Replace nosetests with pytest (#85)

.github/workflows/build.yml

@@ -19,7 +19,7 @@ jobs:
         python-version: '3.11.x'
     - name: Setup Python
       run: |
-        python3 -m pip install Cython numpy scipy matplotlib nose-py3 setuptools==69.1.0
+        python3 -m pip install Cython numpy scipy matplotlib pytest setuptools==69.1.0
     - name: Install system
       run: |
         sudo apt-get -y install cmake liblapack-dev libsuitesparse-dev libhypre-dev
@@ -44,4 +44,4 @@ 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
     - name: Test
-      run: python3 -m nose --verbose tests/* tests/solvers/*
+      run: pytest 

CHANGELOG

@@ -1,8 +1,10 @@
 --- CHANGELOG ---
 
---- Assimulo-3.5.x ---
+--- Assimulo-FUTURE---
     * Added get_sundials_version function (import from assimulo.solvers.sundials).
     * Fixed bug that Radau5ODE would not count state events in statistics.
+    * Removed tests from the Assimulo installation.
+    * Changed testing framework from `nose` to `pytest`.
 
 --- Assimulo-3.5.2 ---
     * Allow to build without distutils for Python>=3.12 support

INSTALL

@@ -20,8 +20,7 @@ Installation is performed using the command:
 	'python setup.py install --sundials-home=/path/to/sundials --blas-home=/path/to/blas --lapack-home=/path/to/lapack'
 
 Assimulo is then installed under Python dist-packages. 
-To test the installation, browse to the tests folder and do a 'nosetests'.
-(The testing needs additionally the python-nose package)
+To test the installation, run "pytest".
 
 For more information regarding Assimulo and the installation procedure, 
 please visit: http://www.jmodelica.org/assimulo

doc/sphinx/source/installation.rst

@@ -60,11 +60,11 @@ the section troubleshooting see :ref:`instTrouble` should be consulted before in
 
 .. note::
 
-    To test Assimulo, go into the tests folder and type::
+    To test Assimulo, type::
     
-        nosetests
+        pytest
         
-    Which requires python-nose.
+    Which requires pytest.
 
 Windows
 ==========
@@ -90,9 +90,9 @@ After a successful installation, the package will be located in pythons dist-pac
 
     To test Assimulo, go into the tests folder and type::
     
-        nosetests
+        pytest .
         
-    Which requires python-nose.
+    Which requires pytest.
 
 
 .. _instTrouble:

examples/cvode_basic.py

@@ -16,7 +16,6 @@
 # along with this program. If not, see <http://www.gnu.org/licenses/>.
 
 import numpy as np
-import nose
 from assimulo.solvers import CVode
 from assimulo.problem import Explicit_Problem
 
@@ -66,8 +65,8 @@ def f(t,y):
         pl.show()
 
     #Basic test
-    nose.tools.assert_almost_equal(y2[-1][0], 0.00347746, 5)
-    nose.tools.assert_almost_equal(exp_sim.get_last_step(), 0.0222169642893, 3)
+    assert abs(y2[-1][0] - 0.00347746) < 1e-5
+    assert abs(exp_sim.get_last_step() - 0.0222169642893) < 1e-3
 
     return exp_mod, exp_sim
 

examples/cvode_basic_backward.py

@@ -16,7 +16,6 @@
 # along with this program. If not, see <http://www.gnu.org/licenses/>.
 
 import numpy as np
-import nose
 from assimulo.solvers import CVode
 from assimulo.problem import Explicit_Problem
 
@@ -62,7 +61,7 @@ def f(t,y):
         pl.show()
 
     #Basic test
-    nose.tools.assert_almost_equal(y[-1][0], 4.00000000, 3)
+    assert abs(y[-1][0] - 4.0) < 1e-3
 
     return exp_mod, exp_sim
 

examples/cvode_gyro.py

@@ -16,7 +16,6 @@
 # along with this program. If not, see <http://www.gnu.org/licenses/>.
 
 import numpy as np
-import nose
 from assimulo.problem import Explicit_Problem
 from assimulo.solvers import CVode
 
@@ -83,8 +82,8 @@ def f(t, u):
         pl.show()
 
