Upgrade to Python 3.11, Cython3 (#81)

.github/workflows/build.yml

@@ -12,10 +12,15 @@ jobs:
       matrix:
         sundials_version: [2.7.0, 3.2.0]
     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
         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
@@ -38,5 +43,4 @@ jobs:
     - name: Build
       run: 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: Test
-      run: nosetests3 tests
-
+      run: python3 -m nose --verbose tests/* tests/solvers/*

CHANGELOG

@@ -1,7 +1,9 @@
 --- CHANGELOG ---
---- Assimulo-3.4.4 ---
+--- Assimulo-3.5.0 ---
     * Changed "numpy.float" to equivalent "numpy.float64" due to DeprecationWarnings in numpy >= 1.20.
     * Improved examples with sparse jacobians by omitting the zeros in the jacobians.
+    * Upgraded to Cython >= 3.
+    * Removed deprecated build option "sundials_with_superlu", which is checked automatically.
 
 --- Assimulo-3.4.3 ---
     * Improved compliance with newer scipy version by instead using corresponding numpy calls when more suitable.

INSTALL

@@ -6,10 +6,10 @@ INSTALL
 =======
 
 *REQUIREMENTS
-	- Python-2.7/3.* (with headers)
+	- Python-3 (with headers)
 	- Numpy, Scipy, Pylab
 	- Sundials-2.5/2.6/3.1/4.1
-	- Cython >= 0.18
+	- Cython >= 3
     - C-compiler
     - Fortran-compiler
     - BLAS

doc/sphinx/source/changelog.rst

@@ -3,6 +3,24 @@
 Changelog
 ==========
 
+--- Assimulo-3.5.0 ---
+    * Changed "numpy.float" to equivalent "numpy.float64" due to DeprecationWarnings in numpy >= 1.20.
+    * Improved examples with sparse jacobians by omitting the zeros in the jacobians.
+    * Upgraded to Cython >= 3.
+    * Removed deprecated build option "sundials_with_superlu", which is checked automatically.
+
+--- Assimulo-3.4.3 ---
+    * Improved compliance with newer scipy version by instead using corresponding numpy calls when more suitable.
+
+--- Assimulo-3.4.2 ---
+    * Updated an import statement in one of the examples to resolve compliance issues with scipy 1.10.1.
+
+--- Assimulo-3.4.1 ---
+    * Restored functionality of CVode with 'external_event_detection' = True, which broke with 3.4.0.
+    * CVode now allows rtol = 0.
+    * Added support for CVode (without sensitivities) with non-negative relative tolerance vector.
+      Requires a SUNDIALS installation supporting this, see README.
+
 --- Assimulo-3.4.0 ---
     * Removed Radau5ODE Fortran implementation. 
       This change should be seamless since the C implementation is numerically equivalent.

doc/sphinx/source/installation.rst

@@ -6,16 +6,16 @@ Installation
 
 Dependencies:
 
-- `Python-2.7 / 3.* <http://www.python.org/>`_
-- `Numpy <http://www.scipy.org/Download/>`_ (>1.6.1 for the solver DASP3)
+- `Python-3 <http://www.python.org/>`_
+- `Numpy <http://www.scipy.org/Download/>`_
 - `Scipy <http://www.scipy.org/Download/>`_
 - `Pylab <http://matplotlib.sourceforge.net/>`_
 
 Additional dependencies for compiling from source:
 
-- `Python-2.7 / 3.* <http://www.python.org/>`_ with headers (python-dev package for Ubuntu)
+- `Python-3 <http://www.python.org/>`_ with headers (python-dev package for Ubuntu)
 - `Sundials-2.6/2.7/3.1/4.1 <http://computation.llnl.gov/casc/sundials/main.html>`_ (for 64bits machines, install Sundials using -fPIC)
-- `Cython 0.18 <http://www.cython.org/>`_
+- `Cython 3.0.7 <http://www.cython.org/>`_
 - C compiler
 - Fortran compiler
 - BLAS (only needed for the solver GLIMDA)

doc/sphinx/source/markup.py

@@ -113,7 +113,7 @@ def mark_solvers():
         elif solver[1] == "DAE_OVER":
             file.write('    mod = '+problem_name+'(res, y0, yd0, t0)\n\n')
         else:
-            print "Unknown solver type"
+            print("Unknown solver type")
         file.write('.. note::\n\n')
         file.write('    For complex problems, it is recommended to check the available :doc:`examples <examples>` and the documentation in the problem class, :class:`'+problem_name+ ' <assimulo.problem.'+problem_name+'>`. It is also recommended to define your problem as a subclass of :class:`'+problem_name+ ' <assimulo.problem.'+problem_name+'>`.\n\n')
         file.write('.. warning::\n\n')

examples/__init__.py

@@ -25,6 +25,5 @@
            "mech_system_pendulum", "euler_vanderpol", "cvode_with_parameters_modified",
            "cvode_basic_backward","ida_basic_backward","dasp3_basic", "cvode_with_preconditioning",
            "kinsol_basic","kinsol_with_jac", "radau5dae_time_events", "kinsol_ors", "lsodar_bouncing_ball",
-           "cvode_with_parameters_fcn", "ida_with_user_defined_handle_result", "cvode_with_jac_sparse"]
-
-
+           "cvode_with_parameters_fcn", "ida_with_user_defined_handle_result", "cvode_with_jac_sparse",
+           "radar_basic", "cvode_stability"]

examples/cvode_basic.py

@@ -66,7 +66,7 @@ def f(t,y):
         P.show()
 
