: |
+          sudo apt update && sudo apt install -y xz-utils ninja-build
+          cd toolchain
+          ./install_abacus_toolchain_new.sh --with-dftd4=install --dry-run -j8
+          ./scripts/stage4/install_stage4.sh
+          cd ..
+
       - name: Configure & Build ABACUS (GNU)
         run: |
           git config --global --add safe.directory `pwd`
           export LD_LIBRARY_PATH=${GKLIB_ROOT}/lib:${METIS32_ROOT}/lib:${PARMETIS32_ROOT}/lib:${SUPERLU32_DIST_ROOT}/lib:${PEXSI32_ROOT}/lib:${LD_LIBRARY_PATH}
           export PKG_CONFIG_PATH=${GKLIB_ROOT}/lib/pkgconfig:${METIS32_ROOT}/lib/pkgconfig:${PARMETIS32_ROOT}/lib/pkgconfig:${SUPERLU32_DIST_ROOT}/lib/pkgconfig:${PEXSI32_ROOT}/lib/pkgconfig:${PKG_CONFIG_PATH}
           export CPATH=${GKLIB_ROOT}/include:${METIS32_ROOT}/include:${PARMETIS32_ROOT}/include:${SUPERLU32_DIST_ROOT}/include:${PEXSI32_ROOT}/include:${CPATH}
           export CMAKE_PREFIX_PATH=${PEXSI32_ROOT}:${SUPERLU_DIST32_ROOT}:${PARMETIS32_ROOT}:${METIS32_ROOT}:${GKLIB_ROOT}:${CMAKE_PREFIX_PATH}
+          source toolchain/install/setup
           rm -rf build
-          cmake -B build
+          cmake -B build -G Ninja
           cmake --build build -j2
 
       - name: Install and Soft Link ABACUS

.github/workflows/build_test_cmake.yml

@@ -3,6 +3,10 @@ on:
   push:
   pull_request:
 
+defaults:
+  run:
+    shell: bash
+
 jobs:
   test:
     runs-on: ubuntu-latest
@@ -13,30 +17,38 @@ jobs:
             build_args: ""
             name: "Build with GNU toolchain"
           - tag: intel
+            external_toolchain_args: "--with-intel"
             build_args: ""
             name: "Build with Intel toolchain"
 
           - tag: gnu
-            build_args: "-DENABLE_LIBXC=1 -DENABLE_MLALGO=1 -DENABLE_LIBRI=1"
+            external_toolchain_args: ""
+            build_args: "-DENABLE_LIBXC=ON -DENABLE_MLALGO=ON -DENABLE_LIBRI=ON"
             name: "Build extra components with GNU toolchain"
           - tag: intel
-            build_args: "-DENABLE_LIBXC=1 -DENABLE_PEXSI=1 -DENABLE_MLALGO=1 -DENABLE_LIBRI=1"
+            external_toolchain_args: "--with-intel"
+            build_args: "-DENABLE_LIBXC=ON -DENABLE_PEXSI=ON -DENABLE_MLALGO=ON -DENABLE_LIBRI=ON"
             name: "Build extra components with Intel toolchain"
 
           - tag: cuda
-            build_args: "-DUSE_CUDA=1"
+            external_toolchain_args: ""
+            build_args: "-DUSE_CUDA=ON"
             name: "Build with CUDA support"
           - tag: gnu
-            build_args: "-DENABLE_LCAO=0"
+            external_toolchain_args: ""
+            build_args: "-DENABLE_LCAO=OFF"
             name: "Build without LCAO"
           - tag: gnu
-            build_args: "-DUSE_ELPA=0 "
+            external_toolchain_args: ""
+            build_args: "-DUSE_ELPA=OFF "
             name: "Build without ELPA"
           - tag: gnu
-            build_args: "-DENABLE_MPI=0"
+            external_toolchain_args: ""
+            build_args: "-DENABLE_MPI=OFF"
             name: "Build without MPI"
           - tag: gnu
-            build_args: "-DENABLE_MPI=0 -DENABLE_LCAO=0"
+            external_toolchain_args: ""
+            build_args: "-DENABLE_MPI=OFF -DENABLE_LCAO=OFF"
             name: "Build without LCAO and MPI"
 
     name: ${{ matrix.name }}
@@ -47,13 +59,22 @@ jobs:
         with:
           submodules: recursive
 
