Update user guide and documentation for v1.1.0

.github/workflows/ci-cmake_tests.yml

@@ -11,8 +11,20 @@ jobs:
       run:
         shell: bash -l {0}
     steps:
-      - uses: actions/checkout@v3
-      - uses: conda-incubator/setup-miniconda@v2
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+
+      # When re-running a PR job, GitHub Actions uses the merge commit created at
+      # the time of the original run, not a fresh merge with the latest target branch.
+      # This step ensures we always test against the most recent target branch.
+      - name: Merge with latest target branch (pull_request only)
+        if: github.event_name == 'pull_request'
+        run: |
+          git fetch origin ${{ github.event.pull_request.base.ref }}
+          git merge --no-edit origin/${{ github.event.pull_request.base.ref }}
+
+      - uses: conda-incubator/setup-miniconda@v3
         with:
           # Specify python version your environment will have. Remember to quote this, or
           # YAML will think you want python 3.1 not 3.10

.github/workflows/clang-format-check.yml

@@ -7,9 +7,21 @@ jobs:
     name: Formatting Check
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
+      with:
+        fetch-depth: 0
+
+    # When re-running a PR job, GitHub Actions uses the merge commit created at
+    # the time of the original run, not a fresh merge with the latest target branch.
+    # This step ensures we always test against the most recent target branch.
+    - name: Merge with latest target branch (pull_request only)
+      if: github.event_name == 'pull_request'
+      run: |
+        git fetch origin ${{ github.event.pull_request.base.ref }}
+        git merge --no-edit origin/${{ github.event.pull_request.base.ref }}
+
     - name: Run clang-format style check for C/C++/Protobuf programs.
-      uses: jidicula/clang-format-action@v4.11.0
+      uses: jidicula/clang-format-action@v4.16.0
       with:
         clang-format-version: '14'
         check-path: '.'

.github/workflows/conda_build.yml

@@ -16,13 +16,24 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        os: [ubuntu-latest, macos-13, macos-latest]
+        os: [ubuntu-latest, macos-15-intel, macos-latest]
     defaults:
       run:
         shell: bash -l {0}
 
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
+      with:
+        fetch-depth: 0
+
+    # When re-running a PR job, GitHub Actions uses the merge commit created at
+    # the time of the original run, not a fresh merge with the latest target branch.
+    # This step ensures we always test against the most recent target branch.
+    - name: Merge with latest target branch (pull_request only)
+      if: github.event_name == 'pull_request'
+      run: |
+        git fetch origin ${{ github.event.pull_request.base.ref }}
+        git merge --no-edit origin/${{ github.event.pull_request.base.ref }}
 
     - uses: conda-incubator/setup-miniconda@v3
       with:

.github/workflows/conda_build_release.yml

@@ -13,10 +13,10 @@ jobs:
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        os: [ubuntu-latest, macos-13, macos-latest]
+        os: [ubuntu-latest, macos-15-intel, macos-latest]
 
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
 
     - uses: conda-incubator/setup-miniconda@v3
       with:

.github/workflows/coverity-scan.yml

@@ -15,9 +15,9 @@ jobs:
         shell: bash
 
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
 
-    - uses: conda-incubator/setup-miniconda@v2
+    - uses: conda-incubator/setup-miniconda@v3
       with:
         # Specify python version your environment will have. Remember to quote this, or
         # YAML will think you want python 3.1 not 3.10
@@ -33,9 +33,9 @@ jobs:
     - name: Install dependencies
       shell: bash -l {0}
       run: |
-        mamba install _openmp_mutex=*=*_llvm cmake make boost git compilers numpy mkl mkl-include mkl-service pybind11 libblas=*=*mkl gtest
+        mamba install cmake make boost compilers blas=*=mkl pybind11 arpack
 
-        cmake -S ${{github.workspace}} -B ${{github.workspace}}/build -DCMAKE_INSTALL_PREFIX=/home/runner/works/Cytnx_lib -DUSE_MKL=on -DUSE_HPTT=on -DHPTT_ENABLE_FINE_TUNE=on -DHPTT_ENABLE_AVX=on -DBUILD_PYTHON=on -DCMAKE_EXPORT_COMPILE_COMMANDS=1 -DRUN_TESTS=on
+        cmake -S ${{github.workspace}} -B ${{github.workspace}}/build -DCMAKE_INSTALL_PREFIX=/home/runner/works/Cytnx_lib --preset=mkl-cpu
 
