Docker build reorder and update

Dockerfile

@@ -38,8 +38,8 @@ echo "c.NotebookApp.ip = '*'" >> /root/.jupyter/jupyter_notebook_config.py
 WORKDIR /usr/local/
 
 # setup scripts and python codes - these are to be automatically updated on the github
-ADD https://github.com/garethkennedy/MECSim_Analytics/archive/master.tar.gz /usr/local/git_codes.tar.gz
-RUN tar xvfz git_codes.tar.gz
+#ADD https://github.com/garethkennedy/MECSim_Analytics/archive/master.tar.gz /usr/local/git_codes.tar.gz
+#RUN tar xvfz git_codes.tar.gz
 # outputs to ~/MECSim_Analytics-master
 RUN rm -rf git_codes.tar.gz
 #RUN mv MECSim_Analytics-master/* .
@@ -54,6 +54,7 @@ WORKDIR /usr/local/MECSim_Analytics-master/
 # copy required directories
 COPY input/* /usr/local/input/
 COPY python/* /usr/local/python/
+COPY docs/* /usr/local/docs/
 COPY input_templates/* /usr/local/input_templates/
 COPY script/* /usr/local/script/
 # copy specific files
@@ -76,6 +77,9 @@ RUN ./MECSim.exe
 RUN head output/log.txt
 RUN tail output/log.txt
 
+# create py versions of default notebooks
+RUN jupyter nbconvert --to python --template=python.tpl python/*
+
 # prepare and test entry script
 #COPY MECSim_Analytics-master/entry_script/entry_script.sh .
 RUN chmod +x entry_script.sh
@@ -90,6 +94,8 @@ WORKDIR /usr/local/external/
 RUN mkdir input
 RUN mkdir python
 RUN mkdir script
+RUN mkdir input_templates
+RUN mkdir docs
 
 WORKDIR /usr/local/
 

entry_script/entry_script.sh

@@ -10,15 +10,13 @@ ls -lrt external/*
 echo "User prompting? Changes saved?"
 
 cp external/input/* input/
+cp external/input_templates/* input_templates/
+cp external/docs/* docs/
 cp external/python/* python/
 cp external/script/* script/
 # 2: copy back to the mapped directories. Thus they will have the most up to date versions AND any gaps filled in with default files stored in the docker image
-cp input/* external/input/
-cp python/* external/python/
-cp script/* external/script/
+# only done in jupyter mode - note that this could cause unexpected behaviour if user was using incorrect dir to update and use script mode?
 
-# convert all ipynb to py
-jupyter nbconvert --to python --template=python.tpl python/*
 
 # Entry point script for MECSim docker. 
 
@@ -27,6 +25,10 @@ if [ "$1" == "--script" ]; then
   ls -lrt script/*
   dos2unix script/*.sh
   chmod +x script/*.sh
+
+  # convert all ipynb to py
+  jupyter nbconvert --to python --template=python.tpl python/*
+
   ./script/run_mecsim_script.sh
 elif [ "$1" == "--single" ]; then
   echo "Running a single MECSim experiment:"
@@ -39,16 +41,38 @@ elif [ "$1" == "--single" ]; then
   [[ -e MECSimOutput_Pot.txt ]] && cp MECSimOutput_Pot.txt output/
 elif [ "$1" == "--jupyter" ]; then
   echo "Running a jupyter notebook env:"
+  # 2: copy back to the mapped directories (from above) 
+  cp input/* external/input/
+  cp input_templates/* external/input_templates/
+  cp docs/* external/docs/
+  cp python/* external/python/
+  cp script/* external/script/
+
+  # convert all ipynb to py
+  jupyter nbconvert --to python --template=python.tpl python/*
+
   dos2unix script/*.sh
   chmod +x script/*.sh
   ./script/run_jupyter_script.sh
 elif [ "$1" == "--update" ]; then
   echo "Updating all python and jupyter notebooks in your local python directory using latest versions from the github repository ( https://github.com/garethkennedy/MECSim_Analytics/tree/master/python ). CAUTION this will overwrite any notebooks with the same names in your local python directory. As a failsafe the existing contents of python/ are copied to python/backup"
-  cd python
-  mkdir backup
-  cp * backup
-  curl -L https://codeload.github.com/garethkennedy/MECSim_Analytics/tar.gz/master | tar -xz --strip=2 MECSim_Analytics-master/python
-  cd ..
+  # 2: copy back to the mapped directories (from above) 
+  cp input/* external/input/
+  cp input_templates/* external/input_templates/
+  cp docs/* external/docs/
+  cp python/* external/python/
+  cp script/* external/script/
+
+  backup_dirs='python
+  input_templates'
+  for this_dir in $backup_dirs;
+  do
+    cd $this_dir
+    mkdir backup
+    cp * backup
+    curl -L https://codeload.github.com/garethkennedy/MECSim_Analytics/tar.gz/master | tar -xz --strip=2 MECSim_Analytics-master/$this_dir
+    cd ..
+  done
 else
   echo "Welcome to MECSim docker"
   echo ""

