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[Internship Project]: Zakia Yahya #713

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GemmaTuron opened this issue Jun 21, 2023 · 80 comments
Closed
5 tasks

[Internship Project]: Zakia Yahya #713

GemmaTuron opened this issue Jun 21, 2023 · 80 comments
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@miquelduranfrigola @GemmaTuron

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@GemmaTuron
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Summary

Hello,

This is a public issue for a virtual daily stand-up. We will use this to briefly share the tasks of the day and the challenges and advances made, so that we can ensure smooth support from the Ersilia mentors and alignment between daily tasks and overall internship goals.

Scope

Initiative 🐋

Objective(s)

Internship goals:

  • Learn how to work in an Open Source Community
  • Improve the infrastructure of the Ersilia Model Hub
  • Improve the usability and platform compatibility of Ersilia Models, mainly via Docker Images
  • Learn about AI/ML models for drug discovery
  • Identify new relevant AI/ML models and datasets and add them to this discussion
  • Incorporate new AI/ML models in the Hub
  • Improve the documentation of the Ersilia Model Hub for users
  • Improve the documentation of the Ersilia Model Hub for developers

Team

Role & Responsibility Username(s)
Intern @ZakiaYahya
Mentor @DhanshreeA
Coordinator @GemmaTuron

Timeline

Before starting your work, line up a few tasks and short description. This should not take long. For example, it could be something like:
Wednesday 21st June

  • Create Intern daily task tracker
  • Update the Ersilia GitHub Project
  • Make sure Git Actions start upon success of the other workflows
  • Work on the documentation for model testing
  • Attend the Drug Discovery intro by WCAIR

Documentation

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@GemmaTuron
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In this example, following the tasks of Wednesday 21st June:

  • Create Intern daily task tracker
  • Update the Ersilia GitHub Project
  • Make sure Git Actions start upon success of the other workflows
  • Work on the documentation for model testing
  • Attend the Drug Discovery intro by WCAIR

I have created all the templates for the Interns, spend a couple of hours revising the GitHub Project and updating the tasks. I have been working on identifying the bug in the GitActions, solved in this issue.
I have set a meeting with @miquelduranfrigola to discuss in detail his comments on the Model testing discussion but I haven't been able to start writing yet, i am to do so by the end of the week.
Looking forward to the WCAIR next lesson!

Pro tip: adding the links to the issues and discussions you mention will be very helpful!

@ZakiaYahya
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ZakiaYahya commented Jun 21, 2023 •
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@GemmaTuron @DhanshreeA

Today Tasks List: Wednesday, June 21, 2023

Model refactoring eos2r5e is still under work, try to complete it as soon as possible. Done testing of model eos31ve on CLI and COLAB, testing on DockerHub rightnow.
Thanks.

@GemmaTuron
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Great thanks Zakia, I am giving you an extra model just because won't be able to review until my morning tomorrow and you probably start working earlier than I do in your timezone. Just in case you finish your previous tasks

@GemmaTuron
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Hi @ZakiaYahya

Please look at this issue. There is so much more information you can add when a workflow is failing, I have written an example of the level of detail you should be aiming for, I hope this is helpful.

@ZakiaYahya
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ZakiaYahya commented Jun 22, 2023 •
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Hello @GemmaTuron @DhanshreeA

Today Tasks List: Thursday, June 22, 2023

  • Refactoring Model eos2re5
  • Refactoring Model eos2b6f
  • Testing Model eos5505

Due to slower network today, my work has been affected. I have done refactoring of model eos2re5 , it is working both locally and inside ersilia --repo-path, but unable to push changes till now due to internet. I'll open PR as soon as i successfully pushes the changes in the repo.
Now, working on model refactoring eos2b6f, try running it locally but encountering errors, working on it. Once i get why the error is happening i'll let you know in detail.
Trying to do model testing eos5505 simultaneously. Able to run it on colab somehow but due to unstable internet it is taking way too long in fetching from ersilia. Once it done i'll post the results in the relevant issue.
I hope my internet get stable by tomorrow.
Thanks.
Thanks.

