Fix compilation error and invalid chunk bug for large simulation data #19

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lekez2005 wants to merge 17 commits into henjo:master from lekez2005:master

.gitignore

            
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    *.lo

    *.la

    .vscode/

    build/

    *.o

    *.so

    .deps

    .libs

    aclocal.m4

    autom4te.cache

    configure

    Makefile

    Makefile.in

    INSTALL

    m4

    py-compile

    config.*

    src/psftest

    test/test_psfdataset

    missing

    ltmain.sh

    libtool

    libpsf.pc

    libpsf-uninstalled.pc

    depcomp

    *~

CMakeLists.txt

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+    # https://stackoverflow.com/questions/17511496/how-to-create-a-shared-library-with-cmake
+    # https://github.com/giuliopaci/cmake-tutorial/blob/master/CMakeLists.txt
+    cmake_minimum_required(VERSION 3.12)
+    project(libpsf VERSION 0.3
+        DESCRIPTION "Load Cadence Spectre PSF simulation data"
+        LANGUAGES CXX)
+    option(WITH_PYTHON "Build python bindings" ON)
+    set(CMAKE_CXX_STANDARD 11)
+    set(CMAKE_CXX_STANDARD_REQUIRED True)
+    set(CMAKE_EXPORT_COMPILE_COMMANDS ON)
+    if(CMAKE_PROJECT_NAME STREQUAL PROJECT_NAME)
+        include(CTest)
+    endif()
+    add_subdirectory(src)
+    add_subdirectory(test)
+    if(WITH_PYTHON)
+        add_subdirectory(bindings)
+    endif()

ChangeLog

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Makefile.am

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NEWS

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README.rst

            
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    @@ -3,34 +3,44 @@ libpsf is a c++ library that reads Cadence PSF waveform files
  
    Install

    =======

    Install prerequisits

    Install prerequisites

    --------------------

    If building without python binding, only cmake and boost are required

    On a debian based system you can run the following to install the 

    - On a debian based system you can run the following to install the 

    packages needed to build libpsf:

    sudo apt-get install autoconf automake libtool libboost-all-dev python-numpy-dev 

        $ sudo apt-get install cmake libboost-all-dev python-numpy-dev cython cppunit

    - Otherwise conda can be used to install the following packages:

        $ conda install python numpy cython cmake

        Then install boost libraries and set

        $ export BOOST_LOC=<BOOST_LOCATION>

    Build and install

    -----------------

    To build and install the library::

    - From root directory, create build directory

       ./autogen.sh

       make

       sudo make install

        $ mkdir build && cd build

    - Run cmake configuration

    To build the python extension::

        $ cmake .. -DCMAKE_INSTALL_PREFIX=$CONDA_PREFIX -DCMAKE_BUILD_TYPE=RELEASE -DWITH_PYTHON=ON

       ./autogen.sh --with-python

       make

       sudo make install

        `CONDA_PREFIX` is the destination where you want libpsf to be installed

        To build without the python binding, just set `-DWITH_PYTHON=OFF`

    - Build

        $ make

    - To run tests, [cppunit](https://www.freedesktop.org/wiki/Software/cppunit) is required.

        $ ctest

    Running the tests

    -----------------

    Install cppunit, then compile and run the tests in the test dir::

        `ctest --verbose` to see individual test result outputs

    - Install

        sudo apt-get install libcppunit-dev

        cd test

        make

        ./test_psfdataset

        $ make install

autogen.sh

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bindings/CMakeLists.txt

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		add_subdirectory(python)

bindings/Makefile.am

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bindings/python/.gitignore

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+    libpsf.cpp
+    libpsf.h
+    *.pyc

