Clarify the docker commands for compilation (#106)

* Clarify the docker commands for compilation

This is the very first time I use docker, and I'm learning. Thas `pwd` told me nothing, I thought it was a password. 

But the correct value is the project path.

I was able to compile after this fix:
```bat
C:\full-path-to-my-biosim4-folder\biosim4\>docker run --rm -ti -v C:\full-path-to-my-biosim4-folder\biosim4:/app --name biosim biosim4 make
test -d bin/Debug || mkdir -p bin/Debug
test -d obj/Debug/src || mkdir -p obj/Debug/src
c++ -Wall -pedantic -std=c++17 -fexceptions -fopenmp -I/usr/include/opencv4  -g -c src/analysis.cpp -o obj/Debug/src/analysis.o
c++ -Wall -pedantic -std=c++17 -fexceptions -fopenmp -I/usr/include/opencv4  -g -c src/basicTypes.cpp -o obj/Debug/src/basicTypes.o
c++ -Wall -pedantic -std=c++17 -fexceptions -fopenmp -I/usr/include/opencv4  -g -c src/createBarrier.cpp -o obj/Debug/src/createBarrier.o
c++ -Wall -pedantic -std=c++17 -fexceptions -fopenmp -I/usr/include/opencv4  -g -c src/endOfGeneration.cpp -o obj/Debug/src/endOfGeneration.o
c++ -Wall -pedantic -std=c++17 -fexceptions -fopenmp -I/usr/include/opencv4  -g -c src/endOfSimStep.cpp -o obj/Debug/src/endOfSimStep.o
c++ -Wall -pedantic -std=c++17 -fexceptions -fopenmp -I/usr/include/opencv4  -g -c src/executeActions.cpp -o obj/Debug/src/executeActions.o
c++ -Wall -pedantic -std=c++17 -fexceptions -fopenmp -I/usr/include/opencv4  -g -c src/feedForward.cpp -o obj/Debug/src/feedForward.o
c++ -Wall -pedantic -std=c++17 -fexceptions -fopenmp -I/usr/include/opencv4  -g -c src/genome-compare.cpp -o obj/Debug/src/genome-compare.o
c++ -Wall -pedantic -std=c++17 -fexceptions -fopenmp -I/usr/include/opencv4  -g -c src/genome.cpp -o obj/Debug/src/genome.o
c++ -Wall -pedantic -std=c++17 -fexceptions -fopenmp -I/usr/include/opencv4  -g -c src/getSensor.cpp -o obj/Debug/src/getSensor.o
c++ -Wall -pedantic -std=c++17 -fexceptions -fopenmp -I/usr/include/opencv4  -g -c src/grid.cpp -o obj/Debug/src/grid.o
c++ -Wall -pedantic -std=c++17 -fexceptions -fopenmp -I/usr/include/opencv4  -g -c src/imageWriter.cpp -o obj/Debug/src/imageWriter.o
c++ -Wall -pedantic -std=c++17 -fexceptions -fopenmp -I/usr/include/opencv4  -g -c src/indiv.cpp -o obj/Debug/src/indiv.o
c++ -Wall -pedantic -std=c++17 -fexceptions -fopenmp -I/usr/include/opencv4  -g -c src/main.cpp -o obj/Debug/src/main.o
c++ -Wall -pedantic -std=c++17 -fexceptions -fopenmp -I/usr/include/opencv4  -g -c src/params.cpp -o obj/Debug/src/params.o
c++ -Wall -pedantic -std=c++17 -fexceptions -fopenmp -I/usr/include/opencv4  -g -c src/peeps.cpp -o obj/Debug/src/peeps.o
c++ -Wall -pedantic -std=c++17 -fexceptions -fopenmp -I/usr/include/opencv4  -g -c src/random.cpp -o obj/Debug/src/random.o
c++ -Wall -pedantic -std=c++17 -fexceptions -fopenmp -I/usr/include/opencv4  -g -c src/signals.cpp -o obj/Debug/src/signals.o
c++ -Wall -pedantic -std=c++17 -fexceptions -fopenmp -I/usr/include/opencv4  -g -c src/simulator.cpp -o obj/Debug/src/simulator.o
c++ -Wall -pedantic -std=c++17 -fexceptions -fopenmp -I/usr/include/opencv4  -g -c src/spawnNewGeneration.cpp -o obj/Debug/src/spawnNewGeneration.o
c++ -Wall -pedantic -std=c++17 -fexceptions -fopenmp -I/usr/include/opencv4  -g -c src/survival-criteria.cpp -o obj/Debug/src/survival-criteria.o
c++ -Wall -pedantic -std=c++17 -fexceptions -fopenmp -I/usr/include/opencv4  -g -c src/unitTestBasicTypes.cpp -o obj/Debug/src/unitTestBasicTypes.o
c++ -Wall -pedantic -std=c++17 -fexceptions -fopenmp -I/usr/include/opencv4  -g -c src/unitTestConnectNeuralNetWiringFromGenome.cpp -o obj/Debug/src/unitTestConnectNeuralNetWiringFromGenome.o
c++ -Wall -pedantic -std=c++17 -fexceptions -fopenmp -I/usr/include/opencv4  -g -c src/unitTestGridVisitNeighborhood.cpp -o obj/Debug/src/unitTestGridVisitNeighborhood.o
c++ -o bin/Debug/biosim4 obj/Debug/src/analysis.o obj/Debug/src/basicTypes.o obj/Debug/src/createBarrier.o obj/Debug/src/endOfGeneration.o obj/Debug/src/endOfSimStep.o obj/Debug/src/executeActions.o obj/Debug/src/feedForward.o obj/Debug/src/genome-compare.o obj/Debug/src/genome.o obj/Debug/src/getSensor.o obj/Debug/src/grid.o obj/Debug/src/imageWriter.o obj/Debug/src/indiv.o obj/Debug/src/main.o obj/Debug/src/params.o obj/Debug/src/peeps.o obj/Debug/src/random.o obj/Debug/src/signals.o obj/Debug/src/simulator.o obj/Debug/src/spawnNewGeneration.o obj/Debug/src/survival-criteria.o obj/Debug/src/unitTestBasicTypes.o obj/Debug/src/unitTestConnectNeuralNetWiringFromGenome.o obj/Debug/src/unitTestGridVisitNeighborhood.o -lopencv_core -lopencv_video -lopencv_videoio -lgomp -lpthread -fopenmp