     #Basic tests
-    nose.tools.assert_almost_equal(y[-1][0], 692.800241862)
-    nose.tools.assert_almost_equal(y[-1][8], 7.08468221e-1)
+    assert abs(y[-1][0] - 692.800241862) < 1e-6
+    assert abs(y[-1][8] - 7.08468221e-1) < 1e-6
 
     return exp_mod, exp_sim    
 

examples/cvode_stability.py

@@ -16,7 +16,6 @@
 # along with this program. If not, see <http://www.gnu.org/licenses/>.
 
 import numpy as np
-import nose
 from assimulo.solvers import CVode
 from assimulo.problem import Explicit_Problem
 
@@ -89,7 +88,7 @@ def f(t,y):
 
     #Basic test
     x1 = y[:,0]
-    nose.tools.assert_less(np.abs(float(x1[-1]) - 1.8601438), 1e-1)
+    assert np.abs(float(x1[-1]) - 1.8601438) < 1e-1
 
     return exp_mod, exp_sim
 

examples/cvode_with_disc.py

@@ -16,7 +16,6 @@
 # along with this program. If not, see <http://www.gnu.org/licenses/>.
 
 import numpy as np
-import nose
 from assimulo.solvers import CVode
 from assimulo.problem import Explicit_Problem
 
@@ -156,14 +155,11 @@ def run_example(with_plots=True):
         pl.show()
 
     #Basic test
-    nose.tools.assert_almost_equal(y[-1][0],8.0)
-    nose.tools.assert_almost_equal(y[-1][1],3.0)
-    nose.tools.assert_almost_equal(y[-1][2],2.0)
+    assert abs(y[-1][0] - 8.0) < 1e-6
+    assert abs(y[-1][1] - 3.0) < 1e-6
+    assert abs(y[-1][2] - 2.0) < 1e-6
 
     return exp_mod, exp_sim
 
 if __name__=="__main__":
     mod,sim = run_example()
-
-
-

examples/cvode_with_initial_sensitivity.py

@@ -16,7 +16,6 @@
 # along with this program. If not, see <http://www.gnu.org/licenses/>.
 
 import numpy as np
-import nose
 from assimulo.solvers import CVode
 from assimulo.problem import Explicit_Problem
 
@@ -123,10 +122,10 @@ def f(t, y, p):
         pl.show()
 
     #Basic test
-    nose.tools.assert_almost_equal(y[-1][0], 1577.6552477, 5)
-    nose.tools.assert_almost_equal(y[-1][1], 611.9574565, 5)
-    nose.tools.assert_almost_equal(y[-1][2], 2215.88563217, 5)
-    nose.tools.assert_almost_equal(exp_sim.p_sol[0][1][0], 1.0)
+    assert abs(y[-1][0] - 1577.6552477)      < 1e-5
+    assert abs(y[-1][1] - 611.9574565)       < 1e-5
+    assert abs(y[-1][2] - 2215.88563217)     < 1e-5
+    assert abs(exp_sim.p_sol[0][1][0] - 1.0) < 1e-6
 
     return exp_mod, exp_sim
 

examples/cvode_with_jac.py

@@ -16,7 +16,6 @@
 # along with this program. If not, see <http://www.gnu.org/licenses/>.
 
 import numpy as np
-import nose
 from assimulo.solvers import CVode
 from assimulo.problem import Explicit_Problem
 
@@ -78,8 +77,8 @@ def jac(t,y):
         pl.show()
 
     #Basic tests
-    nose.tools.assert_almost_equal(y[-1][0],-121.75000000,4)
-    nose.tools.assert_almost_equal(y[-1][1],-49.100000000)
+    assert abs(y[-1][0] + 121.75000000) < 1e-4
+    assert abs(y[-1][1] + 49.100000000) < 1e-6
 
     return exp_mod, exp_sim
 

examples/cvode_with_jac_sparse.py

@@ -17,7 +17,6 @@
 
 import numpy as np
 import scipy.sparse as sps
-import nose
 from assimulo.solvers import CVode
 from assimulo.problem import Explicit_Problem
 
@@ -93,7 +92,7 @@ def jac(t,y):
         pl.show()
 
