🐛 Bug: fetching models from github fails

[arnaucoma24]

Describe the bug.

Hi! I'm trying to fetch several models from the Ersilia Model Hub using a conda env I just created by cloning the Ersilia repository (python 3.12). Am I doing something wrong? I tried models eos5axz, eos4wt0 and eos2gw4 -all of them failed :(

`(ersilia) acomajuncosa@dante:/aloy/home/acomajuncosa/Ersilia/code/ersilia$ ersilia -v fetch eos5axz --from_github
16:01:19 | DEBUG    | Trying to get metadata from: /home/acomajuncosa/eos/dest/eos5axz
⬇️  Fetching model eos5axz: morgan-counts
16:01:20 | INFO     | Detected Python 3.12. Verifying setuptools...
16:01:20 | INFO     | Setuptools is already installed.
16:01:20 | DEBUG    | Initialized with URL: None
16:01:20 | DEBUG    | Getting model source
16:01:20 | DEBUG    | Model getting fetched from GitHub
16:01:20 | INFO     | Model doesn't exist on your system, fetching it now.
16:01:20 | DEBUG    | Starting fetching procedure
16:01:20 | DEBUG    | Fetching in your system, not from DockerHub
16:01:20 | DEBUG    | Deciding fetcher (BentoML or FastAPI)
16:01:21 | DEBUG    | Fetching using BentoML
16:01:21 | DEBUG    | Checking if the model is installable with BentoML
16:01:21 | DEBUG    | Starting fetching procedure
16:01:21 | INFO     | GitHub CLI is not installed. Ersilia can work without it, but we highly recommend that you install this tool.
16:01:21 | DEBUG    | Git LFS is installed
Updated git hooks.
Git LFS initialized.
16:01:21 | DEBUG    | Git LFS has been activated
16:01:22 | DEBUG    | Connected to the internet
16:01:22 | DEBUG    | Conda is installed
16:01:22 | DEBUG    | EOS Home path exists
16:01:22 | INFO     | Starting delete of model eos5axz
16:01:22 | DEBUG    | Attempting Bento delete
16:01:22 | DEBUG    | No BentoML Catalog available
16:01:22 | INFO     | Deleting conda environment eos5axz
16:01:23 | DEBUG    | Attempting temporary folder delete
16:01:23 | DEBUG    | Attempting lake delete (local)
16:01:23 | DEBUG    | Deleting /home/acomajuncosa/eos/isaura/lake/eos5axz_local.h5
16:01:23 | DEBUG    | Attempting lake delete (public)
16:01:23 | DEBUG    | Deleting /home/acomajuncosa/eos/isaura/lake/eos5axz_public.h5
16:01:23 | INFO     | Removing docker images and stopping containers related to eos5axz
16:01:23 | DEBUG    | Model entry eos5axz was not available in the fetched models registry
16:01:23 | SUCCESS  | Model eos5axz deleted successfully
16:01:23 | DEBUG    | Getting repository
Cloning into 'eos5axz'...
remote: Enumerating objects: 37, done.
remote: Counting objects: 100% (21/21), done.
remote: Compressing objects: 100% (19/19), done.
remote: Total 37 (delta 3), reused 10 (delta 0), pack-reused 16 (from 1)
Unpacking objects: 100% (37/37), 43.71 KiB | 497.00 KiB/s, done.
rm: cannot remove '/tmp/ersilia-otum4fqr': Is a directory
16:01:24 | INFO     | 🚀 Model starting...
16:01:24 | DEBUG    | Preparing inner template if necessary
16:01:24 | DEBUG    | The pack.py file already exists
16:01:24 | DEBUG    | The Dockerfile file already exists
16:01:24 | DEBUG    | The src folder already exists
16:01:24 | DEBUG    | Changing python version if necessary
16:01:24 | DEBUG    | {'version': '0.11.0', 'slim': False, 'python': 'py310'}
16:01:24 | DEBUG    | User is not root
16:01:24 | DEBUG    | Copying example file if available
16:01:24 | DEBUG    | Example file exists
16:01:24 | DEBUG    | Getting model parameters
16:01:24 | DEBUG    | Done getting model
16:01:24 | DEBUG    | Check if model can be run with vanilla (system) code (i.e. dockerfile has no installs)
16:01:24 | DEBUG    | Check bentoml and python version
16:01:24 | INFO     | BentoML version {'version': '0.11.0', 'slim': False, 'python': 'py310'}
16:01:24 | DEBUG    | Custom Ersilia BentoML is used, no need for modifying protobuf version
16:01:24 | DEBUG    | Model needs some installs
16:01:24 | DEBUG    | Checking if only python/conda install will be sufficient
16:01:24 | DEBUG    | Mode: conda
16:01:24 | DEBUG    | BentoML path exists! Removing it: /home/acomajuncosa/bentoml/repository/eos5axz
16:01:24 | DEBUG    | Attempting Bento delete
16:01:24 | DEBUG    | No BentoML Catalog available
16:01:24 | DEBUG    | Trying to remove path: /home/acomajuncosa/bentoml/repository/eos5axz
16:01:24 | DEBUG    | ...successfully
16:01:24 | DEBUG    | Initializing conda packer
16:01:24 | DEBUG    | Packing model with Conda
16:01:24 | DEBUG    | Writing install commands
16:01:24 | DEBUG    | Run commands: ['pip install rdkit==2022.9.5', 'pip install numpy==1.26.4']
16:01:24 | DEBUG    | Writing install commands in /home/acomajuncosa/eos/dest/eos5axz/model_install_commands.sh
16:01:24 | DEBUG    | Setting up
16:01:24 | DEBUG    | Installs file /home/acomajuncosa/eos/dest/eos5axz/model_install_commands.sh
16:01:24 | DEBUG    | Conda environment eos5axz
16:01:25 | DEBUG    | Environment eos5axz does not exist
16:01:25 | INFO     | Cloning base conda environment and adding model dependencies
Source:      /home/acomajuncosa/programs/anaconda3/envs/eosbase-bentoml-0.11.0-py310
Destination: /home/acomajuncosa/programs/anaconda3/envs/eos5axz
Packages: 24
Files: 6154
Preparing transaction: done
Verifying transaction: done
Executing transaction: done
#
# To activate this environment, use
#
#     $ conda activate eos5axz
#
# To deactivate an active environment, use
#
#     $ conda deactivate

