Upgrade to Python3.11 + Cython3 (#213)

Co-authored-by: Robin Andersson <[email protected]>

.github/workflows/build.yml

@@ -9,10 +9,15 @@ jobs:
   linux:
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
+    - uses: actions/setup-python@v4
+      with:
+        python-version: '3.11.x'
+    - name: Setup Python
+      run: |
+        python3 -m pip install Cython numpy scipy matplotlib nose-py3
     - name: Install system
       run: |
-        sudo apt-get -y install python3-scipy python3-setuptools python3-nose cython3 python3-matplotlib
         sudo apt-get -y install cmake liblapack-dev libsuitesparse-dev libhypre-dev
         sudo cp -v /usr/lib/x86_64-linux-gnu/libblas.so /usr/lib/x86_64-linux-gnu/libblas_OPENMP.so
     - name: Install superlu
@@ -35,9 +40,8 @@ jobs:
         sudo make install
     - name: Install assimulo
       run: |
-        cd /tmp
-        curl -fSsL https://github.com/modelon-community/Assimulo/archive/Assimulo-3.4.1.tar.gz | tar xz
-        cd Assimulo-Assimulo-3.4.1
+        git clone --depth 1 -b dev-pm-python_upgrade https://github.com/modelon-community/Assimulo /tmp/Assimulo
+        cd /tmp/Assimulo
         python3 setup.py install --user --sundials-home=/usr --blas-home=/usr/lib/x86_64-linux-gnu/ --lapack-home=/usr/lib/x86_64-linux-gnu/ --superlu-home=/usr --extra-fortran-compile-flags="-fallow-argument-mismatch"
     - name: Install fmilib
       run: |
@@ -55,5 +59,4 @@ jobs:
       run: |
         rm src/pyfmi/__init__.py
         cp -rv src/pyfmi/tests/files tests
-        nosetests3 tests
-
+        python3 -m nose --verbose tests/*

CHANGELOG

@@ -3,6 +3,7 @@
     * Removed utilities related to the obsolete FMUX model interface.
     * Removed no longer required dependency on lxml.
     * Unified result handling and allowed the master algorithm to use all available result handlers
+    * Upgraded to Cython3.
 
 --- PyFMI-2.11.0 ---
     * Refactored result handling for dynamic_diagnostics. It is now possible use dynamic_diagnostics with a custom result handler.

setup.cfg

@@ -1,13 +1,13 @@
 [options]
 setup_requires =
     setuptools
-    numpy >= 1.17
-    cython >= 0.29.13
+    numpy >= 1.26.3
+    cython >= 3.0
 
 install_requires =
-    numpy >= 1.17
-    scipy >= 1.3
-    cython >= 0.29.13
-    nose >= 1.3.7
+    numpy >= 1.26.3
+    scipy >= 1.11.4
+    cython >= 3.0.7
+    nose-py3 >= 1.6.3
     matplotlib > 3
-    assimulo >= 3.2
+    assimulo >= 3.5.0

setup.py

@@ -33,13 +33,13 @@
     from Cython.Distutils import build_ext
     from Cython.Build import cythonize
 except ImportError:
-    raise Exception("Please upgrade to a newer Cython version, >= 0.15.")
+    raise Exception("Please upgrade to a newer Cython version, >= 3.")
 
 
 NAME = "PyFMI"
 AUTHOR = "Modelon AB"
 AUTHOR_EMAIL = ""
-VERSION = "3.0-dev"
+VERSION = "2.12.0"
 LICENSE = "LGPL"
 URL = "https://github.com/modelon-community/PyFMI"
 DOWNLOAD_URL = "https://github.com/modelon-community/PyFMI/releases"
@@ -73,7 +73,7 @@
 -------------
 - `FMI Library (at least 2.0.1) <https://github.com/modelon-community/fmi-library>`_
 - `Python-headers (usually included on Windows, python-dev on Ubuntu)`_
-- `Python 3.7 or newer`_
+- `Python 3.11 or newer`_
 - Python package dependencies are listed in file setup.cfg.
 
