edit ruff errors in nbs

ur-whitelab · Feb 22, 2025 · c4648c8 · c4648c8
1 parent a024bd0
commit c4648c8
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Showing 24 changed files with 48 additions and 54 deletions.
diff --git a/notebooks/experiments/Robustness/claude-3-5-sonnet-20240620/prompt10.ipynb b/notebooks/experiments/Robustness/claude-3-5-sonnet-20240620/prompt10.ipynb
@@ -7,8 +7,7 @@
    "outputs": [],
    "source": [
     "from mdcrow import MDCrow\n",
-    "import os \n",
-    "import mdtraj as md"
+    "import os "
    ]
   },
   {

diff --git a/notebooks/experiments/Robustness/claude-3-5-sonnet-20240620/prompt8.ipynb b/notebooks/experiments/Robustness/claude-3-5-sonnet-20240620/prompt8.ipynb
@@ -7,8 +7,7 @@
    "outputs": [],
    "source": [
     "from mdcrow import MDCrow\n",
-    "import os \n",
-    "import mdtraj as md"
+    "import os "
    ]
   },
   {

diff --git a/notebooks/experiments/Robustness/claude-3-5-sonnet-20240620/prompt9.ipynb b/notebooks/experiments/Robustness/claude-3-5-sonnet-20240620/prompt9.ipynb
@@ -7,8 +7,7 @@
    "outputs": [],
    "source": [
     "from mdcrow import MDCrow\n",
-    "import os \n",
-    "import mdtraj as md"
+    "import os "
    ]
   },
   {

diff --git a/notebooks/experiments/Robustness/claude-3-opus/prompt10.ipynb b/notebooks/experiments/Robustness/claude-3-opus/prompt10.ipynb
@@ -7,8 +7,7 @@
    "outputs": [],
    "source": [
     "from mdcrow import MDCrow\n",
-    "import os \n",
-    "import mdtraj as md"
+    "import os "
    ]
   },
   {

diff --git a/notebooks/experiments/Robustness/gpt-4o-2024-08-06/prompt1.ipynb b/notebooks/experiments/Robustness/gpt-4o-2024-08-06/prompt1.ipynb
@@ -150,7 +150,7 @@
    "source": [
     "import re\n",
     "import os\n",
-    "match = re.search(rf\"1LYZ_\\d+\", paths_and_descriptions)\n",
+    "match = re.search(r\"1LYZ_\\d+\", paths_and_descriptions)\n",
     "file_id = match.group(0)\n",
     "pdb_path = registry.get_mapped_path(file_id)\n",
     "assert os.path.exists(pdb_path)\n",
@@ -251,7 +251,7 @@
    "source": [
     "import re\n",
     "import os\n",
-    "match = re.search(rf\"1LYZ_\\d+\", paths_and_descriptions)\n",
+    "match = re.search(r\"1LYZ_\\d+\", paths_and_descriptions)\n",
     "file_id = match.group(0)\n",
     "pdb_path = registry.get_mapped_path(file_id)\n",
     "assert os.path.exists(pdb_path)\n",

diff --git a/notebooks/experiments/Robustness/gpt-4o-2024-08-06/prompt2.ipynb b/notebooks/experiments/Robustness/gpt-4o-2024-08-06/prompt2.ipynb
@@ -174,7 +174,7 @@
     "import os\n",
     "import re\n",
     "\n",
-    "match = re.search(rf\"1LYZ_\\d+\", paths_and_descriptions)\n",
+    "match = re.search(r\"1LYZ_\\d+\", paths_and_descriptions)\n",
     "file_id = match.group(0)\n",
     "pdb_path = registry.get_mapped_path(file_id)\n",
     "assert os.path.exists(pdb_path)\n",
@@ -327,7 +327,7 @@
     "import os\n",
     "import re\n",
     "\n",
-    "match = re.search(rf\"1LYZ_\\d+\", paths_and_descriptions)\n",
+    "match = re.search(r\"1LYZ_\\d+\", paths_and_descriptions)\n",
     "file_id = match.group(0)\n",
     "pdb_path = registry.get_mapped_path(file_id)\n",
     "assert os.path.exists(pdb_path)\n",

