Inclusion of an overhauled version of the first PyXspec walkthrough notebook

[DavidT3]

The first step in making the PyXspec tutorials and demonstrations available through HEASARC-tutorials (and thus on Fornax as well), a revamped version of the first PyXspec walkthrough notebook.

The overall content currently remains the same, no major sections have been added or removed (though we might consider some changes on that front).

All plotting code has been altered.

Some previous bugs have been fixed (the contour plot had mislabeled axes, and wasn't showing the 1, 2, and 3 sigma levels that was claimed in the commentary).

More commentary has been added at certain points.

The notebook has been put into the markdown format required by HEASARC-tutorials, and now matches the template in style. Sections and subsections have been introduced.

Science review checklist

• Does using high-energy data make up a significant part of the tutorial?
• Is there a use case in the introduction that motivates the code?
• Does the code do what the introduction says it is going to do?
• Is it scientifically accurate?
• Have all necessary references to literature been included?

Formatting checklist

• Did you base your notebook on the HEASARC-tutorials template?
• Are all sections in the HEASARC-tutorial template included in your notebook?
• Is the notebook title compact and informative? It will be the name of the notebook on the HEASARC website!
• Have you populated the notebook front-matter (the metadata at the top of the notebook)?
• Is the kernel specified in the front-matter (e.g., heasoft, sas, ciao) correct for the notebook?
• Have you added an entry for your notebook in the *_index.md file for the containing directory?
• Is all plotting matplotlib (or alternative) plotting code in isolated cells, and do they have the metadata required to collapse the code when the notebook/website is viewed?

Tech review checklist

• Documentation:
  • Is every function documented?
  • Do all code cells have corresponding narratives/comments?
  • Are all code comments of a purely technical nature? All narratives should be in Markdown cells.
  • Did you populate the 'Runtime' section?
• Notebook execution, error handling, etc.:
  • Does the notebook run end-to-end, out of the box?
  • Are errors handled appropriately, with try/except statements that are narrow in scope?
  • Have warnings been dealt with appropriately, preferably by updating the code to avoid them (i.e., not by simply silencing them)?
• Efficiency:
  • Is data accessed from the cloud where possible?
  • Is the code parallelized where possible?
  • If the notebook is intended to be scaled up, does it do that efficiently?
  • Is memory usage optimized where possible?
• Cleanup:
  • Have blocks of code that need to be re-used been turned into functions and placed in the 'global setup'-'function' section?
  • Has unused code been removed (e.g., unused functions and commented-out lines)?
  • Are comment lines wrapped so all fit within a max of 90 - 100 characters per line?
  • Do plots use color-blind friendly palettes for plotting? Try this simulator for a visual check.

[DavidT3]

Happily it executed fine - time for polishing.

I've added the 'skip-doc-build' label to disable triggering automatic rebuilds on any commits I make until the badge is removed. The free resources we get from CircleCI are limited, so we try to be as efficient as possible.

[DavidT3]

**The nH problem - ** the notebook points to a column density value of $4x10^{22}$, but I'm not sure where that comes from. The nhtool (from all 3 currently available maps) result is around 1.25

This is an important part of the demonstration that leads into showing how/why you might construct and fit a two-additive-component model, but the reason may be a little artificial as it stands.

I would be alright with that, but actually in the new version of the separate-model-component plot I also show the data, and it is still a pretty poor fit at the low end. Possible some of this is driven by my changing to TBabs, but something needs to change about this I think.

I'll see how fixing it at the current nH result from nhtool changes things.

[DavidT3]

@xspector @krutkow @c181gordon

I've added you all as potential reviewers - the notebook as it stands is pretty complete, though I admit that I now have XSPEC/notebook fatigue and it might still need some more attention particularly towards the end.

Something I wanted to talk about is the multi-additive-component model demonstration in this notebook; the column density currently used for the fixed nH is quite a bit larger than the current HI4PI value from nH, which sort of undermines the point being made about how the absorbed powerlaw is under predicting soft counts (particularly because the two-additive-component fit doesn't look like much of a better fit).

Clearly the tutorial needs a demonstration of a two continuum component fit, but any thoughts on what we should do about that?