16:01:35 | DEBUG    | Run commandlines on eos5axz
16:01:35 | DEBUG    | python -m pip --disable-pip-version-check install rdkit==2022.9.5
python -m pip --disable-pip-version-check install numpy==1.26.4
python -m pip --disable-pip-version-check install git+https://github.com/ersilia-os/bentoml-ersilia.git

16:01:36 | DEBUG    | Activating base environment
16:01:36 | DEBUG    | Current working directory: /home/acomajuncosa/eos/dest/eos5axz
16:01:36 | DEBUG    | Running bash /tmp/ersilia-ndkbt7s0/script.sh 2>&1 | tee -a /tmp/ersilia-azknz76u/command_outputs.log
Collecting rdkit==2022.9.5
  Using cached rdkit-2022.9.5-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (3.9 kB)
Requirement already satisfied: numpy in /home/acomajuncosa/programs/anaconda3/envs/eos5axz/lib/python3.10/site-packages (from rdkit==2022.9.5) (2.2.2)
Collecting Pillow (from rdkit==2022.9.5)
  Using cached pillow-11.1.0-cp310-cp310-manylinux_2_28_x86_64.whl.metadata (9.1 kB)
Using cached rdkit-2022.9.5-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (29.4 MB)
Using cached pillow-11.1.0-cp310-cp310-manylinux_2_28_x86_64.whl (4.5 MB)
Installing collected packages: Pillow, rdkit
Successfully installed Pillow-11.1.0 rdkit-2022.9.5
Collecting numpy==1.26.4
  Using cached numpy-1.26.4-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (61 kB)
Using cached numpy-1.26.4-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (18.2 MB)
Installing collected packages: numpy
  Attempting uninstall: numpy
    Found existing installation: numpy 2.2.2
    Uninstalling numpy-2.2.2:
      Successfully uninstalled numpy-2.2.2
Successfully installed numpy-1.26.4
Collecting git+https://github.com/ersilia-os/bentoml-ersilia.git
  Cloning https://github.com/ersilia-os/bentoml-ersilia.git to /tmp/pip-req-build-gast8v62
  Running command git clone --filter=blob:none --quiet https://github.com/ersilia-os/bentoml-ersilia.git /tmp/pip-req-build-gast8v62
  Resolved https://github.com/ersilia-os/bentoml-ersilia.git to commit d9d9f342294da3f1a69c9e81adb17f77bc010aac
  Installing build dependencies: started
  Installing build dependencies: finished with status 'done'
  Getting requirements to build wheel: started
  Getting requirements to build wheel: finished with status 'done'
  Preparing metadata (pyproject.toml): started
  Preparing metadata (pyproject.toml): finished with status 'done'
Requirement already satisfied: docker in /home/acomajuncosa/programs/anaconda3/envs/eos5axz/lib/python3.10/site-packages (from bentoml==0.11.0) (7.1.0)
Requirement already satisfied: alembic in /home/acomajuncosa/programs/anaconda3/envs/eos5axz/lib/python3.10/site-packages (from bentoml==0.11.0) (1.14.1)
Requirement already satisfied: packaging in /home/acomajuncosa/programs/anaconda3/envs/eos5axz/lib/python3.10/site-packages (from bentoml==0.11.0) (24.2)
Requirement already satisfied: boto3 in /home/acomajuncosa/programs/anaconda3/envs/eos5axz/lib/python3.10/site-packages (from bentoml==0.11.0) (1.36.11)
Requirement already satisfied: psutil in /home/acomajuncosa/programs/anaconda3/envs/eos5axz/lib/python3.10/site-packages (from bentoml==0.11.0) (6.1.1)
Requirement already satisfied: cerberus in /home/acomajuncosa/programs/anaconda3/envs/eos5axz/lib/python3.10/site-packages (from bentoml==0.11.0) (1.3.7)
Requirement already satisfied: sqlalchemy in /home/acomajuncosa/programs/anaconda3/envs/eos5axz/lib/python3.10/site-packages (from bentoml==0.11.0) (2.0.37)
Requirement already satisfied: sqlalchemy-utils in /home/acomajuncosa/programs/anaconda3/envs/eos5axz/lib/python3.10/site-packages (from bentoml==0.11.0) (0.41.2)
Requirement already satisfied: tabulate in /home/acomajuncosa/programs/anaconda3/envs/eos5axz/lib/python3.10/site-packages (from bentoml==0.11.0) (0.9.0)
Requirement already satisfied: humanfriendly in /home/acomajuncosa/programs/anaconda3/envs/eos5axz/lib/python3.10/site-packages (from bentoml==0.11.0) (10.0)
Requirement already satisfied: flask in /home/acomajuncosa/programs/anaconda3/envs/eos5axz/lib/python3.10/site-packages (from bentoml==0.11.0) (3.1.0)
Requirement already satisfied: chardet in /home/acomajuncosa/programs/anaconda3/envs/eos5axz/lib/python3.10/site-packages (from bentoml==0.11.0) (5.2.0)
Requirement already satisfied: numpy in /home/acomajuncosa/programs/anaconda3/envs/eos5axz/lib/python3.10/site-packages (from bentoml==0.11.0) (1.26.4)
Requirement already satisfied: multidict in /home/acomajuncosa/programs/anaconda3/envs/eos5axz/lib/python3.10/site-packages (from bentoml==0.11.0) (6.1.0)
Requirement already satisfied: requests in /home/acomajuncosa/programs/anaconda3/envs/eos5axz/lib/python3.10/site-packages (from bentoml==0.11.0) (2.32.3)
Requirement already satisfied: python-json-logger in /home/acomajuncosa/programs/anaconda3/envs/eos5axz/lib/python3.10/site-packages (from bentoml==0.11.0) (3.2.1)
Requirement already satisfied: ruamel.yaml in /home/acomajuncosa/programs/anaconda3/envs/eos5axz/lib/python3.10/site-packages (from bentoml==0.11.0) (0.18.10)
Requirement already satisfied: werkzeug in /home/acomajuncosa/programs/anaconda3/envs/eos5axz/lib/python3.10/site-packages (from bentoml==0.11.0) (3.1.3)
Requirement already satisfied: protobuf<3.19,>=3.8.0 in /home/acomajuncosa/programs/anaconda3/envs/eos5axz/lib/python3.10/site-packages (from bentoml==0.11.0) (3.18.3)
Requirement already satisfied: prometheus_client in /home/acomajuncosa/programs/anaconda3/envs/eos5axz/lib/python3.10/site-packages (from bentoml==0.11.0) (0.21.1)
Requirement already satisfied: Mako in /home/acomajuncosa/programs/anaconda3/envs/eos5axz/lib/python3.10/site-packages (from alembic->bentoml==0.11.0) (1.3.8)
