Fixed file paths

aspuru-guzik-group · Aug 11, 2022 · f867fe8 · f867fe8
1 parent ee3d602
commit f867fe8
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Showing 3 changed files with 14 additions and 14 deletions.
diff --git a/models_jupyter/hill-climbing.ipynb b/models_jupyter/hill-climbing.ipynb
@@ -15,9 +15,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "%%sh\n",
-    "git clone https://github.com/gkwt/hill-climbing-lstm.git\n",
-    "cd hill-climbing-lstm"
+    "!git clone https://github.com/gkwt/hill-climbing-lstm.git"
    ]
   },
   {
@@ -34,7 +32,9 @@
    "outputs": [],
    "source": [
     "import sys, os\n",
-    "sys.path.append('../..')\n",
+    "ROOT_DIR = '..'\n",
+    "sys.path.append(ROOT_DIR)\n",
+    "sys.path.append('hill-climbing-lstm')\n",
     "\n",
     "from tartarus import pce\n",
     "\n",
@@ -87,12 +87,12 @@
    "outputs": [],
    "source": [
     "# define parameters\n",
-    "data_path       = '../../datasets/hce.csv'\n",
+    "data_path       = os.path.join(ROOT_DIR, 'datasets/hce.csv')\n",
     "string_type     = 'selfies' # 'smiles'\n",
     "num_workers     = 6\n",
     "\n",
     "# get the data\n",
-    "smi_list, sfs_list = utils.get_lists(data_path, sep=',', header=1, smiles_name='smiles')\n",
+    "smi_list, sfs_list = utils.get_lists(data_path, sep=',', header='infer', smiles_name='smiles')\n",
     "if string_type == 'selfies':\n",
     "    str_list = sfs_list\n",
     "    dm = SELFIESDataModule(str_list, batch_size = 128, num_workers = num_workers)\n",

diff --git a/models_jupyter/janus.ipynb b/models_jupyter/janus.ipynb
@@ -13,8 +13,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "%%sh\n",
-    "pip install janus-ga"
+    "!pip install janus-ga"
    ]
   },
   {

diff --git a/models_jupyter/reinvent.ipynb b/models_jupyter/reinvent.ipynb
@@ -15,9 +15,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "%%sh\n",
-    "git clone https://github.com/gkwt/reinvent-benchmarking.git\n",
-    "cd reinvent-benchmarking"
+    "!git clone https://github.com/gkwt/reinvent-benchmarking.git"
    ]
   },
   {
@@ -41,7 +39,10 @@
    "outputs": [],
    "source": [
     "import sys, os\n",
-    "sys.path.append('../..')\n",
+    "ROOT_DIR = '..'\n",
+    "sys.path.append(ROOT_DIR)\n",
+    "sys.path.append('reinvent-benchmarking')\n",
+    "\n",
     "\n",
     "from tartarus import pce\n",
     "\n",
@@ -85,10 +86,10 @@
    "outputs": [],
    "source": [
     "\n",
-    "data_path = '../../datasets'\n",
+    "data_path = os.path.join(ROOT_DIR, 'datasets')\n",
     "filename = 'hce.csv'\n",
     "sep = ','\n",
-    "header = 1\n",
+    "header = 'infer'\n",
     "smile_name = 'smiles'\n",
     "\n",
     "# dataset load\n",