Merge pull request #429 from Cytnx-dev/dev-master

merge dev-master

.github/workflows/ci-cmake_pytests.yml

@@ -0,0 +1,100 @@
+name: Tests and Codecov
+
+on:
+  workflow_dispatch:
+
+jobs:
+  BuildAndTest:
+    runs-on: ubuntu-latest
+
+    defaults:
+      run:
+        shell: bash -l {0}
+
+    steps:
+    - uses: actions/checkout@v3
+
+    - uses: conda-incubator/setup-miniconda@v2
+      with:
+        # Specify python version your environment will have. Remember to quote this, or
+        # YAML will think you want python 3.1 not 3.10
+        python-version: "3.11"
+        # This uses *miniforge*, rather than *minicond*. The primary difference is that
+        # the defaults channel is not enabled at all
+        miniforge-version: latest
+        # These properties enable the use of mamba, which is much faster and far less error
+        # prone than conda while being completely compatible with the conda CLI
+        use-mamba: true
+        mamba-version: "*"
+
+    - 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 beartype
+        mamba install gcovr gtest
+
+    - name: CPU info
+      shell: bash -l {0}
+      run: lscpu
+
+    - name: Configure CMake
+      shell: bash -l {0}
+      run: cmake -S ${{github.workspace}} -B ${{github.workspace}}/build -DCMAKE_INSTALL_PREFIX=/home/runner/work/Cytnx_lib -DUSE_MKL=on -DUSE_HPTT=on -DHPTT_ENABLE_FINE_TUNE=on -DHPTT_ENABLE_AVX=off -DBUILD_PYTHON=on -DCMAKE_EXPORT_COMPILE_COMMANDS=1 -DRUN_TESTS=on
+
+    - name: Build
+      shell: bash -l {0}
+      working-directory: ${{github.workspace}}/build
+      run: |
+        cmake --version
+        cmake --build . -j `nproc`
+
+    - name: Install
+      shell: bash -l {0}
+      working-directory: ${{github.workspace}}/build
+      run: |
+        make install
+
+    - name: Set python path
+      run: |
+        echo "PYTHONPATH=/home/runner/work/Cytnx_lib" >> $GITHUB_ENV
+
+    - name: Test with pytest
+      shell: bash -l {0}
+      run: |
+        pip install pytest pytest-cov
+        pytest pytests/ --doctest-modules --junitxml=junit/test-results.xml --cov=com --cov-report=xml --cov-report=html
+
+    # - name: Run CTest
+    #   shell: bash -l {0}
+    #   working-directory: ${{github.workspace}}/build
+    #   run: GTEST_COLOR=1 ctest --output-on-failure --output-junit junit.xml
+
+    # - name: Run gcovr
+    #   shell: bash -l {0}
+    #   working-directory: ${{github.workspace}}/build
+    #   run: |
+    #     gcovr -r .. . --xml gcovr.xml -e ".*_deps.*$"
+
+    # - name: Upload coverage to Codecov
+    #   uses: codecov/codecov-action@v3
+    #   with:
+    #     #token: ${{ secrets.CODECOV_TOKEN }} # not required for public repos
+    #     #directory: ${{runner.workspace}}/build
+    #     files: ${{github.workspace}}/build/gcovr.xml # optional
+    #     #working-directory: ${{runner.workspace}}/build
+    #     #root_dir: ${{runner.workspace}}
+    #     fail_ci_if_error: true # optional (default = false)
+    #     verbose: true # optional (default = false)
+    #     #version: "v0.1.15"
+
+    #- name: Upload gcovr files
+    #  uses: actions/upload-artifact@v3
+    #  with:
+    #    name: CMakeError.log
+    #    path: /home/runner/work/Cytnx/Cytnx/build/CMakeFiles/CMakeError.log
+
+    #- name: Upload junit files
+    #  uses: actions/upload-artifact@v3
+    #  with:
+    #    name: junit_xml
+    #    path: ${{github.workspace}}/build/junit.xml

.github/workflows/ci-cmake_tests.yml

@@ -34,8 +34,9 @@ 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
+        mamba install _openmp_mutex=*=*_llvm cmake make boost git compilers numpy mkl mkl-include mkl-service pybind11 libblas=*=*mkl beartype
         mamba install gcovr gtest
+        mamba install pytest pytest-cov
 
     - name: CPU info
       shell: bash -l {0}
@@ -64,9 +65,9 @@ jobs:
         gcovr -r .. . --xml gcovr.xml -e ".*_deps.*$"
 
     - name: Upload coverage to Codecov
-      uses: codecov/codecov-action@v3
+      uses: codecov/codecov-action@v4
       with:
-        #token: ${{ secrets.CODECOV_TOKEN }} # not required for public repos
+        token: ${{ secrets.CODECOV_TOKEN }} # not required for public repos
         #directory: ${{runner.workspace}}/build
         files: ${{github.workspace}}/build/gcovr.xml # optional
         #working-directory: ${{runner.workspace}}/build
@@ -75,6 +76,21 @@ jobs:
         verbose: true # optional (default = false)
         #version: "v0.1.15"
 
