Feature/improved warnings

[colonesej]

Description

Improved warnings formmating and messages for users with hints on where to change things.

Note: DeprecationWarnings had to be set to default as they are ignored by default
Note: warning formatting will make text appear in yellow on most terminals but this has not been extensively tested.

New deprecation warning on TroikaHost submit arguments

[DeprecationWarning] /Users/mojp/github/pyflow/pyflow/host.py:1180
/my_suite/init/deploy_data/git_sample: tmpdir' is deprecated in TroikaHost, use 'tmpdir_size' instead

When defining submit arguments to LocalHost

[DeprecationWarning] /Users/mojp/github/pyflow/pyflow/host.py:1180
/my_suite/init/deploy_data/mars_sample: tmpdir' is deprecated in TroikaHost, use 'tmpdir_size' instead

When using out option for a node

[DeprecationWarning] /Users/mojp/github/pyflow/pyflow/nodes.py:1071
'out' option is deprecated for nodes, use the log_directory option in the host instead

Contributor Declaration

By opening this pull request, I affirm the following:

• All authors agree to the Contributor License Agreement.
• The code follows the project's coding standards.
• I have performed self-review and added comments where needed.
• I have added or updated tests to verify that my changes are effective and functional.
• I have run all existing tests and confirmed they pass.