Comments (10)
Hello preritt,
Thanks for your interest in the benchmark. If you would like to download the entire benchmark at once to access the raw .npy files, they are available at the following gcp bucket:
https://github.com/rail-berkeley/design-bench/blob/new-api/design_bench/disk_resource.py#L7
This post may be of interest if you are not familiar with gsutil:
https://stackoverflow.com/questions/58581873/how-to-download-an-entire-bucket-in-gcp
Generally speaking, the dataset files are downloaded as needed from gcp when design_bench.make is called. Could you share the full script producing the error, and the full stack trace?
Warm regards,
Brandon
from design-bench.
Hi Brandon,
Sorry for the delayed response.
Thanks for the information!
Here is the code I used
import design_bench
# task = design_bench.make('TGFP-Transformer-v0')
# task = design_bench.make('TFBind8-Exact-v0')
task = design_bench.make('ChEMBL-ResNet-v0')
This is the error
`Traceback (most recent call last):
File "/BerkleyDesignBenchVer01/testBerkleyV1.py", line 12, in <module>
task = design_bench.make('ChEMBL-ResNet-v0')
File "/BerkleyDesignBenchV1/lib/python3.7/site-packages/design_bench/registration.py", line 328, in make
oracle_kwargs=oracle_kwargs, **kwargs)
File "/BerkleyDesignBenchV1/lib/python3.7/site-packages/design_bench/registration.py", line 157, in make
oracle_kwargs=oracle_kwargs, **kwargs)
File "BerkleyDesignBenchV1/lib/python3.7/site-packages/design_bench/registration.py", line 111, in make
oracle_kwargs=oracle_kwargs_final, **kwargs)
File "BerkleyDesignBenchV1/lib/python3.7/site-packages/design_bench/task.py", line 245, in __init__
dataset = import_name(dataset)(**kwargs)
File "BerkleyDesignBenchV1/lib/python3.7/site-packages/design_bench/datasets/discrete/chembl_dataset.py", line 310, in __init__
soft_interpolation=soft_interpolation, **kwargs)
File "/BerkleyDesignBenchV1/lib/python3.7/site-packages/design_bench/datasets/discrete_dataset.py", line 279, in __init__
super(DiscreteDataset, self).__init__(*args, **kwargs)
File "/BerkleyDesignBenchV1/lib/python3.7/site-packages/design_bench/datasets/dataset_builder.py", line 470, in __init__
for i, y in enumerate(self.iterate_samples(return_x=False)):
File "/BerkleyDesignBenchV1/lib/python3.7/site-packages/design_bench/datasets/dataset_builder.py", line 865, in iterate_samples
return_x=return_x, return_y=return_y):
File "/BerkleyDesignBenchV1/lib/python3.7/site-packages/design_bench/datasets/dataset_builder.py", line 762, in iterate_batches
y_shard_data = self.get_shard_y(shard_id)
File "BerkleyDesignBenchV1/lib/python3.7/site-packages/design_bench/datasets/dataset_builder.py", line 566, in get_shard_y
return np.load(self.y_shards[shard_id].disk_target)
File "BerkleyDesignBenchV1/lib/python3.7/site-packages/numpy/lib/npyio.py", line 416, in load
fid = stack.enter_context(open(os_fspath(file), "rb"))
FileNotFoundError: [Errno 2] No such file or directory: 'BerkleyDesignBenchV1/lib/python3.7/site-packages/design_bench_data/chembl-GI50-CHEMBL1964047/chembl-y-2.npy'`
I'll try the GCP method and get back in case of error.
Thank you so much for your response!
from design-bench.
Could you try calling design_bench.make
on a ChEMBL task with the following format:
https://github.com/rail-berkeley/design-bench/blob/new-api/design_bench/__init__.py#L809
For example, design_bench.make("ChEMBL_MCHC_CHEMBL3885882_MorganFingerprint-RandomForest-v0")
from design-bench.
I tried the following:
task =design_bench.make("ChEMBL_MCHC_CHEMBL3885882_MorganFingerprint-RandomForest-v0")
However, I got the following error now.