diff --git a/notebooks/experiments/Robustness/gpt-4o-2024-08-06/prompt4.ipynb b/notebooks/experiments/Robustness/gpt-4o-2024-08-06/prompt4.ipynb
@@ -8731,7 +8731,7 @@
    ],
    "source": [
     "from IPython.display import Image\n",
-    "match = re.search(rf\"fig0_\\d+\", paths_and_descriptions)\n",
+    "match = re.search(r\"fig0_\\d+\", paths_and_descriptions)\n",
     "fig_id = match.group(0)\n",
     "fig_path = registry.get_mapped_path(fig_id)\n",
     "assert os.path.exists(fig_path), \"This figure does not exist.\"\n",
@@ -16760,7 +16760,7 @@
    ],
    "source": [
     "from IPython.display import Image\n",
-    "match = re.search(rf\"fig0_\\d+\", paths_and_descriptions)\n",
+    "match = re.search(r\"fig0_\\d+\", paths_and_descriptions)\n",
     "fig_id = match.group(0)\n",
     "fig_path = registry.get_mapped_path(fig_id)\n",
     "assert os.path.exists(fig_path), \"This figure does not exist.\"\n",

diff --git a/notebooks/experiments/Robustness/llama-v3p1-405b-instruct/prompt1.ipynb b/notebooks/experiments/Robustness/llama-v3p1-405b-instruct/prompt1.ipynb
@@ -148,7 +148,7 @@
    "source": [
     "import re\n",
     "import os\n",
-    "match = re.search(rf\"1LYZ_\\d+\", paths_and_descriptions)\n",
+    "match = re.search(r\"1LYZ_\\d+\", paths_and_descriptions)\n",
     "file_id = match.group(0)\n",
     "pdb_path = registry.get_mapped_path(file_id)\n",
     "assert os.path.exists(pdb_path)\n",
@@ -255,7 +255,7 @@
    "source": [
     "import re\n",
     "import os\n",
-    "match = re.search(rf\"1LYZ_\\d+\", paths_and_descriptions)\n",
+    "match = re.search(r\"1LYZ_\\d+\", paths_and_descriptions)\n",
     "file_id = match.group(0)\n",
     "pdb_path = registry.get_mapped_path(file_id)\n",
     "assert os.path.exists(pdb_path)\n",

diff --git a/notebooks/experiments/Robustness/llama-v3p1-405b-instruct/prompt2.ipynb b/notebooks/experiments/Robustness/llama-v3p1-405b-instruct/prompt2.ipynb
@@ -188,7 +188,7 @@
     "import os\n",
     "import re\n",
     "\n",
-    "match = re.search(rf\"1LYZ_\\d+\", paths_and_descriptions)\n",
+    "match = re.search(r\"1LYZ_\\d+\", paths_and_descriptions)\n",
     "file_id = match.group(0)\n",
     "pdb_path = registry.get_mapped_path(file_id)\n",
     "assert os.path.exists(pdb_path)\n",
@@ -338,7 +338,7 @@
     "import os\n",
     "import re\n",
     "\n",
-    "match = re.search(rf\"1LYZ_\\d+\", paths_and_descriptions)\n",
+    "match = re.search(r\"1LYZ_\\d+\", paths_and_descriptions)\n",
     "file_id = match.group(0)\n",
     "pdb_path = registry.get_mapped_path(file_id)\n",
     "assert os.path.exists(pdb_path)\n",

diff --git a/notebooks/experiments/Robustness/llama-v3p1-405b-instruct/prompt4.ipynb b/notebooks/experiments/Robustness/llama-v3p1-405b-instruct/prompt4.ipynb
@@ -8825,7 +8825,7 @@
    ],
    "source": [
     "from IPython.display import Image\n",
-    "match = re.search(rf\"fig0_\\d+\", paths_and_descriptions)\n",
+    "match = re.search(r\"fig0_\\d+\", paths_and_descriptions)\n",
     "fig_id = match.group(0)\n",
     "fig_path = registry.get_mapped_path(fig_id)\n",
     "assert os.path.exists(fig_path), \"This figure does not exist.\"\n",
@@ -16984,7 +16984,7 @@
    ],
    "source": [
     "from IPython.display import Image\n",
-    "match = re.search(rf\"fig0_\\d+\", paths_and_descriptions)\n",
+    "match = re.search(r\"fig0_\\d+\", paths_and_descriptions)\n",
     "fig_id = match.group(0)\n",
     "fig_path = registry.get_mapped_path(fig_id)\n",
     "assert os.path.exists(fig_path), \"This figure does not exist.\"\n",

diff --git a/notebooks/experiments/main_experiments/gpt-4-1106-preview/exp_22.ipynb b/notebooks/experiments/main_experiments/gpt-4-1106-preview/exp_22.ipynb
@@ -102,7 +102,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 5,
+   "execution_count": null,
    "metadata": {},
    "outputs": [
     {
@@ -114,12 +114,12 @@
     }
    ],
    "source": [
+    "import mdtraj as md\n",
     "trajectory_path = registry.ckpt_dir + registry.get_mapped_path(\"rec0_114115\").split(\"ckpt_66\")[1]\n",
     "topology_path = registry.ckpt_dir + registry.get_mapped_path(\"top_sim0_114113\").split(\"ckpt_66\")[1]\n",
     "assert os.path.exists(trajectory_path), \"Trajectory file not found\"\n",
     "assert os.path.exists(topology_path), \"Topology file not found\"\n",
     "\n",
-    "import mdtraj as md\n",
     "traj = md.load(trajectory_path, top=topology_path)\n",
     "print(f\"Simulation with :{traj.n_atoms} for {traj.n_frames} frames.\")"
    ]

