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datamol-io · Oct 27, 2023 · af88fcc · af88fcc
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diff --git a/docs/tutorials/design-with-safe.ipynb b/docs/tutorials/design-with-safe.ipynb
@@ -7,47 +7,49 @@
    "outputs": [],
    "source": [
     "%load_ext autoreload\n",
-    "%autoreload 2"
-   ]
-  },
-  {
-   "cell_type": "markdown",
-   "metadata": {},
-   "source": [
-    "!!! info\n",
-    "\n",
-    "    Pretrained checkpoint for autoregressive only models are available at : `gs://valence-experiments/safe/generative-model/`"
+    "%autoreload 2\n"
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": 2,
+   "execution_count": 1,
    "metadata": {},
    "outputs": [],
    "source": [
     "import os\n",
-    "os.environ[\"TOKENIZERS_PARALLELISM\"] = \"false\""
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": 3,
-   "metadata": {},
-   "outputs": [],
-   "source": [
+    "\n",
+    "\n",
+    "os.environ[\"TOKENIZERS_PARALLELISM\"] = \"false\"\n",
+    "\n",
+    "\n",
     "import safe as sf\n",
-    "import datamol as dm\n",
-    "from safe.trainer.data_utils import get_dataset\n",
-    "from safe import SAFEDesign"
+    "import datamol as dm\n"
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": 4,
+   "execution_count": 2,
    "metadata": {},
-   "outputs": [],
+   "outputs": [
+    {
+     "ename": "HFValidationError",
+     "evalue": "Repo id must be in the form 'repo_name' or 'namespace/repo_name': '/home/hadim/.cache/safe/default_model'. Use `repo_type` argument if needed.",
+     "output_type": "error",
+     "traceback": [
+      "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
+      "\u001b[0;31mHFValidationError\u001b[0m                         Traceback (most recent call last)",
+      "\u001b[1;32m/home/hadim/Code/valence/Libs/safe/docs/tutorials/design-with-safe.ipynb Cell 3\u001b[0m line \u001b[0;36m1\n\u001b[0;32m----> <a href='vscode-notebook-cell:/home/hadim/Code/valence/Libs/safe/docs/tutorials/design-with-safe.ipynb#W4sZmlsZQ%3D%3D?line=0'>1</a>\u001b[0m designer \u001b[39m=\u001b[39m sf\u001b[39m.\u001b[39;49mSAFEDesign\u001b[39m.\u001b[39;49mload_default(verbose\u001b[39m=\u001b[39;49m\u001b[39mTrue\u001b[39;49;00m)\n",
+      "File \u001b[0;32m~/Code/valence/Libs/safe/safe/sample.py:89\u001b[0m, in \u001b[0;36mSAFEDesign.load_default\u001b[0;34m(cls, verbose, model_dir, device)\u001b[0m\n\u001b[1;32m     87\u001b[0m \u001b[39mif\u001b[39;00m model_dir \u001b[39mis\u001b[39;00m \u001b[39mNone\u001b[39;00m \u001b[39mor\u001b[39;00m \u001b[39mnot\u001b[39;00m model_dir:\n\u001b[1;32m     88\u001b[0m     model_dir \u001b[39m=\u001b[39m \u001b[39mcls\u001b[39m\u001b[39m.\u001b[39m_DEFAULT_MODEL_PATH\n\u001b[0;32m---> 89\u001b[0m model \u001b[39m=\u001b[39m SAFEDoubleHeadsModel\u001b[39m.