Update the documentation (SMTorg#669)

* fix smt-dse

* ruff

* fix import

* fix imports and doc

* Update notebook references

Signed-off-by: Emmanuel Ferdman <[email protected]>

* fix notebooks by emmanuel ferdman

* fix link

---------

Signed-off-by: Emmanuel Ferdman <[email protected]>
Co-authored-by: Emmanuel Ferdman <[email protected]>

doc/_src_docs/applications/Mixed_Hier_usage.rstx

@@ -39,15 +39,16 @@ The design space is then defined from a list of design variables and implements
 Hierarchical variables
 ----------------------
 
-The design space definition uses the framework of Audet et al. [2]_ to manage both mixed-discrete variables and
+The design space definition uses the framework of [2]_ to manage both mixed-discrete variables and
 hierarchical variables. We distinguish dimensional (or meta) variables which are a special type of variables that may
 affect the dimension of the problem and decide if some other decreed variables are acting or non-acting.
 
 Additionally, it is also possible to define value constraints that explicitly forbid two variables from having some
 values simultaneously or for a continuous variable to be greater than another. 
 This can be useful for modeling incompatibility relationships: for example, engines can't be 
-installed on the back of the fuselage (vs on the wings) if a normal tail (vs T-tail) is selected. Note: this feature
-is only available if ConfigSpace has been installed: `pip install smt[cs]`
+installed on the back of the fuselage (vs on the wings) if a normal tail (vs T-tail) is selected.
+
+Note: this feature is only available if smt_design_space_ext has been installed: `pip install smt-design-space-ext`
 
 The hierarchy relationships are specified after instantiating the design space:
 
@@ -103,6 +104,6 @@ Example of mixed integer context usage
 References
 ----------
 
-.. [1] Saves, P. and Diouane, Y. and Bartoli, N. and Lefebvre, T. and Morlier, J. (2022). A general square exponential kernel to handle mixed-categorical variables for Gaussian process. AIAA Aviation 2022 Forum. 
+.. [1] Saves, P. and Lafage, R. and Bartoli, N. and Diouane, Y. and Bussemaker, J. and Lefebvre, T. and Hwang, J. and Morlier, J. and Martins, J. (2024). SMT 2.0: A Surrogate Modeling Toolbox with a focus on Hierarchical and Mixed Variables Gaussian Processes. Advances in Engineering Sofware.
 
-.. [2] Audet, C., Hallé-Hannan, E. and Le Digabel, S. A General Mathematical Framework for Constrained Mixed-variable Blackbox Optimization Problems with Meta and Categorical Variables. Oper. Res. Forum 4, 12 (2023). 
+.. [2] Hallé-Hannan, E. and  Audet, C., and Diouane, Y. and  Le Digabel, S. and Saves, P. (2024). A graph-structured distance for heterogeneous datasets with meta variable, Neurocomputing.

doc/_src_docs/getting_started.rstx

@@ -34,9 +34,9 @@ Notebooks
 Several notebooks are available to get up to speed with SMT:
 
 * `General <https://github.com/SMTorg/smt/blob/master/tutorial/SMT_Tutorial.ipynb>`_
-* `Handling of Noise <https://github.com/SMTorg/smt/blob/master/tutorial/SMT_Noise.ipynb>`_
-* `Handling of Mixed Integer variables <https://github.com/SMTorg/smt/blob/master/tutorial/SMT_MixedInteger_Engineering_applications.ipynb>`_
-* `Efficient Global Optimization application <https://github.com/SMTorg/smt/blob/master/tutorial/SMT_EGO_application.ipynb>`_
+* `Handling of Noise <https://github.com/SMTorg/smt/blob/master/tutorial/Misc/SMT_Noise.ipynb>`_
+* `Handling of Mixed Integer variables <https://github.com/SMTorg/smt/blob/master/tutorial/MixedInteger/SMT_MixedInteger_Engineering_applications.ipynb>`_
+* `Efficient Global Optimization application <https://github.com/SMTorg/smt/blob/master/tutorial/SBO/SMT_EGO_application.ipynb>`_
 