 Optional
@@ -90,9 +90,10 @@
 
 copy_args = sys.argv[1:]
 
-if os.getenv("FMIL_HOME"): #Check for if there exists and environment variable that specifies FMIL
-    incdirs = os.path.join(os.getenv("FMIL_HOME"), 'include')
-    libdirs = os.path.join(os.getenv("FMIL_HOME"), 'lib')
+fmil_home = os.getenv("FMIL_HOME")
+if fmil_home: #Check for environment variable that specifies FMIL
+    incdirs = os.path.join(fmil_home, 'include')
+    libdirs = os.path.join(fmil_home, 'lib')
 else:
     incdirs = ""
     libdirs = ""
@@ -153,7 +154,6 @@
             debug_flag = False
         copy_args.remove(x)
 
-
 if not incdirs:
     raise Exception("FMI Library cannot be found. Please specify its location, either using the flag to the setup script '--fmil-home' or specify it using the environment variable FMIL_HOME.")
 
@@ -214,29 +214,35 @@ def check_extensions():
     incl_path = [".", "src", os.path.join("src", "pyfmi")]
     #FMI PYX
     ext_list += cythonize([os.path.join("src", "pyfmi", "fmi.pyx")], 
-                    include_path = incl_path)
+                    include_path = incl_path,
+                    compiler_directives={'language_level' : "3str"})
 
     #FMI UTIL
     ext_list += cythonize([os.path.join("src", "pyfmi", "fmi_util.pyx")], 
-                    include_path = incl_path)
+                    include_path = incl_path,
+                    compiler_directives={'language_level' : "3str"})
 
     #FMI Extended PYX
     ext_list += cythonize([os.path.join("src", "pyfmi", "fmi_extended.pyx")], 
-                    include_path = incl_path)
+                    include_path = incl_path,
+                    compiler_directives={'language_level' : "3str"})
 
     #FMI Coupled PYX
     ext_list += cythonize([os.path.join("src", "pyfmi", "fmi_coupled.pyx")], 
-                    include_path = incl_path)
+                    include_path = incl_path,
+                    compiler_directives={'language_level' : "3str"})
 
     #Simulation interface PYX
     ext_list += cythonize([os.path.join("src", "pyfmi", "simulation", "assimulo_interface.pyx")], 
-                    include_path = incl_path)
+                    include_path = incl_path,
+                    compiler_directives={'language_level' : "3str"})
 
     #MASTER PYX
     compile_time_env = {'WITH_OPENMP': with_openmp}
     ext_list += cythonize([os.path.join("src", "pyfmi", "master.pyx")], 
                     include_path = incl_path, 
-                    compile_time_env=compile_time_env)
+                    compile_time_env=compile_time_env,
+                    compiler_directives={'language_level' : "3str"})
 
     for i in range(len(ext_list)):
 

src/common/core.py

@@ -149,7 +149,7 @@ def _exec_algorithm(self, module, algorithm, options):
             Exception if algorithm is not a subclass of 
             common.algorithm_drivers.AlgorithmBase.
         """
-        from .algorithm_drivers import AlgorithmBase
+        from pyfmi.algorithm_drivers import AlgorithmBase
 
         if isinstance(algorithm, str):
             module = __import__(module, globals(), locals(), [algorithm], 0)
@@ -182,7 +182,7 @@ def _exec_simulate_algorithm(self,
             Exception if algorithm is not a subclass of 
             common.algorithm_drivers.AlgorithmBase.
         """
-        from .algorithm_drivers import AlgorithmBase
+        from pyfmi.algorithm_drivers import AlgorithmBase
 
         if isinstance(algorithm, str):
             module = __import__(module, globals(), locals(), [algorithm], 0)

src/common/io.py

@@ -371,20 +371,20 @@ class ResultWriter():
     Base class for writing results to file.
     """
 
-    def write_header():
+    def write_header(self):
         """
         The header is intended to be used for writing general information about
         the model. This is intended to be called once.
         """
         pass
 
-    def write_point():
+    def write_point(self):
         """
         This method does the writing of the actual result.
         """
         pass
 
-    def write_finalize():
+    def write_finalize(self):
         """
         The finalize method can be used to for instance close the file.
         """

src/common/log/__init__.py

@@ -19,7 +19,7 @@
 The log analysis toolkit. 
 """
 
-from .parser import parse_xml_log, parse_xml_log, extract_xml_log, parse_fmu_xml_log
-from .prettyprinter import prettyprint_to_file
+from pyfmi.common.log.parser import parse_xml_log, parse_xml_log, extract_xml_log, parse_fmu_xml_log
+from pyfmi.common.log.prettyprinter import prettyprint_to_file
 