bindings/python/CMakeLists.txt

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+    find_package(Python COMPONENTS Interpreter Development)
+    find_program(CYTHON_EXECUTABLE NAMES cython cython3
+        HINTS ${_python_path})
+    # find_program(Python REQUIRED COMPONENTS Interpreter Development NumPy)
+    # https://bloerg.net/posts/cmake-and-distutils/
+    if( Python_EXECUTABLE AND CYTHON_EXECUTABLE)
+        MESSAGE( STATUS "numpy headers found at: ${Python_NumPy_INCLUDE_DIRS}")
+        MESSAGE( STATUS "cython found at: ${CYTHON_EXECUTABLE}")
+        # set variables for setup.py.in
+        get_target_property(LIBPSF_BUILD_DIR psf BINARY_DIR)
+        get_target_property(LIBPSF_INCLUDE psf INCLUDE_DIRECTORIES)
+        set(SETUP_PY_IN "${CMAKE_CURRENT_SOURCE_DIR}/setup.py.in")
+        set(SETUP_PY    "${CMAKE_CURRENT_BINARY_DIR}/setup.py")
+        set(DEPS setup.py.in psfpython.h psfpython.cc libpsf.pyx cpp_defs.pxd)
+        set(OUTPUT      "${CMAKE_CURRENT_BINARY_DIR}/build/timestamp")
+        configure_file(${SETUP_PY_IN} ${SETUP_PY})
+        # build commands
+        add_custom_command(OUTPUT ${OUTPUT}
+                           COMMAND ${Python_EXECUTABLE} ${SETUP_PY} build_ext --inplace
+                           COMMAND ${Python_EXECUTABLE} ${SETUP_PY} bdist_wheel
+                           COMMAND ${CMAKE_COMMAND} -E touch ${OUTPUT}
+                           DEPENDS ${DEPS})
+        add_custom_target(python_binding ALL DEPENDS ${OUTPUT})
+        add_dependencies(python_binding psf)
+        # install binding
+        install(CODE "execute_process(COMMAND ${Python_EXECUTABLE} ${SETUP_PY} install)")
+        install(DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/dist
+                DESTINATION ${CMAKE_CURRENT_SOURCE_DIR})
+        # tests
+        if(CMAKE_PROJECT_NAME STREQUAL PROJECT_NAME AND BUILD_TESTING)
+            add_test(NAME python_test
+                     COMMAND ${Python_EXECUTABLE} -m unittest test_psfdataset.py -v
+                     WORKING_DIRECTORY "${CMAKE_CURRENT_SOURCE_DIR}/tests")
+            set_tests_properties(python_test PROPERTIES
+                                  ENVIRONMENT PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}:$ENV{PYTHONPATH})
+        endif()
+    else()
+        MESSAGE( WARNING "python/numpy/cython include not found, skipping python bindings")
+    endif()

bindings/python/Makefile.am

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bindings/python/__init__.py

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bindings/python/cpp_defs.pxd

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+    # https://cython.readthedocs.io/en/latest/src/userguide/wrapping_CPlusPlus.html
+    # https://stackoverflow.com/a/10121232
+    # https://stackoverflow.com/a/29002414
+    from cpython.ref cimport PyObject
+    from libcpp cimport bool
+    from libcpp.string cimport string
+    from libcpp.vector cimport vector
+    cdef extern from "psf.h":
+        cdef cppclass PSFVector
+        cdef cppclass PSFBase
+    cdef extern from "psfpython.h":
+        cdef void raise_py_error()
+        cdef cppclass PropertyMap
+    cdef extern from "psf.h":
+        cdef cppclass PSFDataSet:
+            PSFDataSet(string) except +raise_py_error
+            int get_nsweeps()  except +raise_py_error
+            int get_sweep_npoints() except +raise_py_error
+            const vector[string] get_signal_names() except +raise_py_error
+            const vector[string] get_sweep_param_names() except +raise_py_error
+            PSFVector* get_sweep_values() except +raise_py_error
+            PSFBase *get_signal(string name) except +raise_py_error
+            PropertyMap& get_signal_properties(string name) except +raise_py_error
+            PropertyMap& get_header_properties() except +raise_py_error
+            bool is_swept() except +raise_py_error
+            void close() except +raise_py_error
+            void open() except +raise_py_error
+            void set_invertstruct(bool value) except +raise_py_error
+            bool get_invertstruct() except +raise_py_error