test -d bin/Release || mkdir -p bin/Release
test -d obj/Release/src || mkdir -p obj/Release/src
c++ -Wall -pedantic -std=c++17 -fexceptions -fopenmp -I/usr/include/opencv4  -O3 -c src/analysis.cpp -o obj/Release/src/analysis.o
c++ -Wall -pedantic -std=c++17 -fexceptions -fopenmp -I/usr/include/opencv4  -O3 -c src/basicTypes.cpp -o obj/Release/src/basicTypes.o
c++ -Wall -pedantic -std=c++17 -fexceptions -fopenmp -I/usr/include/opencv4  -O3 -c src/createBarrier.cpp -o obj/Release/src/createBarrier.o
c++ -Wall -pedantic -std=c++17 -fexceptions -fopenmp -I/usr/include/opencv4  -O3 -c src/endOfGeneration.cpp -o obj/Release/src/endOfGeneration.o
c++ -Wall -pedantic -std=c++17 -fexceptions -fopenmp -I/usr/include/opencv4  -O3 -c src/endOfSimStep.cpp -o obj/Release/src/endOfSimStep.o
c++ -Wall -pedantic -std=c++17 -fexceptions -fopenmp -I/usr/include/opencv4  -O3 -c src/executeActions.cpp -o obj/Release/src/executeActions.o
c++ -Wall -pedantic -std=c++17 -fexceptions -fopenmp -I/usr/include/opencv4  -O3 -c src/feedForward.cpp -o obj/Release/src/feedForward.o
c++ -Wall -pedantic -std=c++17 -fexceptions -fopenmp -I/usr/include/opencv4  -O3 -c src/genome-compare.cpp -o obj/Release/src/genome-compare.o
c++ -Wall -pedantic -std=c++17 -fexceptions -fopenmp -I/usr/include/opencv4  -O3 -c src/genome.cpp -o obj/Release/src/genome.o
c++ -Wall -pedantic -std=c++17 -fexceptions -fopenmp -I/usr/include/opencv4  -O3 -c src/getSensor.cpp -o obj/Release/src/getSensor.o
c++ -Wall -pedantic -std=c++17 -fexceptions -fopenmp -I/usr/include/opencv4  -O3 -c src/grid.cpp -o obj/Release/src/grid.o
c++ -Wall -pedantic -std=c++17 -fexceptions -fopenmp -I/usr/include/opencv4  -O3 -c src/imageWriter.cpp -o obj/Release/src/imageWriter.o
c++ -Wall -pedantic -std=c++17 -fexceptions -fopenmp -I/usr/include/opencv4  -O3 -c src/indiv.cpp -o obj/Release/src/indiv.o
c++ -Wall -pedantic -std=c++17 -fexceptions -fopenmp -I/usr/include/opencv4  -O3 -c src/main.cpp -o obj/Release/src/main.o
c++ -Wall -pedantic -std=c++17 -fexceptions -fopenmp -I/usr/include/opencv4  -O3 -c src/params.cpp -o obj/Release/src/params.o
c++ -Wall -pedantic -std=c++17 -fexceptions -fopenmp -I/usr/include/opencv4  -O3 -c src/peeps.cpp -o obj/Release/src/peeps.o
c++ -Wall -pedantic -std=c++17 -fexceptions -fopenmp -I/usr/include/opencv4  -O3 -c src/random.cpp -o obj/Release/src/random.o
c++ -Wall -pedantic -std=c++17 -fexceptions -fopenmp -I/usr/include/opencv4  -O3 -c src/signals.cpp -o obj/Release/src/signals.o
c++ -Wall -pedantic -std=c++17 -fexceptions -fopenmp -I/usr/include/opencv4  -O3 -c src/simulator.cpp -o obj/Release/src/simulator.o
c++ -Wall -pedantic -std=c++17 -fexceptions -fopenmp -I/usr/include/opencv4  -O3 -c src/spawnNewGeneration.cpp -o obj/Release/src/spawnNewGeneration.o
c++ -Wall -pedantic -std=c++17 -fexceptions -fopenmp -I/usr/include/opencv4  -O3 -c src/survival-criteria.cpp -o obj/Release/src/survival-criteria.o
c++ -Wall -pedantic -std=c++17 -fexceptions -fopenmp -I/usr/include/opencv4  -O3 -c src/unitTestBasicTypes.cpp -o obj/Release/src/unitTestBasicTypes.o
c++ -Wall -pedantic -std=c++17 -fexceptions -fopenmp -I/usr/include/opencv4  -O3 -c src/unitTestConnectNeuralNetWiringFromGenome.cpp -o obj/Release/src/unitTestConnectNeuralNetWiringFromGenome.o
c++ -Wall -pedantic -std=c++17 -fexceptions -fopenmp -I/usr/include/opencv4  -O3 -c src/unitTestGridVisitNeighborhood.cpp -o obj/Release/src/unitTestGridVisitNeighborhood.o
c++ -o bin/Release/biosim4 obj/Release/src/analysis.o obj/Release/src/basicTypes.o obj/Release/src/createBarrier.o obj/Release/src/endOfGeneration.o obj/Release/src/endOfSimStep.o obj/Release/src/executeActions.o obj/Release/src/feedForward.o obj/Release/src/genome-compare.o obj/Release/src/genome.o obj/Release/src/getSensor.o obj/Release/src/grid.o obj/Release/src/imageWriter.o obj/Release/src/indiv.o obj/Release/src/main.o obj/Release/src/params.o obj/Release/src/peeps.o obj/Release/src/random.o obj/Release/src/signals.o obj/Release/src/simulator.o obj/Release/src/spawnNewGeneration.o obj/Release/src/survival-criteria.o obj/Release/src/unitTestBasicTypes.o obj/Release/src/unitTestConnectNeuralNetWiringFromGenome.o obj/Release/src/unitTestGridVisitNeighborhood.o -lopencv_core -lopencv_video -lopencv_videoio -lgomp -lpthread -fopenmp -O3 -s
```

