Closed steveowk closed 5 months ago
Hello. This action, the "hasunmappedradicalatom" was introduce in rxnutils 1.2. Could it be that you have an old version rxnutils installed in your environment? Could try to do "pip install -U reaction-utils"?
Hello
Thanks for the response. After the update, the error is not there. However, the template extraction pipeline still fails (while executing template_pipeline.sh)
Did you install a Jupyter kernel?
ipython kernel install --name "aizynthtrain" --user
Hello
Yes.
I have rerun the train env set-up but have the same error.
I find this very peculiar. We just pushed a new version. Could you try and re-install (or at least git pull + poetry update)?
Hello, I'm having the same problem with kernelspec. After following your suggestions (git pull & poetry update), no improvement. I tried to specify the python_kernel in aizynthtrain/utils/configs.py in class TemplatePipelineConfig(BaseModel): like this python_kernel: str = "aizynthtrain" --> no improvement.
A check with the command (jupyter kernelspec list) showed me that the kernel exists. output = aizynthtrain /home/.local/share/jupyter/kernels/aizynthtrain
Hello.
We encountered the same issue with our internal setup, and we found a solution. It is not elegant but it works for now
The thing is that is requires a new feature in the papermill
package that has not been released, but this worked for us
conda activate aizynthtrain
python -m pip uninstall papermill
python -m pip install git+https://github.com/nteract/papermill.git
Thank you, this problem is solved on my side.
Hi, Seeking help with an issue on template extraction (step 4). A key seems to be missing from a dict. (see the attached)![error](https://github.com/MolecularAI/aizynthtrain/assets/13416443/6b3a3d94-03f4-446a-b8c2-95be22842e96)
Been able to generate the uspto mapped csv successfully.
Thanks.