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Update bootstrap_linux.bash to work with Debian 13 - Trixie #86

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04b8bb1
Update bootstrap_linux.bash to work with Debian 13 - Trixie
Ejler Feb 11, 2026
b110124
Python 3-only changes to sockets
Ejler Feb 12, 2026
f14f50f
os.chdir is no longer part of pathlib, but the effect is already hand…
Ejler Feb 12, 2026
5c9dc90
Bootstrap_linux: install numpy via pip instead of as a system package
Ejler Feb 12, 2026
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47 changes: 17 additions & 30 deletions PyExpLabSys/common/sockets.py
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Original file line number Diff line number Diff line change
Expand Up @@ -57,11 +57,9 @@
# Queue was renamed to queue in Python 3
import queue as Queue
import logging
import six
from .utilities import call_spec_string
from .system_status import SystemStatus
from ..settings import Settings
from .supported_versions import python2_and_3

# Instantiate module logger
LOGGER = logging.getLogger(__name__)
Expand All @@ -71,9 +69,6 @@
# Instantiate a global system status object
SYSTEM_STATUS = SystemStatus()

# Indicate Python 2/3
python2_and_3(__file__)

# Instantiate settings object
SETTINGS = Settings()
LOGGER.debug("Settings loaded with the following values: %s", SETTINGS.settings)
Expand Down Expand Up @@ -200,9 +195,9 @@ def _single_value(self, command):

elif command == 'json' and name in DATA[self.port]['data']:
if self._old_data(name):
out = six.text_type(json.dumps(OLD_DATA))
out = json.dumps(OLD_DATA)
else:
out = six.text_type(json.dumps(DATA[self.port]['data'][name]))
out = json.dumps(DATA[self.port]['data'][name])
# The command is unknown
else:
out = UNKNOWN_COMMAND
Expand Down Expand Up @@ -239,7 +234,7 @@ def _all_values(self, command):
else:
data = DATA[self.port]['data'][codename]
points.append(data)
out = six.text_type(json.dumps(points))
out = json.dumps(points)
# Return a raw string with all measurements in codenames order including names
elif command == 'raw_wn':
strings = []
Expand All @@ -258,25 +253,23 @@ def _all_values(self, command):
for codename in DATA[self.port]['codenames']:
if self._old_data(codename):
datacopy[codename] = OLD_DATA
out = six.text_type(json.dumps(datacopy))
out = json.dumps(datacopy)
# Return all codesnames in a raw string
elif command == 'codenames_raw':
out = ','.join(DATA[self.port]['codenames'])
# Return a list with all codenames encoded as a json string
elif command == 'codenames_json':
out = six.text_type(json.dumps(DATA[self.port]['codenames']))
out = json.dumps(DATA[self.port]['codenames'])
# Return the socket server name
elif command == 'name':
out = DATA[self.port]['name']
# Return status of system and all socket servers
elif command == 'status':
out = six.text_type(
json.dumps(
{
'system_status': SYSTEM_STATUS.complete_status(),
'socket_server_status': socket_server_status(),
}
)
out = json.dumps(
{
'system_status': SYSTEM_STATUS.complete_status(),
'socket_server_status': socket_server_status(),
}
)
# The command is not known
else:
Expand Down Expand Up @@ -686,13 +679,11 @@ def handle(self):
commands = ['json_wn#', 'raw_wn#', 'name', 'status', 'commands']
return_value = '{}#{}'.format(PUSH_RET, json.dumps(commands))
elif request == 'status':
return_value = six.text_type(
json.dumps(
{
'system_status': SYSTEM_STATUS.complete_status(),
'socket_server_status': socket_server_status(),
}
)
return_value = json.dumps(
{
'system_status': SYSTEM_STATUS.complete_status(),
'socket_server_status': socket_server_status(),
}
)
elif request.count('#') != 1:
return_value = '{}#{}'.format(PUSH_ERROR, UNKNOWN_COMMAND)
Expand Down Expand Up @@ -939,7 +930,7 @@ def _format_return_raw_dict(argument):
# Check all values in list are of same type
types = [type(element) for element in value]
element_type = types[0]
element_type_name = six.text_type(element_type.__name__)
element_type_name = element_type.__name__
if types != len(types) * [element_type]:
message = (
'With return format raw, value in list must have same type'
Expand All @@ -953,13 +944,9 @@ def _format_return_raw_dict(argument):
value_string = ''
else:
# Single element conversion
element_type_name = six.text_type(type(value).__name__)
element_type_name = type(value).__name__
value_string = '{}'.format(str(value))

