Updating tutorials to match version 3.0

Author: patronov

.idea/ReinventCommunity.iml

@@ -49,7 +49,6 @@ dependencies:
   - jupyter_console=6.1.0=py_1
   - jupyter_core=4.6.3=py37hc8dfbb8_1
   - kiwisolver=1.2.0=py37h99015e2_0
-  - ld_impl_linux-64=2.34=h53a641e_0
   - libblas=3.8.0=14_openblas
   - libcblas=3.8.0=14_openblas
   - libclang=9.0.1=default_hde54327_0
@@ -105,6 +104,7 @@ dependencies:
   - pyparsing=2.4.7=pyh9f0ad1d_0
   - pyqt=5.12.3=py37hcca6a23_1
   - pyrsistent=0.16.0=py37h8f50634_0
+  - pyspark
   - python=3.7.6=h8356626_5_cpython
   - python-dateutil=2.8.1=py_0
   - python_abi=3.7=1_cp37m

.idea/inspectionProfiles/profiles_settings.xml

@@ -5,10 +5,10 @@
    "metadata": {},
    "source": [
     "> **How to run this notebook (command-line)?**\n",
-    "1. Install the `reinvent_shared.v2.1` environment:\n",
-    "`conda env create -f reinvent_shared.yml`\n",
+    "1. Install the `ReinventCommunity` environment:\n",
+    "`conda env create -f environment.yml`\n",
     "2. Activate the environment:\n",
-    "`conda activate reinvent_shared.v2.1`\n",
+    "`conda activate ReinventCommunity`\n",
     "3. Execute `jupyter`:\n",
     "`jupyter notebook`\n",
     "4. Copy the link to a browser\n",
@@ -380,8 +380,8 @@
    "outputs": [],
    "source": [
     "configuration[\"parameters\"][\"reinforcement_learning\"] = {\n",
-    "    \"prior\": os.path.join(reinvent_dir, \"data/augmented.prior\"),\n",
-    "    \"agent\": os.path.join(reinvent_dir, \"data/augmented.prior\"),\n",
+    "    \"prior\": os.path.join(ipynb_path, \"models/augmented.prior\"),\n",
+    "    \"agent\": os.path.join(ipynb_path, \"models/augmented.prior\"),\n",
     "    \"n_steps\": 300,\n",
     "    \"sigma\": 128,\n",
     "    \"learning_rate\": 0.0001,\n",

.idea/misc.xml

@@ -5,10 +5,10 @@
    "metadata": {},
    "source": [
     "> **How to run this notebook (command-line)?**\n",
-    "1. Install the `reinvent_shared.v2.1` environment:\n",
-    "`conda env create -f reinvent_shared.yml`\n",
+    "1. Install the `ReinventCommunity` environment:\n",
+    "`conda env create -f environment.yml`\n",
     "2. Activate the environment:\n",
-    "`conda activate reinvent_shared.v2.1`\n",
+    "`conda activate ReinventCommunity`\n",
     "3. Execute `jupyter`:\n",
     "`jupyter notebook`\n",
     "4. Copy the link to a browser\n",
@@ -106,7 +106,7 @@
     "# provide your input dataset that will be used for training \n",
     "#we use a purged dataset provided with this repo\n",
     "\n",
-    "input_SMILES_path = os.path.join(reinvent_dir, \"data/chembl.filtered.smi\") \n",
+    "input_SMILES_path = os.path.join(ipynb_path, \"data/chembl.filtered.smi\") \n",
     "output_model_path = os.path.join(output_dir, \"empty_model.ckpt\")\n",
     "\n",
     "# add the \"parameters\" block\n",