Refresh logging

[garrettwrong]

Closes #212 .

Most of the competing logging implementation was removed in #283 , so this PR isn't too big, nice.

• Converts logger assignments to __file__. We may have one specific place it would be reasonable to deviate from that convention that I am aware of (the tutorials), but it is not necessary the way I have implemented logging here (timestamped logfiles).
• Convert to config file style from a a dictionary style. This moves configuration out of the source code.
• Removes duplicated logging config in pytest.ini, also fixes the stdout out duplication under pytest -s.
• Adds fileHandler with configurable filename.
• Tee stream, >=DEBUG to file and >=INFO to console.
• ISO datetime format in log, and close to it for filename (: presents a problem, replaced with -)
• add levelname

One point of discussion is regarding the default log filename. This initial PR will drop a timestamped file name for each process where aspire package is imported. This is pretty common, but can be a little noisy. That is, if you are frantically developing and running tests, you might get many small files in your directory to rm *.log, instead of one big one...

Alternatively it is possible to turn off writing the file by default, and use a simple bool option like log_to_file in config.ini. This would shield users from the python logging configuration, which might seem complicated. (It isn't but certainly has nothing to do with CryoEM). This is easy to implement if desired.

As it stands the log filenames look like aspire-2020-10-08T14-50-13.456577.log, with a snippet example attached showing the new format.
ex.log

[garrettwrong]

I went through error, warning, and info messages. Made just a few adjustments (mainly errors that should also raise). I also updated the developer guide a little based on this PR.

The only point keeping this PR a draft is regarding the log file default. Mainly do we want multiple (individually timestamped) log files, a single log file, or no file as the default of ASPIRE. @janden do you have any preference? Currently the PR has the multiple timestamped setup. Thanks

[janden]

I would personally prefer to not log to file by default, but this will be very useful for bug reports. Timestamped log files I think are good for that reason too. Would a reasonable compromise be for log files to end up in a subdirectory (like logs/)?

[garrettwrong]

Sure I'll set that up, thanks.