changed something

linux/04_docker.md

@@ -2,8 +2,37 @@
 ---------------
 
 - basically Linux virtual machines
+- a virtual machine functions as if you had a different computer sitting on your desk,
+  but it's emulated
 - can be combine with the host (internet access, memory,...) -> VERY fast
 - but run just fine on windows via wsl
 - images vs containers
 **example**: ur_simple_control dockerfile
 - go over all the flags used there
+
+### Installing docker on Windows
+-------------------------------
+1. install wsl with "wsl --install" in powershell administrator, more at [microsoft website](https://learn.microsoft.com/en-us/windows/wsl/install)
+2. install docker on windows (with wsl option, should be default), more at [docker website](https://docs.docker.com/desktop/install/windows-install/)
+3. create the docker account, some options require it
+
+### slightly more detailed info
+--------------------------------
+To oversimplify, Docker is virtualisation software which allows
+one to programatically set up a Linux virtual machine.
+A virtual machine is a emulation of a full computer, and it runs similarly to other
+programs on the host machine (your computer and its OS).
+By default, the virtual machine has no information about the host machine - it is as if
+you had a different computer sitting on your desk. For our purposes, some sharing will be necessary.
+This includes things like internet access and sharing of files and folders.
+
+A docker image is specification of a virtual machine,
+while a docker container is an instance of that machine (similar to classes and objects
+in programming). You can have multiple containers running the same image.
+A Dockerfile is a specific kind of file where a Docker image is defined. 
+The Dockerfile provided in this repository will create an image with all the software 
+needed to simulate and use the UR robot. 
+If you want to install additional software within your Docker, you will need to either update
+the Dockerfile and re-build the image, or use a persistent container, otherwise
+all of the installed software will be deleted when you close the container 
+(as it happens on university computers). 

ur_simple_control/01_basic_info_and_intended_audience.md

 ## basic info
+---------------
 
 - pure python
 - alternative to ros
@@ -14,4 +15,33 @@
 i.e. people strong in engineering math, but no necessarily software engineering
 - currently only has support for UR5e and velocity control, but expensions are comming soon
 - will get rewritten to C++ and have python bindings via pybind-11 for the official release
-- easy installation with docker (demonstrate)
+- easy installation with docker 
+
+## note on real time
+--------------------------
+We will not even attempt to use software with real-time guarantees.
+This makes all our programs inherently unpredictable due to the lack
+of hard real-time execution guarantees. 
+However, this has not yet caused a problem for our purposes.
+Furthermore, since we are only building experimental set-ups,
+not fully autonomous solutions, unpredictable behavior caused by
+programming mistakes is what we really need to worry about.
+
+### installation instructions
+----------------------------
+Here are the steps to get to your container running.  
+On windows:
+1. install wsl with "wsl --install" in powershell administrator, more at https://learn.microsoft.com/en-us/windows/wsl/install
+2. install docker on windows (with wsl option, should be default)
+3. create the docker accout 
+4. open docker desktop, navigate to Settings (by user/account button) -> Resources -> Network -> click on enable host networking
+5. open wsl (type wsl in powershell) and navigate to git folder (now in wsl) with "cd /mnt/Users/YOURUSERNAME/PATH_TO_GIT_FOLDER"
+
+After docker is installed: 
+6. build the image with "docker build -t ur_simple_control ."
+7. to run the image FIRST RUN "xhost +" EVERY TIME, THEN RUN  "docker run --rm -it --net=host -e DISPLAY=$DISPLAY -v /tmp:/tmp ur_simple_control /bin/zsh"
+8. verify installation by running an example with --visualize-manipulator and --real-time-plotting arguments
+9. if you want to make persistent changes to the code from the docker, you need to use the -v argument in docker run to share the folder
+   with the code between your native OS (host) and the docker container. 
+   in particular, use -v [path_to_folder_on_host]:[path_to_that_folder_in_docker_container]:rw .
+   notice the :rw at the end. this allows for both the host and the container to modify the files (otherwise they will be read-only).

ur_simple_control/03_pinocchio.md

 ## pinocchio 
+--------------
+pinocchio has functions with some advanced math, like Lie groups.  while it's
+certainly a plus to learn them, you don't need to. you can just use the forward
+kinematics and calculating jacobian functions, and do ther rest of the math
+with eigen or numpy.
+
+Content:
 - look at their documentation, do their tutorials if you want more
 - data and model
 - load robot as urdf
@@ -7,3 +14,24 @@
 - cheatsheet overview
 - forwardKinematics 
 - just mention dynamics calls
+
+## general documentation
+-------------------------------
+[pinocchio documentation](https://gepettoweb.laas.fr/doc/stack-of-tasks/pinocchio/master/doxygen-html/index.html)
+
+## native installation procedure
+-------------------------------
+just follow the steps (copy-paste commands into terminal) listed 
+[here](https://stack-of-tasks.github.io/pinocchio/download.html) .
+NOTE: if using own compilation of pinocchio, make sure you compile with mpi 
+and whatever else is needed to run algorithms in parallel.
+you won't be able to run in 500Hz on a single core. also note that
+the compilation required 13GB of RAM on my system. 
+
+## tutorials
+-------------------------------
+- [probably the best introduction to pinocchio](https://github.com/ymontmarin/_tps_robotique)
+- [pinocchio with casadi](https://github.com/nmansard/jnrh2023) - use the provided Docker, very difficult to install the exact software version used in the tutorial
+- [exercises offered on documentation webstite](https://gepettoweb.laas.fr/doc/stack-of-tasks/pinocchio/master/doxygen-html/md_doc_d-practical-exercises_intro.html)
+
+