@ZakiaYahya
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ZakiaYahya commented Jun 23, 2023 •
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Hello @GemmaTuron @DhanshreeA

Tasks List: Friday, June 23, 2023

Will try to work on ERROR: Could not install packages due to an OSError: [Errno 28] No space left on device on weekend.

@GemmaTuron
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Hi @ZakiaYahya !

Thanks, make sure to eliminate all the other Ersilia Models you have been working with running the ersilia delete command, and revise your conda envs as well after doing this. It will free up space in your system

@ZakiaYahya
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Hello @GemmaTuron
Right, i'll delete it all by today.
Thanks.

@DhanshreeA
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Hi @ZakiaYahya I went through your update on eos44zp. Your PR has been simply closed (and not merged) since the model was fairly recent and only required the missing workflow files. Gemma has added them in a separate commit.

Regarding eos2re5, I have left comments on the issue in that repository. The issues with docker build seem to be coming from using conda command through Docker's RUN directives. I will also have to look more into that - but for the time being I have linked a resource that should be useful in understanding what is going on. Also, the model isn't fully cleaned and there are a few more files that should be removed.

@ZakiaYahya
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ZakiaYahya commented Jun 26, 2023 •
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Hello @GemmaTuron @DhanshreeA

Tasks List: Monday, June 26, 2023

I have done model testing and Re-refactor model eos2b6f again with newer version of RDkit that is compatible. I have open PR on it. I'm currently working on model eos2re5 that is failing at after merging as well going through model eos44zp "Space allocation problem" as well but still didn't able to resolve it.
Thanks.

@GemmaTuron
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Hi @ZakiaYahya !
the space problem is related to GitHub actions, can you check for today's meeting what are the limits on Git Actions and we'll discuss what to do?

@ZakiaYahya
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Hello @GemmaTuron
Yes, i'm working on it. Different forums mention different cache sizes but most of them mentioned that they are now offering Upto 10Gb for workflow actions. I've gone through different forums, we will discuss it in today's meeting

@ZakiaYahya
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ZakiaYahya commented Jun 27, 2023 •
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Hello @GemmaTuron @miquelduranfrigola @DhanshreeA
After going into detail, i found three solutions to either free up pre-cached tools or by using swap space technique and i'll discuss it in today's general meeting these three workarounds
(1) Removing pre-cached tools from the github runner: actions/runner-images#2840 (comment)
(2) Adding Swap-Space: https://github.com/pierotofy/set-swap-space
(3) Deleting Pre-cached tools + Swap-space (by doing this available memory is around ~31GB): https://github.com/jlumbroso/free-disk-space/releases/tag/v1.1.0

Thanks

@miquelduranfrigola
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This is great stuff, @ZakiaYahya - I have never explored these options. Let me invoke @honeyankit and @GrantBirki from GitHub, let's see if they have additional feedback.

@ZakiaYahya
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Thank @miquelduranfrigola
Yeah sure, it would be very helpful.

@GrantBirki
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Hey there! I have never explored these options either so I would be curious to follow along with your PRs and see how it all works!

@ZakiaYahya
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ZakiaYahya commented Jun 27, 2023 •
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Hello @GemmaTuron @DhanshreeA

Tasks List: Tuesday, June 27, 2023

Try to search more workaround on Out-of-Memory problem in github actions. Will work on new model refactoring eos46ev tomorrow. Model eos2v11 is still under working, so once it done, i'll test it.
Thanks.

@miquelduranfrigola
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Thanks @ZakiaYahya - awesome progress

@ZakiaYahya
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ZakiaYahya commented Jun 28, 2023 •
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Hello @GemmaTuron @DhanshreeA

Tasks List: Wednesday, June 28, 2023

Model eos2re5: After changes and open PR again, it still fails at "Upload to DockerHub" but now it's not giving previous error i.e. CommandNotFoundError: Your shell has not been properly configured to use 'conda activate'., now it's giving different error but still related to conda i.e. 'CondaEnvironmentService' object has no attribute 'pid'. Still working on this.

Didn't able to do some work on Out-of-Memory issue in model eos44zp, will do it once done with model refactoring eos46ev.
Thanks.

@GemmaTuron
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@ZakiaYahya !