Requirement already satisfied: typing-extensions>=4 in /home/acomajuncosa/programs/anaconda3/envs/eos5axz/lib/python3.10/site-packages (from alembic->bentoml==0.11.0) (4.12.2)
Requirement already satisfied: greenlet!=0.4.17 in /home/acomajuncosa/programs/anaconda3/envs/eos5axz/lib/python3.10/site-packages (from sqlalchemy->bentoml==0.11.0) (3.1.1)
Requirement already satisfied: botocore<1.37.0,>=1.36.11 in /home/acomajuncosa/programs/anaconda3/envs/eos5axz/lib/python3.10/site-packages (from boto3->bentoml==0.11.0) (1.36.11)
Requirement already satisfied: jmespath<2.0.0,>=0.7.1 in /home/acomajuncosa/programs/anaconda3/envs/eos5axz/lib/python3.10/site-packages (from boto3->bentoml==0.11.0) (1.0.1)
Requirement already satisfied: s3transfer<0.12.0,>=0.11.0 in /home/acomajuncosa/programs/anaconda3/envs/eos5axz/lib/python3.10/site-packages (from boto3->bentoml==0.11.0) (0.11.2)
Requirement already satisfied: urllib3>=1.26.0 in /home/acomajuncosa/programs/anaconda3/envs/eos5axz/lib/python3.10/site-packages (from docker->bentoml==0.11.0) (2.3.0)
Requirement already satisfied: charset-normalizer<4,>=2 in /home/acomajuncosa/programs/anaconda3/envs/eos5axz/lib/python3.10/site-packages (from requests->bentoml==0.11.0) (3.4.1)
Requirement already satisfied: idna<4,>=2.5 in /home/acomajuncosa/programs/anaconda3/envs/eos5axz/lib/python3.10/site-packages (from requests->bentoml==0.11.0) (3.10)
Requirement already satisfied: certifi>=2017.4.17 in /home/acomajuncosa/programs/anaconda3/envs/eos5axz/lib/python3.10/site-packages (from requests->bentoml==0.11.0) (2025.1.31)
Requirement already satisfied: Jinja2>=3.1.2 in /home/acomajuncosa/programs/anaconda3/envs/eos5axz/lib/python3.10/site-packages (from flask->bentoml==0.11.0) (3.1.5)
Requirement already satisfied: itsdangerous>=2.2 in /home/acomajuncosa/programs/anaconda3/envs/eos5axz/lib/python3.10/site-packages (from flask->bentoml==0.11.0) (2.2.0)
Requirement already satisfied: click>=8.1.3 in /home/acomajuncosa/programs/anaconda3/envs/eos5axz/lib/python3.10/site-packages (from flask->bentoml==0.11.0) (8.1.8)
Requirement already satisfied: blinker>=1.9 in /home/acomajuncosa/programs/anaconda3/envs/eos5axz/lib/python3.10/site-packages (from flask->bentoml==0.11.0) (1.9.0)
Requirement already satisfied: MarkupSafe>=2.1.1 in /home/acomajuncosa/programs/anaconda3/envs/eos5axz/lib/python3.10/site-packages (from werkzeug->bentoml==0.11.0) (3.0.2)
Requirement already satisfied: ruamel.yaml.clib>=0.2.7 in /home/acomajuncosa/programs/anaconda3/envs/eos5axz/lib/python3.10/site-packages (from ruamel.yaml->bentoml==0.11.0) (0.2.12)
Requirement already satisfied: python-dateutil<3.0.0,>=2.1 in /home/acomajuncosa/programs/anaconda3/envs/eos5axz/lib/python3.10/site-packages (from botocore<1.37.0,>=1.36.11->boto3->bentoml==0.11.0) (2.9.0.post0)
Requirement already satisfied: six>=1.5 in /home/acomajuncosa/programs/anaconda3/envs/eos5axz/lib/python3.10/site-packages (from python-dateutil<3.0.0,>=2.1->botocore<1.37.0,>=1.36.11->boto3->bentoml==0.11.0) (1.17.0)
16:01:45 | DEBUG    | Collecting rdkit==2022.9.5
  Using cached rdkit-2022.9.5-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (3.9 kB)
Requirement already satisfied: numpy in /home/acomajuncosa/programs/anaconda3/envs/eos5axz/lib/python3.10/site-packages (from rdkit==2022.9.5) (2.2.2)
Collecting Pillow (from rdkit==2022.9.5)
  Using cached pillow-11.1.0-cp310-cp310-manylinux_2_28_x86_64.whl.metadata (9.1 kB)
Using cached rdkit-2022.9.5-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (29.4 MB)
Using cached pillow-11.1.0-cp310-cp310-manylinux_2_28_x86_64.whl (4.5 MB)
Installing collected packages: Pillow, rdkit
Successfully installed Pillow-11.1.0 rdkit-2022.9.5
Collecting numpy==1.26.4
  Using cached numpy-1.26.4-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (61 kB)
Using cached numpy-1.26.4-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (18.2 MB)
Installing collected packages: numpy
  Attempting uninstall: numpy
    Found existing installation: numpy 2.2.2
    Uninstalling numpy-2.2.2:
      Successfully uninstalled numpy-2.2.2
Successfully installed numpy-1.26.4
Collecting git+https://github.com/ersilia-os/bentoml-ersilia.git
  Cloning https://github.com/ersilia-os/bentoml-ersilia.git to /tmp/pip-req-build-gast8v62
  Running command git clone --filter=blob:none --quiet https://github.com/ersilia-os/bentoml-ersilia.git /tmp/pip-req-build-gast8v62
  Resolved https://github.com/ersilia-os/bentoml-ersilia.git to commit d9d9f342294da3f1a69c9e81adb17f77bc010aac
  Installing build dependencies: started
  Installing build dependencies: finished with status 'done'
  Getting requirements to build wheel: started
  Getting requirements to build wheel: finished with status 'done'
  Preparing metadata (pyproject.toml): started
  Preparing metadata (pyproject.toml): finished with status 'done'
Requirement already satisfied: docker in /home/acomajuncosa/programs/anaconda3/envs/eos5axz/lib/python3.10/site-packages (from bentoml==0.11.0) (7.1.0)
Requirement already satisfied: alembic in /home/acomajuncosa/programs/anaconda3/envs/eos5axz/lib/python3.10/site-packages (from bentoml==0.11.0) (1.14.1)
Requirement already satisfied: packaging in /home/acomajuncosa/programs/anaconda3/envs/eos5axz/lib/python3.10/site-packages (from bentoml==0.11.0) (24.2)
Requirement already satisfied: boto3 in /home/acomajuncosa/programs/anaconda3/envs/eos5axz/lib/python3.10/site-packages (from bentoml==0.11.0) (1.36.11)
Requirement already satisfied: psutil in /home/acomajuncosa/programs/anaconda3/envs/eos5axz/lib/python3.10/site-packages (from bentoml==0.11.0) (6.1.1)
