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Merge pull request #58 from datamol-io/wandb-load
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Load from wandb
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@maclandrol
maclandrol authored Sep 10, 2024
2 parents f28b97a + e7cf16b commit e9f2f63
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322 changes: 322 additions & 0 deletions docs/tutorials/load-from-wandb.ipynb
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"source": [
"%load_ext autoreload\n",
"%autoreload 2"
]
},
{
"cell_type": "code",
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"metadata": {},
"outputs": [],
"source": [
"from safe.sample import SAFEDesign"
]
},
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"/Users/emmanuel.noutahi/miniconda3/envs/safe/lib/python3.12/site-packages/huggingface_hub/file_download.py:1150: FutureWarning: `resume_download` is deprecated and will be removed in version 1.0.0. Downloads always resume when possible. If you want to force a new download, use `force_download=True`.\n",
" warnings.warn(\n"
]
}
],
"source": [
"model = SAFEDesign.load_default()"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"## Upload models to wandb\n",
"\n",
"SAFE models can be uploaded to wandb with the `upload_to_wandb` function. You can define a general \"SAFE_WANDB_PROJECT\" env variable to save all of your models to that project. \n",
"\n",
"Make sure that you are login into your wandb account:\n",
"\n",
"```bash\n",
"wandb login --relogin $WANDB_API_KEY\n",
"```"
]
},
{
"cell_type": "code",
"execution_count": 4,
"metadata": {},
"outputs": [],
"source": [
"from safe.io import upload_to_wandb"
]
},
{
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"name": "stdout",
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"text": [
"env: WANDB_SILENT=False\n",
"env: SAFE_WANDB_PROJECT=safe-models\n",
"[2024-09-10 13:42:46,004] [INFO] [real_accelerator.py:203:get_accelerator] Setting ds_accelerator to mps (auto detect)\n"
]
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"W0910 13:42:46.257000 8343047168 torch/distributed/elastic/multiprocessing/redirects.py:28] NOTE: Redirects are currently not supported in Windows or MacOs.\n",
"Failed to detect the name of this notebook, you can set it manually with the WANDB_NOTEBOOK_NAME environment variable to enable code saving.\n",
"\u001b[34m\u001b[1mwandb\u001b[0m: Currently logged in as: \u001b[33mmaclandrol\u001b[0m (\u001b[33mvalencelabs\u001b[0m). Use \u001b[1m`wandb login --relogin`\u001b[0m to force relogin\n"
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"wandb version 0.17.9 is available! To upgrade, please run:\n",
" $ pip install wandb --upgrade"
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"Tracking run with wandb version 0.16.6"
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"Run data is saved locally in <code>/Users/emmanuel.noutahi/Code/safe/nb/wandb/run-20240910_134247-72wmn5st</code>"
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"Syncing run <strong><a href='https://wandb.ai/valencelabs/safe-models/runs/72wmn5st' target=\"_blank\">absurd-disco-1</a></strong> to <a href='https://wandb.ai/valencelabs/safe-models' target=\"_blank\">Weights & Biases</a> (<a href='https://wandb.me/run' target=\"_blank\">docs</a>)<br/>"
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" View project at <a href='https://wandb.ai/valencelabs/safe-models' target=\"_blank\">https://wandb.ai/valencelabs/safe-models</a>"
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" View run at <a href='https://wandb.ai/valencelabs/safe-models/runs/72wmn5st' target=\"_blank\">https://wandb.ai/valencelabs/safe-models/runs/72wmn5st</a>"
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"\u001b[34m\u001b[1mwandb\u001b[0m: Adding directory to artifact (/var/folders/rl/wwcfdj4x0pg293bfqszl970r0000gq/T/tmpy8r3mrzg)... Done. 0.6s\n"
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" View run <strong style=\"color:#cdcd00\">absurd-disco-1</strong> at: <a href='https://wandb.ai/valencelabs/safe-models/runs/72wmn5st' target=\"_blank\">https://wandb.ai/valencelabs/safe-models/runs/72wmn5st</a><br/> View project at: <a href='https://wandb.ai/valencelabs/safe-models' target=\"_blank\">https://wandb.ai/valencelabs/safe-models</a><br/>Synced 6 W&B file(s), 0 media file(s), 5 artifact file(s) and 0 other file(s)"
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"Find logs at: <code>./wandb/run-20240910_134247-72wmn5st/logs</code>"
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"source": [
"%env WANDB_SILENT=False\n",
"%env SAFE_WANDB_PROJECT=safe-models\n",
"\n",
"upload_to_wandb(model.model, model.tokenizer, artifact_name=\"default-safe-zinc\", slicer=\"BRICS/Partition\", aliases=[\"paper\"])"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"## Loading models from wandb"
]
},
{
"cell_type": "code",
"execution_count": 3,
"metadata": {},
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{
"name": "stdout",
"output_type": "stream",
"text": [
"env: SAFE_MODEL_ROOT=/Users/emmanuel.noutahi/.cache/wandb/safe/\n"
]
},
{
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"text": [
"\u001b[34m\u001b[1mwandb\u001b[0m: Downloading large artifact default-safe-zinc:latest, 333.22MB. 5 files... \n",
"\u001b[34m\u001b[1mwandb\u001b[0m: 5 of 5 files downloaded. \n",
"Done. 0:0:0.7\n"
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}
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"source": [
"%env SAFE_MODEL_ROOT=/Users/emmanuel.noutahi/.cache/wandb/safe/\n",
"designer = SAFEDesign.load_from_wandb(\"safe-models/default-safe-zinc\")"
]
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" 0%| | 0/1 [00:00<?, ?it/s]"
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"/Users/emmanuel.noutahi/miniconda3/envs/safe/lib/python3.12/site-packages/transformers/tokenization_utils_base.py:1601: FutureWarning: `clean_up_tokenization_spaces` was not set. It will be set to `True` by default. This behavior will be depracted in transformers v4.45, and will be then set to `False` by default. For more details check this issue: https://github.com/huggingface/transformers/issues/31884\n",
" warnings.warn(\n",
"/Users/emmanuel.noutahi/miniconda3/envs/safe/lib/python3.12/site-packages/transformers/generation/configuration_utils.py:615: UserWarning: `num_beams` is set to 1. However, `early_stopping` is set to `True` -- this flag is only used in beam-based generation modes. You should set `num_beams>1` or unset `early_stopping`.\n",
" warnings.warn(\n"
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"designer.de_novo_generation(10)"
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1 change: 1 addition & 0 deletions safe/__init__.py
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from .sample import SAFEDesign
from .tokenizer import SAFETokenizer, split
from .viz import to_image
from .io import upload_to_wandb
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