diff --git a/notebooks/experiments/main_experiments/gpt-4-turbo-2024-04-09/exp_22.ipynb b/notebooks/experiments/main_experiments/gpt-4-turbo-2024-04-09/exp_22.ipynb
@@ -226,7 +226,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 5,
+   "execution_count": null,
    "metadata": {},
    "outputs": [
     {
@@ -238,12 +238,13 @@
     }
    ],
    "source": [
+    "import mdtraj as md\n",
+    "\n",
     "trajectory_path = registry.get_mapped_path(\"rec0_215117\")\n",
     "topology_path = registry.get_mapped_path(\"top_sim0_215114\")\n",
     "assert os.path.exists(trajectory_path), \"Trajectory file not found\"\n",
     "assert os.path.exists(topology_path), \"Topology file not found\"\n",
     "\n",
-    "import mdtraj as md\n",
     "traj = md.load(trajectory_path, top=topology_path)\n",
     "print(f\"Simulation with :{traj.n_atoms} for {traj.n_frames} frames. Total time: {traj.time[-1]*0.002} ps\")"
    ]

diff --git a/.../gpt-4-turbo-2024-04-09/exp_25 copy.ipynb → ...ments/gpt-4-turbo-2024-04-09/exp_25.ipynb b/.../gpt-4-turbo-2024-04-09/exp_25 copy.ipynb → ...ments/gpt-4-turbo-2024-04-09/exp_25.ipynb
@@ -322,7 +322,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 8,
+   "execution_count": null,
    "metadata": {},
    "outputs": [
     {
@@ -339,7 +339,7 @@
    ],
    "source": [
     "from IPython.display import Image\n",
-    "Image(filename=path_oxygenated)"
+    "Image(filename=path_oxygenated) # noqa: F821 - ignore this ruff error"
    ]
   },
   {

diff --git a/notebooks/experiments/main_experiments/gpt-4o-2024-08-06/exp_10.ipynb b/notebooks/experiments/main_experiments/gpt-4o-2024-08-06/exp_10.ipynb
@@ -172,7 +172,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 10,
+   "execution_count": null,
    "id": "4b9220de-6a3c-4db9-8768-68298ece63a6",
    "metadata": {},
    "outputs": [
@@ -196,10 +196,11 @@
     }
    ],
    "source": [
+    "from IPython.display import Image\n",
+    "\n",
     "rmsd_path_ = registry.get_mapped_path(\"fig0_043015\")\n",
     "path = '/Users/jorgemedina/Desktop/md-agent/ckpt/ckpt_29' + rmsd_path_.split(\"ckpt/ckpt_29\")[1]\n",
     "print(path)\n",
-    "from IPython.display import Image\n",
     "Image(path)"
    ]
   },

diff --git a/notebooks/experiments/main_experiments/gpt-4o-2024-08-06/exp_11.ipynb b/notebooks/experiments/main_experiments/gpt-4o-2024-08-06/exp_11.ipynb
@@ -1,16 +1,5 @@
 {
  "cells": [
-  {
-   "cell_type": "code",
-   "execution_count": 1,
-   "id": "b0fcba3a",
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "import time \n",
-    "# time.sleep(4000)"
-   ]
-  },
   {
    "cell_type": "code",
    "execution_count": 2,

diff --git a/notebooks/experiments/main_experiments/gpt-4o-2024-08-06/exp_13.ipynb b/notebooks/experiments/main_experiments/gpt-4o-2024-08-06/exp_13.ipynb
@@ -195,7 +195,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 10,
+   "execution_count": null,
    "id": "21b81076",
    "metadata": {},
    "outputs": [
@@ -212,6 +212,8 @@
     }
    ],
    "source": [
+    "from IPython.display import Image\n",
+    "\n",
     "path1_ = registry.get_mapped_path(\"fig0_180235\")\n",
     "path2_ = registry.get_mapped_path(\"fig0_180233\")\n",
     "path3_ = registry.get_mapped_path(\"fig0_180237\")\n",
@@ -222,7 +224,6 @@
     "path_3 = '/Users/jorgemedina/Desktop/md-agent/ckpt/ckpt_32' + path3_.split(\"ckpt/ckpt_32\")[1]\n",
     "path_4 = '/Users/jorgemedina/Desktop/md-agent/ckpt/ckpt_32' + path4_.split(\"ckpt/ckpt_32\")[1]\n",
     "\n",
-    "from IPython.display import Image\n",
     "Image(filename=path_1)"
    ]
   },

