Modifies the docs to account for the api change

docs/poli-docs/_build/.jupyter_cache/executed/8d4497d872605fedd707c447b2e6c83f/base.ipynb → docs/poli-docs/_build/.jupyter_cache/executed/4158632ea056a4b647992ecd2d975233/base.ipynb

@@ -9,7 +9,7 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "['aloha', 'foldx_rfp_lambo', 'foldx_sasa', 'foldx_stability', 'foldx_stability_and_sasa', 'gfp_select', 'penalized_logp_lambo', 'rdkit_logp', 'rdkit_qed', 'toy_continuous_problem', 'white_noise']\n"
+      "['aloha', 'dockstring', 'foldx_stability', 'gfp_select', 'rdkit_logp', 'rdkit_qed', 'toy_continuous_problem', 'white_noise']\n"
      ]
     }
    ],
@@ -27,7 +27,7 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "['aloha', 'dockstring', 'drd3_docking', 'foldx_rfp_lambo', 'foldx_sasa', 'foldx_stability', 'foldx_stability_and_sasa', 'gfp_cbas', 'gfp_select', 'penalized_logp_lambo', 'rasp', 'rdkit_logp', 'rdkit_qed', 'sa_tdc', 'super_mario_bros', 'toy_continuous_problem', 'white_noise']\n"
+      "['aloha', 'dockstring', 'drd3_docking', 'foldx_rfp_lambo', 'foldx_sasa', 'foldx_stability', 'foldx_stability_and_sasa', 'gfp_cbas', 'gfp_select', 'penalized_logp_lambo', 'rasp', 'rdkit_logp', 'rdkit_qed', 'rfp_foldx_stability_and_sasa', 'sa_tdc', 'super_mario_bros', 'toy_continuous_problem', 'white_noise']\n"
      ]
     }
    ],
@@ -51,20 +51,28 @@
    "source": [
     "from poli import objective_factory\n",
     "\n",
-    "problem_info, f, x0, y0, _ = objective_factory.create(name=\"white_noise\")"
+    "f, x0, y0 = objective_factory.create(name=\"white_noise\")"
    ]
   },
   {
    "cell_type": "code",
    "execution_count": 4,
    "metadata": {},
    "outputs": [
+    {
+     "name": "stderr",
+     "output_type": "stream",
+     "text": [
+      "/Users/sjt972/anaconda3/envs/poli-docs2/lib/python3.9/site-packages/tqdm/auto.py:21: TqdmWarning: IProgress not found. Please update jupyter and ipywidgets. See https://ipywidgets.readthedocs.io/en/stable/user_install.html\n",
+      "  from .autonotebook import tqdm as notebook_tqdm\n"
+     ]
+    },
     {
      "name": "stdout",
      "output_type": "stream",
      "text": [
       "x0: [['1' '2' '3']]\n",
-      "y0: [[0.57433265]]\n"
+      "y0: [[-1.16173153]]\n"
      ]
     }
    ],
@@ -89,7 +97,7 @@
     {
      "data": {
       "text/plain": [
-       "array([['1', '4', '3']], dtype='<U1')"
+       "array([['1', '2', '6']], dtype='<U1')"
       ]
      },
      "execution_count": 5,
@@ -139,7 +147,7 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "[['6' '2' '6']]\n"
+      "[['1' '3' '0']]\n"
      ]
     }
    ],

docs/poli-docs/_build/.jupyter_cache/executed/f2885123d5acde20c7d317555d2324d1/base.ipynb → docs/poli-docs/_build/.jupyter_cache/executed/446bf9e357d4c8f4d26df02b81ac5e1a/base.ipynb

@@ -15,6 +15,31 @@
    "execution_count": 2,
    "metadata": {},
    "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "poli 🧪: creating environment poli__dockstring from dockstring/environment.yml\n"
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "poli 🧪: creating environment poli__dockstring from dockstring/environment.yml\n",
+      "poli 🧪: running registration of dockstring from environment poli__dockstring\n"
+     ]
+    },
+    {
+     "name": "stderr",
+     "output_type": "stream",
+     "text": [
+      "/Users/sjt972/Projects/poli/src/poli/core/registry.py:258: UserWarning: Environment poli__dockstring already exists. Will not create it.\n",
+      "  warnings.warn(f\"Environment {env_name} already exists. Will not create it.\")\n",
+      "/Users/sjt972/Projects/poli/src/poli/core/registry.py:269: UserWarning: Running the following command: conda run -n poli__dockstring python /Users/sjt972/Projects/poli/src/poli/objective_repository/dockstring/register.py. \n",
+      "  warnings.warn(\"Running the following command: %s. \" % command)\n"
+     ]
+    },
     {
      "name": "stdout",
      "output_type": "stream",
@@ -35,7 +60,7 @@
    "source": [
     "from poli import create\n",
     "\n",
-    "problem_info, f, x0, y0, _ = create(\n",
+    "f, x0, y0 = create(\n",
     "    name=\"dockstring\",\n",
     "    target_name=\"drd2\"  # The target protein.\n",
     ")"
@@ -117,7 +142,7 @@
     }
    ],
    "source": [
-    "problem_info, f_logp, x0_logp, y0_logp, _ = create(\n",
+    "f_logp, x0_logp, y0_logp = create(\n",
     "    name=\"rdkit_logp\"\n",
     ")"
    ]

docs/poli-docs/_build/.jupyter_cache/executed/337c7c885331149f43b36d28321ff9e7/base.ipynb → docs/poli-docs/_build/.jupyter_cache/executed/77a7224ddb3ccfbecfc8f0fd017624f9/base.ipynb

@@ -194,28 +194,12 @@
     ]
    },
    "outputs": [
-    {
-     "name": "stderr",
-     "output_type": "stream",
-     "text": [
-      "/Users/sjt972/anaconda3/envs/poli-docs/lib/python3.9/site-packages/tqdm/auto.py:21: TqdmWarning: IProgress not found. Please update jupyter and ipywidgets. See https://ipywidgets.readthedocs.io/en/stable/user_install.html\n",
-      "  from .autonotebook import tqdm as notebook_tqdm\n"
-     ]
-    },
-    {
-     "name": "stderr",
-     "output_type": "stream",
-     "text": [
-      "2023-12-22 12:10:31,253\tINFO util.py:154 -- Missing packages: ['ipywidgets']. Run `pip install -U ipywidgets`, then restart the notebook server for rich notebook output.\n"
-     ]
-    },
     {
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "WARNING:tensorflow:From /Users/sjt972/anaconda3/envs/poli-docs/lib/python3.9/site-packages/tensorflow/python/compat/v2_compat.py:108: disable_resource_variables (from tensorflow.python.ops.variable_scope) is deprecated and will be removed in a future version.\n",
-      "Instructions for updating:\n",
-      "non-resource variables are not supported in the long term\n"
+      "poli 🧪: Creating the objective from the repository.\n",
+      "poli 🧪: initializing the observer.\n"
      ]
     }
    ],
@@ -226,7 +210,7 @@
     "observer = SimpleObserver()\n",
     "\n",
     "# We instantiate the objective function\n",
-    "problem_info, f, x0, y0, _ = objective_factory.create(\n",
+    "f, x0, y0 = objective_factory.create(\n",
     "    name=\"aloha\",\n",
     "    observer=observer,\n",
     ")"