update tests for design_space, run notebook for next week smt2 paper …

…release and update setup.py (#488)
SMTorg · Dec 1, 2023 · 4b31350 · 4b31350
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diff --git a/setup.py b/setup.py
@@ -1,9 +1,10 @@
 """
-Author: Dr. John T. Hwang <[email protected]>
-        Dr. Mohamed A. Bouhlel <[email protected]>
+Author: John T. Hwang <[email protected]>
+        Mohamed A. Bouhlel <[email protected]>
         Remi Lafage <[email protected]>
         Lucas Alber <[email protected]>
-
+        Paul Saves <[email protected]>
+        
 This package is distributed under New BSD license.
 """
 from setuptools import setup, Extension
@@ -90,8 +91,8 @@
     version=__version__,
     description="The Surrogate Modeling Toolbox (SMT)",
     long_description=LONG_DESCRIPTION,
-    author="Mohamed Amine Bouhlel et al.",
-    author_email="[email protected]",
+    author="Remi Lafage et al.",
+    author_email="[email protected]",
     license="BSD-3",
     classifiers=[_f for _f in CLASSIFIERS.split("\n") if _f],
     packages=[
@@ -116,7 +117,7 @@
             "ConfigSpace~=0.6.1",
         ],
     },
-    python_requires=">=3.7",
+    python_requires=">=3.8",
     zip_safe=False,
     ext_modules=ext,
     url="https://github.com/SMTorg/smt",  # use the URL to the github repo

diff --git a/smt/utils/test/test_design_space.py b/smt/utils/test/test_design_space.py
@@ -201,7 +201,7 @@ def test_design_space(self):
         )
         self.assertEqual(len(ds.design_variables), 4)
         if HAS_CONFIG_SPACE:
-            self.assertEqual(len(ds._cs.get_hyperparameters()), 4)
+            self.assertEqual(len(list(ds._cs.values())), 4)
         self.assertTrue(np.all(~ds.is_conditionally_acting))
         if HAS_CONFIG_SPACE:
             x, is_acting = ds.sample_valid_x(3, random_state=42)
@@ -539,6 +539,24 @@ def _is_conditionally_acting(self) -> np.ndarray:
                     RuntimeError, lambda: ds.sample_valid_x(10, random_state=42)
                 )
 
+    def test_check_conditionally_acting_2(self):
+        for simulate_no_cs in [True, False]:
+            with simulate_no_config_space(simulate_no_cs):
+                ds = DesignSpace(
+                    [
+                        CategoricalVariable(["A", "B", "C"]),  # x0
+                        CategoricalVariable(["E", "F"]),  # x1
+                        IntegerVariable(0, 1),  # x2
+                        FloatVariable(0, 1),  # x3
+                    ],
+                    seed=42,
+                )
+                ds.declare_decreed_var(
+                    decreed_var=0, meta_var=1, meta_value="E"
+                )  # Activate x3 if x0 == A
+
+                ds.sample_valid_x(10, random_state=42)
+
     @unittest.skipIf(
         not HAS_CONFIG_SPACE, "Hierarchy ConfigSpace dependency not installed"
     )
@@ -549,7 +567,7 @@ def test_restrictive_value_constraint(self):
                 IntegerVariable(0, 2),
             ]
         )
-        assert ds._cs.get_hyperparameters()[0].default_value == 1
+        assert list(ds._cs.values())[0].default_value == 1
 
         ds.add_value_constraint(var1=0, value1=1, var2=0, value2=1)
         ds.sample_valid_x(100, random_state=42)

