Add autolink to docs

conf.py

@@ -4,18 +4,11 @@
 project = "MACH-Aero Documentation"
 
 # -- General configuration -----------------------------------------------------
-# Specify the baseurls for the projects I want to link to
-repos = [
-    "pygeo",
-    "pyoptsparse",
-    "baseclasses",
-    "idwarp",
-    "adflow",
-    "pyhyp",
-    "multipoint",
-    "pyspline",
-]
-intersphinx_mapping = {r: (f"https://mdolab-{r}.readthedocs-hosted.com/en/latest", None) for r in repos}
+# autolink
+extensions.extend(["sphinx_codeautolink"])
+codeautolink_concat_default = True
+codeautolink_warn_on_missing_inventory = True
+codeautolink_warn_on_failed_resolve = True
 
 # bibtex
 bibtex_bibfiles = [

machAeroTutorials/aero_adflow.rst

@@ -33,6 +33,7 @@ Then copy the code from each of the following sections into this file.
 Import libraries
 ----------------
 .. literalinclude:: ../tutorial/aero/analysis/aero_run.py
+   :language: py
    :start-after: # rst Imports
    :end-before: # rst ADflow options
 
@@ -50,6 +51,7 @@ The ``analysis`` option here will simply run a single ADflow analysis, and the `
 ADflow options
 --------------
 .. literalinclude:: ../tutorial/aero/analysis/aero_run.py
+   :language: py
    :start-after: # rst ADflow options
    :end-before: # rst Start ADflow
 
@@ -64,6 +66,7 @@ We strongly recommend going over the descriptions and tips on solvers and solver
 Create solver
 -------------
 .. literalinclude:: ../tutorial/aero/analysis/aero_run.py
+   :language: py
    :start-after: # rst Start ADflow
    :end-before: # rst Create AeroProblem
 
@@ -75,6 +78,7 @@ Also, ADflow can write airfoil data for a given set of slices along the wing usi
 Set flow conditions
 -------------------
 .. literalinclude:: ../tutorial/aero/analysis/aero_run.py
+    :language: py
     :start-after: # rst Create AeroProblem
     :end-before: # rst Run ADflow
 
@@ -87,6 +91,7 @@ Some available functions include ``'cl'``, ``'cd'``, ``'cmz'``, ``'lift'``, and
 Single analysis
 ---------------
 .. literalinclude:: ../tutorial/aero/analysis/aero_run.py
+    :language: py
     :start-after: # rst Run ADflow
     :end-before: # rst Create polar arrays
 
@@ -103,45 +108,38 @@ The only difference is that the analysis is now done within a loop.
 
 
 .. literalinclude:: ../tutorial/aero/analysis/aero_run.py
+    :language: py
     :start-after: # rst Create polar arrays
     :end-before: # rst Start loop
 
 We start by creating a list of the angle of attack values that we wish to analyze.
 In this case we use the ``numpy.linspace`` function to create a uniformly-spaced array with six whole number entries from 0 -- 5.
-We also create the empty lists for storing the lift and drag coefficients. 
+We also create the empty lists for storing the lift and drag coefficients.
 The lift and drag data will be appended to these lists as the flow solutions are completed.
 
 
 .. literalinclude:: ../tutorial/aero/analysis/aero_run.py
+    :language: py
     :start-after: # rst Start loop
-    :end-before: # rst update AP
+    :end-before: # rst Print polar
 
 Having created the input array and data storage lists, we can now loop over the desired angles of attack to evaluate the polar.
 We accomplish this by using the builtin ``for`` loop structure in python.
 
-
-.. literalinclude:: ../tutorial/aero/analysis/aero_run.py
-    :start-after: # rst update AP
-    :end-before: # rst Run ADflow polar
-
 Now for each angle of attack, we update two attributes of the aero problem.
 We update the name to include the current angle of attack.
 This allow the filenames of the lift distribution, slices, volume solution and surface solution to be updated with the current angle of attack, making it easier to keep track of the output files.
 We also update the alpha parameter, which is the attribute of the AeroProblem that represents the angle of attack.
 
-
-.. literalinclude:: ../tutorial/aero/analysis/aero_run.py
-    :start-after: # rst Run ADflow polar
-    :end-before: # rst Print polar
-
-Running the solver is identical to the simple single point example. 
+Running the solver is identical to the simple single point example.
 We simply call the ``CFDSolver`` instance with the current AeroProblem.
 This causes the CFD solver to be updated with the values of that AeroProblem prior to solving the flow.
 We then use the same ``EvalFunctions`` call to integrate the surface forces to get the lift and drag coefficients.
 The difference is that here, we append the coefficients from ``funcs`` into the ``CLList`` and ``CDList`` variables, so that they can be used later.
 