bindings/python/dist/libpsf-0.3-cp37-cp37m-linux_x86_64.whl

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bindings/python/libpsf.pyx

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+    # distutils: language = c++
+    # cython: language_level=2
+    from libcpp cimport bool
+    from cpython.ref cimport PyObject
+    from cpp_defs cimport PSFVector, PSFBase, PropertyMap
+    from cpp_defs cimport PSFDataSet as C_PSFDataSet
+    cimport numpy as np
+    np.import_array()
+    cdef extern from "psfpython.h":
+        cdef np.ndarray psfvector_to_numpy_array(PSFVector *vec, bool copy)
+        cdef object psfbase_to_numpy_array(PSFBase *d)
+        cdef object propertymap_to_python(PropertyMap& propmap)
+    class FileOpenError(RuntimeError):
+        pass
+    class NotFound(RuntimeError):
+        pass
+    class DataSetNotOpen(RuntimeError):
+        pass
+    class UnknownType(RuntimeError):
+        pass
+    class IncorrectChunk(RuntimeError):
+        pass
+    cdef public PyObject* fileOpenError = <PyObject*>FileOpenError
+    cdef public PyObject* notFoundError = <PyObject*>NotFound
+    cdef public PyObject* notOpenError = <PyObject*>DataSetNotOpen
+    cdef public PyObject* unknownTypeError = <PyObject*>UnknownType
+    cdef public PyObject* incorrectChunkError = <PyObject*>IncorrectChunk
+    cdef to_unicode(str_):
+        return str_.encode('UTF-8')
+    cdef bytes_to_string(str_list):
+        return map(lambda x: x.decode('UTF-8'), str_list)
+    cdef class PSFDataSet:
+        cdef C_PSFDataSet *obj
+        def __cinit__(self, filename):
+            self.obj = new C_PSFDataSet(to_unicode(filename))
+        def __dealloc__(self):
+            del self.obj
+        def get_nsweeps(self):
+            """Return the number of sweeps"""
+            return self.obj.get_nsweeps()
+        def get_sweep_npoints(self):
+            """Return the number of points in the sweep"""
+            return self.obj.get_sweep_npoints()
+        def get_signal_names(self):
+            """Return a list of signal names"""
+            return bytes_to_string(self.obj.get_signal_names())
+        def get_sweep_param_names(self):
+            """Parameters that have been swept"""
+            return bytes_to_string(self.obj.get_sweep_param_names())
+        def get_sweep_values(self):
+            """Numpy array of swept values"""
+            return psfvector_to_numpy_array(self.obj.get_sweep_values(), False)
+        def get_signal(self, signal):
+            """Numpy array of signal values"""
+            return psfbase_to_numpy_array(self.obj.get_signal(to_unicode(signal)))
+        def get_signal_properties(self, signal):
+            """Properties of a non swept signal
+            Throws NotFound exception for non_swept datasets so check self.is_swept
+            first
+            """
+            return propertymap_to_python(self.obj.get_signal_properties(to_unicode(signal)))
+        def get_header_properties(self):
+            """Dict of header [rp[ertoes and values"""
+            return propertymap_to_python(self.obj.get_header_properties())
+        def is_swept(self):
+            """Is the data swept"""
+            return self.obj.is_swept()
+        def close(self):
+            """Close PSF Data Set"""
+            self.obj.close()
+        def open(self):
+            """Open PSF Data Set"""
+            self.obj.open()
+        def set_invertstruct(self, bool value):
+            """Set invert struct"""
+            self.obj.set_invertstruct(value)
+        def get_invertstruct(self):
+            """Get invert struct"""
+            return self.obj.get_invertstruct()

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