Traceback (most recent call last):
File "condaEnvs/BerkleyDesignBenchV1/lib/python3.7/site-packages/design_bench/registration.py", line 201, in spec
return self.task_specs[task_name]
KeyError: 'ChEMBL_MCHC_CHEMBL3885882_MorganFingerprint-RandomForest-v0'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "perspectaTestsVer2/perspectaV1/myCodesV9Della/BerkleyDesignBenchVer01/testBerkleyV1.py", line 13, in <module>
task =design_bench.make("ChEMBL_MCHC_CHEMBL3885882_MorganFingerprint-RandomForest-v0")
File "condaEnvs/BerkleyDesignBenchV1/lib/python3.7/site-packages/design_bench/registration.py", line 328, in make
oracle_kwargs=oracle_kwargs, **kwargs)
File "condaEnvs/BerkleyDesignBenchV1/lib/python3.7/site-packages/design_bench/registration.py", line 155, in make
return self.spec(task_name).make(
File "condaEnvs/BerkleyDesignBenchV1/lib/python3.7/site-packages/design_bench/registration.py", line 232, in spec
UNKNOWN_MESSAGE.format(task_name))
ValueError: No registered task with name: ChEMBL_MCHC_CHEMBL3885882_MorganFingerprint-RandomForest-v0
from design-bench.
Could you check which version number of the benchmark you have installed?
from design-bench.
It is 2.0.12
design-bench 2.0.12 pypi_0 pypi
from design-bench.
The latest version of the benchmark is 2.0.20, could you try that version?
from design-bench.
I have the correct version now:
design-bench 2.0.20 pypi_0 pypi
Not sure why, but now I get an import error when using:
import design_bench
runcell(0, '/BerkleyDesignBenchVer01/testBerkleyV1.py')
Traceback (most recent call last):
File "/BerkleyDesignBenchVer01/testBerkleyV1.py", line 8, in <module>
import design_bench
File "condaEnvs/BerkleyDesignBenchV1/lib/python3.7/site-packages/design_bench/__init__.py", line 766, in <module>
feature_extractor=MorganFingerprintFeatures(dtype=np.int32),
File "condaEnvs/BerkleyDesignBenchV1/lib/python3.7/site-packages/design_bench/oracles/feature_extractors/morgan_fingerprint_features.py", line 74, in __init__
os.path.join(DATA_DIR, 'smiles_vocab.txt'))
File "condaEnvs/BerkleyDesignBenchV1/lib/python3.7/site-packages/deepchem/feat/smiles_tokenizer.py", line 89, in __init__
self.max_len_single_sentence = self.max_len - 2
AttributeError: 'SmilesTokenizer' object has no attribute 'max_len'
from design-bench.
Ah, this can happen if an incompatible version of deepchem is installed. Can you try installing the version of deepchem listed here: https://github.com/brandontrabucco/design-baselines/blob/master/requirements.txt#L29
I'm not sure if that's the only package that may need an update, so perhaps check the whole requirements file.
from design-bench.
Thanks a lot! I did a pip install on the requirements and it resolved the issue.
from design-bench.
Related Issues (2)
Recommend Projects
-
React
A declarative, efficient, and flexible JavaScript library for building user interfaces.
-
Vue.js
🖖 Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
-
Typescript
TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
-
TensorFlow
An Open Source Machine Learning Framework for Everyone
-
Django
The Web framework for perfectionists with deadlines.
-
Laravel
A PHP framework for web artisans
-
D3
Bring data to life with SVG, Canvas and HTML. 📊📈🎉
-
Recommend Topics
-
javascript
JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
-
web
Some thing interesting about web. New door for the world.
-
server
A server is a program made to process requests and deliver data to clients.
-
Machine learning
Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
-
Visualization
Some thing interesting about visualization, use data art
-
Game
Some thing interesting about game, make everyone happy.
Recommend Org
-
Facebook
We are working to build community through open source technology. NB: members must have two-factor auth.
-
Microsoft
Open source projects and samples from Microsoft.
-
Google
Google ❤️ Open Source for everyone.
-
Alibaba
Alibaba Open Source for everyone
-
D3
Data-Driven Documents codes.
-
Tencent
China tencent open source team.
from design-bench.