[WIP] Docker build #33

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TomekFraczek wants to merge 24 commits into develop from docker-build

config.bat

-Original file line number
+Diff line change
@@ -0,0 +1,9 @@
+    @echo off
+    IF "%~1"=="" (
+    	echo "No docker container name given!"
+    	EXIT /B 2
+    ) ELSE (
+    	docker run -it --name configuration-inator %1 python config/make_config.py
+    	docker commit configuration-inator %1
+    )

config.sh

-Original file line number
+Diff line change
@@ -0,0 +1,7 @@
+    #! /bin/bash
+    if [$# -eq 0]; then
+    	echo "No docker image name given!"
+    else
+    	docker run -it --name configuration-inator $1 python config/make_config.py;
+    	docker commit configuration-inator $1;
+    fi

config/make_config.py

            
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                      Diff line number
                      Diff line change
                  
    @@ -1,8 +1,9 @@
  
    #!/usr/bin/python

    '''

    Executable script to create the configuration file for the BMI3D code, a text file called '$BMI3D/config_files/config' 

    Executable script to create the configuration file for the BMI3D code, a text file called '$BMI3D/config/config'

    '''

    import os

    import sys

    from collections import OrderedDict

    stuff = OrderedDict()

    @@ -14,24 +15,32 @@
  
    stuff['plexon IP address'] = dict(addr='10.0.0.13', port=6000)

    stuff['update_rates'] = dict(hdf_hz=60)

    # Add an optional commandline flag to make setup non-interactive

    use_defaults = '-y' in sys.argv or '--use-defaults' in sys.argv

    from db import settings

    databases = list(settings.DATABASES.keys())

    for dbname in databases:

        stuff['db_config_%s' % dbname] = dict(data_path='/storage')

    for db_name in databases:

        stuff[f'db_config_{db_name}'] = dict(data_path='/storage')

    config_filename = '$BMI3D/config_files/config'

    config_filename = '$BMI3D/config/config'

    config_fh = open(os.path.expandvars(config_filename), 'w')

    for system_name, system_opts in list(stuff.items()):

        config_fh.write('[%s]\n' % system_name)

        config_fh.write(f'[{system_name}]\n')

        print(system_name)

        for option, default in list(system_opts.items()):

            print(option, default)

            opt_val = input("Enter value for '%s' (default=%s): " % (option, str(default)))

            if opt_val == '':

            if use_defaults:

                print(f"  Using default ({default}) for {option}")

                opt_val = default

            config_fh.write('%s = %s\n' % (option, opt_val))

            else:

                opt_val = input(f"  Enter value for '{option}' (default={default}): ")

                if opt_val == '':

                    opt_val = default

            config_fh.write(f'{option} = {opt_val}\n')

        config_fh.write('\n')

        print()

config/namelist.py

            
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                      Diff line number
                      Diff line change
                  
    @@ -2,12 +2,17 @@
  
    Lookup table for features, generators and tasks for experiments

    '''

    ## Get the list of experiment features

    from .featurelist import features

    ## Get the list of tasks

    from .tasklist import tasks

    # Get the list of experiment features

    try:

        from .featurelist import features

    except (ImportError, ModuleNotFoundError):

        features = {}

    # Get the list of tasks

    try:

        from .tasklist import tasks

    except (ImportError, ModuleNotFoundError):

        tasks = {}

    # Derive generator functions from the tasklist (all generatorfunctions should be staticmethods of a task)

    generator_names = []

    @@ -67,4 +72,4 @@ def __getitem__(self, name):
  
    ################################################################################

    ################################################################################

    from .bmilist import *
      
    # from .bmilist import *

db/runserver.sh

            
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    @@ -15,7 +15,7 @@ if [ -z "$BMI3D" ]
  
    fi

    #Check /storage (exist )

    storage=$(python $BMI3D/config_files/check_storage.py 2>&1)

    storage=$(python $BMI3D/config/check_storage.py 2>&1)

    if [ $storage == 'False' ]; then

        echo "/storage does not exist --> if on Ismore, must mount"

        exit 1

    @@ -28,8 +28,8 @@ if [ `ps aux | grep "manage.py runserver" | grep python | wc -l` -gt 0 ]; then
  
    fi

    # Check that a config file is in the correct place, $BMI3D/config

    if [ ! -e $BMI3D/config_files/config ]; then 

        echo "ERROR: cannot find config file! Did you run $BMI3D/config_files/make_config.py?"

    if [ ! -e $BMI3D/config/config ]; then

        echo "ERROR: cannot find config file! Did you run $BMI3D/config/make_config.py?"

        exit 1

    fi

install/docker/bmi3d.base.dockerfile

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+Diff line change
@@ -0,0 +1,55 @@
+    ##### ################################################################### ####
+    ##### ---- Starting point when any os dependencies have been changed ---- ####
+    ##### ################################################################### ####
+    FROM python:3
+    #### Connect up third-party repositories (rabbitmq and erlang)
+    RUN curl -s https://packagecloud.io/install/repositories/rabbitmq/rabbitmq-server/script.deb.sh | bash
+    RUN echo "deb http://dl.bintray.com/rabbitmq-erlang/debian bionic erlang" \
+    	>> /etc/apt/sources.list.d/bintray.erlang.list
+    RUN apt-get -y update
+    ##### Install required ubuntu packages
+    RUN apt-get install -y \
+    	smbclient \
+    	cifs-utils \
+    	bison \
+    	flex \
+    	openssh-server \
+    	libusb-dev\
+    	libcomedi-dev \
+    	python-comedilib  \
+    	swig \
+    	isc-dhcp-server \
+    	sqlite3 \
+    	vim
+    # Install rabbitmq with it's erlang dependencies
+    RUN apt-get install -y --allow-unauthenticated \
+        erlang-base-hipe \
+        erlang-asn1 \
+        erlang-crypto \
+        erlang-eldap \
+        erlang-ftp \
+        erlang-inets \
+        erlang-mnesia \
+        erlang-os-mon \
+        erlang-parsetools \
+        erlang-public-key \
+        erlang-runtime-tools \
+        erlang-snmp \
+        erlang-ssl \
+        erlang-syntax-tools \
+        erlang-tftp \
+        erlang-tools \
+        erlang-xmerl \
+        rabbitmq-server
+    ####### Set up directories
+    RUN mkdir -v -p /code/src/
+    RUN mkdir -v -p /backup && chown root /backup
+    RUN mkdir -v -p /storage/plots && chown -R root /storage\
+    RUN mkdir -v -p /code/bmi3d/log