* Clarified how to run commands in docker

I was trying to run OpenCV and CMake directly on windows, added clarification for docker users.

* Added cmake installation

* Update README.md

Co-authored-by: Michael Pilosov <[email protected]>

* Update README.md

Co-authored-by: Michael Pilosov <[email protected]>

---------

Co-authored-by: David R. Miller <[email protected]>
Co-authored-by: Michael Pilosov <[email protected]>

Dockerfile

@@ -8,12 +8,13 @@ RUN apt-get update && apt-get install -yqq \
 	&& apt-get clean \
 	&& rm -rf /var/lib/apt/lists/*
 
-RUN apt-get update && apt install -yqq python3-igraph
+RUN apt-get update && apt-get install -yqq python3-igraph
 
 RUN apt-get update && apt-get install -yqq \
 	cimg-dev \
 	gnuplot \
 	libopencv-dev \
+	cmake \
 	&& apt-get clean \
 	&& rm -rf /var/lib/apt/lists/*
 

README.md

@@ -239,7 +239,7 @@ To build a Docker environment in which you can compile the program:
 docker build -t biosim4 .
 ```
 
-You can then compile the program with an ephemeral container:
+You can then compile the program with an ephemeral container. Note that `pwd` stands for the fullpath of your `biosim4` project, something like `C:/full-path-in-windows/to-your/biosim4-folder/biosim4` in Windows, or `/home/user/project-path/biosim4/` in Linux/MacOS:
 
 ```sh
 docker run --rm -ti -v `pwd`:/app --name biosim biosim4 make
@@ -250,8 +250,14 @@ When you exit the container, the files compiled in your container files will per
 
 A `CMakeList.txt` file is provided to allow development, build, test, installation and packaging with the CMake tool chain and all IDE's that support CMake. 
 
-To build with cmake you need to install cmake. Once installed use the procedure below:
+To build with cmake you need to install cmake. 
 
+If you're using docker, `cmake` is already installed in the image. So, you can directly open its terminal to use it:
+```sh
+docker run --rm -ti -v `pwd`:/app --name biosim biosim4 bash
+```
+
+Once cmake is installed use the procedure below:
 ```sh
 mkdir build
 cd build