# We always call it str
if sys.version_info[0] == 2 and element_type_name == 'unicode':
element_type_name = 'str'

# Check that the element type makes sense for raw conversion
if element_type_name not in ['int', 'float', 'bool', 'str']:
message = (
Expand Down
3 changes: 0 additions & 3 deletions bin/autostart.py
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Original file line number Diff line number Diff line change
Expand Up @@ -73,9 +73,6 @@ def main():
args = parse_args()
config_file_path = find_config(args)

# Change current working directory to config dir
pathlib.os.chdir(config_file_path.parent)

# Parse XML config file
etree_object = XML.parse(config_file_path)
xml = etree_object.getroot()
Expand Down
105 changes: 55 additions & 50 deletions bootstrap/bootstrap_linux.bash
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Original file line number Diff line number Diff line change
Expand Up @@ -6,21 +6,26 @@
# EDIT POINT START: Edit here to change what the script does #
##############################################################

# Install virtual python environment in ~/$PELS_ENV
PELS_ENV=.pels

# apt install packages line 1, general packages
#
apt1="openssh-server emacs graphviz screen i2c-tools vim-nox"
apt1="emacs-nox graphviz screen i2c-tools vim-nox"

# apt install packages line 2, python extensions
#
# NOTE: This line used to contain colorama, but it is a dependency of
# pip, so it will be installed anyway
apt2="python3-pip python3-numpy black"
# NOTE: This line used to contain colorama, but it was a dependency of
# pip, so it will be installed anyway. Only used on Windows systems?
apt2="python3-pip python3-venv black"

# apt install packages that has possibly changed name, written in list form and installed one at at time
declare -a apt3=("libpython3-dev" "python3-dev")
# https://pypi.org/project/mysqlclient/
declare -a apt3=("libpython3-dev" "python3-dev default-libmysqlclient-dev build-essential pkg-config")
# for rhel, you need python3-devel mysql-devel pkgconfig instead to be able to pip mysqlclient

# packages to be installed by pip
pip3packages="minimalmodbus pyusb python-usbtmc pyserial pyyaml mysqlclient"
pip3packages="minimalmodbus pyusb python-usbtmc pyserial pyyaml mysqlclient numpy"
# Put packages into this array, whose installation sometimes fail
declare -a pip3problempackages=("pylint")

Expand All @@ -37,16 +42,13 @@ if [ -d $machine_dir ]; then
cd $machine_dir
fi
pistatus.py
if [ -f ~/'$PELS_ENV'/bin/activate ]; then
source ~/'$PELS_ENV'/bin/activate
fi
'

# These lines will be added to ~/.bash_aliases
bash_aliases="
alias sagi=\"sudo apt-get install\"
alias sagr=\"sudo apt-get remove\"
alias acs=\"apt-cache search\"
alias sagu=\"sudo apt-get update\"
alias sagup=\"sudo apt-get upgrade\"
alias sagdu=\"sudo apt-get dist-upgrade\"
alias ll=\"ls -lh\"
alias df=\"df -h\"
alias emacs-nolint=\"emacs -q --load ~/PyExpLabSys/bootstrap/.emacs-simple\"
Expand Down Expand Up @@ -87,6 +89,7 @@ abelec Setup device to use daq-modules from AB Electronics (NOT part of all
dash Install packages for dash
qt Setup GUI environment: Qt and Qwt (for plots)
"

##################
# EDIT POINT END #
##################
Expand Down Expand Up @@ -200,69 +203,66 @@ fi

# Install packages
if [ $1 == "install" ] || [ $1 == "all" ];then
# Verified for Debian 13 - Trixie
echo
echobold "===> INSTALLING PACKAGES"
echoblue "---> Updating package archive information"

# Update, but only if it has not just been done (within the last
# 10 hours), since it actually takes a while on a RPi.
#
# NOTE. The method is based on checking the last modification of
# the apt cache file, which may not the perfect method, we will
# test it and see
last_update=`stat /var/cache/apt/pkgcache.bin --format="%Y"`
now=`date +%s`
since_last_update=$((now-last_update))
if [ $since_last_update -gt 36000 ];then
sudo apt-get update
else
echoblue "Skipping, since it was done" $(($since_last_update/3600)) "hours ago"
fi
# Update - it does not take that long on newer hardware and the old
# method seemingly did not work when run on a fresh minimal installation.
sudo apt update

aptgetprefix='sudo apt-get -y'
aptprefix='sudo apt -y'

echoblue "---> Upgrade all existing packages"
$aptgetprefix dist-upgrade
$aptprefix full-upgrade
echoblue "---> Installing packages"
echoblue "----> Install: $apt1"
$aptgetprefix install $apt1
$aptprefix install $apt1
echoblue "----> Install: $apt2"
$aptgetprefix install $apt2
$aptprefix install $apt2

