more fixes

Cleanup

removed pytest as requirement from examples

Removing tests from the Assimulo installation

Adding pytest config; adjusted instructions

simplified workflow file

Changed if in test to skipif

Added missing reason in skipif

.github/workflows/build.yml

@@ -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: pytest --verbose tests/
+      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

@@ -20,7 +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, run "pytest tests/".
+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

@@ -60,9 +60,9 @@ 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::
     
-        pytest .
+        pytest
         
     Which requires pytest.
 

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 pytest
 from assimulo.solvers import CVode
 from assimulo.problem import Explicit_Problem
 
@@ -66,8 +65,8 @@ def f(t,y):
         pl.show()
 
     #Basic test
-    assert y2[-1][0] == pytest.approx(0.00347746, abs = 1e-5)
-    assert exp_sim.get_last_step() == pytest.approx(0.0222169642893, abs = 1e-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 pytest
 from assimulo.solvers import CVode
 from assimulo.problem import Explicit_Problem
 
@@ -62,7 +61,7 @@ def f(t,y):
         pl.show()
 
     #Basic test
-    assert y[-1][0] == pytest.approx(4.00000000, abs = 1e-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 pytest
 from assimulo.problem import Explicit_Problem
 from assimulo.solvers import CVode
 
@@ -83,8 +82,8 @@ def f(t, u):
         pl.show()
 
     #Basic tests
-    assert y[-1][0] == pytest.approx(692.800241862)
-    assert y[-1][8] == pytest.approx(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 pytest
 from assimulo.solvers import CVode
 from assimulo.problem import Explicit_Problem
 

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 pytest
 from assimulo.solvers import CVode
 from assimulo.problem import Explicit_Problem
 
@@ -156,9 +155,9 @@ def run_example(with_plots=True):
         pl.show()
 
     #Basic test
-    assert y[-1][0] == pytest.approx(8.0)
-    assert y[-1][1] == pytest.approx(3.0)
-    assert y[-1][2] == pytest.approx(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
 

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 pytest
 from assimulo.solvers import CVode
 from assimulo.problem import Explicit_Problem
 
@@ -123,10 +122,10 @@ def f(t, y, p):
         pl.show()
 
     #Basic test
-    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)
+    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 pytest
 from assimulo.solvers import CVode
 from assimulo.problem import Explicit_Problem
 
@@ -78,8 +77,8 @@ def jac(t,y):
         pl.show()
 
     #Basic tests
-    assert y[-1][0] == pytest.approx(-121.75000000, abs = 1e-4)
-    assert y[-1][1] == pytest.approx(-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 pytest
 from assimulo.solvers import CVode
 from assimulo.problem import Explicit_Problem
 
@@ -93,7 +92,7 @@ def jac(t,y):
         pl.show()
 
     #Basic tests
-    assert y[-1][0] == pytest.approx(0.9851, abs = 1e-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 pytest
 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
-    assert y[-1][0] == pytest.approx(-121.75000000, abs = 1e-4)
-    assert y[-1][1] == pytest.approx(-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 pytest
 from assimulo.solvers import CVode
 from assimulo.problem import Explicit_Problem
 
@@ -87,12 +86,13 @@ def f(t, y, p):
         pl.show()  
 
     #Basic test
-    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)
+    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 pytest
 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
-    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)
+    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 pytest
 from assimulo.solvers import CVode
 from assimulo.problem import Explicit_Problem
 
@@ -85,11 +84,12 @@ def f(t, y, p):
         pl.show()  
 
     #Basic test
-    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 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 pytest
 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
-    assert y[-1,0] == pytest.approx(3.11178295, abs = 1e-4)
-    assert y[-1,1] == pytest.approx(3.19318992, abs = 1e-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 pytest
 
 try:
     from assimulo.solvers import DASP3ODE
@@ -100,7 +99,7 @@ def dzdt(t,y,z):
         pl.show()
 
     #Basic test
-    assert y[-1,0] == pytest.approx( 10.860063849896818, abs = 1e-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 pytest
 from assimulo.solvers import Dopri5
 from assimulo.problem import Explicit_Problem
 
@@ -56,7 +55,7 @@ def f(t,y):
         pl.show()
 
     #Basic test
-    assert y[-1][0] == pytest.approx(0.02695199, abs = 1e-5)
+    assert abs(y[-1][0] - 0.02695199) < 1e-5
 
     return exp_mod, exp_sim
 

examples/dopri5_with_disc.py

@@ -16,7 +16,6 @@
 # along with this program. If not, see <http://www.gnu.org/licenses/>.
 
 import numpy as np
-import pytest
 from assimulo.solvers import Dopri5
 from assimulo.problem import Explicit_Problem
 
@@ -155,9 +154,9 @@ def run_example(with_plots=True):
         pl.show()
 
     #Basic test
-    assert y[-1][0] == pytest.approx(8.0)
-    assert y[-1][1] == pytest.approx(3.0)
-    assert y[-1][2] == pytest.approx(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
 

examples/euler_basic.py

@@ -16,7 +16,6 @@
 # along with this program. If not, see <http://www.gnu.org/licenses/>.
 
 import numpy as np
-import pytest
 from assimulo.solvers import ExplicitEuler
 from assimulo.problem import Explicit_Problem
 
@@ -61,7 +60,7 @@ def f(t,y):
         pl.show()
 
     #Basic test
-    assert y2[-1][0] == pytest.approx(0.02628193)
+    assert abs(y2[-1][0] - 0.02628193) < 1e-6
 
     return exp_mod, exp_sim
 

examples/euler_vanderpol.py

@@ -16,7 +16,6 @@
 # along with this program. If not, see <http://www.gnu.org/licenses/>.
 
 import numpy as np
-import pytest
 from assimulo.solvers import ImplicitEuler
 from assimulo.problem import Explicit_Problem