Great progress, a lot on your plate so don't worry, focus on the issues one by one. If you need help with the eos46ev ping me and I'll try to provide further guidance I won't be assigning new models to you so you can focus on the eos44zp

@ZakiaYahya
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Thanks @GemmaTuron
I'll try to first test eos46ev with latest ersilia version. Then i'll let you know. It seems like @Febie is also encountering the same problem as i encountered in eos46ev. Regarding model eos44zp, i'm thinking of trying swap-space workaround rather than deleting pre-cached tools as it deletes some of packages that we required like python.

@ZakiaYahya
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ZakiaYahya commented Jun 29, 2023 •
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Hello @GemmaTuron @DhanshreeA

Tasks List: Thursday, June 29, 2023

Tested eos46ev for various single smile inputs updated here. Now i'm focusing on above mentioned three unresolved issues.
Thanks.

@GemmaTuron
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Thanks for the update @ZakiaYahya !
I'll test eos46ev on my side as well

@ZakiaYahya
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ZakiaYahya commented Jun 30, 2023 •
edited by DhanshreeA
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Hello @GemmaTuron @DhanshreeA

Tasks List: Friday, June 30, 2023

Open PR again on model eos44zp with added swap-space. Working on conda-issue in model eos2re5. Let me know @GemmaTuron when you test single inputs for model eos46ev, i've kept it in hold for now. Will start working on model refactoring eos6pbf once done with conda-issue.
Thanks.

@ZakiaYahya
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ZakiaYahya commented Jul 3, 2023 •
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Hello @GemmaTuron @DhanshreeA

Tasks List: Monday, July 3, 2023

Did model refactoring eos6pbf and open PR on it today. Modified test-model.yml for model eos44zp as discussed and open PR on it. Tested model eos7asg and update it on relevant issue. Working on model investigation eos46ev in detail, along with working on conda-issue in model eos2re5 as well.
Thanks

@GemmaTuron
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Hi @ZakiaYahya

The space in git actions is not easy to solve, let's try to talk about it today in the meeting. Focus for today on investigating the eos46ev and the conda issue on eos2re5 and if you are done with all let me know!

@ZakiaYahya
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Right @GemmaTuron, I'm working on it. Will let you know once it done.
Thanks.

@DhanshreeA
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DhanshreeA commented Jul 4, 2023 •
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Sorry for hijacking the conversation here a bit, but @GrantBirki could you tell us how much persistent storage space do GitHub runners get on our plan? I couldn't find much that says anything about it. I ask because configuring any amount of swap space would be limited by how much storage we actually have. And can we increase it, if yes, how? And is it possible to increase it specifically for a single model repository and not all of them?

@ZakiaYahya
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ZakiaYahya commented Jul 18, 2023 •
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Hello @GemmaTuron @DhanshreeA

Tasks List: Monday, July 17, 2023

Model eos1579: Today i tried different versions of signaturizer (1.1.11 and 1.1.13), as tensorflow-Hub install automatically with version 0.14.0 and it requires protobuf version >=3.19.6 which is not compatible with bentoML as it requires protobuf version >=3.8,<3.19, so here the clash occurs. As ersilia automatically resolves clashes that occur between bentoML and protobuf so i search on tensorflow-hub that fits with protobuf version that is compatible with bentoML too. The installed version of tensorflow-Hub is 0.14.0 which is the latest one so I tried degrading the tensorflow-Hub manually in Dockerfile to version 0.12.0 which requires protobuf version 3.17.3 which is also compatible with bentoML requirements but somehow it is not working either, i'm still working on it.

Thanks

@ZakiaYahya
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ZakiaYahya commented Jul 18, 2023 •
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Hello @GemmaTuron @DhanshreeA

Tasks List: Tuesday, July 18, 2023

Model eos1579: Done quite a lot of debugging in resolving protobuf-bentoML-tensorflow-HUB dependancy issue but the problem that causes the model to fail in Ersilia CLI is in service.py, as the service.py is doing slicing on wrong input list which is empty that's why it is giving Cannot choose from an empty sequence. Model is working now and i've open PR on it as well,, i've explained all changes and how i resolved errors in detail here

Will start working from tomorrow on Clean UP & Dockerization eos481p, Debugging Model eos7ack and Model Testing eos5axz.
Thanks.