prepare_docker_build.sh

@@ -0,0 +1,29 @@
+#!/bin/bash
+docker='/c/gfk/EChem/StatisticalAnalysis/Docker_build/MECSim'
+
+# copy docker build instructions file
+cp Dockerfile $docker
+# scripts includes running jupyter (run_jupyter_script.sh) and a default run_mecsim_script.sh
+# also a sample skeleton file (Master.sk)
+mkdir $docker/script
+cp script/* $docker/script
+# sample skeleton files for different mechanisms (copy over Master.sk)
+mkdir $docker/input_templates
+cp input_templates/* $docker/input_templates
+# documentation (updatable via github via docker)
+mkdir $docker/docs
+cp docs/* $docker/docs
+# sample single run MECSim input file (Master.inp)
+mkdir $docker/input
+cp input/* $docker/input
+# MECSim source code for build (removed from docker container post-compile)
+mkdir $docker/src
+cp src/* $docker/src
+# script to specify docker container functionality at run time
+mkdir $docker/entry_script
+cp entry_script/* $docker/entry_script
+# python scripts that can be editted by user or updated from git
+mkdir $docker/python
+cp python/*.ipynb $docker/python
+
+# what about the scripts to run the docker container correctly?

run_docker_win_cmd_jupyter.bat

@@ -1 +1 @@
-docker run -v %cd%/input:/usr/local/external/input -v %cd%/output:/usr/local/output -v %cd%/python:/usr/local/external/python -v %cd%/script:/usr/local/external/script --rm --name mecsim_container -p 8888:8888 -it mecsim --jupyter
+docker run -v %cd%/input:/usr/local/external/input -v %cd%/output:/usr/local/output -v %cd%/python:/usr/local/external/python -v %cd%/docs:/usr/local/external/docs -v %cd%/input_templates:/usr/local/external/input_templates -v %cd%/script:/usr/local/external/script --rm --name mecsim_container -p 8888:8888 -it mecsim --jupyter

run_docker_win_cmd_single.bat

@@ -1 +1 @@
-docker run -v %cd%/input:/usr/local/input -v %cd%/output:/usr/local/output -v %cd%/python:/usr/local/python -v %cd%/script:/usr/local/script -it mecsim --single
+docker run -v %cd%/input:/usr/local/input -v %cd%/output:/usr/local/output -it mecsim --single

script/run_jupyter_script.sh

@@ -1,10 +1,11 @@
 #!/bin/bash
 
 PYTHON_CODE_DIR='python/'
+EXTERNAL_DIR='external/'
 
 # Script to run a single MECSim execution. Working directory of wherever this script is called (/ in docker)
 echo "In sample customizable MECSim script..."
 echo "Any python codes to be put in $PYTHON_CODE_DIR"
 echo "jupyter notebook test"
 #jupyter notebook --port=80 --no-browser --ip=0.0.0.0 --allow-root
-jupyter notebook --port=8888 --no-browser --allow-root
+jupyter notebook --notebook-dir=$EXTERNAL_DIR --port=8888 --no-browser --allow-root