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animikhroy / rk_toolkit_pipeline_diagrams

Master-repository for all code related to "A Novel Approach to Topological Graph Theory with R-K Diagrams and Gravitational Wave Analysis"
https://arxiv.org/abs/2201.06923
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R-K Workbench Missing #17

Closed animikhroy closed 2 years ago

animikhroy commented 2 years ago

@andorsk upon review there's always been an important section of the paper involving the R-K Workbench that was referenced in multiple sections including the Novel Approach, Computational Pipeline and Case Studies. I have added this to the documentation and methods google doc (https://docs.google.com/document/d/1dB_YSAV-rW3i0Jk1aHKDU5fPjcrS1OZlqdVvUJiGWx0/edit?usp=sharing) that @Ashxyz998 and I are currently preparing as follows:

R-K Workbench:

In order to help users get started quicker, we provide a docker image called R-K Workbench (https://github.com/andorsk/rk-workbench) which wraps the ML-Workspace (https://github.com/ml-tooling/ml-workspace) with packages relevant to building R-K Models and R-K Diagrams built into the core image. The README file contains details on how to use it for the purpose of independent use by researchers and programmers to customize and apply the R-K Pipeline to various scientific and business use-cases.

However, I can't seem to find the relevant code with the docker image that was previously provided on this link: https://github.com/ml-tooling/ml-workspace as referenced in our paper and wanted to seek your help in locating that page with its corresponding files for adding it to the R-K Toolkit folder on this repo: https://github.com/animikhroy/rk_toolkit_pipeline_diagrams/

We can update the link on the documentation accordingly.

andorsk commented 2 years ago

I added you to the repo. https://github.com/andorsk/rk-workbench/

ghost commented 2 years ago

Hey Andor, can I have the access to the workbench too, @animikhroy asked me to add it to the rktookit submodule

animikhroy commented 2 years ago

@Ashxyz998 Thanks for the update! Could you please delete this comment form this issue and add it to the issue #15 instead of this one? You may tag us both there instead of here for the review thanks!

andorsk commented 2 years ago

@Ashxyz998 added you to the Workbench too

andorsk commented 2 years ago

I'm closing the issue, as both you guys have access to the repo.

animikhroy commented 2 years ago

@andorsk Thanks I have access to the main repo now but I have other access issues and concerns form the peer reviewers' POV for the rk-workbench even after forking the repo as listed below:

1) There is a help me find things section with links to these items listed below BUT there is no access to the following sections:

  1. [Documentation]()
  2. [RK Toolkit API]()
  3. [User Guide]()
  4. [Examples]()

So clicking on them shows the page not found error message.

2) The examples folder has the store_sales repo as a submodule but there is no access to that either and I do not know exactly which version this is so I would request to update the link and redirect it to the new store sales code in : https://github.com/animikhroy/rk_toolkit_pipeline_diagrams/tree/main/02_notebooks/rk_general_applications or suggest an appropriate alternative for all the examples and references to store sales in the rk-workbench repo such as in case of .gitmodules and requirements.txt,

3) The Docker File and a few other places have direct references to andor@henosisknot.com however this link is also currently invalid so I would request to update this with something valid for reference purposes.

animikhroy commented 2 years ago

@andorsk @Ashxyz998 I have reopened this issue to address my concerns in the above comment and they are mostly directed to @andorsk to provide clarity and guidance in order to address the 3 problems. @Ashxyz998 can help to address some of these issues if required but I would let @andorsk take that call!

andorsk commented 2 years ago
  1. @animikhroy you are already a member of the store_sales repo. Not all the links are live/work because they were probably placeholders for a TODO that was never done.
  2. You do have access to the store_sales sub module and it was linked correctly over git. https://github.com/andorsk/store_sales/tree/ac255de1f07798454504dabeec1641a5c3cdf514 That being said: This is really old. Most of it has been migrated to the updated notebook. I would suggested just tossing that example and using the other example, that we used for the notebook, as a reference point.
  3. The dockerfile has a reference to the maintainer: MAINTAINER Andor Kesselman andor@henosisknot.com. That's standard. Not sure what you're asking about here.
animikhroy commented 2 years ago
  1. @animikhroy you are already a member of the store_sales repo. Not all the links are live/work because they were probably placeholders for a TODO that was never done.

