Conversion to pytest; work in progress

work in progress; more conversion

Cleanup

removing redundant testattr

removing warnings

Resolving DeprecationWarnings in tests

Fixing issue in 1 test; more deprecation issues

Replaced commented-out tests with appropriate pytest.mark.skip

Cleanup; some more minor Deprecations

Review fixes

.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 --verbose tests/

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 tests/".
 
 For more information regarding Assimulo and the installation procedure, 
 please visit: http://www.jmodelica.org/assimulo

doc/sphinx/source/installation.rst

@@ -62,9 +62,9 @@ the section troubleshooting see :ref:`instTrouble` should be consulted before in
 
     To test Assimulo, go into the tests folder and 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 +16,7 @@
 # along with this program. If not, see <http://www.gnu.org/licenses/>.
 
 import numpy as np
-import nose
+import pytest
 from assimulo.solvers import CVode
 from assimulo.problem import Explicit_Problem
 
@@ -66,8 +66,8 @@ 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 y2[-1][0] == pytest.approx(0.00347746, abs = 1e-5)
+    assert exp_sim.get_last_step() == pytest.approx(0.0222169642893, abs = 1e-3)
 
     return exp_mod, exp_sim
 

examples/cvode_basic_backward.py

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

examples/cvode_gyro.py

@@ -16,7 +16,7 @@
 # along with this program. If not, see <http://www.gnu.org/licenses/>.
 
 import numpy as np
-import nose
+import pytest
 from assimulo.problem import Explicit_Problem
 from assimulo.solvers import CVode
 
@@ -83,8 +83,8 @@ 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 y[-1][0] == pytest.approx(692.800241862)
+    assert y[-1][8] == pytest.approx(7.08468221e-1)
 
     return exp_mod, exp_sim    
 

examples/cvode_stability.py

@@ -16,7 +16,7 @@
 # along with this program. If not, see <http://www.gnu.org/licenses/>.
 
 import numpy as np
-import nose
+import pytest
 from assimulo.solvers import CVode
 from assimulo.problem import Explicit_Problem
 
@@ -89,7 +89,7 @@ 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 +16,7 @@
 # along with this program. If not, see <http://www.gnu.org/licenses/>.
 
 import numpy as np
-import nose
+import pytest
 from assimulo.solvers import CVode
 from assimulo.problem import Explicit_Problem
 
@@ -156,14 +156,11 @@ 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 y[-1][0] == pytest.approx(8.0)
+    assert y[-1][1] == pytest.approx(3.0)
+    assert y[-1][2] == pytest.approx(2.0)
 
     return exp_mod, exp_sim
 
 if __name__=="__main__":
     mod,sim = run_example()
-
-
-

examples/cvode_with_initial_sensitivity.py

@@ -16,7 +16,7 @@
 # along with this program. If not, see <http://www.gnu.org/licenses/>.
 
 import numpy as np
-import nose
+import pytest
 from assimulo.solvers import CVode
 from assimulo.problem import Explicit_Problem
 
@@ -123,10 +123,10 @@ 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 y[-1][0] == pytest.approx(1577.6552477, abs = 1e-5)
+    assert y[-1][1] == pytest.approx(611.9574565, abs = 1e-5)
+    assert y[-1][2] == pytest.approx(2215.88563217, abs = 1e-5)
+    assert exp_sim.p_sol[0][1][0] == pytest.approx(1.0)
 
     return exp_mod, exp_sim
 

examples/cvode_with_jac.py

@@ -16,7 +16,7 @@
 # along with this program. If not, see <http://www.gnu.org/licenses/>.
 
 import numpy as np
-import nose
+import pytest
 from assimulo.solvers import CVode
 from assimulo.problem import Explicit_Problem
 
@@ -78,8 +78,8 @@ 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 y[-1][0] == pytest.approx(-121.75000000, abs = 1e-4)
+    assert y[-1][1] == pytest.approx(-49.100000000)
 
     return exp_mod, exp_sim
 

examples/cvode_with_jac_sparse.py

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

examples/cvode_with_jac_spgmr.py

@@ -16,7 +16,7 @@
 # along with this program. If not, see <http://www.gnu.org/licenses/>.
 
 import numpy as np
-import nose
+import pytest
 from assimulo.solvers import CVode
 from assimulo.problem import Explicit_Problem
 
@@ -85,8 +85,8 @@ 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 y[-1][0] == pytest.approx(-121.75000000, abs = 1e-4)
+    assert y[-1][1] == pytest.approx(-49.100000000)
 
     return exp_mod, exp_sim
 

examples/cvode_with_parameters.py

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

examples/cvode_with_parameters_fcn.py

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

examples/cvode_with_parameters_modified.py

@@ -16,7 +16,7 @@
 # along with this program. If not, see <http://www.gnu.org/licenses/>.
 
 import numpy as np
-import nose
+import pytest
 from assimulo.solvers import CVode
 from assimulo.problem import Explicit_Problem
 
@@ -30,9 +30,9 @@ 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 +85,11 @@ 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 y[-1][0] == pytest.approx(9.05518032e-01, abs = 1e-4)
+    assert y[-1][1] == pytest.approx(2.24046805e-05, abs = 1e-4)
+    assert y[-1][2] == pytest.approx(9.44595637e-02, abs = 1e-4)
+    assert exp_sim.p_sol[0][-1][0] == pytest.approx(-1.8761, abs = 1e-2) #Values taken from the example in Sundials
+    assert exp_sim.p_sol[1][-1][0] == pytest.approx(2.9614e-06, abs = 1e-8)
 
     return exp_mod, exp_sim
 

examples/cvode_with_preconditioning.py

@@ -20,7 +20,7 @@
 """
 
 import numpy as np
-import nose
+import pytest
 from assimulo.solvers import CVode
 from assimulo.problem import Explicit_Problem
 
@@ -107,8 +107,8 @@ 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 y[-1,0] == pytest.approx(3.11178295, abs = 1e-4)
+    assert y[-1,1] == pytest.approx(3.19318992, abs = 1e-4)
 
     return exp_mod, exp_sim
 

examples/dasp3_basic.py

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

examples/dopri5_basic.py

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