Swtich to use python's standard `logging` pacakge for logging

[zhuchcn]

Description

This is to make the logging message more standardized and professional. We now can use --debug-level in any moPepGen command. --debug-level INFO will print basic messages (those with the logger.info() call), and --debug-level DEBUG will print debug messages (logger.debug()). And setting --debug-level 0 or --quiet will show no message.

Here is an example output of callVariant:

python -m moPepGen.cli callVariant \
    -i \
        test/files/vep/vep_gSNP.gvf \
        test/files/vep/vep_gINDEL.gvf \
        test/files/fusion/star_fusion.gvf \
    --index-dir test/files/index \
    -o test/files/vep/test3.fasta \
    --debug-level DEBUG
[ 2024-02-29 18:11:47 ] [ moPepGen - INFO ] moPepGen callVariant started
[ 2024-02-29 18:11:47 ] [ moPepGen - INFO ] Reference indices loaded.
[ 2024-02-29 18:11:47 ] [ moPepGen - INFO ] Using GVF file: test/files/vep/vep_gSNP.gvf
[ 2024-02-29 18:11:47 ] [ moPepGen - INFO ] Using GVF file: test/files/vep/vep_gINDEL.gvf
[ 2024-02-29 18:11:47 ] [ moPepGen - INFO ] Using GVF file: test/files/fusion/star_fusion.gvf
[ 2024-02-29 18:11:47 ] [ moPepGen - INFO ] Variants sorted
[ 2024-02-29 18:11:47 ] [ moPepGen - DEBUG ] ['ENST00000614167.2']
[ 2024-02-29 18:11:47 ] [ moPepGen - DEBUG ] ['ENST00000614168.2']
[ 2024-02-29 18:11:47 ] [ moPepGen - DEBUG ] ['ENST00000622235.5']
[ 2024-02-29 18:11:47 ] [ moPepGen - DEBUG ] ['ENST00000642151.1']
[ 2024-02-29 18:11:47 ] [ moPepGen - DEBUG ] ['ENST00000624155.2']
[ 2024-02-29 18:11:47 ] [ moPepGen - INFO ] Variant peptide FASTA file written to disk.
[ 2024-02-29 18:11:47 ] [ moPepGen - INFO ] rss=79.59 MiB, vms=395.6 MiB, wallclock=0:00:01.180000, system=0:00:00.720000, cpu_usage=101.2%

Closes #594

Checklist

• [ ] This PR does NOT contain PHI or germline genetic data. A repo may need to be deleted if such data is uploaded. Disclosing PHI is a major problem.
• [ ] This PR does NOT contain molecular files, compressed files, output files such as images (e.g. .png, .jpeg), .pdf, .RData, .xlsx, .doc, .ppt, or other non-plain-text files. To automatically exclude such files using a .gitignore file, see here for example.
• [ ] I have read the code review guidelines and the code review best practice on GitHub check-list.
• [ ] The name of the branch is meaningful and well formatted following the standards, using [AD_username (or 5 letters of AD if AD is too long)]-[brief_description_of_branch].
• [ ] I have added the major changes included in this pull request to the CHANGELOG.md under the next release version or unreleased, and updated the date.
• [ ] All test cases passed locally.