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Local dataset #208
Local dataset #208
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Check out this pull request on See visual diffs & provide feedback on Jupyter Notebooks. Powered by ReviewNB |
Thanks @1511878618 will give this a review. @rg314 Paging for a consult on the failing docker build. It seems
Any ideas? |
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LGTM, happy to merge if we can resolve this docker issue - I think it's unrelated and probably caused by some version drift.
Thanks again for a great PR!
…ocal_dataset comment jupyter command of Dockerfile and just interact by shell or vscode remote ssh
Ok, I comment the jupyter command since i could use ssh or vscode to connect the container. The reason of the bug, i guess, is that no commands in Dockerfile would install jupyter-nbextension. And in my view, it is not necessary quesstion since it is a support for extension of jupyter notebook while jupyter lab may be a better choice of it.
I'll try to find which package for jupyter notebook and makes it works if we do use jupyter-nbextension.
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发件人: "a-r-j/graphein" ***@***.***>;
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主题: Re: [a-r-j/graphein] Local dataset (PR #208)
Thanks @1511878618 will give this a review.
@rg314 Paging for a consult on the failing docker build. It seems
RUN jupyter nbextension enable --py widgetsnbextension is throwing an error:
Jupyter command `jupyter-nbextension` not found. The command '/bin/sh -c jupyter nbextension enable --py widgetsnbextension' returned a non-zero code: 1 Service 'graphein-cpu' failed to build : Build failed
Any ideas?
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Hey @1511878618, I agree that it's unnecessary however I'd kept it in so the example notebooks could be run in a containerized environment out of the box. The reason being it make it really easy for new users to quickly spin up a container and have the code running. As you say jupyter lab might be a better choice but then you'd need to test that the notebooks run in the containerized env. I would just fix the line rather than commenting it out. I'll leave this up to @a-r-j Let me know if you have any other questions. |
And woooooops, i closed this comment. 🤣 I reopen it, and I commited the changes of Dockerfile, if you are interested it. |
Thanks @rg314 I'm inclined to leave it in (and it looks like @1511878618 has figured it out!). I'm just a little confused as to why this issue emerged now; perhaps it's been unbundled from some other dependency? This hasn't been a problem before and we've not touched dependencies/the dockerfile for quite some time. |
Maybe the version is not specified for these packages like below shows:
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I'm not much of a docker user but this sounds smart. If you and @rg314 agree on this then I'm happy to do that |
Off the top of my head I don't have a quick fix but I'm sure someone else has run into the same problem with the notebook. If you can fix by specifying the old version this would be good. From which line are you suggesting to move to Docker hub? It maybe that in the future the version of pytorch needs to be bumped with means someone would need to manage that image on docker hub (not ideal). If you can fix by setting the version that I can have a look in 3 hours. |
Ok, i'm not sure whether i can find the specific version of each package. Hmmmm, i think the best choice in my mind is add Actually, i have no idea about how to manage the version of packages which are needed in our project and how to make sure it still works with latest version of them. |
Looks like it's working. Would you be able to fix the failing dataloader test @1511878618 ? |
Ok, I'll try later, as i'm not familiar with pytest, so maybe a long time 🤣 |
Fixed in 1511878618#1 @1511878618. @a-r-j I also had to fix some bits with the SSL. I think there's something wrong with the SSL certs on regnetworkweb.org. |
Fixed Dockerfile and unit tests
Ok, Thanks a lot for this ! 👍 👍 |
Codecov Report
@@ Coverage Diff @@
## master #208 +/- ##
==========================================
+ Coverage 40.27% 47.86% +7.59%
==========================================
Files 48 92 +44
Lines 2811 5534 +2723
==========================================
+ Hits 1132 2649 +1517
- Misses 1679 2885 +1206
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Thanks for the great PR @rg314 @1511878618 |
SonarCloud Quality Gate failed.
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* add load local pdb_files to ProteinGraphDataset * load local pdb_files from a list * test and black and isort and add CHANGELOG.md * docstring formatting * comment jupyter; just run and ssh or vscode to interact with container * install dependency of jupyter nbextension * Fixed Dockerfile and unit tests * Update chage log Co-authored-by: xutingfeng <xutingfeng@big.ac.cn> Co-authored-by: Arian Jamasb <arjamasb@gmail.com> Co-authored-by: ryan <ryan.greenhalgh@hotmail.co.uk> Co-authored-by: Nicktf <49584439+1511878618@users.noreply.github.com> Co-authored-by: xutingfeng <xutingfeng@big.ac.cn> Co-authored-by: ryan <ryan.greenhalgh@hotmail.co.uk>
* fix disulphide bond node filtering #205 * Local dataset (#208) (#211) * add load local pdb_files to ProteinGraphDataset * load local pdb_files from a list * test and black and isort and add CHANGELOG.md * docstring formatting * comment jupyter; just run and ssh or vscode to interact with container * install dependency of jupyter nbextension * Fixed Dockerfile and unit tests * Update chage log Co-authored-by: xutingfeng <xutingfeng@big.ac.cn> Co-authored-by: Arian Jamasb <arjamasb@gmail.com> Co-authored-by: ryan <ryan.greenhalgh@hotmail.co.uk> Co-authored-by: Nicktf <49584439+1511878618@users.noreply.github.com> Co-authored-by: xutingfeng <xutingfeng@big.ac.cn> Co-authored-by: ryan <ryan.greenhalgh@hotmail.co.uk> * fix typo Co-authored-by: Nicktf <49584439+1511878618@users.noreply.github.com> Co-authored-by: xutingfeng <xutingfeng@big.ac.cn> Co-authored-by: ryan <ryan.greenhalgh@hotmail.co.uk>
Reference Issues/PRs
No related issues/PRs
What does this implement/fix? Explain your changes
support for loading local pdb files by
ProteinGraphDataset
andInMemoryProteinGraphDataset
.What testing did you do to verify the changes in this PR?
python -m py.test tests/
, a part result of testing is as below:Pull Request Checklist
./CHANGELOG.md
file (if applicable)./graphein/tests/*
directories (if applicable)./notebooks/
(if applicable)python -m py.test tests/
and make sure that all unit tests pass (for small modifications, it might be sufficient to only run the specific test file, e.g.,python -m py.test tests/protein/test_graphs.py
)black .
andisort .