Add `updateIndex`

[zhuchcn]

Description

Command updateIndex added to create a new canonical peptide pool to an existing moPepGen index directory. So the index directory now can support multiple canonical peptide pools. When callVariant is called, the correct canonical peptide pool that matches with the input cleavage parameters (including enzyme) will be loaded. And of cause it will fail if such a canonical peptide doesn't exist.

The index dir looks like this now:

test/files/index
├── annotation.gtf
├── annotation_gene.idx
├── annotation_tx.idx
├── canonical_peptides_001.pkl
├── canonical_peptides_002.pkl
├── coding_transcripts.pkl
├── genome.pkl
├── metadata.json
└── proteome.pkl

The metadata.json looks like this now:

{
  "version": {
    "python": "3.8.17",
    "biopython": "1.82",
    "mopepgen": "1.3.0"
  },
  "canonical_pools": [
    {
      "filename": "canonical_peptides_001.pkl",
      "index": 1,
      "cleavage_params": {
        "enzyme": "trypsin",
        "exception": "trypsin_exception",
        "miscleavage": 2,
        "min_mw": 500.0,
        "min_length": 7,
        "max_length": 25
      }
    },
    {
      "filename": "canonical_peptides_002.pkl",
      "index": 2,
      "cleavage_params": {
        "enzyme": "lysc",
        "exception": null,
        "miscleavage": 2,
        "min_mw": 500.0,
        "min_length": 7,
        "max_length": 25
      }
    }
  ],
  "source": "GENCODE"
}

Closes #853

Checklist

• [X] 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.
• [X] 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.
• [X] I have read the code review guidelines and the code review best practice on GitHub check-list.
• [X] 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].
• [X] 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.
• [X] All test cases passed locally.

[zhuchcn]

I put more detail to the PR description a little bit. The documentation site will be built automatically after the PR is merged. I added a page, and I don't think users need to know too much detail of how canonical peptides are organized. The software already provides enough information.