\u001b[39;49mfrom_pretrained(model_dir)\n\u001b[1;32m     90\u001b[0m tokenizer \u001b[39m=\u001b[39m SAFETokenizer\u001b[39m.\u001b[39mload(os\u001b[39m.\u001b[39mpath\u001b[39m.\u001b[39mjoin(model_dir, \u001b[39m\"\u001b[39m\u001b[39mtokenizer.json\u001b[39m\u001b[39m\"\u001b[39m))\n\u001b[1;32m     91\u001b[0m gen_config \u001b[39m=\u001b[39m GenerationConfig\u001b[39m.\u001b[39mfrom_pretrained(model_dir)\n",
+      "File \u001b[0;32m~/local/micromamba/envs/safe/lib/python3.11/site-packages/transformers/modeling_utils.py:2507\u001b[0m, in \u001b[0;36mPreTrainedModel.from_pretrained\u001b[0;34m(cls, pretrained_model_name_or_path, config, cache_dir, ignore_mismatched_sizes, force_download, local_files_only, token, revision, use_safetensors, *model_args, **kwargs)\u001b[0m\n\u001b[1;32m   2504\u001b[0m \u001b[39mif\u001b[39;00m commit_hash \u001b[39mis\u001b[39;00m \u001b[39mNone\u001b[39;00m:\n\u001b[1;32m   2505\u001b[0m     \u001b[39mif\u001b[39;00m \u001b[39mnot\u001b[39;00m \u001b[39misinstance\u001b[39m(config, PretrainedConfig):\n\u001b[1;32m   2506\u001b[0m         \u001b[39m# We make a call to the config file first (which may be absent) to get the commit hash as soon as possible\u001b[39;00m\n\u001b[0;32m-> 2507\u001b[0m         resolved_config_file \u001b[39m=\u001b[39m cached_file(\n\u001b[1;32m   2508\u001b[0m             pretrained_model_name_or_path,\n\u001b[1;32m   2509\u001b[0m             CONFIG_NAME,\n\u001b[1;32m   2510\u001b[0m             cache_dir\u001b[39m=\u001b[39;49mcache_dir,\n\u001b[1;32m   2511\u001b[0m             force_download\u001b[39m=\u001b[39;49mforce_download,\n\u001b[1;32m   2512\u001b[0m             resume_download\u001b[39m=\u001b[39;49mresume_download,\n\u001b[1;32m   2513\u001b[0m             proxies\u001b[39m=\u001b[39;49mproxies,\n\u001b[1;32m   2514\u001b[0m             local_files_only\u001b[39m=\u001b[39;49mlocal_files_only,\n\u001b[1;32m   2515\u001b[0m             token\u001b[39m=\u001b[39;49mtoken,\n\u001b[1;32m   2516\u001b[0m             revision\u001b[39m=\u001b[39;49mrevision,\n\u001b[1;32m   2517\u001b[0m             subfolder\u001b[39m=\u001b[39;49msubfolder,\n\u001b[1;32m   2518\u001b[0m             _raise_exceptions_for_missing_entries\u001b[39m=\u001b[39;49m\u001b[39mFalse\u001b[39;49;00m,\n\u001b[1;32m   2519\u001b[0m             _raise_exceptions_for_connection_errors\u001b[39m=\u001b[39;49m\u001b[39mFalse\u001b[39;49;00m,\n\u001b[1;32m   2520\u001b[0m         )\n\u001b[1;32m   2521\u001b[0m         commit_hash \u001b[39m=\u001b[39m extract_commit_hash(resolved_config_file, commit_hash)\n\u001b[1;32m   2522\u001b[0m     \u001b[39melse\u001b[39;00m:\n",