     - name: Download Coverity Build Tool
       shell: bash -l {0}

.github/workflows/docs.yml

@@ -40,7 +40,7 @@ jobs:
       - name: Deploy
         uses: peaceiris/actions-gh-pages@v3
         with:
-          publish_branch: gh-pages  
+          publish_branch: gh-pages
           personal_token: ${{ secrets.PAGES_PAT }}
           external_repository: Cytnx-dev/Cytnx_doc
           publish_dir: docs/build/

CMakeLists.txt

@@ -146,7 +146,7 @@ endfunction()
 
 include(CMakeDependentOption)
 
-set(CMAKE_INSTALL_PREFIX "/usr/local/cytnx" CACHE PATH "Destination path for installation")
+set(CMAKE_INSTALL_PREFIX "~/.local/cytnx" CACHE PATH "Destination path for installation")
 option(BUILD_PYTHON "Build Python API. Requires Python and pybind11 installed." ON)
 option(BACKEND_TORCH "Use PyTorch as a backend container for tensors." OFF)
 cmake_dependent_option(USE_MKL "Use MKL as a BLAS provider otherwise use OpenBLAS." OFF "NOT BACKEND_TORCH" OFF)
@@ -317,14 +317,14 @@ endif()
 # #######
 IF(BUILD_PYTHON)
   find_package (Python COMPONENTS Interpreter Development)
-  find_package(pybind11 REQUIRED)
+  find_package(pybind11 3.0.0 QUIET)
 
   if(NOT pybind11_FOUND)
     include(FetchContent)
     FetchContent_Declare(
       pybind11_sources
       GIT_REPOSITORY https://github.com/pybind/pybind11.git
-      GIT_TAG v2.11.1
+      GIT_TAG v3.0.1
     )
 
     FetchContent_GetProperties(pybind11_sources)
@@ -339,7 +339,7 @@ IF(BUILD_PYTHON)
     endif()
   endif()
 
-  pybind11_add_module(pycytnx SHARED pybind/cytnx.cpp
+  pybind11_add_module(pycytnx MODULE pybind/cytnx.cpp
     pybind/generator_py.cpp
     pybind/storage_py.cpp
     pybind/tensor_py.cpp
@@ -357,13 +357,31 @@ IF(BUILD_PYTHON)
     pybind/ncon_py.cpp
   )
   target_link_libraries(pycytnx PUBLIC cytnx)
+
+  # On macOS, Python extensions should NOT link to libpython
+  # Use -undefined dynamic_lookup to resolve symbols from the running interpreter
+  if(APPLE)
+    target_link_options(pycytnx PRIVATE "-undefined" "dynamic_lookup")
+  endif()
   set_target_properties(pycytnx PROPERTIES OUTPUT_NAME cytnx)
   message(STATUS "pybind11 include dir: ${CUTENSOR_LIBRARY_DIRS}")
   message(STATUS "pybind11 include dir: ${CUQUANTUM_LIBRARY_DIRS}")
-  set_target_properties(pycytnx
-    PROPERTIES
-    INSTALL_RPATH "${CUTENSOR_LIBRARY_DIRS};${CUQUANTUM_LIBRARY_DIRS}"
-  )
+  message(STATUS "pybind11 include dir: ${LAPACK_LIBRARY_DIRS}")
+  message(STATUS "pybind11 include dir: ${LAPACKE_LIBRARY_DIRS}")
+  # Configure RPATH for macOS to make the Python extension relocatable
+  if(APPLE)
+    set_target_properties(pycytnx
+      PROPERTIES
+      BUILD_WITH_INSTALL_RPATH TRUE
+      INSTALL_RPATH_USE_LINK_PATH TRUE
+      INSTALL_RPATH "@loader_path;@loader_path/../../../lib;${CMAKE_INSTALL_PREFIX}/lib"
+    )
+  else()
+    set_target_properties(pycytnx
+      PROPERTIES
+      INSTALL_RPATH "${CMAKE_INSTALL_RPATH};${CMAKE_INSTALL_PREFIX}/lib"
+    )
+  endif()
 
   message(STATUS " Build Python Wrapper: YES")
   message(STATUS "  - Python Excutable  : ${PYTHON_EXECUTABLE}")