Added HDF documentation.

airvzxf commented 3 months ago

:pencil: Description

Type: :memo: documentation

Write a complete description of your changes, including the necessary context or any piece of information required to understand your work.

Added the HDF documentation with two main sections: the overview and the extraction of the data in the H5 files.

Also, link issues affected by this pull request by using the keywords: close, closes, closed, fix, fixes, fixed, resolve, resolves or resolved.

:pushpin: Resources

Examples, notebooks, and links to useful references.

Screenshot of my local server

:vertical_traffic_light: Testing

How did you test these changes?

[ ] Testing pipeline
[x] Other method (describe): Manual, I build the docs and run on the local server.
[ ] My changes can't be tested (explain why)

:ballot_box_with_check: Checklist

[ ] I requested two reviewers for this pull request
[x] I updated the documentation according to my changes
[x] I built the documentation by applying the build_docs label

Note: If you are not allowed to perform any of these actions, ping (@) a contributor. @wkerzendorf @andrewfullard @atharva-2001

tardis-bot commented 3 months ago

*beep* *bop*

Hi, human.

The docs workflow has succeeded :heavy_check_mark:

Click here to see your results.

atharva-2001 commented 3 months ago

I'm afraid I can't see the documentation on the website sent by the bot. Is the bot not working correctly? @KasukabeDefenceForce

KasukabeDefenceForce commented 3 months ago

I'm afraid I can't see the documentation on the website sent by the bot. Is the bot not working correctly? @KasukabeDefenceForce

The issue is here, when the LFS setup step is run it checks out the main repo, which is why the documentation generated is based upon the files in the master. https://github.com/tardis-sn/tardis/actions/runs/9266497498/job/25490895572?pr=2630#step:5:15

codecov[bot] commented 3 months ago

Codecov Report

All modified and coverable lines are covered by tests :white_check_mark:

Project coverage is 67.76%. Comparing base (199b03f) to head (0843a55).

:exclamation: Current head 0843a55 differs from pull request most recent head 022f077

Please upload reports for the commit 022f077 to get more accurate results.

Additional details and impacted files

```diff @@ Coverage Diff @@ ## master #2630 +/- ## ======================================= Coverage 67.76% 67.76% ======================================= Files 171 171 Lines 14411 14411 ======================================= Hits 9765 9765 Misses 4646 4646 ```

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jvshields commented 2 months ago

This looks really good to me! My one comment is that I'm not sure the "Extract Data" section really belongs here, or does a great job explaining how to use hdfs in tardis. What's currently there seems more specific to our regression testing, but I don't think somebody would go to the HDF section under I/O to try to find this type of information, and I think a better thing to have here would just be an example of reading an hdf and showing its contents.

airvzxf commented 2 months ago

This looks really good to me! My one comment is that I'm not sure the "Extract Data" section really belongs here, or does a great job explaining how to use hdfs in tardis. What's currently there seems more specific to our regression testing, but I don't think somebody would go to the HDF section under I/O to try to find this type of information, and I think a better thing to have here would just be an example of reading an hdf and showing its contents.

I could split this comment into two different parts. One is the location for this information and the other for the content of this section.

Talking about the location, this is the general structure:

Installation
Quickstart for TARDIS
Tutorials
How-To Guides
Frequently Asked Questions
API

Input/Output
    Configuration (Required Input)
    Reading Models
    Optional Inputs
    Visualization Tools & Widgets
    Additional Outputs

Physics Walkthrough
    Physics Walkthrough Introduction
    Setting Up the Simulation
    Monte Carlo Iteration
    Updating Plasma and Convergence
    Spectrum Generation

Contributing to TARDIS
    Contribution Guidelines
    Developer Workflow
    Developer Tools
    Change Log
    Features In-Progress

Other Resources
    Credits & Publication Policies
    Papers Using TARDIS
    Code Comparison
    References and Glossary

What could be the best place to insert it?

tardis-sn / tardis