+    - name: Install for python tests
+      shell: bash -l {0}
+      working-directory: ${{github.workspace}}/build
+      run: |
+        make install
+
+    - name: Set python path
+      shell: bash -l {0}
+      run: |
+        echo "PYTHONPATH=/home/runner/work/Cytnx_lib" >> $GITHUB_ENV
+
+    - name: Test with pytest
+      shell: bash -l {0}
+      run: |
+        pytest pytests/ --doctest-modules --junitxml=junit/test-results.xml --cov=com --cov-report=xml --cov-report=html
     #- name: Upload gcovr files
     #  uses: actions/upload-artifact@v3
     #  with:

CMakeLists.txt

@@ -231,7 +231,9 @@ endif()
 # ## Python wrapper
 # #######
 IF(BUILD_PYTHON)
-  find_package(PythonInterp REQUIRED)
+  # PythonInterp is removed in newer version of cmake
+  # find_package(PythonInterp REQUIRED)
+  find_package (Python COMPONENTS Interpreter Development)
   find_package(pybind11 REQUIRED)
 
   if(NOT pybind11_FOUND)

Install.sh

@@ -3,7 +3,8 @@
 #=========================================================
 # [Note] Set the destination path for installation in Ins_dest
 #----------------------------------------------
-Ins_dest="/usr/local/cytnx"
+# Ins_dest="/usr/local/cytnx"
+Ins_dest="~/Cytnx_lib"
 FLAG="${FLAG} -DCMAKE_INSTALL_PREFIX=${Ins_dest}"
 #-----------------------------------------------
 
@@ -18,7 +19,7 @@ FLAG="${FLAG} -DCMAKE_INSTALL_PREFIX=${Ins_dest}"
 #        Please follow the guide from official mkl/oneMKL "post-installation" part
 #        to source the proper setvars.sh and/or vars.sh
 #---------------------------
-FLAG="${FLAG} -DUSE_MKL=OFF"
+FLAG="${FLAG} -DUSE_MKL=ON"
 #---------------------------
 # 2-b) use OpenBLAS (DEFAULT = on (by settung DUSE_MKL=OFF above))
 # [Note] By default it will automatically find openblas installed
@@ -154,7 +155,7 @@ FLAG="${FLAG} -DUSE_OMP=OFF"
 #=========================================================
 # [Note] Wheather to run cytnx tests (DEFAULT = OFF)
 #-----------------------------------
-DRUN_TESTS=OFF
+DRUN_TESTS=ON
 FLAG="${FLAG} -DRUN_TESTS=${DRUN_TESTS}"
 #-----------------------------------
 
@@ -190,15 +191,16 @@ FLAG="${FLAG} -DUSE_DEBUG=OFF"
 # Build commands
 #=========================================================
 echo ${FLAG}
-# rm -rf build
+rm -rf build
 mkdir build
 cd build
 cmake ../ ${FLAG} #-DDEV_MODE=on
-make -j${nproc}
+make -j`nproc`
 make install
-#if DRUN_TESTS=ON, run tests
-shopt -s nocasematch
-case "${DRUN_TESTS}" in
- "ON" ) ctest; gcovr -r ../ . --html-details cov.html;;
- *) echo "Tests are skipped";;
-esac
+# if DRUN_TESTS=ON, run tests
+# ctest
+# shopt -s nocasematch
+# case "${DRUN_TESTS}" in
+#  "ON" ) ctest; gcovr -r ../ . --html-details cov.html;;
+#  *) echo "Tests are skipped";;
+# esac

cytnx/Network_conti.py

@@ -1,12 +1,26 @@
 from .utils import *
 from cytnx import *
 
-import imp
-try:
-    imp.find_module('graphviz')
-    from .NetGraph import *
-except ImportError:
+# import imp
+# try:
+#     imp.find_module('graphviz')
+#     from .NetGraph import *
+# except ImportError:
+#     from .NetGraph_empty import *
+
+import importlib
+spec = importlib.util.find_spec("graphviz")
+if spec is None:
+    # print("Can't find the graphviz module.")
     from .NetGraph_empty import *
+else:
+    # If you chose to perform the actual import ...
+    module = importlib.util.module_from_spec(spec)
+    spec.loader.exec_module(module)
+
+    # Adding the module to sys.modules is optional.
+    #sys.modules["graphviz"] = module
+    from .NetGraph import *
 