+      "File \u001b[0;32m~/local/micromamba/envs/safe/lib/python3.11/site-packages/transformers/utils/hub.py:429\u001b[0m, in \u001b[0;36mcached_file\u001b[0;34m(path_or_repo_id, filename, cache_dir, force_download, resume_download, proxies, token, revision, local_files_only, subfolder, repo_type, user_agent, _raise_exceptions_for_missing_entries, _raise_exceptions_for_connection_errors, _commit_hash, **deprecated_kwargs)\u001b[0m\n\u001b[1;32m    426\u001b[0m user_agent \u001b[39m=\u001b[39m http_user_agent(user_agent)\n\u001b[1;32m    427\u001b[0m \u001b[39mtry\u001b[39;00m:\n\u001b[1;32m    428\u001b[0m     \u001b[39m# Load from URL or cache if already cached\u001b[39;00m\n\u001b[0;32m--> 429\u001b[0m     resolved_file \u001b[39m=\u001b[39m hf_hub_download(\n\u001b[1;32m    430\u001b[0m         path_or_repo_id,\n\u001b[1;32m    431\u001b[0m         filename,\n\u001b[1;32m    432\u001b[0m         subfolder\u001b[39m=\u001b[39;49m\u001b[39mNone\u001b[39;49;00m \u001b[39mif\u001b[39;49;00m \u001b[39mlen\u001b[39;49m(subfolder) \u001b[39m==\u001b[39;49m \u001b[39m0\u001b[39;49m \u001b[39melse\u001b[39;49;00m subfolder,\n\u001b[1;32m    433\u001b[0m         repo_type\u001b[39m=\u001b[39;49mrepo_type,\n\u001b[1;32m    434\u001b[0m         revision\u001b[39m=\u001b[39;49mrevision,\n\u001b[1;32m    435\u001b[0m         cache_dir\u001b[39m=\u001b[39;49mcache_dir,\n\u001b[1;32m    436\u001b[0m         user_agent\u001b[39m=\u001b[39;49muser_agent,\n\u001b[1;32m    437\u001b[0m         force_download\u001b[39m=\u001b[39;49mforce_download,\n\u001b[1;32m    438\u001b[0m         proxies\u001b[39m=\u001b[39;49mproxies,\n\u001b[1;32m    439\u001b[0m         resume_download\u001b[39m=\u001b[39;49mresume_download,\n\u001b[1;32m    440\u001b[0m         token\u001b[39m=\u001b[39;49mtoken,\n\u001b[1;32m    441\u001b[0m         local_files_only\u001b[39m=\u001b[39;49mlocal_files_only,\n\u001b[1;32m    442\u001b[0m     )\n\u001b[1;32m    443\u001b[0m \u001b[39mexcept\u001b[39;00m GatedRepoError \u001b[39mas\u001b[39;00m e:\n\u001b[1;32m    444\u001b[0m     \u001b[39mraise\u001b[39;00m \u001b[39mEnvironmentError\u001b[39;00m(\n\u001b[1;32m    445\u001b[0m         \u001b[39m\"\u001b[39m\u001b[39mYou are trying to access a gated repo.\u001b[39m\u001b[39m\\n\u001b[39;00m\u001b[39mMake sure to request access at \u001b[39m\u001b[39m\"\u001b[39m\n\u001b[1;32m    446\u001b[0m         \u001b[39mf\u001b[39m\u001b[39m\"\u001b[39m\u001b[39mhttps://huggingface.co/\u001b[39m\u001b[39m{\u001b[39;00mpath_or_repo_id\u001b[39m}\u001b[39;00m\u001b[39m and pass a token having permission to this repo either \u001b[39m\u001b[39m\"\u001b[39m\n\u001b[1;32m    447\u001b[0m         \u001b[39m\"\u001b[39m\u001b[39mby logging in with `huggingface-cli login` or by passing `token=<your_token>`.\u001b[39m\u001b[39m\"\u001b[39m\n\u001b[1;32m    448\u001b[0m     ) \u001b[39mfrom\u001b[39;00m \u001b[39me\u001b[39;00m\n",