     #Basic test
-    nose.tools.assert_almost_equal(float(y2[-1]), 0.00347746, 5)
+    nose.tools.assert_almost_equal(y2[-1][0], 0.00347746, 5)
     nose.tools.assert_almost_equal(exp_sim.get_last_step(), 0.0222169642893, 3)
 
     return exp_mod, exp_sim

examples/cvode_basic_backward.py

@@ -62,7 +62,7 @@ def f(t,y):
         P.show()
 
     #Basic test
-    nose.tools.assert_almost_equal(float(y[-1]), 4.00000000, 3)
+    nose.tools.assert_almost_equal(y[-1][0], 4.00000000, 3)
 
     return exp_mod, exp_sim
 

examples/cvode_stability.py

@@ -68,7 +68,7 @@ def f(t,y):
     exp_sim = CVode(exp_mod) #Create a CVode solver
 
     #Sets the parameters
-    exp_sim.stablimdet = True
+    exp_sim.stablimit = True
     exp_sim.report_continuously = True
 
     #Simulate
@@ -95,4 +95,3 @@ def f(t,y):
 
 if __name__=='__main__':
     mod,sim = run_example()
-

examples/cvode_with_disc.py

@@ -84,7 +84,7 @@ def handle_event(self, solver, event_info):
 
             event_info = self.check_eIter(b_mode, a_mode)
 
-            if not True in event_info: #Breaks the iteration loop
+            if True not in event_info: #Breaks the iteration loop
                 break
 
     #Helper function for handle_event

examples/cvode_with_parameters.py

@@ -70,7 +70,7 @@ def f(t, y, p):
     exp_sim.discr = 'BDF'
     exp_sim.rtol = 1.e-4
     exp_sim.atol = N.array([1.0e-8, 1.0e-14, 1.0e-6])
-    exp_sim.sensmethod = 'SIMULTANEOUS' #Defines the sensitvity method used
+    exp_sim.sensmethod = 'SIMULTANEOUS' #Defines the sensitivity method used
     exp_sim.suppress_sens = False       #Dont suppress the sensitivity variables in the error test.
     exp_sim.report_continuously = True
 

examples/cvode_with_parameters_fcn.py

@@ -87,7 +87,7 @@ def fsens(t, y, s, p):
     exp_sim.discr = 'BDF'
     exp_sim.rtol = 1.e-4
     exp_sim.atol = N.array([1.0e-8, 1.0e-14, 1.0e-6])
-    exp_sim.sensmethod = 'SIMULTANEOUS' #Defines the sensitvity method used
+    exp_sim.sensmethod = 'SIMULTANEOUS' #Defines the sensitivity method used
     exp_sim.suppress_sens = False       #Dont suppress the sensitivity variables in the error test.
     exp_sim.report_continuously = True
 

examples/cvode_with_parameters_modified.py

@@ -68,7 +68,7 @@ def f(t, y, p):
     exp_sim.discr = 'BDF'
     exp_sim.rtol = 1.e-4
     exp_sim.atol = N.array([1.0e-8, 1.0e-14, 1.0e-6])
-    exp_sim.sensmethod = 'SIMULTANEOUS' #Defines the sensitvity method used
+    exp_sim.sensmethod = 'SIMULTANEOUS' #Defines the sensitivity method used
     exp_sim.suppress_sens = False       #Dont suppress the sensitivity variables in the error test.
     exp_sim.report_continuously = True
 
@@ -95,4 +95,3 @@ def f(t, y, p):
 
 if __name__=='__main__':
     mod,sim = run_example()
-

examples/cvode_with_preconditioning.py

@@ -53,7 +53,7 @@ def prec_setup(t, y, fy, jok, gamma, data):
         A = np.array([[2.0, 1.0], [3.0, 2.0]])
 
         #If jok is false the jacobian data needs to be recomputed
-        if jok == False:
+        if jok is False:
 
             #Extract the diagonal of the jacobian to form a Jacobi preconditioner
             a0 = A[0, 0] * t * np.cos(y[0])
@@ -64,7 +64,7 @@ def prec_setup(t, y, fy, jok, gamma, data):
             return [True, a]
 
         #If jok is true the existing jacobian data can be reused 
-        if jok == True:
+        if jok is True:
 
             #Return false (jacobian data was reused) and the old data
             return [False, data]

examples/dopri5_basic.py

@@ -56,7 +56,7 @@ def f(t,y):
         P.show()
 
