Add show_versions() function for printing debugging information used in issue reports

[seisman]

Description of proposed changes

The show_versions function reports system information, package versions and GMT library information. The output looks like:

PyGMT information:
  version: v0.1.1+20.g4d11e8c.dirty
System information:
  python: 3.7.6 (default, Jan  8 2020, 13:42:34)  [Clang 4.0.1 (tags/RELEASE_401/final)]
  executable: /Users/seisman/.anaconda/bin/python
  machine: Darwin-19.4.0-x86_64-i386-64bit
Dependency information:
  numpy: 1.18.1
  pandas: 1.0.1
  xarray: 0.15.1
  netCDF4: 1.5.3
  packaging: 20.1
  ghostscript: 9.50
  gmt: 6.1.0_ddd829b_2020.05.29
GMT library information:
  binary dir: /Users/seisman/.anaconda/bin
  cores: 8
  grid layout: rows
  library path: /Users/seisman/local/GMT/lib/libgmt.dylib
  padding: 2
  plugin dir: /Users/seisman/local/GMT/lib/gmt/plugins
  share dir: /Users/seisman/local/GMT/share
  version: 6.1.0

TODO:

• Update the github issue template
• Update the pygmt test instructions in the documentation
• Replace print_clib_info() with show_versions in Makefile

Fixes #460

Reminders

• Run make format and make check to make sure the code follows the style guide.
• Add tests for new features or tests that would have caught the bug that you're fixing.
• Add new public functions/methods/classes to doc/api/index.rst.
• Write detailed docstrings for all functions/methods.
• If adding new functionality, add an example to docstrings or tutorials.

[weiji14]

Trying to think of other good ones to print, maybe conda and ghostscript?

[seisman]

I agree with ghostscript, but do we really care about conda version?

[weiji14]

Yeah, let's skip conda. It's looking really good by the way! One more thing we might want is to have it print out a more specific GMT version using (gmt --version?). conda list used to show the build number I think.

[seisman]

One more thing we might want is to have it print out a more specific GMT version using (gmt --version?).

Agree.

conda list used to show the build number I think.

Yes, but conda list is usually slow.

[seisman]

GMT version added. See the first comment for the updated output.

[weiji14]

Great work @seisman, just one small comment to improve the documentation of show_versions. This is what it looks like on my system, the GMT version is duplicated but that's fairly minor:

PyGMT information:
  version: v0.1.1+21.gb55250e.dirty
System information:
  python: 3.7.6 | packaged by conda-forge | (default, Mar 23 2020, 23:03:20)  [GCC 7.3.0]
  executable: /home/weiji/miniconda3/envs/pygmt/bin/python
  machine: Linux-4.19.0-8-amd64-x86_64-with-debian-10.4
Dependency information:
  numpy: 1.18.4
  pandas: 1.0.4
  xarray: 0.15.1
  netCDF4: 1.5.3
  packaging: 20.4
  ghostscript: 9.22
  gmt: 6.0.0
GMT library information:
  binary dir: /home/weiji/miniconda3/envs/pygmt/bin
  cores: 2
  grid layout: rows
  library path: /home/weiji/miniconda3/envs/pygmt/lib/libgmt.so
  padding: 2
  plugin dir: /home/weiji/miniconda3/envs/pygmt/lib/gmt/plugins
  share dir: /home/weiji/miniconda3/envs/pygmt/share/gmt
  version: 6.0.0

There should be room to add extra stuff to this going forward. Would be great ot print out what's in gmt.conf but that's low priority right now.

[seisman]

This is what it looks like on my system, the GMT version is duplicated but that's fairly minor:

Yes, the two GMT versions are different if

• users are using the GMT master branch
• there are multiple GMT installed, and the loaded library is different from the in the command line

There should be room to add extra stuff to this going forward. Would be great ot print out what's in gmt.conf but that's low priority right now.

We perhaps can wrap the gmt defaults module, but I agree it's very low priority.