Update dev manual scripts for python3

[mlouielu]

Summary of this Pull Request (PR)

Update dev manual scripts for python3.

This PR tend to addressed #433 (comment) issue for Python 3 to build dev manual.

The major consideration is the different behavior (I didn't take a close look, but I believe is because set/dict ordering, Python 3 ensure dict order) causing dot file difference: #433 (comment)

Intent for your PR

Choose one (Mandatory):

• This PR is for a code-review and is intended to get feedback, but not to be pulled yet.
• This PR is mature, and ready to be integrated into the repo.

Reviewers (Mandatory):

@gparmer

Code Quality

As part of this pull request, I've considered the following:

Style:

I am using psf/black for style format. This can be removed by dropping c4de0ef

Code Craftsmanship:

• [-] I've made an attempt to remove all redundant code
• [-] I've considered ways in which my changes might impact existing code, and cleaned it up
• [-] I've formatted the code in an effort to make it easier to read (proper error handling, function use, etc...)
• [-] I've commented appropriately where code is tricky
• [-] I agree that there is no "throw-away" code, and that code in this PR is of high quality

Testing

Running under Python 2.7 and Python 3.9