Primerdriver

Changelog

CLI
- Rewrite `primerdriver` as a Python module
- Use `black` for auto-formatting
- Improve CLI logging
- Build CLI into a standalone package for Windows and Linux (installing dependencies no longer needed unless you want to make a contribution, just download the appropriate binary for your system)

Web app
- Merge backend and frontend code into this monorepo
- App has been containerized
- Migrated to GCP Cloud Run

⚠️ Security update

This release mostly updates vulnerable `node` dependencies (refer to PRs 14-26).

General
- 📦 Switch to `pipenv` as package and environment manager.
- 🗑️ Cleanup root directory structure by moving JS plugin configs (i.e., `eslintrc`, `babelrc`) to `package.json`.

CLI
- ✨ Rename `pdcli.py` to `primerdriver.py`. Program can now be invoked transparently as `primerdriver`.

Welcome to PrimerDriver's first minor version update!

CLI
- Created `version.py` to handle versioning in compliance with [SemVer](http://semver.org/).
- Fixed a UX snag wherein passing no arguments (i.e., `python pdcli.py`) causes the program to end non-gracefully. The default behavior now calls the help view instead.
- Fixed a bug where a request from web which results in no valid primers being found raises a `TypeError` instead of the error string, thereby returning an HTTP code 500.

Web
- The design app as been completely redesigned. Using tighter [React.js](https://reactjs.org) integration, the app is now an SPA on the landing page.
- The `/result` endpoint has been deprecated.
- The `PrimerDesign` API is now exposed on the `/api` endpoint. Primer design queries can now be performed directly via HTTP `POST` requests (e.g., using XHRs or `curl`).

PrimerDriver's first minor version update, release candidate 1. Changes in progress are as follows:

Pipeline
- Switched CI provider to [CircleCI](https://circleci.com).
- Added coverage reports c/o [Codecov](https://codecov.io).
- Added visual testing c/o [Percy](https://percy.io).

CLI
- Created `version.py` to handle versioning in compliance with [SemVer](http://semver.org/).
- Exposed the `PrimerClass` API on `/api` which can be accesed by an HTTP `POST` request.

Web
- Converted the `/design` page to a React SPA on `/index`
- The `/result` endpoint and `/design` page are deprecated

Welcome to the first official release of PrimerDriver! Here are all the available features, built up since day one:

- Command line interface with an interactive mode and a single-command mode
- Primer characterization of user-provided sequence, either manually typed or by FASTA file
- DNA & protein-based primer design, which also accepts either manual or FASTA input
- Saving results to HTML, FASTA, CSV, and plain text
- Ability for batch primer design when using as part of a Shell script
- Fully working web application (at https://primerdriver.herokuapp.com/) (*Note*: File inputs and outputs are not available on the web app...yet)

Changelog:
- DNA-based design is fully functional for all SDM, with complementary and overlapping
- Support output for `csv`, `html`, `fasta`, and `json`
- Protein-based design works with substitution only, with IUPAC protein codes