Requirement already satisfied: cerberus in /home/acomajuncosa/programs/anaconda3/envs/eos5axz/lib/python3.10/site-packages (from bentoml==0.11.0) (1.3.7)
Requirement already satisfied: sqlalchemy in /home/acomajuncosa/programs/anaconda3/envs/eos5axz/lib/python3.10/site-packages (from bentoml==0.11.0) (2.0.37)
Requirement already satisfied: sqlalchemy-utils in /home/acomajuncosa/programs/anaconda3/envs/eos5axz/lib/python3.10/site-packages (from bentoml==0.11.0) (0.41.2)
Requirement already satisfied: tabulate in /home/acomajuncosa/programs/anaconda3/envs/eos5axz/lib/python3.10/site-packages (from bentoml==0.11.0) (0.9.0)
Requirement already satisfied: humanfriendly in /home/acomajuncosa/programs/anaconda3/envs/eos5axz/lib/python3.10/site-packages (from bentoml==0.11.0) (10.0)
Requirement already satisfied: flask in /home/acomajuncosa/programs/anaconda3/envs/eos5axz/lib/python3.10/site-packages (from bentoml==0.11.0) (3.1.0)
Requirement already satisfied: chardet in /home/acomajuncosa/programs/anaconda3/envs/eos5axz/lib/python3.10/site-packages (from bentoml==0.11.0) (5.2.0)
Requirement already satisfied: numpy in /home/acomajuncosa/programs/anaconda3/envs/eos5axz/lib/python3.10/site-packages (from bentoml==0.11.0) (1.26.4)
Requirement already satisfied: multidict in /home/acomajuncosa/programs/anaconda3/envs/eos5axz/lib/python3.10/site-packages (from bentoml==0.11.0) (6.1.0)
Requirement already satisfied: requests in /home/acomajuncosa/programs/anaconda3/envs/eos5axz/lib/python3.10/site-packages (from bentoml==0.11.0) (2.32.3)
Requirement already satisfied: python-json-logger in /home/acomajuncosa/programs/anaconda3/envs/eos5axz/lib/python3.10/site-packages (from bentoml==0.11.0) (3.2.1)
Requirement already satisfied: ruamel.yaml in /home/acomajuncosa/programs/anaconda3/envs/eos5axz/lib/python3.10/site-packages (from bentoml==0.11.0) (0.18.10)
Requirement already satisfied: werkzeug in /home/acomajuncosa/programs/anaconda3/envs/eos5axz/lib/python3.10/site-packages (from bentoml==0.11.0) (3.1.3)
Requirement already satisfied: protobuf<3.19,>=3.8.0 in /home/acomajuncosa/programs/anaconda3/envs/eos5axz/lib/python3.10/site-packages (from bentoml==0.11.0) (3.18.3)
Requirement already satisfied: prometheus_client in /home/acomajuncosa/programs/anaconda3/envs/eos5axz/lib/python3.10/site-packages (from bentoml==0.11.0) (0.21.1)
Requirement already satisfied: Mako in /home/acomajuncosa/programs/anaconda3/envs/eos5axz/lib/python3.10/site-packages (from alembic->bentoml==0.11.0) (1.3.8)
Requirement already satisfied: typing-extensions>=4 in /home/acomajuncosa/programs/anaconda3/envs/eos5axz/lib/python3.10/site-packages (from alembic->bentoml==0.11.0) (4.12.2)
Requirement already satisfied: greenlet!=0.4.17 in /home/acomajuncosa/programs/anaconda3/envs/eos5axz/lib/python3.10/site-packages (from sqlalchemy->bentoml==0.11.0) (3.1.1)
Requirement already satisfied: botocore<1.37.0,>=1.36.11 in /home/acomajuncosa/programs/anaconda3/envs/eos5axz/lib/python3.10/site-packages (from boto3->bentoml==0.11.0) (1.36.11)
Requirement already satisfied: jmespath<2.0.0,>=0.7.1 in /home/acomajuncosa/programs/anaconda3/envs/eos5axz/lib/python3.10/site-packages (from boto3->bentoml==0.11.0) (1.0.1)
Requirement already satisfied: s3transfer<0.12.0,>=0.11.0 in /home/acomajuncosa/programs/anaconda3/envs/eos5axz/lib/python3.10/site-packages (from boto3->bentoml==0.11.0) (0.11.2)
Requirement already satisfied: urllib3>=1.26.0 in /home/acomajuncosa/programs/anaconda3/envs/eos5axz/lib/python3.10/site-packages (from docker->bentoml==0.11.0) (2.3.0)
Requirement already satisfied: charset-normalizer<4,>=2 in /home/acomajuncosa/programs/anaconda3/envs/eos5axz/lib/python3.10/site-packages (from requests->bentoml==0.11.0) (3.4.1)
Requirement already satisfied: idna<4,>=2.5 in /home/acomajuncosa/programs/anaconda3/envs/eos5axz/lib/python3.10/site-packages (from requests->bentoml==0.11.0) (3.10)
Requirement already satisfied: certifi>=2017.4.17 in /home/acomajuncosa/programs/anaconda3/envs/eos5axz/lib/python3.10/site-packages (from requests->bentoml==0.11.0) (2025.1.31)
Requirement already satisfied: Jinja2>=3.1.2 in /home/acomajuncosa/programs/anaconda3/envs/eos5axz/lib/python3.10/site-packages (from flask->bentoml==0.11.0) (3.1.5)
Requirement already satisfied: itsdangerous>=2.2 in /home/acomajuncosa/programs/anaconda3/envs/eos5axz/lib/python3.10/site-packages (from flask->bentoml==0.11.0) (2.2.0)
Requirement already satisfied: click>=8.1.3 in /home/acomajuncosa/programs/anaconda3/envs/eos5axz/lib/python3.10/site-packages (from flask->bentoml==0.11.0) (8.1.8)
Requirement already satisfied: blinker>=1.9 in /home/acomajuncosa/programs/anaconda3/envs/eos5axz/lib/python3.10/site-packages (from flask->bentoml==0.11.0) (1.9.0)
Requirement already satisfied: MarkupSafe>=2.1.1 in /home/acomajuncosa/programs/anaconda3/envs/eos5axz/lib/python3.10/site-packages (from werkzeug->bentoml==0.11.0) (3.0.2)
Requirement already satisfied: ruamel.yaml.clib>=0.2.7 in /home/acomajuncosa/programs/anaconda3/envs/eos5axz/lib/python3.10/site-packages (from ruamel.yaml->bentoml==0.11.0) (0.2.12)
Requirement already satisfied: python-dateutil<3.0.0,>=2.1 in /home/acomajuncosa/programs/anaconda3/envs/eos5axz/lib/python3.10/site-packages (from botocore<1.37.0,>=1.36.11->boto3->bentoml==0.11.0) (2.9.0.post0)
Requirement already satisfied: six>=1.5 in /home/acomajuncosa/programs/anaconda3/envs/eos5axz/lib/python3.10/site-packages (from python-dateutil<3.0.0,>=2.1->botocore<1.37.0,>=1.36.11->boto3->bentoml==0.11.0) (1.17.0)