diff --git a/tutorial/NotebookRunTestCases_Paper_SMT_v2.ipynb b/tutorial/NotebookRunTestCases_Paper_SMT_v2.ipynb
@@ -57,7 +57,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 1,
    "id": "fff43855",
    "metadata": {},
    "outputs": [],
@@ -125,10 +125,19 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 2,
    "id": "ccc49c3b",
    "metadata": {},
-   "outputs": [],
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "Pred_RMSE on the training points 1.0052501496058814e-12\n",
+      "Var_RMSE on the training points 1.6419278095185747e-12\n"
+     ]
+    }
+   ],
    "source": [
     "def f_neu(x1, x2, x3):\n",
     "    return 2 * x1 + x2 - 0.5 * x3\n",
@@ -202,10 +211,21 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 3,
    "id": "9fc88694",
    "metadata": {},
-   "outputs": [],
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "[1.3098127  0.69714044 2.19224095] [1.3098127  0.69714044 2.19224095]\n",
+      "The outputs must be similar (inactive variables have no effect) 0.0\n",
+      "[-1.39420965] [10.45248007]\n",
+      "The outputs must be different (active variables have effect) 11.846689716902546\n"
+     ]
+    }
+   ],
    "source": [
     "#To check of some inactive variables have no effect on the output\n",
     "xv1=np.array([\n",
@@ -234,10 +254,22 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 4,
    "id": "c122b735",
    "metadata": {},
-   "outputs": [],
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "Activation function ['ISRLU', 'SELU', 'ReLU ']\n",
+      "Batch size  [3, 4, 5]\n",
+      "Number of hidden neurons -1st layer  [2, 2, 2]\n",
+      "Number of hidden neurons -2nd layer [0, 1, 1]\n",
+      "Number of hidden neurons -3rd layer [0, 0, 5]\n"
+     ]
+    }
+   ],
    "source": [
     "#To have access to the \"real\" values of the input space variables\n",
     "x2_decoded = design_space.decode_values(xv1, i_dv=2)\n",
@@ -295,10 +327,29 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 5,
    "id": "1b3c3727",
    "metadata": {},
-   "outputs": [],
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "\u001b[33mWARNING: Ignoring invalid distribution -umpy (/stck/psaves/miniconda3/lib/python3.8/site-packages)\u001b[0m\u001b[33m\n",
+      "\u001b[0mName: numba\n",
+      "Version: 0.58.1\n",
+      "Summary: compiling Python code using LLVM\n",
+      "Home-page: https://numba.pydata.org\n",
+      "Author: \n",
+      "Author-email: \n",
+      "License: BSD\n",
+      "Location: /stck/psaves/miniconda3/lib/python3.8/site-packages\n",
+      "Requires: importlib-metadata, llvmlite, numpy\n",
+      "Required-by: \n",
+      "Numba used or not in your environment= %USE_NUMBA_JIT%\n"
+     ]
+    }
+   ],
    "source": [
     "#to check if numba is available\n",
     "!pip show numba\n",
@@ -308,15 +359,57 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 7,
    "id": "b2d505b5",
    "metadata": {},
-   "outputs": [],
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "Design space:\n",
+      "x0: Cat [0, 1, 2, 3]\n",
+      "x1: Ord [0, 1]\n",
+      "x2: Float (0, 100)\n",
+      "x3: Float (0, 100)\n",
+      "x4: Float (0, 100)\n",
+      "x5: Float (0, 100)\n",
+      "x6: Float (0, 100)\n",
+      "x7: Int (0, 2)\n",
+      "x8: Int (0, 2)\n",
+      "x9: Int (0, 2)\n",
+      "x10: Int (0, 2)\n",
+      "for  15 points time is =  0.0018038749694824219\n"
+     ]
+    },
+    {
+     "ename": "IndexError",
+     "evalue": "index 11 is out of bounds for axis 0 with size 11",
+     "output_type": "error",
+     "traceback": [
+      "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
+      "\u001b[0;31mInactiveHyperparameterSetError\u001b[0m            Traceback (most recent call last)",
+      "\u001b[0;32m~/smt/smt/utils/design_space.py\u001b[0m in \u001b[0;36m_get_correct_config\u001b[0;34m(self, vector)\u001b[0m\n\u001b[1;32m    968\u001b[0m             \u001b[0;32mtry\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 969\u001b[0;31m                 \u001b[0mconfig\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mis_valid_configuration\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m    970\u001b[0m                 \u001b[0;32mreturn\u001b[0m \u001b[0mconfig\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
+      "\u001b[0;32m~/miniconda3/lib/python3.8/site-packages/ConfigSpace/configuration.py\u001b[0m in \u001b[0;36mis_valid_configuration\u001b[0;34m(self)\u001b[0m\n\u001b[1;32m    128\u001b[0m         \"\"\"\n\u001b[0;32m--> 129\u001b[0;31m         c_util.check_configuration(\n\u001b[0m\u001b[1;32m    130\u001b[0m             \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mconfig_space\u001b[0m\u001b[0;34m,\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
+      "\u001b[0;32m~/miniconda3/lib/python3.8/site-packages/ConfigSpace/c_util.pyx\u001b[0m in \u001b[0;36mConfigSpace.c_util.check_configuration\u001b[0;34m()\u001b[0m\n",
+      "\u001b[0;32m~/miniconda3/lib/python3.8/site-packages/ConfigSpace/c_util.pyx\u001b[0m in \u001b[0;36mConfigSpace.c_util.check_configuration\u001b[0;34m()\u001b[0m\n",
+      "\u001b[0;31mInactiveHyperparameterSetError\u001b[0m: Hyperparameter is inactive but has a value set as 0.5.\nx8, Type: UniformInteger, Range: [0, 2], Default: 1",
+      "\nDuring handling of the above exception, another exception occurred:\n",
+      "\u001b[0;31mIndexError\u001b[0m                                Traceback (most recent call last)",
