add development instructions

DEVELOPMENT.md

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+# Developing HADDOCK3
+
+This file provides information on how to setup a development environment for HADDOCK3.
+
+- [System requirements](#system-requirements)
+  - [Python3.9](#python39)
+  - [CNS](#cns)
+  - [git](#git)
+  - [gcc](#gcc)
+  - [OpenMPI](#openmpi)
+- [Setting up the development environment](#setting-up-the-development-environment)
+  - [Clone the repository](#clone-the-repository)
+  - [Link CNS binary](#link-cns-binary)
+  - [Install shipped C++ dependencies](#install-shipped-c-dependencies)
+    - [fcc](#fcc)
+    - [fast-rmsdmatrix](#fast-rmsdmatrix)
+  - [Python environment](#python-environment)
+  - [Install Python dependencies](#install-python-dependencies)
+  - [Running tests](#running-tests)
+
+## System requirements
+
+- Python 3.9
+- CNS
+- git
+- gcc
+- OpenMPI
+
+### Installing system dependencies
+
+Below the instructions are provided for a Ubuntu system using `apt-get`. If you are using a different system, please refer to the respective package manager - `yum`, `dnf`, `pacman`, `homebrew`, `port`, etc.
+
+#### Python3.9
+
+Conda is NOT recommended for development. Instead, install and compile Python 3.9 from source.
+
+On a __Linux-based system__ you can install Python 3.9 with the following commands:
+```bash
+wget https://www.python.org/ftp/python/3.9.6/Python-3.9.6.tgz
+tar -xf Python-3.9.6.tgz
+cd Python-3.9.6
+./configure --enable-optimizations
+sudo make altinstall -j 8
+```
+
+Then `python3.9` should be available on your system at `/usr/local/bin/python3.9`
+
+On __OSX__, use rather [brew](https://brew.sh) to install Python 3.9:
+
+```bash
+brew install [email protected]
+```
+
+Then `python3.9` should be available on your system at `/opt/homebrew/bin/python3.9`
+
+
+#### CNS
+
+Please refer to the [CNS installation instructions](docs/CNS.md).
+
+#### Git
+
+On a __Linux-based__ system:
+
+```bash
+sudo apt-get install git
+```
+
+#### gcc
+
+On a __Linux-based__ system:
+
+```bash
+sudo apt-get install gcc
+```
+
+#### OpenMPI 
+
+On a __Linux-based__ system:
+
+```bash
+sudo apt-get install openmpi-bin libopenmpi3 libopenmpi-dev
+```
+__Note__ that this step is not required on OSX.
+
+
+## Setting up the development environment
+
+### Clone the repository
+
+```bash
+git clone --recursive https://github.com/haddocking/haddock3.git
+```
+
+### Link CNS binary
+
+```bash
+mkdir haddock3/bin
+ln -s /path/to/cns_solve_1.3/bin/cns haddock3/bin/cns
+```
+
+### Install shipped C++ dependencies
+
+#### fcc
+
+```bash
+cd src/fcc/src
+make
+cd ../../../
+```
+
+#### fast-rmsdmatrix
+
+```bash
+cd src/fast-rmsdmatrix/src
+make fast-rmsdmatrix
+cd ../../../
+```
+
+### Python environment
+
+We recomend you use Python's native virtual environment to manage the dependencies.
+
+```bash
+/usr/local/bin/python3.9 -m venv .venv
+source .venv/bin/activate
+```
+
+On __OSX__ the command would be:
+
+```bash
+/opt/homebrew/bin/python3.9 -m venv .venv
+source .venv/bin/activate
+```
+
+
+### Install Python dependencies
+
+Install both project dependencies and test dependencies using pip.
+
+```bash
+pip install -r requirements.txt &&
+  pip install \
+    coverage==7.2.5 \
+    pytest==7.3.1 \
+    pytest-cov==4.0.0 \
+    hypothesis==6.75.1 \
+    pytest-mock==3.12.0 \
+    fastapi==0.110.1 \
+    httpx==0.27.0 \
+    mpi4py==3.1.6
+```
+
+Install haddock3 in development mode.
+
+```bash
+python setup.py develop
+```
+
+## Running tests
+
+Simply run the following command to run the tests.
+
+```bash
+pytest
+```