Fixes and improvements for SPAM and volmap, 3d grids

[drroe]

This PR has multiple fixes and improvements related to SPAM, volmap and reading/writing 3D data.

• The online help and manual documentation are greatly improved for both.
• The volmap command now creates a data set for the peaks data. This means that among other things you can run spam and volmap in the same cpptraj run. This could include running volmap several times with the same peak data and different settings.
• Some checks have been introduced into spam to trap "bad" peaks (poor occupancy, extremely large energies, etc) that previously could lead to the code producing nonsense or failing outright.
• OpenDX data can now be read in single (the previous behavior) or double precision if desired.
• OpenDX output now respects if the format of a data set has been changed (via e.g. dataset precision) from the default of %g.
• Enable divide and multiply for 3D datasets.

Miscellaneous fixes:

• Improve Tinker format recognition.

[AmberJenkins]

The PGI build in Jenkins failed.

[drroe]

Weird - Jenkins says PGI failed again, but it clearly passed.

[drroe]

Travis-CI mac framework is having issues:

Error: Failure while executing; `tar xof /Users/travis/Library/Caches/Homebrew/downloads/9e4ec3ec2b678643fc676aad73df9fd9e838a4d764ecba365714e1e7f5852631--nss-3.56.high_sierra.bottle.tar.gz -C /var/folders/nz/vv4_9tw56nv9k3tkvyszvwg80000gn/T/d20200821-83344-mhy1fh` exited with 1. Here's the output:

tar: Error opening archive: Failed to open '/Users/travis/Library/Caches/Homebrew/downloads/9e4ec3ec2b678643fc676aad73df9fd9e838a4d764ecba365714e1e7f5852631--nss-3.56.high_sierra.bottle.tar.gz'

I'll try to restart in a bit I guess...

[drroe]

😠 The Mac stuff is still failing

[drroe]

OK, the real error is a few lines above:

==> Downloading https://homebrew.bintray.com/bottles/nss-3.56.high_sierra.bottle

curl: (22) The requested URL returned error: 404 Not Found

Error: Failed to download resource "nss"

Download failed: https://homebrew.bintray.com/bottles/nss-3.56.high_sierra.bottle.tar.gz

Warning: Bottle installation failed: building from source.

Indeed, trying that URL results in a The requested path was not found. So right now I'm stuck.

[drroe]

Looks like Mac builds on Travis are finally working again!

[swails]

Weird - Jenkins says PGI failed again, but it clearly passed.

It actually didn't pass. The problem is that if that stage itself failed, then the entire pipeline would fail (which we don't want). If you click on the green PGI stage in the Blue Ocean UI, you will see the individual steps, and the build/test step is red:

The PR post is placed in the catch part of a try/catch control block in the Jenkinsfile, so it's only accessible when the steps before it fail.

The whole point behind having the pipeline post to a PR when the PGI build fails is so we can be notified if it didn't pass without making the whole Jenkins pipeline fail (which would block it from building the libcpptraj docker image and testing pytraj against it).

As an aside, the latest master build doesn't work with pytraj it seems. @hainm, are you aware of this?

[hainm]

As an aside, the latest master build doesn't work with pytraj it seems. @hainm, are you aware of this?

The error is here: FAILED test_analysis/test_jcoupling.py::test_jcoupling - ValueError
And I think @drroe already fixed that in Amber-MD/pytraj#1547

[drroe]

It actually didn't pass.

@swails you're 100% right! Thanks - I think I've found the issue, should be fixed by #839 (I hope).