Changes to move the parsing to the ouput from the screen instead of the log file.

[JPchico]

During the development we discovered that the log file and the stdout print the same information except for warnings and errors, which are only printed in stdout.

To ensure that we can make use of the warnings and errors, the parsing file has been changed from the log file to use the redirected stdout, which is lammps.out.

The information obtained should be the same, but the amount of retrieved files will be less, and the information parsed richer.

The log file can still be retrieved by adding it to the list of additionally retrieved files if the user wishes to do so.

[codecov]

Codecov Report

Merging #84 (199231d) into develop (2eace50) will decrease coverage by 0.25%.
The diff coverage is 76.31%.

@@             Coverage Diff             @@
##           develop      #84      +/-   ##
===========================================
- Coverage    88.90%   88.65%   -0.25%     
===========================================
  Files           19       19              
  Lines         1451     1455       +4     
===========================================
  Hits          1290     1290              
- Misses         161      165       +4     

Flag	Coverage Δ
pytests	88.65% <76.31%> (-0.25%)	⬇️

Flags with carried forward coverage won't be shown. Click here to find out more.

Impacted Files	Coverage Δ
aiida_lammps/parsers/inputfile.py	87.23% <ø> (ø)
aiida_lammps/parsers/raw.py	84.61% <66.66%> (ø)
aiida_lammps/parsers/parse_raw/lammps_output.py	89.06% <69.23%> (ø)
aiida_lammps/parsers/base.py	85.22% <78.57%> (ø)
aiida_lammps/calculations/base.py	96.26% <100.00%> (-0.09%)	⬇️
aiida_lammps/calculations/raw.py	100.00% <100.00%> (ø)
aiida_lammps/parsers/parse_raw/__init__.py	100.00% <100.00%> (ø)

[JPchico]

@chrisjsewell, @sphuber I have changed the parsing to make use of the redirected stdout instead of the log file. The reason behind this is to make sure that we can parse the warnings and errors, which do not seem to be printed in the log file.

We can then use the warnings and errors in the parsing to give the information to the user and or to give proper exit codes related to actual lammps errors

[sphuber]

Thanks @JPchico looks good to me