 
 .. literalinclude:: ../tutorial/aero/analysis/aero_run.py
+    :language: py
     :start-after: # rst Print polar
 
 Once we complete the loop and evaluate all of the desired flow conditions, we can print the completed data set to the screen.

machAeroTutorials/aero_pygeo.rst

@@ -38,12 +38,14 @@ We need to import the pyGeo library in order to use its functions.
 The pyGeo library, along with all other MACH libraries, should be importable because its code is located in a directory which is exposed to the system environment variable PYTHON_PATH.
 
 .. literalinclude:: ../tutorial/aero/geometry/generate_wing.py
+    :language: py
     :start-after: # rst Imports
     :end-before: # rst Airfoil file
 
 Wing Definition
 ---------------
 .. literalinclude:: ../tutorial/aero/geometry/generate_wing.py
+    :language: py
     :start-after: # rst Airfoil file
     :end-before: # rst Wing definition
 
@@ -76,12 +78,14 @@ An offset in the x-y plane can be added to this position with the ``offset`` arr
 In this case, we don't want to apply any rotation (the rotation options shown below would be for rotation about the airfoil leading edge points and the units are degrees) or offset.
 
 .. literalinclude:: ../tutorial/aero/geometry/generate_wing.py
+    :language: py
     :start-after: # rst Wing definition
     :end-before: # rst Run pyGeo
 
 Call pyGeo
 ----------
 .. literalinclude:: ../tutorial/aero/geometry/generate_wing.py
+    :language: py
     :start-after: # rst Run pyGeo
     :end-before: # rst Write output files
 
@@ -92,11 +96,12 @@ Write output files
 ------------------
 There are three options for writing the geometry surface definition to file.
 
-    1. Write a dat file to view wing in Tecplot.
-    2. Write an IGES file. This can be converted to a TIN file in ICEM.
-    3. Write a TIN file directly from pyGeo.
+    #. Write a dat file to view wing in Tecplot.
+    #. Write an IGES file. This can be converted to a TIN file in ICEM.
+    #. Write a TIN file directly from pyGeo.
 
 .. literalinclude:: ../tutorial/aero/geometry/generate_wing.py
+   :language: py
    :start-after: # rst Write output files
 
 Run it yourself!

machAeroTutorials/aero_pyhyp.rst

@@ -32,6 +32,7 @@ Then copy the code from each of the following sections into this file.
 Import libraries
 ----------------
 .. literalinclude:: ../tutorial/aero/meshing/volume/run_pyhyp.py
+   :language: py
    :start-after: # rst Imports
    :end-before: # rst general
 
@@ -45,6 +46,7 @@ Here we will point a few of the more basic options.
 For pyHyp, the options can be organized like so:
 
 .. literalinclude:: ../tutorial/aero/meshing/volume/run_pyhyp.py
+    :language: py
     :start-after: # rst general
     :end-before: # rst grid
 
@@ -68,6 +70,7 @@ General options:
         Name given to wall surfaces. If a dictionary is submitted, each wall patch can have a different name. This can help the user to apply certain operations to specific wall patches in ADflow.
 
 .. literalinclude:: ../tutorial/aero/meshing/volume/run_pyhyp.py
+    :language: py
     :start-after: # rst grid
     :end-before: # rst pseudo
 
@@ -88,21 +91,25 @@ More information can be found in the :doc:`pyHyp documentation <pyhyp:index>`.
 For example, ``epsE`` may be of interest when dealing with concave corners.
 
 .. literalinclude:: ../tutorial/aero/meshing/volume/run_pyhyp.py
+    :language: py
     :start-after: # rst pseudo
     :end-before: # rst smoothing
 
 .. literalinclude:: ../tutorial/aero/meshing/volume/run_pyhyp.py
+    :language: py
     :start-after: # rst smoothing
     :end-before: # rst solution
 
 .. literalinclude:: ../tutorial/aero/meshing/volume/run_pyhyp.py
+    :language: py
     :start-after: # rst solution
     :end-before: # rst run pyHyp
 
 Running pyHyp is quite simple, as shown below.
 After the mesh extrusion is done, we can write the volume mesh with the ``writeCGNS`` function.
 
 .. literalinclude:: ../tutorial/aero/meshing/volume/run_pyhyp.py
+    :language: py
     :start-after: # rst run pyHyp
 
 Run it yourself!

machAeroTutorials/airfoilopt_ffd.rst

@@ -25,18 +25,21 @@ Create the following empty runscript in the current directory.
 Import Packages
 ===============
 .. literalinclude:: ../tutorial/airfoilopt/ffd/genFFD.py
+    :language: py
     :start-after: # rst Import
     :end-before: # rst Load
 
 Load Airfoil
 ============
 .. literalinclude:: ../tutorial/airfoilopt/ffd/genFFD.py
+    :language: py
     :start-after: # rst Load
     :end-before: # rst UpperLower
 
 The following two functions are used to get the upper and lower points of the airfoil. 
 
