How to install single packages in a workspace?

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"installing" something (either with catkin_make or with catkin_tools) will always copy installable artefacts to the install space. With catkin_tools, catkin clean does indeed clear that directory out, unless you specify specific spaces to be deleted only (ie: with --log, --build, --devel and/or --install).

That is rather brittle though (if/when someone forgets to pass those options your install space will be cleaned out again).

If it is not possible, what is the canonical way to deal with this? Build the packages to be installed in an intermediate workspace, and then extend another workspace? Build them in /opt/ros/melodic/?

Best practice would be -- apart from using an internal buildfarm, releasing those packages and installing them that way -- to create an underlay workspace that your regular workspace extends. You'd use workspace overlaying, like so:

/opt/ros/$ROS_DISTRO
└── /path/to/your/underlay_ws
    └── /path/to/your/regular_ws

In this setup, vanilla $ROS_DISTRO would be the install space populated by the .deb packages you install using apt (or built from sources on some platforms). You then build the underlay workspace with the packages that you "always need". You then activate the underlay workspace (either source /path/to/your/underlay_ws/install/setup.bash or by using catkin config --extend (recommended)) and build your regular_ws.

A catkin clean of regular_ws will only clean out your regular workspace. It will not touch any underlays.

Finally:

• underlay_ws can of course have any name, it doesn't need to be called underlay_ws
• it can also be located anywhere (here in my lab we have several underlays which are located in /opt/ros fi)
• if you have machines that are exact duplicates of each other, you could even share your underlay workspaces, avoiding the need to build the workspaces on all machines (but if you go this far, you might start looking into generating .debs)