Cleanup and Docs (#7)

- Updated README.md to only include installation and run details
- Moved developer details to DEVELOPMENT.md
- Added missing test project dependencies to pyproject.toml
- Cleanup unused stuff from cookiecutter template
- Added 'Getting Started' details to readthedocs docs
- Added more documentation to backend classes

Author: PardhavMaradani

DEVELOPMENT.md

@@ -0,0 +1,227 @@
+# Development
+
+This page contains developer instructions to build and maintain `mdadash`.
+
+- [Installation](#installation)
+  - [With `conda`](#with-conda)
+  - [With `pip`](#with-pip)
+- [Run](#run)
+- [Develop](#develop)
+  - [Frontend](#frontend)
+  - [Backend](#backend)
+- [Lint checks](#lint-checks)
+  - [Frontend](#frontend)
+  - [Backend](#backend)
+- [Tests](#tests)
+  - [Frontend](#frontend)
+  - [Backend](#backend)
+- [Code Coverage](#code-coverage)
+  - [Frontend](#frontend)
+  - [Backend](#backend)
+- [Build](#build)
+- [Verify GitHub actions locally](#verify-github-actions-locally)
+- [Docs](#docs)
+
+### Installation
+
+To build mdadash from source,we highly recommend using virtual environments. If possible, we strongly recommend that you use [Anaconda](https://docs.conda.io/en/latest/) as your package manager. Below we provide instructions both for `conda` and for `pip`.
+
+#### With conda
+
+Ensure that you have [conda](https://docs.conda.io/projects/conda/en/latest/user-guide/install/index.html) installed.
+
+Create a virtual environment and activate it:
+
+```sh
+conda create --name mdadash
+conda activate mdadash
+```
+
+Install the development, testing and documentation dependencies:
+
+```sh
+conda env update --name mdadash --file devtools/conda-envs/dev_env.yaml
+conda env update --name mdadash --file devtools/conda-envs/test_env.yaml
+conda env update --name mdadash --file docs/requirements.yaml
+```
+
+Build this package from source:
+
+```sh
+pip install -e .
+```
+
+If you want to update your dependencies (which can be risky!), run:
+
+```sh
+conda update --all
+```
+
+And when you are finished, you can exit the virtual environment with:
+
+```sh
+conda deactivate
+```
+
+#### With pip
+
+To build the package from source, run:
+
+```sh
+pip install .
+```
+
+If you want to create a development environment, install
+the dependencies required for tests and docs with:
+
+```sh
+pip install ".[dev,test,doc]"
+```
+
+### Run
+
+> The frontend code needs to be built before running the backend server. This can be done as follows:
+
+```sh
+cd mdadash/frontend
+npm install
+npm run build
+```
+
+To run the dashboard server:
+
+```sh
+mdadash --topology <topology_filename> --trajectory <trajectory_url>
+```
+
+To see the options available:
+
+```sh
+mdadash --help
+```
+
+### Develop
+
+#### Frontend
+
+Developer instructions for `frontend` code can be found [here](mdadash/frontend/README.md).
+
+#### Backend
+
+- Use the `editable` installation above (`pip install -e .`)
+
+### Lint checks
+
+#### Frontend
+
+```sh
+npm run lint --prefix mdadash/frontend
+```
+
+#### Backend
+
+```sh
+ruff check
+```
+
+### Tests
+
+#### Frontend
+
+```sh
+npm run test:unit --prefix mdadash/frontend -- --run
+```
+
+#### Backend
+
+```sh
+pytest -v
+```
+
+### Code Coverage
+
+#### Frontend
+
+```sh
+cd mdadash/frontend
+npx vitest --run --coverage
+```
+
+The coverage details will be shown on the console. Open `coverage/index.html` to view the interactive coverage report in the browser.
+
+#### Backend
+
+To see coverage output on the console:
+
+```sh
+pytest -v --cov=mdadash
+```
+
+To write coverage output to `html` file:
+
+```sh
+pytest -v --cov=mdadash --cov-report=html
+```
+
+Open `htmlcov/index.html` to view the coverage report in the browser.
+
+### Build
+
+To build this package:
+
+```sh
+rm -rf mdadash.egg-info dist && python -m build
+```
+
+To verify the created wheel in an isolated environment:
+
+```sh
+uv run --refresh --with path.to.whl mdadash <options>
+```
+
+To check the created distribution:
+
+```sh
+twine check dist/*
+```
+
+### Verify GitHub actions locally
+
+GitHub actions can be verified locally using [act](https://github.com/nektos/act).
+
+> Note that this requires [Docker](https://www.docker.com). Running on Mac needs an additional param `--container-architecture linux/arm64`. To bypass the repo name check, you can pass `--env GITHUB_REPOSITORY=MDAnalysis/mdadash`. Both these can be set in `~/.actrc` as well.
+
+To list the jobs:
+
+```sh
+act -l
+```
+
+To run a job (eg: `pylint_check`):
+
+```sh
+act -j pylint_check
+```
+
+To run all jobs:
+
+```sh
+act
+```
+
+### Docs
+
+Setting up the docs environment:
+
+```sh
+conda env update --name mdadash --file docs/requirements.yaml
+```
+
+Building docs locally:
+
+```sh
+cd docs
+make clean && make html
+```
+
+Open `docs/_build/html/index.html` to view the docs in the browser.