16:01:45 | DEBUG    | Activation done
16:01:45 | DEBUG    | Creating environment YAML file
16:01:47 | DEBUG    | Storing Conda environment in the local environment database
16:01:47 | DEBUG    | Done with the Conda setup
16:01:47 | DEBUG    | Using environment eos5axz
16:01:47 | DEBUG    | Running command: python pack.py
16:01:47 | DEBUG    | Run commandlines on eos5axz
16:01:47 | DEBUG    | 
        python pack.py
        
16:01:48 | DEBUG    | Activating base environment
16:01:48 | DEBUG    | Current working directory: /home/acomajuncosa/eos/dest/eos5axz
16:01:48 | DEBUG    | Running bash /tmp/ersilia-sx5h1j0p/script.sh 2>&1 | tee -a /tmp/ersilia-zbdmji31/command_outputs.log
[2025-02-03 16:01:48,864] WARNING - Python 3.10.16 found in current environment is not officially supported by BentoML. The docker base image used is'bentoml/model-server:0.11.0' which will use conda to install Python 3.10.16 in the build process. Supported Python versions are: f3.6, 3.7, 3.8
[2025-02-03 16:01:49,874] INFO - BentoService bundle 'eos5axz:20250203160149_D0982D' saved to: /home/acomajuncosa/bentoml/repository/eos5axz/20250203160149_D0982D
16:01:50 | DEBUG    | [2025-02-03 16:01:48,864] WARNING - Python 3.10.16 found in current environment is not officially supported by BentoML. The docker base image used is'bentoml/model-server:0.11.0' which will use conda to install Python 3.10.16 in the build process. Supported Python versions are: f3.6, 3.7, 3.8
[2025-02-03 16:01:49,874] INFO - BentoService bundle 'eos5axz:20250203160149_D0982D' saved to: /home/acomajuncosa/bentoml/repository/eos5axz/20250203160149_D0982D

