Update Installing the OBITools3

Installing-the-OBITools3.md

@@ -1,4 +1,37 @@
-The OBITools3 are now available to download from git, and will soon be on Nix ([pull request](https://github.com/NixOS/nixpkgs/pull/69644)).
+The OBITools3 are now available to download from git and PyPI.
+
+# Install with pip
+
+First, make sure you have installed: **python3, python3-venv, pip**
+
+Then you can install the OBITools3 in a virtual environment:
+
+```
+  python3 -m venv obi3-env
+  source obi3-env/bin/activate
+  pip3 install --upgrade pip setuptools wheel Cython
+  pip3 install --pre --upgrade OBITools3
+```
+
+If you get this error from having previously installed the deprecated alpha version:
+
+  `ERROR: Cannot uninstall 'OBITools3'. It is a distutils installed project and thus we cannot accurately determine which files belong to it which would lead to only a partial uninstall.`
+
+You can remove the deprecated installation with (change Python version if needed):
+
+```
+  rm -rf /Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/OBITools3-0.0.*
+
+  rm -rf /Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/obitools3
+```
+
+Test the installation with:
+
+		obi test
+
+Once installed, you will need to be in the virtual environment to run commands (`source obi3-env/bin/activate`), or add the `obi` command to your `PATH`.
+
+# Install with git
 
 First, make sure you have installed: **python3, python3-venv, git, CMake**