     #Basic tests
-    nose.tools.assert_almost_equal(y[-1][0],0.9851,3)
+    assert abs(y[-1][0] - 0.9851) < 1e-3
 
     return exp_mod, exp_sim
 

examples/cvode_with_jac_spgmr.py

@@ -16,7 +16,6 @@
 # along with this program. If not, see <http://www.gnu.org/licenses/>.
 
 import numpy as np
-import nose
 from assimulo.solvers import CVode
 from assimulo.problem import Explicit_Problem
 
@@ -85,8 +84,8 @@ def jacv(t,y,fy,v):
         pl.show()
 
     #Basic tests
-    nose.tools.assert_almost_equal(y[-1][0],-121.75000000,4)
-    nose.tools.assert_almost_equal(y[-1][1],-49.100000000)
+    assert abs(y[-1][0] + 121.75000000) < 1e-4
+    assert abs(y[-1][1] + 49.100000000) < 1e-6
 
     return exp_mod, exp_sim
 

examples/cvode_with_parameters.py

@@ -16,7 +16,6 @@
 # along with this program. If not, see <http://www.gnu.org/licenses/>.
 
 import numpy as np
-import nose
 from assimulo.solvers import CVode
 from assimulo.problem import Explicit_Problem
 
@@ -87,12 +86,13 @@ def f(t, y, p):
         pl.show()  
 
     #Basic test
-    nose.tools.assert_almost_equal(y[-1][0], 9.05518032e-01, 4)
-    nose.tools.assert_almost_equal(y[-1][1], 2.24046805e-05, 4)
-    nose.tools.assert_almost_equal(y[-1][2], 9.44595637e-02, 4)
-    nose.tools.assert_almost_equal(exp_sim.p_sol[0][-1][0], -1.8761, 2) #Values taken from the example in Sundials
-    nose.tools.assert_almost_equal(exp_sim.p_sol[1][-1][0], 2.9614e-06, 8)
-    nose.tools.assert_almost_equal(exp_sim.p_sol[2][-1][0], -4.9334e-10, 12)
+    assert abs(y[-1][0] - 9.05518032e-01) < 1e-4
+    assert abs(y[-1][1] - 2.24046805e-05) < 1e-4
+    assert abs(y[-1][2] - 9.44595637e-02) < 1e-4
+    # Values taken from the example in Sundials
+    assert abs(exp_sim.p_sol[0][-1][0] + 1.8761) < 1e-2
+    assert abs(exp_sim.p_sol[1][-1][0] - 2.9614e-06) < 1e-8
+    assert abs(exp_sim.p_sol[2][-1][0] + 4.9334e-10) < 1e-12
 
     return exp_mod, exp_sim
 

examples/cvode_with_parameters_fcn.py

@@ -16,7 +16,6 @@
 # along with this program. If not, see <http://www.gnu.org/licenses/>.
 
 import numpy as np
-import nose
 from assimulo.solvers import CVode
 from assimulo.problem import Explicit_Problem
 
@@ -104,12 +103,13 @@ def fsens(t, y, s, p):
         pl.show()  
 
     #Basic test
-    nose.tools.assert_almost_equal(y[-1][0], 9.05518032e-01, 4)
-    nose.tools.assert_almost_equal(y[-1][1], 2.24046805e-05, 4)
-    nose.tools.assert_almost_equal(y[-1][2], 9.44595637e-02, 4)
-    nose.tools.assert_almost_equal(exp_sim.p_sol[0][-1][0], -1.8761, 2) #Values taken from the example in Sundials
-    nose.tools.assert_almost_equal(exp_sim.p_sol[1][-1][0], 2.9614e-06, 8)
-    nose.tools.assert_almost_equal(exp_sim.p_sol[2][-1][0], -4.9334e-10, 12)
+    assert abs(y[-1][0] - 9.05518032e-01) < 1e-4
+    assert abs(y[-1][1] - 2.24046805e-05) < 1e-4
+    assert abs(y[-1][2] - 9.44595637e-02) < 1e-4
+    #Values taken from the example in Sundials
+    assert abs(exp_sim.p_sol[0][-1][0] + 1.8761) < 1e-2
+    assert abs(exp_sim.p_sol[1][-1][0] - 2.9614e-06) < 1e-8
+    assert abs(exp_sim.p_sol[2][-1][0] + 4.9334e-10) < 1e-12
 
     return exp_mod, exp_sim
 

examples/cvode_with_parameters_modified.py

@@ -16,7 +16,6 @@
 # along with this program. If not, see <http://www.gnu.org/licenses/>.
 
