Add simplified installation instructions to README.md.

README.md

@@ -5,32 +5,41 @@
 ##
 
 [![Documentation](https://img.shields.io/badge/GitBook-Docu-lightgrey)](https://app.gitbook.com/@ehjc/s/kallisto/)
-[![License](https://img.shields.io/badge/license-Apache%202-blue)](https://img.shields.io/badge/license-Apache%202-blue)
 [![Maturity Level](https://img.shields.io/badge/Maturity%20Level-ML--1-orange)](https://img.shields.io/badge/Maturity%20Level-ML--1-orange)
 [![Tests](https://github.com/AstraZeneca/kallisto/workflows/Tests/badge.svg)](https://github.com/AstraZeneca/kallisto/actions?workflow=Tests)
 [![codecov](https://codecov.io/gh/AstraZeneca/kallisto/branch/master/graph/badge.svg?token=HI0U0R96X8)](https://codecov.io/gh/AstraZeneca/kallisto)
 [![Language grade: Python](https://img.shields.io/lgtm/grade/python/g/AstraZeneca/kallisto.svg?logo=lgtm&logoWidth=18)](https://lgtm.com/projects/g/AstraZeneca/kallisto/context:python)
 [![status](https://joss.theoj.org/papers/16126cbcfb826bf4810d243a009a6b02/status.svg)](https://joss.theoj.org/papers/16126cbcfb826bf4810d243a009a6b02)
 
-Table of Contents
------------------
+# Table of Contents
 
 - Full Author List
 - Introduction
 - Installation
+- Testing suite
 - Reference
 
-Full Author List
-----------------
+# Full Author List
 
 Eike Caldeweyher and Philipp Pracht
 
-Introduction
-------------
+# Introduction
 
 We developed the `kallisto` program for the efficient and robust calculation of atomic features using molecular geometries either in a ``xmol`` or a ``Turbomole`` format.
 Furthermore, several modelling tools are implemented, e.g., to calculate root-mean squared deviations via quaternions (including rotation matrices), sorting of molecular geometries and many more. All features of ``kallisto`` are described in detail within our [documentation](https://app.gitbook.com/@ehjc/s/kallisto/) ([GitBook repository](https://github.com/f3rmion/gitbook-kallisto)).
 
+Main dependencies
+-----------------
+
+```bash
+click 7.1.2 Composable command line interface toolkit
+numpy 1.20.1 NumPy is the fundamental package for array computing with Python.
+scipy 1.6.0 SciPy: Scientific Library for Python
+└── numpy >=1.16.5
+```
+
+For a list of all dependencies have a look at the pyproject.toml file.
+
 Installation from PyPI
 ----------------------
 
@@ -42,54 +51,103 @@ pip install kallisto
 Installation from Source
 ------------------------
 
-`kallisto` runs on `python3`
+Requirements to install ``kallisto``from sources:
+- [poetry](https://python-poetry.org/docs/#installation)
+- [pyenv](https://github.com/pyenv/pyenv#installation) or [conda](https://docs.conda.io/projects/conda/en/latest/user-guide/install/index.html)
+- python >=3.7
+
+First check that ``poetry`` is running correctly (v1.0.10 at the time of writing)
 
-Python development setup. Install the `pyenv` python version manager:
 ```bash
-curl https://pyenv.run | bash
+> poetry --version
+Poetry version 1.0.10
 ```
-and add this to the `~/.bashrc` and source it:
+
+Create a virtual environment (via ``pyenv`` or ``conda``) and activate it. Afterwards, clone the ``kallisto`` project from GitHub and install it using ``poetry``
+
 ```bash
-export PATH="~/.pyenv/bin:$PATH"
-eval "$(pyenv init -)"
-eval "$(pyenv virtualenv-init -)"
+> git clone [email protected]:AstraZeneca/kallisto.git
+> cd kallisto
+> poetry install
 ```
-Install the latest python versions:
+
+Testing suite
+-------------
+
+The ``kallisto`` project uses [nox](https://nox.thea.codes/en/stable/tutorial.html#installation) as an automated unit test suite, which is therefore an additional dependency.
+
+### Default nox session
+
+The default session includes: linting (lint), type checks (mypy, pytype), and unit tests (tests). 
+
 ```bash
-pyenv install 3.8.2
-pyenv install 3.7.7
-pyenv local 3.8.2 3.7.7
+> nox
 ```
 
-Now we are ready to set up `kallisto`.
-Clone the repository:
+When everything runs smoothly through, you are ready to go! After one successful nox run, we can reuse the created virtual environment via the ``-r`` flag.
+
 ```bash
-git clone [email protected]:AstraZeneca/kallisto.git
+> nox -r
 ```
 
-Install a python dependency manager. We choose to go with `poetry`:
+Different unit test sessions are implemented (check the noxfile.py). They can be called separately via the run session ``-rs`` flag.
+
+### Tests
+
+Run all unit tests that are defined in the /tests directory.
+
+```bash 
+> nox -rs tests
+```
+
+### Lint
+
+``kallisto`` uses the [flake8](https://flake8.pycqa.org/en/latest/) linter (check the .flake8 config file).
+
 ```bash
-curl -sSL https://raw.githubusercontent.com/python-poetry/poetry/master/get-poetry.py | python
-source ~/.poetry/env
+> nox -rs lint
+```
+
+### Black
+
+``kallisto`` uses the [black](https://github.com/psf/black) code formatter.
+
+```bash 
+> nox -rs black
 ```
-or alternatively via `pip`:
+
+### Safety
+
+``kallisto`` checks the security of dependencies via [safety](https://pyup.io/safety/).
+
 ```bash
-pip install --user poetry
+> nox -rs safety
 ```
 
-Now, if you haven't already done so, change into the cloned `kallisto` directory and
-download the dependencies via `poetry`:
+### Mypy
+
+``kallisto`` checks for static types via [mypy](https://github.com/python/mypy) (check the mypy.ini config file).
+
 ```bash
-cd kallisto
-poetry install
+> nox -rs mypy
 ```
 
-Finally install the test automation environment `nox` via ``pip``:
+### Pytype
+
+``kallisto`` furthermore uses [pytype](https://github.com/google/pytype) for type checks.
+
 ```bash
-pip install --user --upgrade nox
+> nox -rs pytype
 ```
 
-Run `nox` to test the setup.
+### Coverage
+
+Unit test [coverage](https://coverage.readthedocs.io/en/coverage-5.4/) can be checked as well.
+
+
+```bash
+> nox -rs coverage
+```
 
 Reference
 ---------