Improved testing & checking on size of generated files

.github/workflows/docker-image-quickrun.yml

@@ -31,3 +31,5 @@ jobs:
         ls -alth
         ls -alth output
         ls -alth output/*
+
+        find output/Siber*/cut*mp4 -maxdepth 1 -size +200k | grep -q . # Fails if not found or too small 

.github/workflows/docker-image.yml

@@ -33,3 +33,6 @@ jobs:
         ls -alth output/*
 
         more output/*/report.json 
+
+        find output/C2_FW*/cut*mp4 -maxdepth 1 -size +300k | grep -q .  # Fails if not found or too small 
+

.gitignore

@@ -4,3 +4,8 @@ output/C2*
 /output/siminfo.py
 /output/wor*
 /output/Sibernetic_*
+/output/W2D*
+/output/alone*
+/output/cube*
+/output/deep*
+/output/master*

Dockerfile_intel

@@ -1,4 +1,4 @@
-FROM ubuntu:22.04
+FROM ubuntu:24.04
 
 LABEL maintainer="David Lung (lungdm@gmail.com); Padraig Gleeson (p.gleeson@gmail.com)"
 
@@ -18,72 +18,76 @@ RUN mkdir -p /etc/sudoers.d && \
   chmod 0440 /etc/sudoers.d/$USER && \
   chown ${uid}:${gid} -R /home/$USER
 
-ENV DEBIAN_FRONTEND noninteractive # TODO: change
+ENV DEBIAN_FRONTEND=noninteractive
 
 
 ################################################################################
 ########     Update/install essential libraries
 
-RUN apt-get update && apt-get install -y --no-install-recommends apt-utils \
+RUN apt-get update
+RUN apt-get install -y --no-install-recommends apt-utils \
   wget nano htop build-essential make git automake autoconf \
-  g++ rpm libtool libncurses5-dev zlib1g-dev bison flex lsb-core \
+  g++ rpm libtool libncurses5-dev zlib1g-dev bison flex \
   sudo xorg openbox x11-xserver-utils \
-  libxext-dev libncurses-dev python3-dev mercurial \
-  freeglut3-dev libglu1-mesa-dev libglew-dev python3-dev python3-pip python3-lxml  python3-scipy python3-tk \
+  libxext-dev libncurses-dev mercurial \
+  freeglut3-dev libglu1-mesa-dev libglew-dev python3-dev python3-pip \
   kmod dkms linux-source linux-headers-generic \
   maven openjdk-8-jdk \
-  python3-setuptools python3-yaml libnuma1 \
+  libnuma1 \
   openmpi-bin  libopenmpi-dev \
-  libgl1-mesa-glx libgl1-mesa-dri libfreetype6-dev \
-  libxft-dev python3-matplotlib unzip ffmpeg xvfb tmux
+  libgl1 libglx-mesa0  libgl1-mesa-dri libfreetype6-dev \
+  libxft-dev  unzip ffmpeg xvfb tmux
 
 #RUN  sudo pip install --upgrade pip
 
 RUN sudo usermod -a -G video $USER
 
 #USER $USER
-ENV HOME /home/$USER
+ENV HOME=/home/$USER
 WORKDIR $HOME
 
-#### TODO: check that this is the best way to switch to py3...
-RUN  sudo update-alternatives --install /usr/bin/python python /usr/bin/python3 10
-RUN  sudo update-alternatives --install /usr/bin/pip pip /usr/bin/pip3 10
 
 
 ################################################################################
 ########     Install NEURON simulator
 
-RUN pip3 install neuron==8.2.6
+RUN sudo pip install neuron==8.2.6  --break-system-packages
 
 
 ################################################################################
 ########     Install c302 for building neuronal network models
 
 RUN git clone https://github.com/openworm/c302.git && \
   cd c302 && \
-  git checkout ow-0.9.5 && \
-  sudo pip install .
+  git checkout ow-0.9.7 && \
+  sudo pip install .  --break-system-packages
 
 # Note: pyNeuroML installed with the above library
 
-RUN pip3 install owmeta-core==0.13.5
-RUN owm bundle remote --user add ow 'https://raw.githubusercontent.com/openworm/owmeta-bundles/master/index.json'
 
 
 ################################################################################
 ########     Install Sibernetic for the worm body model
 
 RUN git clone https://github.com/openworm/sibernetic.git && \
   cd sibernetic && \
-  git checkout ow-0.9.5  # fixed to a specific branch
+  git checkout ow-0.9.7  # fixed to a specific branch
+
+
+################################################################################
+########     Install extra Python dependencies
+
+RUN sudo pip install ruff  --break-system-packages
 
 
 ################################################################################
 ########     Set some paths//environment variables
 
 ENV C302_HOME=$HOME/c302/c302
 ENV SIBERNETIC_HOME=$HOME/sibernetic
-ENV PYTHONPATH=$PYTHONPATH:$HOME/c302:$SIBERNETIC_HOME
+ENV PYTHONPATH=$HOME/c302:$SIBERNETIC_HOME
+
+ENV NEURON_MODULE_OPTIONS=-nogui
 
 
 ################################################################################
@@ -124,7 +128,7 @@ RUN cd sibernetic && \
 COPY ./master_openworm.py $HOME/master_openworm.py
 RUN sudo chown $USER:$USER $HOME/master_openworm.py
 
-RUN echo '\n\nalias cd..="cd .."\nalias h=history\nalias ll="ls -alt"' >> ~/.bashrc
+RUN printf '\n\nalias cd..="cd .."\nalias h=history\nalias ll="ls -alth"\n' >> ~/.bashrc
 
 RUN pip list
 

run-quick.sh

@@ -1,4 +1,5 @@
 #!/bin/bash
+set -ex
 
 #from: https://unix.stackexchange.com/a/129401
 while getopts ":d:p:" opt; do
@@ -16,7 +17,7 @@ OW_OUT_DIR=/home/ow/shared
 HOST_OUT_DIR=$PWD
 version=$(<VERSION) # Read version of Dockerfile from file VERSION
 
-xhost +
+# xhost + # remove for now...
 
 
 NOC302_PART="-e NOC302=1"
@@ -33,6 +34,6 @@ $DURATION_PART \
 --privileged \
 -v $HOST_OUT_DIR:$OW_OUT_DIR:rw \
 openworm/openworm:$version \
-bash -c "DISPLAY=:44 python master_openworm.py"
+bash -c "DISPLAY=:44 python3 master_openworm.py"
 
 docker logs -f openworm_$version

run.sh

@@ -1,4 +1,5 @@
 #!/bin/bash
+set -ex
 
 #from: https://unix.stackexchange.com/a/129401
 while getopts ":d:p:" opt; do
@@ -17,7 +18,7 @@ HOST_OUT_DIR=$PWD
 
 version=$(<VERSION) # Read version of Dockerfile from file VERSION
 
-xhost +
+# xhost + # remove for now...
 
 if [ -z "$duration" ]
 then #duration is not set, don't use it