+      - name: Install external tools from toolchain
+        run: |
+          sudo apt update && sudo apt install -y gfortran ninja-build xz-utils
+          cd toolchain
+          ./install_abacus_toolchain_new.sh --with-dftd4=install --dry-run ${{matrix.external_toolchain_args}}
+          ./scripts/stage4/install_stage4.sh
+          cd ..
+
       - name: Build
         run: |
           git config --global --add safe.directory `pwd`
           export LD_LIBRARY_PATH=${GKLIB_ROOT}/lib:${METIS32_ROOT}/lib:${PARMETIS32_ROOT}/lib:${SUPERLU32_DIST_ROOT}/lib:${PEXSI32_ROOT}/lib:${LD_LIBRARY_PATH}
           export PKG_CONFIG_PATH=${GKLIB_ROOT}/lib/pkgconfig:${METIS32_ROOT}/lib/pkgconfig:${PARMETIS32_ROOT}/lib/pkgconfig:${SUPERLU32_DIST_ROOT}/lib/pkgconfig:${PEXSI32_ROOT}/lib/pkgconfig:${PKG_CONFIG_PATH}
           export CPATH=${GKLIB_ROOT}/include:${METIS32_ROOT}/include:${PARMETIS32_ROOT}/include:${SUPERLU32_DIST_ROOT}/include:${PEXSI32_ROOT}/include:${CPATH}
           export CMAKE_PREFIX_PATH=${PEXSI32_ROOT}:${SUPERLU_DIST32_ROOT}:${PARMETIS32_ROOT}:${METIS32_ROOT}:${GKLIB_ROOT}:${CMAKE_PREFIX_PATH}
+          source toolchain/install/setup
           rm -rf build
-          cmake -B build ${{ matrix.build_args }}
-          cmake --build build -j2
+          cmake -B build -G Ninja ${{ matrix.build_args }}
+          cmake --build build -j $(nproc)

.github/workflows/build_test_makefile.yml

@@ -3,6 +3,10 @@ on:
   push:
   pull_request:
 
+defaults:
+  run:
+    shell: bash
+
 jobs:
   test:
     runs-on: ubuntu-latest

.github/workflows/coverage.yml

@@ -5,6 +5,11 @@ on:
   push:
     tags:
     - 'v*'
+
+defaults:
+  run:
+    shell: bash
+
 jobs:
   test-coverage:
     name: Generate Coverage Report
@@ -18,20 +23,39 @@ jobs:
 
     - name: Install Perl Dependencies and Coverage Tools
       run: |
-        apt update && apt install -y curl jq ca-certificates python3-pip
-        apt install -y lcov perl-modules
-        apt install -y libcapture-tiny-perl libdatetime-perl libjson-perl libperlio-gzip-perl
+        sudo apt update
+        sudo apt install -y \
+          curl \
+          jq \
+          ca-certificates \
+          python3-pip \
+          xz-utils \
+          ninja-build \
+          lcov \
+          perl-modules \
+          libcapture-tiny-perl \
+          libdatetime-perl \
+          libjson-perl \
+          libperlio-gzip-perl
         lcov --version
 
+    - name: Install external tools from toolchain
+      run: |
+        cd toolchain
+        ./install_abacus_toolchain_new.sh --with-dftd4=install --dry-run -j8
+        ./scripts/stage4/install_stage4.sh
+        cd ..
+
     - name: Building with Coverage
       run: |
+        source toolchain/install/setup
         rm -rf build/
         rm -f CMakeCache.txt
 
         mkdir -p build
         chmod -R 755 build/
 
-        cmake -B build \
+        cmake -B build -G Ninja \
           -DENABLE_COVERAGE=ON \
           -DBUILD_TESTING=ON \
           -DENABLE_MLALGO=ON \

.github/workflows/cuda.yml

@@ -4,6 +4,10 @@ on:
   workflow_dispatch:
   pull_request:
 
+defaults:
+  run:
+    shell: bash
+
 concurrency:
   group: ${{ github.workflow }}-${{ github.ref }}
   cancel-in-progress: true
@@ -28,13 +32,21 @@ jobs:
       - name: Install Ccache
         run: |
           sudo apt-get update
-          sudo apt-get install -y ccache
+          sudo apt-get install -y ccache xz-utils ninja-build
+
+      - name: Install external tools from toolchain
+        run: |
+          cd toolchain
+          ./install_abacus_toolchain_new.sh --with-dftd4=install --dry-run -j8
+          ./scripts/stage4/install_stage4.sh
+          cd ..
 
       - name: Configure & Build
         run: |
           nvidia-smi
+          source toolchain/install/setup
           rm -rf build
-          cmake -B build -DUSE_CUDA=ON -DBUILD_TESTING=ON
+          cmake -B build -G Ninja -DUSE_CUDA=ON -DBUILD_TESTING=ON
           cmake --build build -j4
           cmake --install build
 

.github/workflows/devcontainer.yml

@@ -9,6 +9,10 @@ on:
       - 'v*'
   workflow_dispatch:
 
+defaults:
+  run:
+    shell: bash
+
 jobs:
   build_container_and_push:
     runs-on: X64

.github/workflows/doxygen.yml

@@ -10,6 +10,10 @@ on:
   # Allows you to run this workflow manually from the Actions tab
   workflow_dispatch:
 
+defaults:
+  run:
+    shell: bash
+
 # Sets permissions of the GITHUB_TOKEN to allow deployment to GitHub Pages
 permissions:
   contents: read

.github/workflows/dynamic.yml

@@ -5,6 +5,10 @@ on:
     - cron: '0 16 * * 0'
   workflow_dispatch:
 