+      "File \u001b[0;32m~/local/micromamba/envs/safe/lib/python3.11/site-packages/huggingface_hub/utils/_validators.py:110\u001b[0m, in \u001b[0;36mvalidate_hf_hub_args.<locals>._inner_fn\u001b[0;34m(*args, **kwargs)\u001b[0m\n\u001b[1;32m    105\u001b[0m \u001b[39mfor\u001b[39;00m arg_name, arg_value \u001b[39min\u001b[39;00m chain(\n\u001b[1;32m    106\u001b[0m     \u001b[39mzip\u001b[39m(signature\u001b[39m.\u001b[39mparameters, args),  \u001b[39m# Args values\u001b[39;00m\n\u001b[1;32m    107\u001b[0m     kwargs\u001b[39m.\u001b[39mitems(),  \u001b[39m# Kwargs values\u001b[39;00m\n\u001b[1;32m    108\u001b[0m ):\n\u001b[1;32m    109\u001b[0m     \u001b[39mif\u001b[39;00m arg_name \u001b[39min\u001b[39;00m [\u001b[39m\"\u001b[39m\u001b[39mrepo_id\u001b[39m\u001b[39m\"\u001b[39m, \u001b[39m\"\u001b[39m\u001b[39mfrom_id\u001b[39m\u001b[39m\"\u001b[39m, \u001b[39m\"\u001b[39m\u001b[39mto_id\u001b[39m\u001b[39m\"\u001b[39m]:\n\u001b[0;32m--> 110\u001b[0m         validate_repo_id(arg_value)\n\u001b[1;32m    112\u001b[0m     \u001b[39melif\u001b[39;00m arg_name \u001b[39m==\u001b[39m \u001b[39m\"\u001b[39m\u001b[39mtoken\u001b[39m\u001b[39m\"\u001b[39m \u001b[39mand\u001b[39;00m arg_value \u001b[39mis\u001b[39;00m \u001b[39mnot\u001b[39;00m \u001b[39mNone\u001b[39;00m:\n\u001b[1;32m    113\u001b[0m         has_token \u001b[39m=\u001b[39m \u001b[39mTrue\u001b[39;00m\n",
+      "File \u001b[0;32m~/local/micromamba/envs/safe/lib/python3.11/site-packages/huggingface_hub/utils/_validators.py:158\u001b[0m, in \u001b[0;36mvalidate_repo_id\u001b[0;34m(repo_id)\u001b[0m\n\u001b[1;32m    155\u001b[0m     \u001b[39mraise\u001b[39;00m HFValidationError(\u001b[39mf\u001b[39m\u001b[39m\"\u001b[39m\u001b[39mRepo id must be a string, not \u001b[39m\u001b[39m{\u001b[39;00m\u001b[39mtype\u001b[39m(repo_id)\u001b[39m}\u001b[39;00m\u001b[39m: \u001b[39m\u001b[39m'\u001b[39m\u001b[39m{\u001b[39;00mrepo_id\u001b[39m}\u001b[39;00m\u001b[39m'\u001b[39m\u001b[39m.\u001b[39m\u001b[39m\"\u001b[39m)\n\u001b[1;32m    157\u001b[0m \u001b[39mif\u001b[39;00m repo_id\u001b[39m.\u001b[39mcount(\u001b[39m\"\u001b[39m\u001b[39m/\u001b[39m\u001b[39m\"\u001b[39m) \u001b[39m>\u001b[39m \u001b[39m1\u001b[39m:\n\u001b[0;32m--> 158\u001b[0m     \u001b[39mraise\u001b[39;00m HFValidationError(\n\u001b[1;32m    159\u001b[0m         \u001b[39m\"\u001b[39m\u001b[39mRepo id must be in the form \u001b[39m\u001b[39m'\u001b[39m\u001b[39mrepo_name\u001b[39m\u001b[39m'\u001b[39m\u001b[39m or \u001b[39m\u001b[39m'\u001b[39m\u001b[39mnamespace/repo_name\u001b[39m\u001b[39m'\u001b[39m\u001b[39m:\u001b[39m\u001b[39m\"\u001b[39m\n\u001b[1;32m    160\u001b[0m         \u001b[39mf\u001b[39m\u001b[39m\"\u001b[39m\u001b[39m \u001b[39m\u001b[39m'\u001b[39m\u001b[39m{\u001b[39;00mrepo_id\u001b[39m}\u001b[39;00m\u001b[39m'\u001b[39m\u001b[39m. Use `repo_type` argument if needed.