# Install package individually, that may have changed name
for package in "${apt3[@]}";do
echoblue "----> Attempting to install \"$package\" as an individual package"
$aptgetprefix install $package
$aptprefix install $package
done

echoblue "---> Remove un-needed packages, if any"
$aptgetprefix autoremove
$aptprefix autoremove
echoblue "---> Clear apt cache"
$aptgetprefix clean
sudo apt -y clean

echoblue "---> Enable ssh by creating /boot/ssh"
sudo touch /boot/ssh
echogood "+++++> DONE"
fi

# Install extra packages with pip
if [ $1 == "pip" ] || [ $1 == "all" ];then
# Verified for Debian 13 - Trixie
echo
# Test if pip3 is there
PIPEXECUTABLE=`which pip3`

if [ $? -eq 0 ];then
echobold "===> INSTALLING EXTRA PYTHON PACKAGES WITH PIP3"
echoblue "---> Installing: $pip3packages"
sudo $PIPEXECUTABLE install -U $pip3packages
# Individual packages
for package in "${pip3problempackages[@]}";do
echoblue "---> Installing \"$package\" as an invididual package"
sudo $PIPEXECUTABLE install -U $package
done
echogood "+++++> DONE"
# Create virtual Python environment if not existing
if [ ! -d ~/$PELS_ENV ];then
echoblue "Creating virtual environment for PyExpLabSys as $PELS_ENV"
python3 -m venv ~/$PELS_ENV
fi
# Activate virtual environment
if [ -f ~/$PELS_ENV/bin/activate ];then
source ~/$PELS_ENV/bin/activate

# Install packages
echobold "===> INSTALLING EXTRA PYTHON PACKAGES WITH PIP3"
echoblue "---> Installing: $pip3packages"
python -m pip install -U $pip3packages
# Individual packages
for package in "${pip3problempackages[@]}";do
echoblue "---> Installing \"$package\" as an invididual package"
python -m pip install -U $package
done
echogood "+++++> DONE"
else
echobad "pip3 not installed, run install step and then re-try pip step"
echobad "~/$PELS_ENV already exists, but is not a virtual environment for Python"
echobad "Skipping pip installs"
fi
fi

Expand Down Expand Up @@ -309,7 +309,7 @@ $cronline"
fi


# Setup autostart cronjob
# Setup settings
if [ $1 == "settings" ] || [ $1 == "all" ];then
echobold "===> LINKING PYEXPLABSYS SETTINGS FILE IN PLACE"
if [ -f ~/.config/PyExpLabSys/user_settings.yaml ];then
Expand Down Expand Up @@ -349,6 +349,7 @@ fi

# Install extra packages needed for writing docs
if [ $1 == "docs" ];then
# FIXME: Should be updated/removed or is working?
# TODO add sphinx and extra package needed to dependency graph
echobold "===> INSTALLING EXTRA PACKAGES FOR WRITING DOCS"
echo
Expand All @@ -370,6 +371,7 @@ if [ $1 == "docs" ];then
fi

if [ $1 == "wiringpi" ];then
# FIXME: Should be updated/removed or is working?
echobold "===> INSTALLING WIRINGPI"
echoblue "---> Installing wiringpi with apt-get"
sudo apt-get install wiringpi
Expand All @@ -383,9 +385,10 @@ if [ $1 == "wiringpi" ];then
fi

if [ $1 == "abelec" ];then
# FIXME: Should be updated/removed or is working?
# TODO: Improve script to allow multiple executions
echobold "===> INSTALLING EXTRA PACKAGES FOR AB ELECTRONICS"
sudo apt-get install i2c-tools python-smbus
sudo apt install i2c-tools python-smbus
echo

sudo touch /etc/modprobe.d/raspi-blacklist.conf # Make sure file is there before removing
Expand Down Expand Up @@ -439,6 +442,7 @@ fi


if [ $1 == "dash" ];then
# FIXME: Should be updated/removed or is working?
# TODO: Improve script to allow multiple executions
echobold "===> INSTALLING EXTRA PACKAGES FOR DASH"
pip3 install dash==0.28.5 # The core dash backend
Expand All @@ -450,6 +454,7 @@ fi

# GUI section (Qt and Qwt)
if [ $1 == "qt" ];then
# FIXME: Should be updated/removed or is working?
echobold "===> INSTALLING EXTRA PACKAGES FOR GUIS"
echo

Expand Down