@ZakiaYahya
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ZakiaYahya commented Jul 19, 2023 •
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Hello @GemmaTuron @DhanshreeA

Tasks List: Wednesday, July 19, 2023

Tested above models and updated on relevant issues. Working on model refactoring eos481p.

@ZakiaYahya
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ZakiaYahya commented Jul 20, 2023 •
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Hello @GemmaTuron @DhanshreeA

Tasks List: Thursday, July 20, 2023

Model eos481p: Done refactoring of model eos481p and open PR on it as well.
Model eos5axz: Re-tested the model as yesterday it was giving me errors and it was due to AirTable as it was down temporarily. It is working fine on CLI, COLAB and DockerHub.
Today's Meeting: Prepare slides for today's presentation and attend the weekly lab meeting

Kindly assign me new models to work on it.
Thanks.

@ZakiaYahya
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ZakiaYahya commented Jul 21, 2023 •
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Hello @GemmaTuron @DhanshreeA

Tasks List: Friday, July 21, 2023

Model eos8a5g: Refactor the model and tested it with few smiles and even with eml_canonical to ensure that model is working. Tested the model both with run.sh and --repo-path before and after refactoring. The model is working fine. I've Open PR on it.
Model eos9taz: Tested the model before refactoring but didn't understand the outputs it returns. Understanding the model layout.
Model eos7ack: Cloned the repo and tested it with run.sh and --repo-path and with both few smiles and with eml_canonical. It seems like that the model is working fine with few inputs but not not with larger inputs but the problem didn't lies in model coding, it basically the SwissAdme that process few inputs at a time, with larger inputs the server return empty response and hence getting error "empty sequence". But i'll dig more into this model to confirm this thing.

Thanks.

@ZakiaYahya
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ZakiaYahya commented Jul 24, 2023 •
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Hello @GemmaTuron @DhanshreeA

Tasks List: Monday, July 24, 2023

Model eos2re5: Testing it again on CLI, DockerHUB and COLAB to check the issue using ersilia fetch api.
Model eos9taz: First stuck in model understanding conceptually. After that, i'm now refactoring the model, as main.py requires a bit a lot changes in it because initially the code didn't contain any bash file to run main.py. main.py is using argument parser to take Model_path, input_file and Output_file. Need to remove that part so that arguments can pass through run.sh, i'm working on it.

Thanks.

@GemmaTuron
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Hi @ZakiaYahya

Thanks, I've added a new model in case you finish the current one

@ZakiaYahya
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Right @GemmaTuron
Almost done with model eos9taz, just making final commits then will start working on new model.
Thanks

@ZakiaYahya
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ZakiaYahya commented Jul 25, 2023 •
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Hello @GemmaTuron @DhanshreeA

Tasks List: Tuesday, July 25, 2023

@ZakiaYahya
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ZakiaYahya commented Jul 26, 2023 •
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Hello @GemmaTuron @DhanshreeA

Tasks List: Wednesday, July 26, 2023

Model eos4q1a: I have tested the model before doing refactoring the model and it is working fine with run.sh, giving upto 100 generated molecules as a separte columns in output file but when i tested it with Ersilia it is giving me correct output, giving me upto 100 generated molecules as well but in a list format in a single column , not in individual columns. So i'm trying to fix it in service.py before doing refactoring. Here's the detail ersilia-os/eos4q1a#12 (comment)

Model eos2re5: Figure out the First-null-entry issue in the output. It basically stores an extra smiles column in dataframe, which we don't needed in case of fetching from Ersilia as ersilia automatically appends key and input column in a output and input column is basically smiles. So, i just discarded storing smiles in a dataframe in main.py and it is working fine with run.sh, just need to ensure that by testing it with repo-path, so currently i'm fetching the model which took time in case of eos2re5 due to dependancies installation, once it done i'll Open the PR again on it.

Thanks.