 __all__=['parser','tree','prettyprinter']

src/common/log/parser.py

@@ -23,7 +23,7 @@
 import os
 import numpy as np
 from distutils.util import strtobool
-from .tree import *
+from pyfmi.common.log.tree import *
 from pyfmi.fmi_util import python3_flag
 from pyfmi.fmi import FMUException
 

src/common/log/prettyprinter.py

@@ -19,7 +19,7 @@
 """
 
 from numpy import ndarray
-from .tree import *
+from pyfmi.common.log.tree import *
 
 def prettyprint(write, node):
     """Prettyprint a log node to the write callback write."""

src/pyfmi/__init__.py

@@ -21,11 +21,11 @@
 __all__ = ['fmi_algorithm_drivers', 'examples', 'fmi', 'common']
 
 #Import the model class allowing for users to type e.g.,: from pyfmi import FMUModelME1
-from .fmi import load_fmu, FMUModelME1, FMUModelME2
-from .fmi import FMUModelCS1, FMUModelCS2
-from .fmi_coupled import CoupledFMUModelME2
-from .master import Master
-from .fmi_extended import FMUModelME1Extended
+from pyfmi.fmi import load_fmu, FMUModelME1, FMUModelME2
+from pyfmi.fmi import FMUModelCS1, FMUModelCS2
+from pyfmi.fmi_coupled import CoupledFMUModelME2
+from pyfmi.master import Master
+from pyfmi.fmi_extended import FMUModelME1Extended
 import numpy as N
 import os.path
 import sys
@@ -49,7 +49,7 @@ def wrap(func):
 
 
 try:
-    curr_dir = os.path.dirname(os.path.abspath(__file__));
+    curr_dir = os.path.dirname(os.path.abspath(__file__))
     _fpath=os.path.join(curr_dir,'version.txt')
     with open(_fpath, 'r') as f:
         __version__=f.readline().strip()
@@ -178,5 +178,3 @@ def check_packages():
 This package is needed to be able to use the plot-GUI.")
 
             sys.stdout.write("\n\n")
-
-

src/pyfmi/fmi.pxd

@@ -29,7 +29,7 @@ cimport numpy as N
 
 N.import_array()
 
-cimport fmil_import as FMIL
+cimport pyfmi.fmil_import as FMIL
 
 cdef FMIL.fmi_version_enu_t import_and_get_version(FMIL.fmi_import_context_t*, char*, char*, int)
 
@@ -116,7 +116,7 @@ cdef class FMUModelBase(ModelBase):
     cdef FMIL.jm_callbacks* callbacks_standard
 
     #Internal values
-    cdef public object __t
+    cdef public object _t
     cdef public object _file_open
     cdef public object _npoints
     cdef public object _enable_logging
@@ -158,10 +158,11 @@ cdef class FMUModelME1(FMUModelBase):
     cpdef _get_time(self)
     cpdef _set_time(self, FMIL.fmi1_real_t t)
     cpdef get_derivatives(self)
-    cdef int __get_nominal_continuous_states(self, FMIL.fmi1_real_t* xnominal, size_t nx)
+    cdef int _get_nominal_continuous_states_fmil(self, FMIL.fmi1_real_t* xnominal, size_t nx)
     cdef public object _preinit_nominal_continuous_states
 
-cdef class __ForTestingFMUModelME1(FMUModelME1):
+cdef class _ForTestingFMUModelME1(FMUModelME1):
+    cdef int _get_nominal_continuous_states_fmil(self, FMIL.fmi1_real_t* xnominal, size_t nx)
     cpdef set_allocated_fmu(self, int value)
 