 import numpy as np
-import nose
 from assimulo.solvers import CVode
 from assimulo.problem import Explicit_Problem
 
@@ -30,9 +29,9 @@ def run_example(with_plots=True):
 
     .. math:: 
     
-       \dot y_1 &= -p_1 y_1 + p_2 y_2 y_3 \\
-       \dot y_2 &= p_1 y_1 - p_2 y_2 y_3 - p_3 y_2^2 \\
-       \dot y_3 &= p_3  y_2^2
+       \\dot y_1 &= -p_1 y_1 + p_2 y_2 y_3 \\
+       \\dot y_2 &= p_1 y_1 - p_2 y_2 y_3 - p_3 y_2^2 \\
+       \\dot y_3 &= p_3  y_2^2
     
     on return:
     
@@ -85,11 +84,12 @@ def f(t, y, p):
         pl.show()  
 
     #Basic test
-    nose.tools.assert_almost_equal(y[-1][0], 9.05518032e-01, 4)
-    nose.tools.assert_almost_equal(y[-1][1], 2.24046805e-05, 4)
-    nose.tools.assert_almost_equal(y[-1][2], 9.44595637e-02, 4)
-    nose.tools.assert_almost_equal(exp_sim.p_sol[0][-1][0], -1.8761, 2) #Values taken from the example in Sundials
-    nose.tools.assert_almost_equal(exp_sim.p_sol[1][-1][0], 2.9614e-06, 8)
+    assert abs(y[-1][0] - 9.05518032e-01) < 1e-4
+    assert abs(y[-1][1] - 2.24046805e-05) < 1e-4
+    assert abs(y[-1][2] - 9.44595637e-02) < 1e-4
+    # Values taken from the example in Sundials
+    assert abs(exp_sim.p_sol[0][-1][0] + 1.8761) < 1e-2
+    assert abs(exp_sim.p_sol[1][-1][0] - 2.9614e-06) < 1e-8
 
     return exp_mod, exp_sim
 

examples/cvode_with_preconditioning.py

@@ -20,7 +20,6 @@
 """
 
 import numpy as np
-import nose
 from assimulo.solvers import CVode
 from assimulo.problem import Explicit_Problem
 
@@ -107,8 +106,8 @@ def prec_solve(t, y, fy, r, gamma, delta, data):
         exp_sim.plot()
 
     #Basic verification
-    nose.tools.assert_almost_equal(y[-1,0],3.11178295,4)
-    nose.tools.assert_almost_equal(y[-1,1],3.19318992,4)
+    assert abs(y[-1,0] - 3.11178295) < 1e-4
+    assert abs(y[-1,1] - 3.19318992) < 1e-4
 
     return exp_mod, exp_sim
 

examples/dasp3_basic.py

@@ -16,7 +16,6 @@
 # along with this program. If not, see <http://www.gnu.org/licenses/>.
 
 import numpy as np
-import nose
 
 try:
     from assimulo.solvers import DASP3ODE
@@ -100,7 +99,7 @@ def dzdt(t,y,z):
         pl.show()
 
     #Basic test
-    nose.tools.assert_almost_equal(y[-1,0], 10.860063849896818, 3)
+    assert abs(y[-1,0] - 10.860063849896818) < 1e-3
 
     return exp_mod, exp_sim
 

examples/dopri5_basic.py

@@ -16,7 +16,6 @@
 # along with this program. If not, see <http://www.gnu.org/licenses/>.
 
 import numpy as np
-import nose
 from assimulo.solvers import Dopri5
 from assimulo.problem import Explicit_Problem
 
@@ -56,7 +55,7 @@ def f(t,y):
         pl.show()
 
     #Basic test
-    nose.tools.assert_almost_equal(y[-1][0],0.02695199,5)
+    assert abs(y[-1][0] - 0.02695199) < 1e-5
 
     return exp_mod, exp_sim