@ZakiaYahya
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ZakiaYahya commented Jul 27, 2023 •
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Hello @GemmaTuron @DhanshreeA

Tasks List: Thursday, July 27, 2023

Model eos9be7: I have start working on the model, the model is not working even before refactoring due to input format it requires, i have posted some queries on the issue, kindly check it at ersilia-os/eos9be7#1 (comment)

Thanks

@ZakiaYahya
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ZakiaYahya commented Jul 28, 2023 •
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Hello @GemmaTuron @DhanshreeA

Tasks List: Friday, July 28, 2023

Model eos9be7: I have done nothing much today due to unavailability of internet. Trying to parse the data from json input file and getting the fcd scores. The json file is loaded successfully but the fcd is taking it as atom by atom not smiles by smiles. So, basically i'm stuck here. Going through original code to figure it out.

Latest Update: Able to figure it out the correct format of json file to input to main.py, The json file should contain a list that has pair of smiles, for calculation of fcd scores. I've updated in detail at the issue here

Thanks

@ZakiaYahya
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ZakiaYahya commented Jul 31, 2023 •
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Hello @GemmaTuron @DhanshreeA

Tasks List: Monday, July 31, 2023

Model eos9be7: Model is working with run.sh for few smiles as well as for eml_canonical. Incorporated following things in main.py

  1. To start taking CSV file of smiles as an input instead json.
  2. Convert smiles from CSV to pair of smiles so that model handles the input format. In order to avoid the conflict of odd number of smiles from CSV, i incorporated this approach such that if there is N number of smiles in a CSV file, the number of pairs created in JSON file is N-1 regardless of even/odd number of smiles
 [
  ["SMILES1", "SMILES2"],
  ["SMILES2", "SMILES3"],
  ...
]
  1. Store that pairs of smiles in a JSON file and save it in a working directory at the backend for better understanding of pairs creation for new users.
  2. Read that JSON file and handle exceptions like if data is not in a correct format or the file is not present in the directory.
  3. Delete JSON file if needed.

I'm now trying to make this main.py run with --repo-path.
Thanks.

@GemmaTuron
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Hi @ZakiaYahya
Great job, I have merged all your PRs, and assigned some models to test

@ZakiaYahya
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ZakiaYahya commented Aug 1, 2023 •
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Hello @GemmaTuron @DhanshreeA

Tasks List: Tuesday, August 1, 2023

Today most of the time spend meetings and in debugging eos9be7 for input format, and understanding the bentolite.

@ZakiaYahya
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ZakiaYahya commented Aug 2, 2023 •
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Hello @GemmaTuron @DhanshreeA

Tasks List: Wednesday, August 2, 2023

Model Testing: Tested all assigned models i.e. eos1bba, eos157v and eos9c7k on CLI, COLAB and DockerHUB
Model eos9be7: Make it work for multiple inputs in JSON format with runs.h. Replace NAN/inf fcd_scores with None in output, having few queries that i updated at github issue here
Bentolite: Didn't able to work on it, as i was stuck in Docker issue and Colab pyairtable issue and then in model testing. After that did worked on model eos9be7.

@ZakiaYahya
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ZakiaYahya commented Aug 3, 2023 •
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Hello @GemmaTuron @DhanshreeA

Tasks List: Thursday, August 3, 2023

Working on eos9be7, the model is working with both fcd_canonical and fcd_canonical_smiles with run.sh.
Worked on Bentolite today.
Working on model eos9taz to format the output structure.

@ZakiaYahya
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ZakiaYahya commented Aug 4, 2023 •
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Hello @GemmaTuron @DhanshreeA

Tasks List: Friday, August 4, 2023

@ZakiaYahya
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ZakiaYahya commented Aug 7, 2023 •
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Hello @GemmaTuron @DhanshreeA

Tasks List: Monday, August 7, 2023

Model eos9be7: I did model refactoring today, The model is working fine both with run.sh and --repo_path but with JSON file as an input. Waiting for final comments either to make changes to make it work with CSV file as an input as CSV is not parsing that smiles that have dot . operand in it but JSON is. Once it decide i proceed it further.

Model eos9taz: I debugg output format, and the problem is in service.py as it stores generated smile in a list in a output file rather than just simply gives string of smile in a separate column, i did necessary changes in it and make it work so that it simply return a smile string without list in the final output.

