Add a Python parser for diag.out files and fix header formatting

[yut23]

PR summary

This PR adds some Python code that can parse the files and sanitize any duplicate entries (which often occurs when a run is restarted from an earlier checkpoint). It also fixes some mistakes in the gravity_diag.out header formatting, and cleans up some of the other header-writing code.

Additional details

N.B.: Standard streams in C++ are right-justified by default (compared to Python, where numbers are right-justified and strings are left-justified).

• update the header printing code for gravity_diag.out to match the others (the column numbers were 26 characters long instead of 25, and number 8 was missing)
• simplify species formatting for species_diag.out (the previous code was just adding leading spaces)
• update the header field widths for amr_diag.out to match what's used for the data

PR checklist

• test suite needs to be run on this PR
• this PR will change answers in the test suite to more than roundoff level
• all newly-added functions have docstrings as per the coding conventions
• the CHANGES file has been updated, if appropriate
• if appropriate, this change is described in the docs

[zingale]

can you add a short description to the docs about this, perhaps in the visualization section, along with an index entry for the diag files.

[zingale]

Oh, actually it looks like this is the place in the docs:

https://amrex-astro.github.io/Castro/docs/io.html#index-9

[aisclark91]

I just wonder if the source driver modifications alter the output file (adding or removing spaces, etc)?

[yut23]

I just wonder if the source driver modifications alter the output file (adding or removing spaces, etc)?

The gravity_diag.out column numbers are the only things that get changed in the outputs.

[aisclark91]

I approve your PR, my only worry is if this script will work with the existing version of the logs, or with the suggested change version of them?

[yut23]

I made sure it works with both.