+defaults:
+  run:
+    shell: bash
+
 jobs:
   test:
     name: Dynamic analysis
@@ -14,9 +18,17 @@ jobs:
     steps:
       - name: Checkout
         uses: actions/checkout@v7
+      - name: Install external tools from toolchain
+        run: |
+          sudo apt update && sudo apt install -y xz-utils ninja-build
+          cd toolchain
+          ./install_abacus_toolchain_new.sh --with-dftd4=install --dry-run -j8
+          ./scripts/stage4/install_stage4.sh
+          cd ..
       - name: Building
         run: |
-          cmake -B build -DENABLE_ASAN=1 -DENABLE_MLALGO=1 -DENABLE_LIBXC=1
+          source toolchain/install/setup
+          cmake -B build -G Ninja -DENABLE_ASAN=ON -DENABLE_MLALGO=ON -DENABLE_LIBXC=ON
           cmake --build build -j8
           cmake --install build
       - name: Testing

.github/workflows/interface.yml

@@ -3,6 +3,10 @@ name: interface
 on:
   workflow_dispatch:
 
+defaults:
+  run:
+    shell: bash
+
 jobs:
   wannier-interface:
     name: "wannier interface — ${{ matrix.name }}"

.github/workflows/mirror_gitee.yml

@@ -2,6 +2,10 @@ name: Mirror to Gitee Repository
 
 on: [ push, delete, create ]
 
+defaults:
+  run:
+    shell: bash
+
 # Ensures that only one mirror task will run at a time.
 concurrency:
   group: git-mirror

.github/workflows/performance.yml

@@ -3,6 +3,10 @@ name: Performance test
 on:
   workflow_dispatch:
 
+defaults:
+  run:
+    shell: bash
+
 jobs:
   test:
     name: Performance test
@@ -17,7 +21,7 @@ jobs:
         uses: actions/checkout@v7
       - name: Install Requirements
         run: |
-          apt install -y time
+          sudo apt install -y time
       - name: Test
         run: |
           . /opt/intel/oneapi/setvars.sh || :

.github/workflows/pytest.yml

@@ -3,6 +3,10 @@ name: Pyabacus Build and Test
 on:
   pull_request:
 
+defaults:
+  run:
+    shell: bash
+
 jobs:
   test:
     name: PyTest

.github/workflows/test.yml

@@ -36,20 +36,37 @@ jobs:
       - name: Install CI tools
         run: |
           sudo apt-get update
-          sudo apt-get install -y gfortran ccache ca-certificates python-is-python3 python3-pip
+          sudo apt-get install -y \
+            gfortran \
+            ccache \
+            ca-certificates \
+            python-is-python3 \
+            python3-pip \
+            ninja-build \
+            xz-utils
           sudo pip install clang-format clang-tidy
 
-      - name: Install dftd4 from toolchain
+      - name: Install external tools from toolchain
         run: |
           cd toolchain
           ./install_abacus_toolchain_new.sh --with-dftd4=install --dry-run -j8
-          ./scripts/stage4/install_dftd4.sh
+          ./scripts/stage4/install_stage4.sh
           cd ..
 
       - name: Configure
         run: |
           source toolchain/install/setup
-          cmake -B build -DBUILD_TESTING=ON -DENABLE_MLALGO=ON -DENABLE_LIBXC=ON -DENABLE_LIBRI=ON -DENABLE_GOOGLEBENCH=ON -DENABLE_RAPIDJSON=ON  -DCMAKE_EXPORT_COMPILE_COMMANDS=1 -DENABLE_FLOAT_FFTW=ON -DENABLE_DFTD4=ON
+          cmake -B build -G Ninja \
+            -DBUILD_TESTING=ON \
+            -DCMAKE_EXPORT_COMPILE_COMMANDS=ON \
+            -DENABLE_MLALGO=ON \
+            -DENABLE_LIBXC=ON \
+            -DENABLE_LIBRI=ON \
+            -DENABLE_GOOGLEBENCH=ON \
+            -DENABLE_RAPIDJSON=ON \
+            -DENABLE_FLOAT_FFTW=ON \
+            -DENABLE_DFTD4=ON \
+            -Werror=dev
 
 # Temporarily removed because no one maintains this now.
 # And it will break the CI test workflow.

.github/workflows/toolchain_full.yaml

@@ -8,6 +8,11 @@ on:
         description: "Comma-separated variants: gnu,intel,cuda"
         required: false
         default: "gnu,intel,cuda"
+
+defaults:
+  run:
+    shell: bash
+
 jobs:
   full-build-gnu:
     if: contains(inputs.variants || 'gnu,intel,cuda', 'gnu')

.github/workflows/toolchain_quick.yaml

@@ -11,6 +11,11 @@ on:
       - toolchain/**
       - .github/workflows/toolchain_quick.yaml
   workflow_dispatch:
+
+defaults:
+  run:
+    shell: bash
+
 jobs:
   lint-and-sanity:
     runs-on: ubuntu-latest