Bentolite: Working on Bentolite. Had a meeting with miquel today, and we just start testing the changes we have made in Bentolite with model eos7uix which is test model, just to ensure that whether the refactored Bentolite works with Ersilia or not. It is not working with Ersilia rightnow, so we are just debugging things and doing further refactoring.

@ZakiaYahya
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ZakiaYahya commented Aug 8, 2023 •
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Hello @GemmaTuron @DhanshreeA

Tasks List: Tuesday, August 8, 2023

@GemmaTuron
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Hi @ZakiaYahya

I think there are a few model testings assigned to you inaddition to the BEntoLite task. Let me know how you are progressing there!
Also, in addition to your tasks, please try out the test module developed by Riley and Febie and provide feedback in the Slack thread, specifying which model did you test, and if you have any further suggestions for improvement. Thanks!

@ZakiaYahya
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ZakiaYahya commented Aug 9, 2023 •
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Hello @GemmaTuron @DhanshreeA

Tasks List: Wednesday, August 9, 2023

Model eos9be7: I've modified the main.py to read CSV as an input. and it is working fine with run.sh but with --repo-path i got errors while parsing smile_1 and smile_2 in Ersilia CLI while fetching. First i passed this step then i'll try to discard the smiles having dot inside.

Bentolite: Working on bentolite to test model eos7uix but it is giving errors as some config files i.e..cfgfiles are not actually copying from Bentolite to the installed version of Bentolite inside model env created while fetching the model in Ersilia CLI.

Model Testing: Tested the model eos43at in CLI, COLAB and DockerHub. It is working and giving consistent output as well.

Test module: I've tested the new "test module" using model eos3b5e and eos8a5g and the it is working perfectly.

Thanks

@ZakiaYahya
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Hello @GemmaTuron
Yes, i have one model assigned as Model Testing i.e. eos43at, which i'll do it by today. Just updated my Task List for today. Apart from that i'll test the Riley's model as well.
Thanks.

@ZakiaYahya
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ZakiaYahya commented Aug 10, 2023 •
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Hello @GemmaTuron @DhanshreeA

Tasks List: Thursday, August 10, 2023

Model eos9be7: So, i've make the code work with run.sh with changes in main.py so it takes multiple inputs from CSV file rather than JSON. But as service.py is working woth JSON, so model is failing at fetch time with --repo-path. So, i did changes in it but somehow it still not processing smile_1 and smile_2 format at Ersilia CLI. Need help there because i'm stuck here now but i'm trying still to make it work.

Bentolite: Didn't able to resolve configuration files issue as it is not copying while installing, Need suggestion from Miquel to proceed.

Thanks

@ZakiaYahya
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ZakiaYahya commented Aug 11, 2023 •
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Hello @GemmaTuron @DhanshreeA

Tasks List: Friday, August 11, 2023

Model eos9be7: Trying to figure out why Ersilia is not processing multiple_inputs as in my understanding from serve.log there is something wrong with service.py or it's inference_api.py that is not parsing smiles in a format smile_1 and smile_2. Looking further into it. Suggestions required.

Bentolite: Just had a meeting with Miquel and discussed .cfg problem with him, He's now further inverstigate the problem and then i'll proceed it.

Thanks

@ZakiaYahya
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ZakiaYahya commented Aug 14, 2023 •
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Hello @GemmaTuron @DhanshreeA

Tasks List: Monday, August 14, 2023

@ZakiaYahya
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ZakiaYahya commented Aug 16, 2023 •
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Hello @GemmaTuron @DhanshreeA

Tasks List: Tuesday, August 15, 2023

@ZakiaYahya
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Hello @GemmaTuron @DhanshreeA

Tasks List: Wednesday, August 16, 2023

@GemmaTuron
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Hi @ZakiaYahya !
It was great to work with you, thanks so much for your contributions to Ersilia, we hoped you learnt and enjoyed as much as we did! Please, remain engaged with the community and feel free to open any issues or contribute to open ones :)
I'll now close this issue as completed !

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@DhanshreeA @miquelduranfrigola @GrantBirki @ZakiaYahya @GemmaTuron