16:01:50 | DEBUG    | Activation done
16:01:50 | DEBUG    | Previous command successfully run inside eos5axz conda environment
16:01:50 | DEBUG    | Now trying to establish symlinks
16:01:50 | DEBUG    | BentoML location is /home/acomajuncosa/bentoml/repository/eos5axz/20250203160149_D0982D
16:01:50 | DEBUG    | Ersilia Bento location is /home/acomajuncosa/eos/repository/eos5axz/20250203160149_D0982D
16:01:50 | DEBUG    | Building symlinks between /home/acomajuncosa/eos/repository/eos5axz/20250203160149_D0982D and /home/acomajuncosa/bentoml/repository/eos5axz/20250203160149_D0982D
16:01:50 | DEBUG    | Creating model symlink bundle artifacts > dest
16:01:50 | DEBUG    | Creating model_install_commands.sh symlink dest <> bundle
16:01:50 | INFO     | Could not create symbolic link from /home/acomajuncosa/eos/dest/eos5axz/data.h5 to /home/acomajuncosa/eos/isaura/lake/eos5axz_public.h5
16:01:50 | DEBUG    | Run file found in framework: /home/acomajuncosa/eos/repository/eos5axz/20250203160149_D0982D/eos5axz/artifacts/framework/run.sh
16:01:50 | DEBUG    | Run commandlines on eos5axz
16:01:50 | DEBUG    | which python > /tmp/ersilia-yqvf5ih_/tmp.txt
16:01:50 | DEBUG    | Activating base environment
16:01:50 | DEBUG    | Current working directory: /aloy/home/acomajuncosa/Ersilia/code/ersilia
16:01:50 | DEBUG    | Running bash /tmp/ersilia-ehpala5z/script.sh 2>&1 | tee -a /tmp/ersilia-kfzeel2f/command_outputs.log
16:01:50 | DEBUG    | 
16:01:50 | DEBUG    | Activation done
16:01:50 | DEBUG    | Python executable: /home/acomajuncosa/programs/anaconda3/envs/eos5axz/bin/python
16:01:50 | DEBUG    | Conda is needed
16:01:50 | DEBUG    | Checking if model needs to be integrated to a tool
16:01:50 | DEBUG    | Getting model card of eos5axz
16:01:50 | DEBUG    | Trying to get metadata from: /home/acomajuncosa/eos/dest/eos5axz
16:01:50 | DEBUG    | Card saved at /home/acomajuncosa/eos/dest/eos5axz/card.json
16:01:50 | DEBUG    | Saving slug morgan-counts
16:01:50 | DEBUG    | Checking that autoservice works
16:01:50 | DEBUG    | Setting BentoML AutoService for eos5axz
16:01:50 | DEBUG    | No service class provided, deciding automatically
16:01:50 | DEBUG    | No service class file exists in /home/acomajuncosa/eos/repository/eos5axz/20250203160149_D0982D/service_class.txt
16:01:50 | DEBUG    | Pack method is: bentoml
16:01:50 | DEBUG    | Pack method is: bentoml
16:01:50 | DEBUG    | Setting virtual environment at /home/acomajuncosa/eos/dest/eos5axz
16:01:50 | DEBUG    | Pack method is: bentoml
16:01:51 | DEBUG    | Pack method is: bentoml
16:01:51 | DEBUG    | Service class: conda
16:01:51 | DEBUG    | Getting APIs from list file
16:01:51 | DEBUG    | Getting APIs from BentoML
16:01:51 | DEBUG    | Getting APIs from Bento
16:01:51 | DEBUG    | Getting info from BentoML and storing in /tmp/ersilia-rhapl6fn/information.json
🚨🚨🚨 Something went wrong with Ersilia 🚨🚨🚨