install/docker/bmi3d.code.dockerfile

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+Diff line change
@@ -0,0 +1,17 @@
+    #### ##################################################################### #####
+    #### ---- Starting point when only small local changes have been made ---- #####
+    #### ##################################################################### #####
+    FROM bmi3d:python
+    COPY bmi3d/ /code/bmi3d/
+    COPY bmi3d_tasks_analysis/ /code/bmi3d_tasks_analysis/
+    RUN python config/make_config.py --use-defaults && \
+        python db/manage.py makemigrations && \
+        python db/manage.py migrate
+    # Fix all .sh files that might have aquired windows line endings
+    RUN for f in $(find /code/ -name "*.sh"); \
+        do echo "fixing: $f" && sed -i 's/\r$//' $f; \
+        done
+    CMD [ "/bin/bash", "./db/runserver.sh" ]

install/docker/bmi3d.python.dockerfile

-Original file line number
+Diff line change
@@ -0,0 +1,18 @@
+    ##### ################################################################### ####
+    ##### ---- Starting point when python dependencies have been changed ---- ####
+    ##### ################################################################### ####
+    FROM bmi3d:base
+    # --- Expect cache invalidation here if source files have changed --- #
+    COPY bmi3d/requirements.txt /code/bmi3d/requirements.txt
+    WORKDIR /code/bmi3d/
+    ###### Install python dependencies
+    RUN pip install --upgrade pip
+    RUN pip install -r requirements.txt
+    # Set env vars for future reference
+    ENV BMI3D="/code/bmi3d" \
+    	PYTHONPATH="${PYTHONPATH}:/code/bmi3d/:/code/bmi3d_tasks_analysis"

install/docker/src_code_install.sh

-Original file line number
+Diff line change
@@ -0,0 +1,63 @@
+    #!/bin/bash
+    ####### Declare environment variables
+    CODE=/code
+    BMI3D=$CODE/bmi3d ### Directory in which to install the bmi3d software
+    USER=root  # We're in a docker container so root is safe
+    ####### Download any src code
+    git clone https://github.com/sgowda/robotics_toolbox $HOME/code/robotics
+    # Phidgets code
+    #wget https://www.phidgets.com/downloads/phidget22/libraries/linux/libphidget22/libphidget22-1.1.20190417.tar.gz
+    #wget https://www.phidgets.com/downloads/phidget22/libraries/any/Phidget22Python/Phidget22Python_1.1.20190418.zip
+    ####### Install source code, configure software
+    # plexread module
+    #cd $BMI3D/riglib
+    which python
+    #python setup.py install
+    # NIDAQ software -- deprecated!
+    # $HOME/code/bmi3d/riglib/nidaq/build.sh
+    echo "TESTED IF HERE"
+    # Phidgets libraries
+    #cd $CODE/src/
+    #tar xzf libphidget.tar.gz
+    #cd libphidget*
+    #./configure
+    #make
+    #make install
+    #cd $CODE/src/
+    #unzip PhidgetsPython.zip
+    #cd PhidgetsPython
+    #python setup.py install
+    ####### Configure udev rules, permissions
+    # Phidgets
+    #cp $CODE/src/libphidget*/udev/99-phidgets.rules /etc/udev/rules.d
+    #chmod a+r /etc/udev/rules.d/99-phidgets.rules
+    # NIDAQ
+    cp $HOME/code/bmi3d/install/udev/comedi.rules /etc/udev/rules.d/
+    chmod a+r /etc/udev/rules.d/comedi.rules
+    udevadm control --reload-rules
+    # Group permissions
+    usermod -a -G iocard $USER # NIDAQ card belongs to iocard group
+    usermod -a -G dialout $USER # Serial ports belong to 'dialout' group
+    ####### Reconfigure .bashrc
+    sed -i '$a export PYTHONPATH=$PYTHONPATH:$HOME/code/robotics' $HOME/.bashrc
+    sed -i '$a export BMI3D=/home/lab/code/bmi3d' $HOME/.bashrc
+    sed -i '$a source $HOME/code/bmi3d/pathconfig.sh' $HOME/.bashrc
+    source $HOME/.bashrc
+    chown -R $USER ~/.matplotlibs
+    cd $HOME/code/bmi3d/db
+    python manage.py syncdb
+    # Add superuser 'lab' with password 'lab'

requirements.txt

-Original file line number
+Diff line change
@@ Expand Up / @@ -7,15 +7,15 @@ traits @@
     pandas
     patsy
     statsmodels
-    PyOpenGL
-    PyOpenGL-accelerate
+    PyOpenGL
     Django
     pylibftdi
     nitime
     sphinx
     numpydoc
     tornado
     tables
+    sklearn
     pyserial
     h5py
     pygame
@@ Expand Down @@

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