fix doc

.gitignore

+__pycache__/
+*.py[cod]
+\#*\#
+.\#*
+*~
+.env
+*env/
+libclang*so
+Dockerfile
+build/
+*egg-info/
+*png
+test_*/
+git-global-secret
\ No newline at end of file

cloneall.bash

@@ -10,15 +10,13 @@ while getopts "cptlr:" opt
 do
    case "$opt" in
       c ) clona=1 ;;
-      p ) pyinsta=1 ;;
       t ) tmuxa=1 ;;
-      l ) linka=1 ;;
       r ) shift $(( OPTIND - 2 )) && REPOS=($@) && break
    esac
 done
 
-if [ -z "$clona" ] && [ -z "$pyinsta" ] && [ -z "$tmuxa" ] && [ -z "$linka" ];then
-    echo 'usage: ./cloneall.bash -c (clone repos) -p (python install and tests) -t (attach to tmux) -l (full tree of links) -r (repos)'
+if [ -z "$clona" ] && [ -z "$tmuxa" ]; then
+    echo 'usage: ./cloneall.bash -c (clone repos) -t (attach to tmux) -r (repos list, e.g. core io octree) '
     exit 1
 fi
 
@@ -29,37 +27,16 @@ if [ ! -z "$clona" ]; then
        echo "export DEBUG=1" >> .env
     fi
     . .env
-    [[ ! -d "venv" ]] && python3 -mvenv venv
-    . venv/bin/activate
-    pip install --upgrade pip
-    pip install autopep8
-    pip install matplotlib
     for REPO in "${REPOS[@]}"; do
 
 	[[ ! -d "$REPO" ]] && git clone ssh://git@git.ia2.inaf.it/hotwheels/$REPO.git
         pushd $REPO
+	[[ ! -d "venv" ]] && python3 -mvenv venv && . venv/bin/activate && pip install autopep8  && pip install PyYaml
         git switch dev || echo no dev branch
-	if [[ "$REPO" != "gitlab-profile" ]]; then
-	    [ ! -z "$pyinsta" ] && python -mpip install -e .[edit] && python -m hotwheels.checkup hotwheels/
-	fi
         popd
     done
 fi
 
-if [ ! -z "$linka" ]; then
-    mkdir -p full/hotwheels
-    touch full/hotwheels/__init__.py || echo cant touch
-    for f in core/hotwheels/*; do
-	[[ "${f##*/:0:2}" == "__" ]] && continue
-	ln -sf $PWD/$f full/hotwheels/${f##*/}
-    done
-    for REPO in "${REPOS[@]}"; do
-	if [ "$REPO" != "core" ] && [ "$REPO" != "gitlab-profile" ]; then
-	    ln -sf $PWD/$REPO/hotwheels/$REPO full/hotwheels
-	fi
-    done
-fi
-
 if [ ! -z "$tmuxa" ]; then
     
     if ! tmux has-session -t $SESSION_NAME ; then
@@ -77,8 +54,8 @@ if [ ! -z "$tmuxa" ]; then
 	    fi
             # Initialize the environment in the first window
             tmux send-keys -t $SESSION_NAME:$index ". .env" C-m
-            tmux send-keys -t $SESSION_NAME:$index ". venv/bin/activate" C-m
             tmux send-keys -t $SESSION_NAME:$index "cd $PWD/$value" C-m
+            tmux send-keys -t $SESSION_NAME:$index ". venv/bin/activate" C-m
 	    tmux rename-window $value
             
 	done

install_and_test.md

@@ -74,7 +74,7 @@ In case you need to work on many modules, you can clone and install all default
 
 ```bash
 wget https://www.ict.inaf.it/gitlab/hotwheels/gitlab-profile/-/raw/main/cloneall.bash
-./cloneall.bash -cp # will clone and pip-install all hotwheels modules
+bash cloneall.bash -c # will clone all hotwheels modules
 ```
 
 If you want to create a folder with all the modules soft-linked into the folder `hotwheels/*`, add the flag `-l` to `cloneall.bash` to get this folder tree in a folder named `full/hotwheels/*`. This is helpful in navigating the files with the IDE when development has strong refactoring and one need to edit multiple modules.