Error message:

Expecting value: line 1 column 1 (char 0)
If this error message is not helpful, open an issue at:
 - https://github.com/ersilia-os/ersilia
Or feel free to reach out to us at:
 - hello[at]ersilia.io

If you haven't, try to run your command in verbose mode (-v in the CLI)
 - You will find the console log file in: /home/acomajuncosa/eos/current.log
Task exception was never retrieved
future: <Task finished name='Task-1' coro=<ModelFetcher.fetch() done, defined at /aloy/home/acomajuncosa/Ersilia/code/ersilia/ersilia/hub/fetch/fetch.py:345> exception=SystemExit(1)>
Traceback (most recent call last):
  File "/aloy/home/acomajuncosa/Ersilia/code/ersilia/ersilia/utils/exceptions_utils/throw_ersilia_exception.py", line 25, in inner_function
    return func(*args, **kwargs)
           ^^^^^^^^^^^^^^^^^^^^^
  File "/aloy/home/acomajuncosa/Ersilia/code/ersilia/ersilia/hub/fetch/fetch.py", line 203, in _fetch_from_bentoml
    mf.fetch(model_id=self.model_id)
  File "/aloy/home/acomajuncosa/Ersilia/code/ersilia/ersilia/hub/fetch/fetch_bentoml.py", line 213, in fetch
    self._fetch(model_id)
  File "/aloy/home/acomajuncosa/Ersilia/code/ersilia/ersilia/hub/fetch/fetch_bentoml.py", line 171, in _fetch
    self._fetch_not_from_dockerhub(model_id=model_id)
  File "/aloy/home/acomajuncosa/Ersilia/code/ersilia/ersilia/hub/fetch/fetch_bentoml.py", line 154, in _fetch_not_from_dockerhub
    self._check()
  File "/aloy/home/acomajuncosa/Ersilia/code/ersilia/ersilia/hub/fetch/fetch_bentoml.py", line 127, in _check
    mc.check()
  File "/aloy/home/acomajuncosa/Ersilia/code/ersilia/ersilia/hub/fetch/actions/check.py", line 27, in check
    AutoService(self.model_id)
  File "/aloy/home/acomajuncosa/Ersilia/code/ersilia/ersilia/serve/autoservice.py", line 216, in __init__
    self._set_apis()
  File "/aloy/home/acomajuncosa/Ersilia/code/ersilia/ersilia/serve/autoservice.py", line 257, in _set_apis
    for api_name in self.service._get_apis_from_where_available():
                    ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/aloy/home/acomajuncosa/Ersilia/code/ersilia/ersilia/serve/services.py", line 124, in _get_apis_from_where_available
    apis_list = self._get_apis_from_bento()
                ^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/aloy/home/acomajuncosa/Ersilia/code/ersilia/ersilia/serve/services.py", line 98, in _get_apis_from_bento
    info = self._get_info_from_bento()
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/aloy/home/acomajuncosa/Ersilia/code/ersilia/ersilia/serve/services.py", line 92, in _get_info_from_bento
    info = json.load(f)
           ^^^^^^^^^^^^
  File "/home/acomajuncosa/programs/anaconda3/envs/ersilia/lib/python3.12/json/__init__.py", line 293, in load
    return loads(fp.read(),
           ^^^^^^^^^^^^^^^^
  File "/home/acomajuncosa/programs/anaconda3/envs/ersilia/lib/python3.12/json/__init__.py", line 346, in loads
    return _default_decoder.decode(s)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/acomajuncosa/programs/anaconda3/envs/ersilia/lib/python3.12/json/decoder.py", line 338, in decode
    obj, end = self.raw_decode(s, idx=_w(s, 0).end())
               ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/acomajuncosa/programs/anaconda3/envs/ersilia/lib/python3.12/json/decoder.py", line 356, in raw_decode
    raise JSONDecodeError("Expecting value", s, err.value) from None
json.decoder.JSONDecodeError: Expecting value: line 1 column 1 (char 0)

