Fixed paths to code in docs (#443)

* Fixed paths to tests in docs

* Fixed paths to tests in docs that use embed-code

* Had to switch from embed-code to literalinclude since tests no longer in python package

openaerostruct/docs/advanced_features/aerostruct_ffd.rst

@@ -9,5 +9,7 @@ This allows for more general design shape changes and helps sync up geometry cha
 .. warning::
   This example requires `pyGeo`, an external code developed by the MDO Lab. You can install it from `here <https://github.com/mdolab/pygeo>`_.
 
-.. embed-code::
-  openaerostruct.tests.test_aerostruct_ffd.Test.test
+.. literalinclude:: /../../tests/integration_tests/test_aerostruct_ffd.py
+    :start-after: docs checkpoint 0
+    :end-before: docs checkpoint 1
+    :dedent: 8

openaerostruct/docs/advanced_features/ground_effect.rst

@@ -17,8 +17,10 @@ This means that configurations deep in ground effect (small altitude compared to
 
 To enable ground effect, add a :code:`groundplane: True` attribute to your aerosurfaces, like so:
 
-.. embed-code::
-    openaerostruct.tests.test_aero_ground_effect.Test.test
+.. literalinclude:: /../../tests/integration_tests/test_aero_ground_effect.py
+    :start-after: docs checkpoint 0
+    :end-before: docs checkpoint 1
+    :dedent: 8
 
 If groundplane is turned on for an AeroPoint or AeroStructPoint, a new input will be created (height_agl) which represents the distance from the origin (in airplane coordinates) to the ground plane.
 The default value, 8000 meters, produces essentially zero ground effect.

openaerostruct/docs/advanced_features/multiple_surfaces.rst

@@ -6,6 +6,7 @@ Multiple Lifting Surfaces
 It's easily possible to simulate multiple lifting surfaces simultaneously in OpenAeroStruct.
 The most straightforward example is a wing and a tail for a conventional airplane, as shown below, though OpenAeroStruct can handle any arbitrary collection of lifting surfaces.
 
-.. embed-code::
-    openaerostruct.tests.test_multiple_aero_analysis.Test.test
-    :layout: interleave
+.. literalinclude:: /../../tests/integration_tests/test_multiple_aero_analysis.py
+    :start-after: docs checkpoint 0
+    :end-before: docs checkpoint 1
+    :dedent: 8

openaerostruct/docs/advanced_features/multipoint.rst

@@ -11,9 +11,10 @@ Aerodynamic Optimization Example
 --------------------------------
 We optimize the aircraft at two cruise flight conditions below.
 
-.. embed-code::
-    openaerostruct.tests.test_multipoint_aero.Test.test
-    :layout: interleave
+.. literalinclude:: /../../tests/integration_tests/test_multipoint_aero.py
+    :start-after: docs checkpoint 0
+    :end-before: docs checkpoint 1
+    :dedent: 8
 
 
 Aerostructural Optimization Example (Q400)

openaerostruct/docs/advanced_features/multipoint_parallel.rst

@@ -43,7 +43,7 @@ Then, let's set up the problem in the same way as the serial runscript.
 
 Next, we need to add AS_points under a ``ParallelGroup`` instead of directly under the ``prob.model``.
 
-.. literalinclude:: ../../tests/test_multipoint_parallel.py
+.. literalinclude:: /../../tests/integration_tests/test_multipoint_parallel.py
     :dedent: 8
     :start-after: # [rst Setup ParallelGroup (beg)]
     :end-before: # [rst Setup ParallelGroup (end)]
@@ -55,7 +55,7 @@ Among 6 functions, 4 depend only on AS_point_0, and 2 depend only on AS_point_1.
 Therefore, we can form 2 pairs and perform linear solves in parallel.
 We specify ``parallel_deriv_color`` to tell OpenMDAO which function's derivatives can be solved for in parallel.
 
-.. literalinclude:: ../../tests/test_multipoint_parallel.py
+.. literalinclude:: /../../tests/integration_tests/test_multipoint_parallel.py
     :dedent: 8
     :start-after: # [rst Parallel deriv color setup 1 (beg)]
     :end-before: # [rst Parallel deriv color setup 1 (end)]
@@ -64,15 +64,15 @@ Furthermore, we will add another dummy (nonsense) constraint to explain how para
 This dummy constraint (sum of the fuel burns from AS_point_0 and AS_point_1) depends on both AS points.
 In this case, the linear solves of AS_point_0 and AS_point_1 will be parallelized.
 