 import numpy as np
 

example/Accessor/ex.cpp.out

@@ -0,0 +1,21 @@
+
+Total elem: 24
+type  : Double (Float64)
+cytnx device: CPU
+Shape : (2,3,4)
+[[[0.00000e+00 1.00000e+00 2.00000e+00 3.00000e+00 ]
+  [4.00000e+00 5.00000e+00 6.00000e+00 7.00000e+00 ]
+  [8.00000e+00 9.00000e+00 1.00000e+01 1.10000e+01 ]]
+ [[1.20000e+01 1.30000e+01 1.40000e+01 1.50000e+01 ]
+  [1.60000e+01 1.70000e+01 1.80000e+01 1.90000e+01 ]
+  [2.00000e+01 2.10000e+01 2.20000e+01 2.30000e+01 ]]]
+
+
+
+Total elem: 6
+type  : Double (Float64)
+cytnx device: CPU
+Shape : (3,2)
+[[0.00000e+00 1.00000e+00 ]
+ [4.00000e+00 5.00000e+00 ]
+ [8.00000e+00 9.00000e+00 ]]

example/Accessor/example.cpp

@@ -0,0 +1,38 @@
+#include "cytnx.hpp"
+#include <iostream>
+
+using namespace cytnx;
+using namespace std;
+int main() {
+  // 1. handy alias:
+  typedef Accessor ac;
+
+  /*
+      2. Create a Tensor with
+      shape (3,4,5),
+      dtype =Type.Double [default],
+      device=Device.cpu [default]
+  */
+  Tensor A = cytnx::arange(24);
+  A.reshape_({2, 3, 4});
+  cout << A << endl;
+
+  /*
+      3. Accessing elements using accessor
+      This is similar as python slices.
+      -> A[0,:,0:2:1]
+
+  */
+  Tensor B = A(0, ac::all(), ac::range(0, 2, 1));
+  cout << B << endl;
+
+  /* [Note] Conversion from python slice to ac:
+          [::x]   = ac::step(x)
+          [a::x]  = ac::tilend(a,x)
+          [a::]   = ac::tilend(a)
+          [:b:]   = ac::range(0,b,1)
+          [a:b:x] = ac::range(a,b,x)
+  */
+
+  return 0;
+}

example/Accessor/example.cpp.out

@@ -0,0 +1,21 @@
+
+Total elem: 24
+type  : Double (Float64)
+cytnx device: CPU
+Shape : (2,3,4)
+[[[0.00000e+00 1.00000e+00 2.00000e+00 3.00000e+00 ]
+  [4.00000e+00 5.00000e+00 6.00000e+00 7.00000e+00 ]
+  [8.00000e+00 9.00000e+00 1.00000e+01 1.10000e+01 ]]
+ [[1.20000e+01 1.30000e+01 1.40000e+01 1.50000e+01 ]
+  [1.60000e+01 1.70000e+01 1.80000e+01 1.90000e+01 ]
+  [2.00000e+01 2.10000e+01 2.20000e+01 2.30000e+01 ]]]
+
+
+
+Total elem: 6
+type  : Double (Float64)
+cytnx device: CPU
+Shape : (3,2)
+[[0.00000e+00 1.00000e+00 ]
+ [4.00000e+00 5.00000e+00 ]
+ [8.00000e+00 9.00000e+00 ]]

example/Accessor/example.py

@@ -0,0 +1,13 @@
+import sys
+from pathlib import Path
+home = str(Path.home())
+sys.path.append(home + '/Cytnx_lib')
+from cytnx import *
+
+A = arange(24);
+A.reshape_(2,3,4);
+print(A)
+
+
+B = A[0,:,0:2:1]
+print(B)

example/Accessor/example.py.out

@@ -0,0 +1,22 @@
+
+Total elem: 24
+type  : Double (Float64)
+cytnx device: CPU
+Shape : (2,3,4)
+[[[0.00000e+00 1.00000e+00 2.00000e+00 3.00000e+00 ]
+  [4.00000e+00 5.00000e+00 6.00000e+00 7.00000e+00 ]
+  [8.00000e+00 9.00000e+00 1.00000e+01 1.10000e+01 ]]
+ [[1.20000e+01 1.30000e+01 1.40000e+01 1.50000e+01 ]
+  [1.60000e+01 1.70000e+01 1.80000e+01 1.90000e+01 ]
+  [2.00000e+01 2.10000e+01 2.20000e+01 2.30000e+01 ]]]
+
+
+
+
+Total elem: 6
+type  : Double (Float64)
+cytnx device: CPU
+Shape : (3,2)
+[[0.00000e+00 1.00000e+00 ]
+ [4.00000e+00 5.00000e+00 ]
+ [8.00000e+00 9.00000e+00 ]]

example/Bond/.cpp.out

@@ -0,0 +1,17 @@
+Dim = 10 |type: REGULAR
+
+Dim = 5 |type: REGULAR
+
+Dim = 50 |type: REGULAR
+
+Dim = 3 |type: <BRA
+ U1::  +0 +2 -4
+ Z2::  +1 +0 +1
+
+Dim = 4 |type: <BRA
+ U1::  +0 +2 -1 +3
+ Z2::  +0 +1 +1 +0
+
+Dim = 12 |type: <BRA
+ U1::  +0 +2 -1 +3 +2 +4 +1 +5 -4 -2 -5 -1
+ Z2::  +1 +0 +0 +1 +0 +1 +1 +0 +1 +0 +0 +1