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/home/acomajuncosa/programs/anaconda3/envs/ersilia/bin/ersilia", line 8, in <module>
    sys.exit(cli())
             ^^^^^
  File "/home/acomajuncosa/programs/anaconda3/envs/ersilia/lib/python3.12/site-packages/click/core.py", line 1161, in __call__
    return self.main(*args, **kwargs)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/acomajuncosa/programs/anaconda3/envs/ersilia/lib/python3.12/site-packages/click/core.py", line 1082, in main
    rv = self.invoke(ctx)
         ^^^^^^^^^^^^^^^^
  File "/home/acomajuncosa/programs/anaconda3/envs/ersilia/lib/python3.12/site-packages/click/core.py", line 1697, in invoke
    return _process_result(sub_ctx.command.invoke(sub_ctx))
                           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/acomajuncosa/programs/anaconda3/envs/ersilia/lib/python3.12/site-packages/click/core.py", line 1443, in invoke
    return ctx.invoke(self.callback, **ctx.params)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/acomajuncosa/programs/anaconda3/envs/ersilia/lib/python3.12/site-packages/click/core.py", line 788, in invoke
    return __callback(*args, **kwargs)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/aloy/home/acomajuncosa/Ersilia/code/ersilia/ersilia/cli/commands/__init__.py", line 31, in wrapper
    return func(*args, **kwargs)
           ^^^^^^^^^^^^^^^^^^^^^
  File "/aloy/home/acomajuncosa/Ersilia/code/ersilia/ersilia/cli/commands/fetch.py", line 142, in fetch
    fetch_result = _fetch(mf, model_id)
                   ^^^^^^^^^^^^^^^^^^^^
  File "/aloy/home/acomajuncosa/Ersilia/code/ersilia/ersilia/cli/commands/fetch.py", line 37, in _fetch
    res = asyncio.run(mf.fetch(model_id))
          ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/acomajuncosa/programs/anaconda3/envs/ersilia/lib/python3.12/site-packages/nest_asyncio.py", line 30, in run
    return loop.run_until_complete(task)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/acomajuncosa/programs/anaconda3/envs/ersilia/lib/python3.12/site-packages/nest_asyncio.py", line 92, in run_until_complete
    self._run_once()
  File "/home/acomajuncosa/programs/anaconda3/envs/ersilia/lib/python3.12/site-packages/nest_asyncio.py", line 133, in _run_once
    handle._run()
  File "/home/acomajuncosa/programs/anaconda3/envs/ersilia/lib/python3.12/asyncio/events.py", line 88, in _run
    self._context.run(self._callback, *self._args)
  File "/home/acomajuncosa/programs/anaconda3/envs/ersilia/lib/python3.12/asyncio/tasks.py", line 303, in __step
    self.__step_run_and_handle_result(exc)
  File "/home/acomajuncosa/programs/anaconda3/envs/ersilia/lib/python3.12/asyncio/tasks.py", line 314, in __step_run_and_handle_result
    result = coro.send(None)
             ^^^^^^^^^^^^^^^
  File "/aloy/home/acomajuncosa/Ersilia/code/ersilia/ersilia/hub/fetch/fetch.py", line 366, in fetch
    fr = await self._fetch(model_id)
         ^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/aloy/home/acomajuncosa/Ersilia/code/ersilia/ersilia/hub/fetch/fetch.py", line 334, in _fetch
    self._fetch_not_from_dockerhub(model_id=model_id)
  File "/aloy/home/acomajuncosa/Ersilia/code/ersilia/ersilia/utils/exceptions_utils/throw_ersilia_exception.py", line 25, in inner_function
    return func(*args, **kwargs)
           ^^^^^^^^^^^^^^^^^^^^^
  File "/aloy/home/acomajuncosa/Ersilia/code/ersilia/ersilia/hub/fetch/fetch.py", line 228, in _fetch_not_from_dockerhub
    self._fetch_from_bentoml()
  File "/aloy/home/acomajuncosa/Ersilia/code/ersilia/ersilia/utils/exceptions_utils/throw_ersilia_exception.py", line 41, in inner_function
    sys.exit(DEFAULT_ERSILIA_ERROR_EXIT_CODE)
SystemExit: 1
`

Describe the steps to reproduce the behavior

No response

Operating environment

Ubuntu 20.04.3 LTS

[arnaucoma24]

I have repeated the same exact procedure using py 3.10 and everything works smoothly :)
is this something expected?

[GemmaTuron]

Hi @arnaucoma24

Thanks for reporting this, python 3.12 should be working smoothly but it is true that I have encountered some issues as well sometimes. I see you reported a very similar error or the same one a while ago.

I have just now tried fetching eos2gw4 from github on my ubuntu 24.04 in py 3.12 and it worked. So some sanity checks:

• Which version of Ersilia are you using? Did you pull the latest code and pip install -e .?
• I bet this will be the same across all models, for example does eos3b5e also fails with the same error?

If you can in the future add the logs as attached .txt so the conversation will be easier to follow and faster to browse through it.

Please @DhanshreeA have a look, I think this is something we have already identified in the past and solved successfully but I can't recall now.

[GemmaTuron]

and I know you'll need to use the models via conda, but just to be sure, can you try if docker is also failing or that works?

[arnaucoma24]

Hi @GemmaTuron

Thanks for your fast answer! Indeed, I reported a similar error a while ago. However, in this case, I am encountering the error for all the models, apparently. Here some extra info:

• I'm using ersilia, version 0.1.41, pulled from the Ersilia Repository and installed with pip install -e .
• You're right, eos3b5e (and others) are failing with the same error for me.

Regarding the logs, I checked the file /home/acomajuncosa/eos/current.log but looks empty. Is there something am I missing? It seems the problem is fully on my side.

Re: docker. I tried using --from_docker but I don't have docker installed in my system and the fetching failed. I'll try to install it and let you know!

[Abellegese]

Hi @arnaucoma24 this is same problem you mentioned your recent issue. You can do the quick fix as I mentioned there.

[arnaucoma24]

Closing issue as duplicate of #1532