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
@@ -33,13 +37,22 @@ jobs:
           cd interfaces/ASE_interface
           pip install .
 
+      - name: Install external tools from toolchain
+        run: |
+          apt update && apt install -y xz-utils
+          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 --build build -j2

.github/workflows/build_test_cmake.yml

@@ -3,6 +3,10 @@ on:
   push:
   pull_request:
 
+defaults:
+  run:
+    shell: bash
+
 jobs:
   test:
     runs-on: ubuntu-latest
@@ -13,29 +17,37 @@ jobs:
             build_args: ""
             name: "Build with GNU toolchain"
           - tag: intel
+            external_toolchain_args: "--with-intel"
             build_args: ""
             name: "Build with Intel toolchain"
 
           - tag: gnu
+            external_toolchain_args: ""
             build_args: "-DENABLE_LIBXC=1 -DENABLE_MLALGO=1 -DENABLE_LIBRI=1"
             name: "Build extra components with GNU toolchain"
           - tag: intel
+            external_toolchain_args: "--with-intel"
             build_args: "-DENABLE_LIBXC=1 -DENABLE_PEXSI=1 -DENABLE_MLALGO=1 -DENABLE_LIBRI=1"
             name: "Build extra components with Intel toolchain"
 
           - tag: cuda
+            external_toolchain_args: ""
             build_args: "-DUSE_CUDA=1"
             name: "Build with CUDA support"
           - tag: gnu
+            external_toolchain_args: ""
             build_args: "-DENABLE_LCAO=0"
             name: "Build without LCAO"
           - tag: gnu
+            external_toolchain_args: ""
             build_args: "-DUSE_ELPA=0 "
             name: "Build without ELPA"
           - tag: gnu
+            external_toolchain_args: ""
             build_args: "-DENABLE_MPI=0"
             name: "Build without MPI"
           - tag: gnu
+            external_toolchain_args: ""
             build_args: "-DENABLE_MPI=0 -DENABLE_LCAO=0"
             name: "Build without LCAO and MPI"
 
@@ -47,13 +59,22 @@ jobs:
         with:
           submodules: recursive
 
+      - name: Install external tools from toolchain
+        run: |
+          apt update && apt install -y gfortran 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

.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
@@ -18,13 +23,21 @@ jobs:
 
     - name: Install Perl Dependencies and Coverage Tools
       run: |
-        apt update && apt install -y curl jq ca-certificates python3-pip
+        apt update && apt install -y curl jq ca-certificates python3-pip xz-utils
         apt install -y lcov perl-modules
         apt install -y 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
 

.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
@@ -28,11 +32,19 @@ jobs:
       - name: Install Ccache
         run: |
           sudo apt-get update
-          sudo apt-get install -y ccache
+          sudo apt-get install -y ccache xz-utils
+
+      - 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 --build build -j4

.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
@@ -14,8 +18,16 @@ jobs:
     steps:
       - name: Checkout
         uses: actions/checkout@v6
+      - name: Install external tools from toolchain
+        run: |
+          apt update && apt install -y xz-utils
+          cd toolchain
+          ./install_abacus_toolchain_new.sh --with-dftd4=install --dry-run -j8
+          ./scripts/stage4/install_stage4.sh
+          cd ..
       - name: Building
         run: |
+          source toolchain/install/setup
           cmake -B build -DENABLE_ASAN=1 -DENABLE_MLALGO=1 -DENABLE_LIBXC=1
           cmake --build build -j8
           cmake --install build

.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

.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

@@ -39,11 +39,11 @@ jobs:
           sudo apt-get install -y gfortran ccache ca-certificates python-is-python3 python3-pip
           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

.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

.github/workflows/version_check.yml

@@ -3,6 +3,10 @@ on:
   release:
     types: [published]
 
+defaults:
+  run:
+    shell: bash
+
 jobs:
   validate_version:
     runs-on: ubuntu-latest
@@ -42,4 +46,4 @@ jobs:
           if [[ "${{ steps.versions.outputs.prev_tag}}" == "${{ steps.versions.outputs.current_tag }}" ]]; then
             echo "::error::Version unchanged: ${{ steps.versions.outputs.current_tag }}"
             exit 1
-          fi
+          fi