vcell_cli_utils python refactor

[CodeByDrescher]

Background

• Previously, the java codebase in the VCell CLI project interacted with the biosimulators_utils python library through starting a new system process to call and execute a specific python function defined in either status.py or cli.py in VCell CLI Utils. This issue has been partially resolved by creating a CLI Python Manager class to create a single object through which all python interaction is handled from java.
• However, some parts of the python codebase in vcell_cli_utils were never designed to work in a interpretive session, and some python functions would create incredible slowdown when invoked repeatedly in the same interpretive session. This required some calls to python (from java) to continue using the old style of invocation to complete.
• Further, closer inspection of the vcell_cli_utils shows redundant computation and smattering of undocumented side effects that both slow down python and create difficulties in fixing the issues.

Tasks

1. Refactor the functionality of status.py and cli.py in vcell_cli_utils to work in an OOP fashion with new python files. This will allow greater ease in not only reading the code, but also adds additional control over how many objects are created as well as where and when to use or delete them.
2. Refactor ExecuteImpl.java>singleExecVcml(File,File) to integrate the new vcell_cli_utils refactor.
3. Finish updating remaining "old style" python calls to the new style.

[jcschaff]

some java-side refactoring has already been done.

The vcell_cli_utils Python package would benefit from (e.g. Python Typing, MyPy, removal of unused code, and unit tests). After that, we can look at elaborating into a more general library if it is warranted.

Additional packages have also been added to this poetry project (biosimulations_pipeline, omex, vcell_common, vcell_pipeline) ... all with unit tests. but that code is Python centric.