 cdef class FMUModelBase2(ModelBase):
@@ -190,7 +191,7 @@ cdef class FMUModelBase2(ModelBase):
     cdef public list    _save_real_variables_val
     cdef public list    _save_int_variables_val
     cdef public list    _save_bool_variables_val
-    cdef object         __t
+    cdef object         _t
     cdef public object  _pyEventInfo
     cdef char* _fmu_temp_dir
     cdef object         _states_references
@@ -206,7 +207,7 @@ cdef class FMUModelBase2(ModelBase):
     cdef object         _outputs_states_dependencies_kind
     cdef object         _outputs_inputs_dependencies_kind
     cdef object         _A, _B, _C, _D
-    cdef public object         _group_A, _group_B, _group_C, _group_D
+    cdef public object  _group_A, _group_B, _group_C, _group_D
     cdef object         _mask_A
     cdef object         _A_row_ind, _A_col_ind
     cdef public object  _has_entered_init_mode
@@ -234,9 +235,9 @@ cdef class FMUModelBase2(ModelBase):
     cdef int _get_directional_derivative(self, N.ndarray v_ref, N.ndarray z_ref, N.ndarray dv, N.ndarray dz) except -1
     cpdef set_real(self, valueref, values)
     cpdef N.ndarray get_real(self, valueref)
-    cdef int __set_real(self, FMIL.fmi2_value_reference_t* vrefs, FMIL.fmi2_real_t* values, size_t size)
-    cdef int __get_real(self, FMIL.fmi2_value_reference_t* vrefs, size_t size, FMIL.fmi2_real_t* values)
-    cdef int _get_real(self, FMIL.fmi2_value_reference_t[:] valueref, size_t size, FMIL.fmi2_real_t[:] values)
+    cdef int _set_real(self, FMIL.fmi2_value_reference_t* vrefs, FMIL.fmi2_real_t* values, size_t size)
+    cdef int _get_real_by_ptr(self, FMIL.fmi2_value_reference_t* vrefs, size_t size, FMIL.fmi2_real_t* values)
+    cdef int _get_real_by_list(self, FMIL.fmi2_value_reference_t[:] valueref, size_t size, FMIL.fmi2_real_t[:] values)
     cdef int _get_integer(self, FMIL.fmi2_value_reference_t[:] valueref, size_t size, FMIL.fmi2_integer_t[:] values)
     cdef int _get_boolean(self, FMIL.fmi2_value_reference_t[:] valueref, size_t size, FMIL.fmi2_real_t[:] values)
 
@@ -255,11 +256,11 @@ cdef class FMUModelME2(FMUModelBase2):
     cpdef get_derivatives(self)
     cdef public object force_finite_differences
     cdef int _get_derivatives(self, FMIL.fmi2_real_t[:] values)
-    cdef int __get_continuous_states(self, FMIL.fmi2_real_t[:] ndx)
-    cdef int __set_continuous_states(self, FMIL.fmi2_real_t[:] ndx)
+    cdef int _get_continuous_states_fmil(self, FMIL.fmi2_real_t[:] ndx)
+    cdef int _set_continuous_states_fmil(self, FMIL.fmi2_real_t[:] ndx)
     cdef int _get_event_indicators(self, FMIL.fmi2_real_t[:] values)
     cdef int _completed_integrator_step(self, int* enter_event_mode, int* terminate_simulation)
-    cdef int __get_nominal_continuous_states(self, FMIL.fmi2_real_t* xnominal, size_t nx)
+    cdef int _get_nominal_continuous_states_fmil(self, FMIL.fmi2_real_t* xnominal, size_t nx)
     cdef public object _preinit_nominal_continuous_states
 
 cdef class WorkerClass2:
@@ -274,5 +275,11 @@ cdef class WorkerClass2:
     cdef N.ndarray get_real_numpy_vector(self, int index)
     cpdef verify_dimensions(self, int dim)
 
-cdef class __ForTestingFMUModelME2(FMUModelME2):
+cdef class _ForTestingFMUModelME2(FMUModelME2):
+    cdef int _get_real_by_ptr(self, FMIL.fmi2_value_reference_t* vrefs, size_t size, FMIL.fmi2_real_t* values)
+    cdef int _set_real(self, FMIL.fmi2_value_reference_t* vrefs, FMIL.fmi2_real_t* values, size_t size)
+    cdef int _get_real_by_list(self, FMIL.fmi2_value_reference_t[:] valueref, size_t size, FMIL.fmi2_real_t[:] values)
+    cdef int _get_integer(self, FMIL.fmi2_value_reference_t[:] valueref, size_t size, FMIL.fmi2_integer_t[:] values)
+    cdef int _get_boolean(self, FMIL.fmi2_value_reference_t[:] valueref, size_t size, FMIL.fmi2_real_t[:] values)
+    cdef int _get_nominal_continuous_states_fmil(self, FMIL.fmi2_real_t* xnominal, size_t nx)
     cpdef set_initialized_fmu(self, int value)