-.. literalinclude:: ../../tests/test_multipoint_parallel.py
+.. literalinclude:: /../../tests/integration_tests/test_multipoint_parallel.py
     :dedent: 8
     :start-after: # [rst Parallel deriv color setup 2 (beg)]
     :end-before: # [rst Parallel deriv color setup 2 (end)]
 
 Finally, let's change the linear solver from default.
 This step is not necessary and not directly relevant to parallelization, but the ``LinearBlockGS`` solver works better on a fine mesh than the default ``DirectSolver``.
 
-.. literalinclude:: ../../tests/test_multipoint_parallel.py
+.. literalinclude:: /../../tests/integration_tests/test_multipoint_parallel.py
     :dedent: 8
     :start-after: # [rst Change linear solver (beg)]
     :end-before: # [rst Change linear solver (end)]
@@ -81,8 +81,10 @@ This step is not necessary and not directly relevant to parallelization, but the
 Complete runscript
 ------------------
 
-.. embed-code::
-    openaerostruct.tests.test_multipoint_parallel.Test.test_multipoint_MPI
+.. literalinclude:: /../../tests/integration_tests/test_multipoint_parallel.py
+    :start-after: docs checkpoint 0
+    :end-before: docs checkpoint 1
+    :dedent: 8
 
 To run this example in parallel with two processors, use the following command:
 

openaerostruct/docs/aerostructural_tube_walkthrough.rst

@@ -10,6 +10,7 @@ Additionally, we have more variable connections due to the more complex problem
 
 For more details about ``mesh_dict`` and ``surface`` in the following script, see :ref:`Mesh and Surface Dict`.
 
-.. embed-code::
-    openaerostruct.tests.test_aerostruct.Test.test
-    :layout: interleave
+.. literalinclude:: /../../tests/integration_tests/test_aerostruct.py
+    :start-after: docs checkpoint 0
+    :end-before: docs checkpoint 1
+    :dedent: 8

openaerostruct/docs/quick_example.rst

@@ -6,7 +6,7 @@ Quick Example
 Here is an example run script to perform aerodynamic optimization.
 We'll go into more detail later about how to set up a model, define the optimization problem, and postprocess results.
 
-.. embed-code::
-    openaerostruct.tests.test_aero.Test.test
-    :layout: interleave
-
+.. literalinclude:: /../../tests/integration_tests/test_aero.py
+    :start-after: docs checkpoint 0
+    :end-before: docs checkpoint 1
+    :dedent: 8

openaerostruct/docs/struct_example.rst

@@ -9,6 +9,7 @@ Although doing structural-only optimizations is relatively rare, this is a build
 
 For more details about ``mesh_dict`` and ``surf_dict`` in the following script, see :ref:`Mesh and Surface Dict`.
 
-.. embed-code::
-  openaerostruct.tests.test_struct.Test.test
-  :layout: interleave
+.. literalinclude:: /../../tests/integration_tests/test_struct.py
+    :start-after: docs checkpoint 0
+    :end-before: docs checkpoint 1
+    :dedent: 8

openaerostruct/docs/user_reference/v1_v2_conversion.rst

@@ -38,7 +38,7 @@ v1 Script
 v2 Script
 ^^^^^^^^^
 
-.. literalinclude:: /../tests/test_v1_aero_opt.py
+.. literalinclude:: /../../tests/integration_tests/test_v1_aero_opt.py
   :start-after: checkpoint 0
   :end-before: checkpoint 1
   :dedent: 8
@@ -64,7 +64,7 @@ v1 Script
 v2 Script
 ^^^^^^^^^
 
-.. literalinclude:: /../tests/test_v1_aero_opt.py
+.. literalinclude:: /../../tests/integration_tests/test_v1_aero_opt.py
   :start-after: checkpoint 2
   :end-before: checkpoint 3
   :dedent: 8
@@ -92,7 +92,7 @@ v1 Script
 v2 Script
 ^^^^^^^^^
 
-.. literalinclude:: /../tests/test_v1_aero_opt.py
+.. literalinclude:: /../../tests/integration_tests/test_v1_aero_opt.py
   :start-after: checkpoint 4
   :end-before: checkpoint 5
   :dedent: 8
@@ -143,7 +143,7 @@ v1 Script
 v2 Script
 ^^^^^^^^^
 