 Uninstalling
 ------------

setup.py

@@ -107,6 +107,7 @@
         "smt.sampling_methods",
         "smt.utils",
         "smt.applications",
+        "smt.applications.tests",
         "smt.design_space",
         "smt.kernels",
     ],

smt/applications/__init__.py

@@ -6,6 +6,7 @@
 from .vfm import VFM
 from .podi import PODI, SubspacesInterpolation
 from .cckrg import CoopCompKRG
+from .tests.test_mixed_integer import TestMixedInteger
 
 __all__ = [
     "VFM",
@@ -20,4 +21,5 @@
     "PODI",
     "SubspacesInterpolation",
     "CoopCompKRG",
+    "TestMixedInteger",
 ]

smt/applications/tests/__init__.py

@@ -0,0 +1,5 @@
+from .test_mixed_integer import TestMixedInteger
+
+__all__ = [
+    "TestMixedInteger",
+]

smt/applications/tests/test_mixed_integer.py

@@ -801,13 +801,13 @@ def run_hierarchical_design_space_example(self):
         from smt.surrogate_models import KRG, MixHrcKernelType, MixIntKernelType
         from smt.design_space import (
             CategoricalVariable,
-            DesignSpace,
             FloatVariable,
             IntegerVariable,
             OrdinalVariable,
         )
+        from smt_design_space_ext import ConfigSpaceDesignSpaceImpl
 
-        ds = DesignSpace(
+        ds = ConfigSpaceDesignSpaceImpl(
             [
                 CategoricalVariable(
                     ["A", "B"]

smt/design_space/design_space.py

@@ -624,7 +624,7 @@ def __repr__(self):
 
 def raise_config_space():
     raise RuntimeError(
-        "Dependencies are not installed, please install smt_design_space."
+        "Dependencies are not installed, please install smt_design_space_ext."
     )
 
 

tutorial/MFK/SMT_MFK_Noise.ipynb

@@ -4,7 +4,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "<a href=\"https://colab.research.google.com/github/SMTorg/smt/blob/master/tutorial/SMT_MFK_Noise.ipynb\" target=\"_blank\" rel=\"nofollow\"><img src=\"https://colab.research.google.com/assets/colab-badge.svg\" alt=\"Open In Colab\"></a>"
+    "<a href=\"https://colab.research.google.com/github/SMTorg/smt/blob/master/tutorial/MFK/SMT_MFK_Noise.ipynb\" target=\"_blank\" rel=\"nofollow\"><img src=\"https://colab.research.google.com/assets/colab-badge.svg\" alt=\"Open In Colab\"></a>"
    ]
   },
   {

tutorial/Misc/SMT_GP_Sampling.ipynb

@@ -6,7 +6,7 @@
    "metadata": {},
    "source": [
     "\n",
-    "<a href=\"https://colab.research.google.com/github/SMTorg/smt/blob/master/tutorial/SMT_GP_Sampling.ipynb\" target=\"_parent\"><img src=\"https://colab.research.google.com/assets/colab-badge.svg\" alt=\"Open In Colab\"/></a>\n"
+    "<a href=\"https://colab.research.google.com/github/SMTorg/smt/blob/master/tutorial/Misc/SMT_GP_Sampling.ipynb\" target=\"_parent\"><img src=\"https://colab.research.google.com/assets/colab-badge.svg\" alt=\"Open In Colab\"/></a>\n"
    ]
   },
   {

tutorial/Misc/SMT_Noise.ipynb

@@ -7,7 +7,7 @@
    },
    "source": [
     "\n",
-    "<a href=\"https://colab.research.google.com/github/SMTorg/smt/blob/master/tutorial/SMT_Noise.ipynb\" target=\"_parent\"><img src=\"https://colab.research.google.com/assets/colab-badge.svg\" alt=\"Open In Colab\"/></a>"
+    "<a href=\"https://colab.research.google.com/github/SMTorg/smt/blob/master/tutorial/Misc/SMT_Noise.ipynb\" target=\"_parent\"><img src=\"https://colab.research.google.com/assets/colab-badge.svg\" alt=\"Open In Colab\"/></a>"
    ]
   },
   {