diff --git a/notebooks/experiments/main_experiments/gpt-4o-2024-08-06/exp_15.ipynb b/notebooks/experiments/main_experiments/gpt-4o-2024-08-06/exp_15.ipynb
@@ -415,7 +415,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 7,
+   "execution_count": null,
    "metadata": {},
    "outputs": [
     {
@@ -431,8 +431,8 @@
     }
    ],
    "source": [
-    "path_ = registry.get_mapped_path(\"fig0_162840\") + '.png'\n",
     "from IPython.display import Image\n",
+    "path_ = registry.get_mapped_path(\"fig0_162840\") + '.png'\n",
     "Image(filename=path_)"
    ]
   },

diff --git a/notebooks/experiments/main_experiments/gpt-4o-2024-08-06/exp_22.ipynb b/notebooks/experiments/main_experiments/gpt-4o-2024-08-06/exp_22.ipynb
@@ -100,7 +100,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 5,
+   "execution_count": null,
    "metadata": {},
    "outputs": [
     {
@@ -112,12 +112,13 @@
     }
    ],
    "source": [
+    "import mdtraj as md\n",
+    "\n",
     "trajectory_path = registry.ckpt_dir + registry.get_mapped_path(\"rec0_111845\").split(\"ckpt_41\")[1]\n",
     "topology_path = registry.ckpt_dir + registry.get_mapped_path(\"top_sim0_111844\").split(\"ckpt_41\")[1]\n",
     "assert os.path.exists(trajectory_path), \"Trajectory file not found\"\n",
     "assert os.path.exists(topology_path), \"Topology file not found\"\n",
     "\n",
-    "import mdtraj as md\n",
     "traj = md.load(trajectory_path, top=topology_path)\n",
     "print(f\"Simulation with :{traj.n_atoms} for {traj.n_frames} frames.\")"
    ]

diff --git a/notebooks/experiments/main_experiments/gpt-4o-2024-08-06/exp_23.ipynb b/notebooks/experiments/main_experiments/gpt-4o-2024-08-06/exp_23.ipynb
@@ -161,7 +161,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 7,
+   "execution_count": null,
    "metadata": {},
    "outputs": [
     {
@@ -177,9 +177,9 @@
     }
    ],
    "source": [
+    "from IPython.display import Image\n",
     "rdf_path = registry.get_mapped_path(\"fig0_113444\")\n",
     "rdf_path = '/Users/jorgemedina/Desktop/md-agent/ckpt/ckpt_42' + rdf_path.split(\"ckpt/ckpt_42\")[1]\n",
-    "from IPython.display import Image\n",
     "Image(filename=rdf_path)"
    ]
   },

diff --git a/notebooks/experiments/main_experiments/gpt-4o-2024-08-06/exp_24.ipynb b/notebooks/experiments/main_experiments/gpt-4o-2024-08-06/exp_24.ipynb
@@ -133,7 +133,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 8,
+   "execution_count": null,
    "metadata": {},
    "outputs": [
     {
@@ -145,14 +145,15 @@
     }
    ],
    "source": [
+    "import mdtraj as md\n",
+    "\n",
     "trajectory_path = registry.get_mapped_path(\"rec0_104757\")\n",
     "topology_path = registry.get_mapped_path(\"top_sim0_104753\")\n",
     "trajectory_path = '/Users/jorgemedina/Desktop/md-agent/ckpt/ckpt_44' + trajectory_path.split('ckpt/ckpt_44')[1]\n",
     "topology_path = '/Users/jorgemedina/Desktop/md-agent/ckpt/ckpt_44' + topology_path.split('ckpt/ckpt_44')[1]\n",
     "assert os.path.exists(trajectory_path), \"Trajectory file not found\"\n",
     "assert os.path.exists(topology_path), \"Topology file not found\"\n",
     "\n",
-    "import mdtraj as md\n",
     "traj = md.load(trajectory_path, top=topology_path)\n",
     "print(f\"Simulation with :{traj.n_atoms} for {traj.n_frames} frames.\")"
    ]

diff --git a/notebooks/experiments/main_experiments/llama-v3p1-405b-instruct/exp_1.ipynb b/notebooks/experiments/main_experiments/llama-v3p1-405b-instruct/exp_1.ipynb
@@ -431,7 +431,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 17,
+   "execution_count": null,
    "metadata": {},
    "outputs": [
     {
@@ -447,6 +447,7 @@
     }
    ],
    "source": [
+    "from IPython.display import Image\n",
     "Image(filename=path1)"
    ]
   },