Update readme to reflect new setup method

README.rst

@@ -24,9 +24,8 @@ Installation using python virtual environment - recommended
 3. ``python3 -m venv .venv`` - create the virtual environment
 4. ``source .venv/bin/activate`` - activate the virtual environment
 5. ``python3 -m pip install --upgrade pip`` - upgrade version of pip
-6. ``python3 -m pip install -r requirements.txt`` - install dependencies
-7. ``python3 -m pip install .`` - install the pycalibration package (add ``-e`` flag for editable development installation)
-8. ``pip install "git+ssh://git@git.xfel.eu:10022/karaboDevices/pyDetLib.git#egg=XFELDetectorAnalysis&subdirectory=lib"``
+6. ``python3 -m pip install .`` - install the pycalibration package (add ``-e`` flag for editable development installation)
+7. ``pip install "git+ssh://git@git.xfel.eu:10022/karaboDevices/pyDetLib.git#egg=XFELDetectorAnalysis&subdirectory=lib"``
 
 Copy/paste script:
 
@@ -38,19 +37,23 @@ Copy/paste script:
   python3 -m venv .venv
   source .venv/bin/activate
   python3 -m pip install --upgrade pip
-  python3 -m pip install -r requirements.txt
-  python3 -m pip install .  # `-e` flag for editable install
+  python3 -m pip install .  # `-e` flag for editable install, e.g. `pip install -e .`
   python3 -m pip install "git+ssh://git@git.xfel.eu:10022/karaboDevices/pyDetLib.git#egg=XFELDetectorAnalysis&subdirectory=lib/"
 
 
 Installation into user home directory
 =====================================
 
+This is not recommended as `pycalibration` has pinned dependencies for
+stability, if you install it directly into you users home environment then it
+will down/upgrade your local packages, which may cause major issues and may
+**break your local environment**, it is highly recommended to use the venv
+installation method instead.
+
 1. ``git clone ssh://git@git.xfel.eu:10022/detectors/pycalibration.git && cd pycalibration`` - clone the offline calibration package from EuXFEL GitLab
 2. ``module load anaconda/3`` - load the anaconda/3 environment. If installing into other python environments, this step can be skipped
-3. ``pip install -r requirements.txt`` - install all requirements of this tool chain in your home directory
-4. ``pip install .`` - install the pycalibration package (add ``-e`` flag for editable development installation)
-5. ``export PATH=$HOME/.local/bin:$PATH`` - make sure that the home directory is in the PATH environment variable
+3. ``pip install .`` - install the pycalibration package (add ``-e`` flag for editable development installation)
+4. ``export PATH=$HOME/.local/bin:$PATH`` - make sure that the home directory is in the PATH environment variable
 
 Copy/paste script:
 
@@ -59,8 +62,7 @@ Copy/paste script:
   git clone ssh://git@git.xfel.eu:10022/detectors/pycalibration.git
   cd pycalibration
   module load anaconda/3
-  pip install -r requirements.txt --user
-  pip install .  # `-e` flag for editable install, e.g. `pip install -e .`
+  pip install --user .  # `-e` flag for editable install, e.g. `pip install -e .`
   export PATH=$HOME/.local/bin:$PATH
 
 
@@ -89,6 +91,11 @@ Development guidelines can be found on the GitLab Wiki page here: https://git.xf
 Basics
 ======
 
+If you are installing the package for development purposes then you should
+install the optional dependencies as well. Follow the instructions as above, but
+instead of ``pip install .`` use ``pip install ".[test,dev]"`` to install both
+the extras.
+
 The installation instructions above assume that you have set up SSH keys for use
 with GitLab to allow for passwordless clones from GitLab, this way it's possible
 to run ``pip install git+ssh...`` commands and install packages directly from