\u001b[39m\u001b[39m\"\u001b[39m\n\u001b[1;32m    161\u001b[0m     )\n\u001b[1;32m    163\u001b[0m \u001b[39mif\u001b[39;00m \u001b[39mnot\u001b[39;00m REPO_ID_REGEX\u001b[39m.\u001b[39mmatch(repo_id):\n\u001b[1;32m    164\u001b[0m     \u001b[39mraise\u001b[39;00m HFValidationError(\n\u001b[1;32m    165\u001b[0m         \u001b[39m\"\u001b[39m\u001b[39mRepo id must use alphanumeric chars or \u001b[39m\u001b[39m'\u001b[39m\u001b[39m-\u001b[39m\u001b[39m'\u001b[39m\u001b[39m, \u001b[39m\u001b[39m'\u001b[39m\u001b[39m_\u001b[39m\u001b[39m'\u001b[39m\u001b[39m, \u001b[39m\u001b[39m'\u001b[39m\u001b[39m.\u001b[39m\u001b[39m'\u001b[39m\u001b[39m, \u001b[39m\u001b[39m'\u001b[39m\u001b[39m--\u001b[39m\u001b[39m'\u001b[39m\u001b[39m and \u001b[39m\u001b[39m'\u001b[39m\u001b[39m..\u001b[39m\u001b[39m'\u001b[39m\u001b[39m are\u001b[39m\u001b[39m\"\u001b[39m\n\u001b[1;32m    166\u001b[0m         \u001b[39m\"\u001b[39m\u001b[39m forbidden, \u001b[39m\u001b[39m'\u001b[39m\u001b[39m-\u001b[39m\u001b[39m'\u001b[39m\u001b[39m and \u001b[39m\u001b[39m'\u001b[39m\u001b[39m.\u001b[39m\u001b[39m'\u001b[39m\u001b[39m cannot start or end the name, max length is 96:\u001b[39m\u001b[39m\"\u001b[39m\n\u001b[1;32m    167\u001b[0m         \u001b[39mf\u001b[39m\u001b[39m\"\u001b[39m\u001b[39m \u001b[39m\u001b[39m'\u001b[39m\u001b[39m{\u001b[39;00mrepo_id\u001b[39m}\u001b[39;00m\u001b[39m'\u001b[39m\u001b[39m.\u001b[39m\u001b[39m\"\u001b[39m\n\u001b[1;32m    168\u001b[0m     )\n",
+      "\u001b[0;31mHFValidationError\u001b[0m: Repo id must be in the form 'repo_name' or 'namespace/repo_name': '/home/hadim/.cache/safe/default_model'. Use `repo_type` argument if needed."
+     ]
+    }
+   ],
    "source": [
-    "designer = SAFEDesign.load_default(verbose=True)"
+    "designer = sf.SAFEDesign.load_default(verbose=True)\n"
    ]
   },
   {
@@ -182,7 +184,7 @@
     }
    ],
    "source": [
-    "dm.to_image(dm.to_mol(candidate_mol))"
+    "dm.to_image(dm.to_mol(candidate_mol))\n"
    ]
   },
   {
@@ -191,7 +193,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "N_SAMPLES = 100"
+    "N_SAMPLES = 100\n"
    ]
   },
   {
@@ -217,7 +219,7 @@
     }
    ],
    "source": [
-    "generated = designer.de_novo_generation(sanitize=True, n_samples_per_trial=N_SAMPLES)"
+    "generated = designer.de_novo_generation(sanitize=True, n_samples_per_trial=N_SAMPLES)\n"
    ]
   },
   {
@@ -1631,7 +1633,7 @@
     }
    ],
    "source": [
-    "dm.to_image(generated[:20])"
+    "dm.to_image(generated[:20])\n"
    ]
   },
   {
@@ -1708,7 +1710,7 @@
     }
    ],
    "source": [
-    "dm.to_image(scaffold)"
+    "dm.to_image(scaffold)\n"
    ]
   },
   {
@@ -1725,7 +1727,7 @@
     }
    ],
    "source": [
-    "generated = designer.scaffold_decoration(scaffold=scaffold, n_samples_per_trial=N_SAMPLES, n_trials=2, sanitize=True, do_not_fragment_further=True)"