-.. literalinclude:: /../tests/test_v1_aero_opt.py
+.. literalinclude:: /../../tests/integration_tests/test_v1_aero_opt.py
   :start-after: checkpoint 0
   :end-before: checkpoint 5
   :dedent: 8

tests/integration_tests/test_aero_ground_effect.py

@@ -3,6 +3,7 @@
 
 class Test(unittest.TestCase):
     def test(self):
+        # docs checkpoint 0
         import numpy as np
 
         import openmdao.api as om
@@ -107,6 +108,7 @@ def test(self):
         prob.setup()
 
         prob.run_driver()
+        # docs checkpoint 1
 
         assert_near_equal(prob["aero_point_0.wing_perf.CD"][0], 0.03157578980832382, 1e-6)
         assert_near_equal(prob["aero_point_0.wing_perf.CL"][0], 0.5, 1e-6)

tests/integration_tests/test_aerostruct.py

@@ -5,6 +5,7 @@
 
 class Test(unittest.TestCase):
     def test(self):
+        # docs checkpoint 0
         import numpy as np
 
         from openaerostruct.geometry.utils import generate_mesh
@@ -141,11 +142,12 @@ def test(self):
         # Set up the problem
         prob.setup(check=True)
 
+        optResult = prob.run_driver()
+        # docs checkpoint 1
+
         # Inserting a small unit test here. Verify that beta is correctly promoted in an Aerostruct
         # group.
         assert_near_equal(prob["AS_point_0.beta"], 0.0)
-
-        optResult = prob.run_driver()
         assert_opt_successful(self, optResult)
 
         assert_near_equal(prob["AS_point_0.fuelburn"][0], 92523.945549167, 1e-8)

tests/integration_tests/test_aerostruct_ffd.py

@@ -16,6 +16,7 @@
 @unittest.skipUnless(pygeo_flag, "pyGeo is required.")
 class Test(unittest.TestCase):
     def test(self):
+        # docs checkpoint 0
         from openaerostruct.geometry.utils import generate_mesh, write_FFD_file
 
         from openaerostruct.integration.aerostruct_groups import AerostructGeometry, AerostructPoint
@@ -167,6 +168,7 @@ def test(self):
 
         # prob.run_model()
         optResult = prob.run_driver()
+        # docs checkpoint 1
         assert_opt_successful(self, optResult)
 
         assert_near_equal(prob["AS_point_0.fuelburn"][0], 92474.52106288195, 1e-3)

tests/integration_tests/test_multiple_aero_analysis.py

@@ -4,6 +4,7 @@
 
 class Test(unittest.TestCase):
     def test(self):
+        # docs checkpoint 0
         import numpy as np
 
         import openmdao.api as om
@@ -134,6 +135,7 @@ def test(self):
         prob.setup()
 
         prob.run_model()
+        # docs checkpoint 1
 
         assert_near_equal(prob["aero_point_0.wing_perf.CD"][0], 0.03539775778518085, 1e-6)
         assert_near_equal(prob["aero_point_0.wing_perf.CL"][0], 0.5124736932248048, 1e-6)

tests/integration_tests/test_multipoint_aero.py

@@ -4,6 +4,7 @@
 
 class Test(unittest.TestCase):
     def test(self):
+        # docs checkpoint 0
         import numpy as np
         import openmdao.api as om
 
@@ -127,6 +128,7 @@ def test(self):
         # Set up the problem and run optimization.
         prob.setup()
         prob.run_driver()
+        # docs checkpoint 1
 
         assert_near_equal(prob["aero_point_0.wing_perf.CL"][0], 0.45, 1e-6)
         assert_near_equal(prob["aero_point_0.wing_perf.CD"][0], 0.030502881726099183, 1e-6)

tests/integration_tests/test_multipoint_parallel.py

@@ -25,6 +25,7 @@ class Test(unittest.TestCase):
     N_PROCS = 2
 
     def test_multipoint_MPI(self):
+        # docs checkpoint 0
         import numpy as np
         import time
 
@@ -386,6 +387,7 @@ def test_multipoint_MPI(self):
         if MPI.COMM_WORLD.rank == 0:
             print("Analysis runtime: ", run_model_time, "[s]")
             print("Derivatives runtime: ", derivs_time, "[s]")
+        # docs checkpoint 1
 
         # OpenMDAO versions before 3.31 use absolute names as dictionary keys, but versions after
         # use user facing (promoted) names. Handle both cases here.

tests/integration_tests/test_struct.py

@@ -4,6 +4,7 @@
 
 class Test(unittest.TestCase):
     def test(self):
+        # docs checkpoint 0
         import numpy as np
 
         from openaerostruct.geometry.utils import generate_mesh
@@ -66,9 +67,10 @@ def test(self):
         prob.model.add_objective("wing.structural_mass", scaler=1e-5)
 
         # Set up the problem
-        prob.setup(force_alloc_complex=False)
+        prob.setup()
 
         prob.run_driver()
+        # docs checkpoint 1
 
         assert_near_equal(prob["wing.structural_mass"][0], 71088.4682399, 1e-8)