     #Basic test
-    nose.tools.assert_almost_equal(float(y[-1]),0.02695199,5)
+    nose.tools.assert_almost_equal(y[-1][0],0.02695199,5)
 
     return exp_mod, exp_sim
 

examples/dopri5_with_disc.py

@@ -84,7 +84,7 @@ def handle_event(self, solver, event_info):
 
             event_info = self.check_eIter(b_mode, a_mode)
 
-            if not True in event_info: #Breaks the iteration loop
+            if True not in event_info: #Breaks the iteration loop
                 break
 
     #Helper function for handle_event
@@ -163,6 +163,3 @@ def run_example(with_plots=True):
 
 if __name__=="__main__":
     mod,sim = run_example()
-
-
-

examples/euler_basic.py

@@ -61,7 +61,7 @@ def f(t,y):
         P.show()
 
     #Basic test
-    nose.tools.assert_almost_equal(float(y2[-1]), 0.02628193)
+    nose.tools.assert_almost_equal(y2[-1][0], 0.02628193)
 
     return exp_mod, exp_sim
 

examples/euler_vanderpol.py

@@ -92,4 +92,3 @@ def jac(t,y):
 
 if __name__=='__main__':
     mod,sim = run_example()
-

examples/euler_with_disc.py

@@ -84,7 +84,7 @@ def handle_event(self, solver, event_info):
 
             event_info = self.check_eIter(b_mode, a_mode)
 
-            if not True in event_info: #Breaks the iteration loop
+            if True not in event_info: #Breaks the iteration loop
                 break
 
     #Helper function for handle_event
@@ -121,8 +121,6 @@ def init_mode(self, solver):
         solver.y[1] = (-1.0 if solver.sw[1] else 3.0)
         solver.y[2] = (0.0 if solver.sw[2] else 2.0)
 
-
-
 def run_example(with_plots=True):
     r"""
     Example of the use of Euler's method for a differential equation

examples/glimda_vanderpol.py

@@ -17,7 +17,7 @@
 
 import numpy as N
 import nose
-from assimulo.solvers import GLIMDA,IDA
+from assimulo.solvers import GLIMDA
 from assimulo.problem import Implicit_Problem
 
 def run_example(with_plots=True):

examples/ida_basic_backward.py

@@ -62,7 +62,7 @@ def f(t,y,yd):
         P.show()
 
     #Basic test
-    nose.tools.assert_almost_equal(float(y[-1]), 4.00000000, 3)
+    nose.tools.assert_almost_equal(y[-1][0], 4.00000000, 3)
 
     return imp_mod, imp_sim
 

examples/ida_with_disc.py

@@ -87,7 +87,7 @@ def handle_event(self, solver, event_info):
 
             event_info = self.check_eIter(b_mode, a_mode)
 
-            if not True in event_info: #Breaks the iteration loop
+            if True not in event_info: #Breaks the iteration loop
                 break
 
     #Helper function for handle_event
@@ -125,8 +125,6 @@ def init_mode(self, solver):
                                                    #see SUNDIALS IDA documentation
                                                    #on the option 'IDA_YA_YDP_INIT'
 
-
-
 def run_example(with_plots=True):
     r"""
     Example of the use of IDA for an implicit differential equation
@@ -168,6 +166,3 @@ def run_example(with_plots=True):
 
 if __name__=="__main__":
     mod,sim = run_example()
-
-
-

examples/ida_with_initial_sensitivity.py

@@ -79,7 +79,7 @@ def f(t, y, yd,p):
     imp_sim.atol = 1e-6
     imp_sim.pbar = [1,1,1] #pbar is used to estimate the tolerances for the parameters
     imp_sim.report_continuously = True #Need to be able to store the result using the interpolate methods
-    imp_sim.sensmethod = 'SIMULTANEOUS' #Defines the sensitvity method used
+    imp_sim.sensmethod = 'SIMULTANEOUS' #Defines the sensitivity method used
     imp_sim.suppress_sens = False            #Dont suppress the sensitivity variables in the error test.
 
     #Simulate

examples/ida_with_jac.py

@@ -125,4 +125,3 @@ def jac(c,t,y,yd):
 
 if __name__=='__main__':
     mod,sim = run_example()
-

examples/ida_with_parameters.py

@@ -98,4 +98,3 @@ def f(t, y, yd, p):
 
 if __name__=='__main__':
     mod,sim = run_example()
-

examples/ida_with_user_defined_handle_result.py

@@ -115,7 +115,5 @@ def handle_result(solver, t ,y, yd):
 
     return imp_mod, imp_sim
 
-
 if __name__=='__main__':
     mod,sim = run_example()
-

examples/kinsol_basic.py

@@ -15,7 +15,6 @@
 # You should have received a copy of the GNU Lesser General Public License
 # along with this program. If not, see <http://www.gnu.org/licenses/>.
 
-import numpy as N
 import nose
 from assimulo.solvers import KINSOL
 from assimulo.problem import Algebraic_Problem
@@ -53,4 +52,3 @@ def res(y):
 
 if __name__=='__main__':
     mod, solv = run_example()
-