+    "generated = designer.scaffold_decoration(scaffold=scaffold, n_samples_per_trial=N_SAMPLES, n_trials=2, sanitize=True, do_not_fragment_further=True)\n"
    ]
   },
   {
@@ -5994,7 +5996,7 @@
     }
    ],
    "source": [
-    "dm.viz.lasso_highlight_image([dm.to_mol(x) for x in generated[:20]], dm.from_smarts(scaffold))"
+    "dm.viz.lasso_highlight_image([dm.to_mol(x) for x in generated[:20]], dm.from_smarts(scaffold))\n"
    ]
   },
   {
@@ -6059,7 +6061,7 @@
     }
    ],
    "source": [
-    "dm.to_image(superstructure)"
+    "dm.to_image(superstructure)\n"
    ]
   },
   {
@@ -6077,7 +6079,7 @@
    ],
    "source": [
     "generated = designer.super_structure(core=superstructure, n_samples_per_trial=N_SAMPLES, n_trials=1, sanitize=True, do_not_fragment_further=False, attachment_point_depth=3)\n",
-    "#generated"
+    "#generated\n"
    ]
   },
   {
@@ -7225,7 +7227,7 @@
     }
    ],
    "source": [
-    "dm.to_image(generated[:20])"
+    "dm.to_image(generated[:20])\n"
    ]
   },
   {
@@ -7277,7 +7279,7 @@
     }
    ],
    "source": [
-    "dm.to_image(motif)"
+    "dm.to_image(motif)\n"
    ]
   },
   {
@@ -7295,7 +7297,7 @@
    ],
    "source": [
     "# let's make some long sequence\n",
-    "generated = designer.motif_extension(motif=motif, n_samples_per_trial=N_SAMPLES, n_trials=1, sanitize=True, do_not_fragment_further=False, min_length=25, max_length=80)"
+    "generated = designer.motif_extension(motif=motif, n_samples_per_trial=N_SAMPLES, n_trials=1, sanitize=True, do_not_fragment_further=False, min_length=25, max_length=80)\n"
    ]
   },
   {
@@ -8451,7 +8453,7 @@
     }
    ],
    "source": [
-    "dm.to_image(generated[:20])"
+    "dm.to_image(generated[:20])\n"
    ]
   },
   {
@@ -8541,7 +8543,7 @@
     }
    ],
    "source": [
-    "dm.to_image(side_chains)"
+    "dm.to_image(side_chains)\n"
    ]
   },
   {
@@ -10006,7 +10008,7 @@
    ],
    "source": [
     "generated = designer.scaffold_morphing(side_chains=side_chains, n_samples_per_trial=N_SAMPLES, n_trials=1, sanitize=True, do_not_fragment_further=False, random_seed=100)\n",
-    "dm.to_image(generated[:20])"
+    "dm.to_image(generated[:20])\n"
    ]
   },
   {
@@ -10112,7 +10114,7 @@
     }
    ],
    "source": [
-    "dm.to_image(linker_generation)"
+    "dm.to_image(linker_generation)\n"
    ]
   },
   {
@@ -12320,7 +12322,7 @@
    ],
    "source": [
     "generated = designer.linker_generation(*linker_generation, n_samples_per_trial=N_SAMPLES, n_trials=1, sanitize=True, do_not_fragment_further=False, random_seed=100)\n",
-    "dm.to_image(generated[:20])"
+    "dm.to_image(generated[:20])\n"
    ]
   }
  ],
@@ -12340,7 +12342,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.11.4"
+   "version": "3.11.6"
   },
   "orig_nbformat": 4
  },