@andorsk I am a member correct but that is a private repo and the peer-reviewers will not have access to it hence I wanted to seek an alternative. Now that you mention it I understand the issue is that:

  1. [Documentation]()
  2. [RK Toolkit API]()
  3. [User Guide]()
  4. [Examples]()

All of the above was perhaps kept as TODO. So could you guide @Ashxyz998 to briefly add some relevant content for some of the items to be accepted by peer reviewers and then delete the rest of the items on the list to keep things clean and ready for peer review!

  1. You do have access to the store_sales sub module and it was linked correctly over git. https://github.com/andorsk/store_sales/tree/ac255de1f07798454504dabeec1641a5c3cdf514 That being said: This is really old. Most of it has been migrated to the updated notebook. I would suggested just tossing that example and using the other example, that we used for the notebook, as a reference point.

@andorsk I agree with the part that most of it is really old and may not be valid hence I suggested updating the link to the new notebook section on https://github.com/animikhroy/rk_toolkit_pipeline_diagrams/tree/main/02_notebooks/rk_general_applications

should @Ashxyz998 go ahead with this?

  1. The dockerfile has a reference to the maintainer: MAINTAINER Andor Kesselman andor@henosisknot.com. That's standard. Not sure what you're asking about here.

I understand it is standard but your website was not working at that time so the link to it was showing invalid. But I just crosschecked and https://www.henosisknot.com/ is now working okay so ignore this point. No further issues!

andorsk commented 2 years ago

@

  1. @animikhroy you are already a member of the store_sales repo. Not all the links are live/work because they were probably placeholders for a TODO that was never done.

@andorsk I am a member correct but that is a private repo and the peer-reviewers will not have access to it hence I wanted to seek an alternative. Now that you mention it I understand the issue is that:

  1. Documentation
  2. RK Toolkit API
  3. User Guide
  4. Examples

All of the above was perhaps kept as TODO. So could you guide @Ashxyz998 to briefly add some relevant content for some of the items to be accepted by peer reviewers and then delete the rest of the items on the list to keep things clean and ready for peer review!

@animikhroy all these repos are private. If you want to add peers to them you have 2 options:

  1. Make them public ( which as public research, I don't see why you wouldn't ).
  2. Add them to the repo directly.

re: the 1-4, there is nothing specifically. At the bullets are for the most part, self describing of what would need to go into it. There is too many items to bullet. Either take out 1-4, or just work within the intent of the bullet with more specific questions passed if needed.

  1. You do have access to the store_sales sub module and it was linked correctly over git. https://github.com/andorsk/store_sales/tree/ac255de1f07798454504dabeec1641a5c3cdf514 That being said: This is really old. Most of it has been migrated to the updated notebook. I would suggested just tossing that example and using the other example, that we used for the notebook, as a reference point.

@andorsk I agree with the part that most of it is really old and may not be valid hence I suggested updating the link to the new notebook section on https://github.com/animikhroy/rk_toolkit_pipeline_diagrams/tree/main/02_notebooks/rk_general_applications

should @Ashxyz998 go ahead with this?

yes. the example should be updated.

  1. The dockerfile has a reference to the maintainer: MAINTAINER Andor Kesselman andor@henosisknot.com. That's standard. Not sure what you're asking about here.

I understand it is standard but your website was not working at that time so the link to it was showing invalid. But I just crosschecked and https://www.henosisknot.com/ is now working okay so ignore this point. No further issues!

@animikhroy the website should have no relevance to the maintainers email address. As long as the email address works, that's the point. If it's bugging you we can take it out, though there's no reason to do that IMO.

andorsk commented 2 years ago

Creating these issues: https://github.com/andorsk/rk-workbench/issues/1 https://github.com/andorsk/rk-workbench/issues/2

animikhroy commented 2 years ago

@andorsk

1)

a) I do intent to make the following repo: https://github.com/animikhroy/rk_toolkit_pipeline_diagrams public before the peer review submission so this should address the issue.

b) I will review with @Ashxyz998 and get back to you regarding 1-4.

2) Thanks for the confirmation I'll ask @Ashxyz998 to update the example accordingly.

3) It's not bugging me its working fine! lets keep that as it is and as you mentioned the email is also working perfectly at your end so no changes required for this.

andorsk commented 2 years ago

@animikhroy since the initial issue was "R-K Workbench Missing" and that's been resolved, mind if I close out this issue. If there is another issue you can open a new issue. We are very tangent to the original issue description right now.

animikhroy commented 2 years ago

@andorsk I agree now that you have made separate issues on your Github repo that should address my concerns. Could you please assign @Ashxyz998 to those issues and then close this issue? That should be perfectly fine thanks!