 .. literalinclude:: ../tutorial/airfoilopt/ffd/genFFD.py
+    :language: py
     :start-after: # rst UpperLower
     :end-before: # rst FFDBox1
 
@@ -47,6 +50,7 @@ FFD Box Creation
 The FFD box can now be set up. 
 
 .. literalinclude:: ../tutorial/airfoilopt/ffd/genFFD.py
+    :language: py
     :start-after: # rst FFDBox1
     :end-before: # rst FFDBox2
 
@@ -61,6 +65,7 @@ An empty FFD box is created.
 
 
 .. literalinclude:: ../tutorial/airfoilopt/ffd/genFFD.py
+    :language: py
     :start-after: # rst FFDBox2
     :end-before: # rst WriteFile
 
@@ -74,6 +79,7 @@ Writing to File
 ===============
 
 .. literalinclude:: ../tutorial/airfoilopt/ffd/genFFD.py
+    :language: py
     :start-after: # rst WriteFile
 
 Run it yourself!

machAeroTutorials/airfoilopt_mesh.rst

@@ -38,6 +38,7 @@ pyHyp runscript
 Import the pyHyp libraries and numpy.
 
 .. literalinclude:: ../tutorial/airfoilopt/mesh/genMesh.py
+    :language: py
     :start-after: # rst Import
     :end-before: # rst SurfMesh
 
@@ -46,6 +47,7 @@ Surface Mesh Generation
 =======================
 
 .. literalinclude:: ../tutorial/airfoilopt/mesh/genMesh.py
+    :language: py
     :start-after: # rst SurfMesh
     :end-before: # rst GenOptions
 
@@ -65,6 +67,7 @@ Options
 =======
 
 .. literalinclude:: ../tutorial/airfoilopt/mesh/genMesh.py
+    :language: py
     :start-after: # rst GenOptions
     :end-before: # rst GridOptions
 
@@ -87,6 +90,7 @@ General Options
 
 
 .. literalinclude:: ../tutorial/airfoilopt/mesh/genMesh.py
+    :language: py
     :start-after: # rst GridOptions
     :end-before: # rst Run
 
@@ -108,6 +112,7 @@ Running pyHyp and Writing to File
 The following three lines of code extrude the surface mesh and write the resulting volume mesh to a ``.cgns`` file.
 
 .. literalinclude:: ../tutorial/airfoilopt/mesh/genMesh.py
+    :language: py
     :start-after: # rst Run
 
 Run it yourself!

machAeroTutorials/airfoilopt_multipoint.rst

@@ -56,6 +56,7 @@ Specifying parameters for the optimization
 For multipoint optimization, the parameters have to be specified in lists of the same size.
 
 .. literalinclude:: ../tutorial/airfoilopt/multipoint/airfoil_multiopt.py
+    :language: py
     :start-after: # rst parameters (beg)
     :end-before: # rst parameters (end)
 
@@ -65,6 +66,7 @@ This is largely unchanged from the single-point case, since we use a very simila
 The only difference is in defining the variable ``nGroup`` which is used later on to distinguish between the two AeroProblems.
 
 .. literalinclude:: ../tutorial/airfoilopt/multipoint/airfoil_multiopt.py
+    :language: py
     :start-after: # rst multipoint (beg)
     :end-before: # rst multipoint (end)
 
@@ -75,6 +77,7 @@ For more than one AeroProblem, a list needs to be created.
 Each AeroProblem is created with the respective optimization point and appended to the list.
 
 .. literalinclude:: ../tutorial/airfoilopt/multipoint/airfoil_multiopt.py
+    :language: py
     :start-after: # rst aeroproblem (beg)
     :end-before: # rst aeroproblem (end)
 
@@ -86,6 +89,7 @@ The lines that require a call to the an AeroProblem is now put into a for-loop t
 
 
 .. literalinclude:: ../tutorial/airfoilopt/multipoint/airfoil_multiopt.py
+    :language: py
     :start-after: # rst funcs (beg)
     :end-before: # rst funcs (end)
 
@@ -99,6 +103,7 @@ In addition, we use the ``wrt`` keyword to specify the variables that affect eac
 In this case, the ``alpha`` from the other flight conditions do not impact the lift constraint, so they are set to zero.
 
 .. literalinclude:: ../tutorial/airfoilopt/multipoint/airfoil_multiopt.py
+    :language: py
     :start-after: # rst optprob (beg)
     :end-before: # rst optprob (end)