+      "\u001b[0;32m/tmp/ipykernel_3462256/3677463211.py\u001b[0m in \u001b[0;36m<cell line: 13>\u001b[0;34m()\u001b[0m\n\u001b[1;32m     11\u001b[0m \u001b[0mend\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mtime\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mtime\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m     12\u001b[0m \u001b[0mprint\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m\"for \"\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mn_doe\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m\"points time is = \"\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mend\u001b[0m \u001b[0;34m-\u001b[0m \u001b[0mstart\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m---> 13\u001b[0;31m \u001b[0mYt1\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mproblem\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mXt1\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m     14\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m     15\u001b[0m \u001b[0;31m#for 150 points\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
+      "\u001b[0;32m~/smt/smt/problems/problem.py\u001b[0m in \u001b[0;36m__call__\u001b[0;34m(self, x, kx)\u001b[0m\n\u001b[1;32m    109\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    110\u001b[0m         \u001b[0;31m# Correct the design vector and get information about which design variables are active\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 111\u001b[0;31m         \u001b[0mx_corr\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0meval_is_acting\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mdesign_space\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mcorrect_get_acting\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mx\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m    112\u001b[0m         \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0meval_x\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mx_corr\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    113\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n",
+      "\u001b[0;32m~/smt/smt/utils/design_space.py\u001b[0m in \u001b[0;36mcorrect_get_acting\u001b[0;34m(self, x)\u001b[0m\n\u001b[1;32m    273\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    274\u001b[0m         \u001b[0;31m# Correct and get the is_acting matrix\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 275\u001b[0;31m         \u001b[0mx_corrected\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mis_acting\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m_correct_get_acting\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mx\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m    276\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    277\u001b[0m         \u001b[0;31m# Check conditionally-acting status\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
+      "\u001b[0;32m~/smt/smt/utils/design_space.py\u001b[0m in \u001b[0;36m_correct_get_acting\u001b[0;34m(self, x)\u001b[0m\n\u001b[1;32m    899\u001b[0m             \u001b[0mconfigs\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0;34m[\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    900\u001b[0m             \u001b[0;32mfor\u001b[0m \u001b[0mxi\u001b[0m \u001b[0;32min\u001b[0m \u001b[0mx\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 901\u001b[0;31m                 \u001b[0mconfigs\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mappend\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m_get_correct_config\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mxi\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0minv_cs_var_idx\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m    902\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    903\u001b[0m             \u001b[0;31m# Convert Configuration objects to design vectors and get the is_active matrix\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
+      "\u001b[0;32m~/smt/smt/utils/design_space.py\u001b[0m in \u001b[0;36m_get_correct_config\u001b[0;34m(self, vector)\u001b[0m\n\u001b[1;32m    980\u001b[0m                     \u001b[0;31m# Modify the vector and create a new Configuration\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    981\u001b[0m                     \u001b[0mvector\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mconfig\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mget_array\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mcopy\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 982\u001b[0;31m                     \u001b[0;32mwhile\u001b[0m \u001b[0mstr\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mvector\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0mparam_idx\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m)\u001b[0m \u001b[0;34m==\u001b[0m\u001b[0;34m\"nan\"\u001b[0m \u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m    983\u001b[0m                         \u001b[0mparam_idx\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0mparam_idx\u001b[0m\u001b[0;34m+\u001b[0m\u001b[0;36m1\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    984\u001b[0m                     \u001b[0mvector\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0mparam_idx\u001b[0m\u001b[0;34m]\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mnp\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mnan\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
+      "\u001b[0;31mIndexError\u001b[0m: index 11 is out of bounds for axis 0 with size 11"
+     ]
+    }
+   ],
    "source": [
     "#compare the CPU time to build a DOE with 15 or 150 points\n",
     "problem = HierarchicalGoldstein()\n",
     "design_space = problem.design_space\n",
-    "\n",
+    "print(design_space)\n",
     "#for 15 points\n",
     "n_doe = 15\n",
     "design_space.seed = 42\n",