Oakvar

- Fixed console output of ``ov module`` CLI commands.

- Multi-core gene mapping is default.
- Fixed ``ov system setup``, ``ov system config``, and ``ov system md`` to show output.
- Fixed Ctrl-C while ``ov module installbase``.
- Fixed processing default command-line argument.
- Fixed importing ``inout`` and ``admin_util`` by modules.

- Line breaks in annotation results are correctly escaped with ``ov report``. This fixes the issue at https://github.com/KarchinLab/open-cravat/issues/106.
- CLI commands alignment among CLI, Python, and R. For example:

CLI:
bash
>ov module ls

Python:
Python
>import oakvar
>oakvar.ov_module_ls()

R:
R
>devtools::install_github("rkimoakbioinformatics/roakvar")
>library(roakvar)
>ov.module.ls()

- Python ``subprocess`` calls to CLI functions such as ``oakvar.ov_module_ls()`` will return returncode 0 if no error was produced.
- ``ov gui`` will print error messages to stdout if ``—debug`` option is given.
- ``ov module install`` will automatically install PyPI dependencies defined in OakVar modules’ yml files with ``requires_pypi`` or ``pypi_dependency``.- Improved the speed of handling configuration files.
- Improved exception handling.
- Fixed that the number of unique variants did not show on the job table of ``ov gui``.
- Fixed a bug in using ``—package`` option with ``ov run`` and ``ov report``.
- Refactored the mechanism for handling ``—package`` and ``--confpath`` options to ``ov run`` and ``ov report``.
- Refactored the handling of CLI command functions for better alignment among CLI, Python, and R.
- Refactored the code so that no error nor warning is reported by pyright and pylance.

* ``ov system setup`` is the new command to set up OakVar after ``pip install oakvar``. A system conf yaml file can be given as ``ov system setup -f setup.yaml`` for consistent setup.
* ``ov system`` command has been added to handle OakVar system operations.
* System configuration can be defined with environmental variables. All the fields in cravat-system.yml can be defined with environmental variables using a consistent naming convention. For example, the root data directory of OakVar is defined in ``root_dir`` field in cravat-system.yml. An environmental variable ``OV_ROOT_DIR`` will override what is in cravat-system.yml. The OakVar modules directory is defined in ``modules_dir`` field, which can be overridden with ``OV_MODULES_DIR``. The naming convention is ``OV_`` + the upper case version of the system conf field.
* Exception handling has been improved.

* Significantly faster launch of ``ov`` CLI commands
* Python 3.8 is the minimum Python version requirement.
* Refactored codes.
* ``ov run`` and other CLI commands can have ``--md`` option to fix https://github.com/KarchinLab/open-cravat/issues/112.
* The PyPI packages required for a module can be defined with ``requires_pypi`` field in the module's ``yml`` file and they will be automatically installed with ``ov module install``.
* All secondary input fields, including those with ``None`` value, will be provided to annotator modules' ``annotate`` function for consistency in handling them.

* Works with Roakvar, an R wrapper of oakvar. See https://github.com/rkimoakbioinformatics/roakvar.
* Cleaned CLI commands.
* Works with existing OpenCRAVAT modules.
* Overall code refactoring