First version of cameopy:

 - README with list of dependencies
 - Compilation using CMake
 - cameo c++ API downloaded from source if not installed on the machine
 - doxygen for documentation
 - python binding with pybind11
 ** Installation of the python binding not yet fixed **

.clang-format

+BasedOnStyle: LLVM
+IndentWidth: 8
+#UseTab: UT_AlignWithSpaces # available in release later than 9
+UseTab: ForContinuationAndIndentation
+BreakBeforeBraces: Custom
+BraceWrapping:
+	AfterNamespace: false
+AllowShortIfStatementsOnASingleLine: false
+IndentCaseLabels: false
+ColumnLimit: 110
+
+AlignConsecutiveAssignments: true
+AlignConsecutiveDeclarations: false
+AlignTrailingComments: true
+AccessModifierOffset: -8 # It has to be equal to the tab size
+NamespaceIndentation: None
+PointerAlignment: Left
+AlwaysBreakAfterReturnType: None
+
+SortIncludes: false
+
+

.gitignore

+build/

.gitlab-ci.yml

+image: gcc
+variables:
+  GIT_SUBMODULE_STRATEGY: normal
+  
+stages:
+  - build
+  - doc
+  - test
+
+before_script:
+  - git status
+  - mkdir -p build/
+  - cd build/
+
+compile_api:
+  stage: build
+  script:
+    - cmake ..
+    - cmake --build .
+    - cmake -DCAMEOPYTHON_TESTS=ON ..
+    - cmake --build .
+
+test:
+  stage: test
+  script:
+   - cd ..
+   - ./test.sh
+   
+pages:
+  stage: doc
+  script:
+    - cmake ..
+    - cmake --build . --target doc
+    - mv doc/html/ ../public/
+  artifacts:
+    paths:
+      - public
+  only:
+    - master
\ No newline at end of file

.gitmodules

+[submodule "pybind11"]
+	path = pybind11
+	url = git@github.com:pybind/pybind11.git
+[submodule "doctest"]
+	path = doctest
+	url = https://github.com/onqtam/doctest.git

CMakeLists.txt

+cmake_minimum_required(VERSION 3.11.3)
+# Project name and version
+project(cameopy VERSION 1.0.0 LANGUAGES CXX)
+
+include(GNUInstallDirs)
+
+# Want to compile dynamic or static libraries
+set(BUILD_SHARED_LIBS True)
+
+
+include(ExternalProject)
+
+
+option(TESTING "Enable testing" OFF)
+#------------------------------------------------------------ Dependencies
+# 2.4.3 is the version that has been used for development and tests
+find_package(pybind11 2.4.3 QUIET)  
+find_package(cameo 1.1 QUIET)
+#------------------------------------------------------------
+
+
+#------------------------------------------------------------
+if(NOT pybind11_FOUND)
+  message(WARNING "Using PYBIND11 from GIT repository")
+  ExternalProject_Add(pybind11 
+	GIT_REPOSITORY https://github.com/pybind/pybind11.git
+	GIT_TAG v2.5.0
+	GIT_SHALLOW True
+	#INSTALL_COMMAND ""
+	UPDATE_COMMAND ""
+	UPDATE_DISCONNECTED FALSE
+	CMAKE_ARGS -DPYBIND11_TEST=OFF -DPYBIND11_INSTALL=ON -DCMAKE_INSTALL_PREFIX=${CMAKE_CURRENT_BINARY_DIR}/pybind11_install/
+	#I am obliged to perform the install step otherwise some files from pybind are not put together and I don't manage to set it.
+	)
+      ExternalProject_Get_Property(pybind11 install_dir BINARY_DIR)
+
+      list(APPEND DEPENDENT_PACKAGES pybind11)
+  #set(pybind11_DIR ${install_dir})
+  set(pybind11_DIR ${CMAKE_CURRENT_BINARY_DIR}/pybind11_install/share/cmake/pybind11)
+endif()
+
+#------------------------------------------------------------
+if(NOT cameo_FOUND)
+  ExternalProject_Add(cameo
+    GIT_REPOSITORY https://code.ill.fr/cameo/cameo-api-cpp.git
+    #    GIT_TAG master_new
+    GIT_TAG master
+    GIT_REMOTE_NAME cameocpp
+    GIT_SHALLOW True
+    #SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/cameo-api-cpp/
+    INSTALL_DIR ${CMAKE_INSTALL_PREFIX} # this does not work...
+    CMAKE_ARGS -DCMAKE_INSTALL_PREFIX=${CMAKE_INSTALL_PREFIX}
+    #INSTALL_COMMAND "" # this disables the install step for the external project
+    )
+  ExternalProject_Get_Property(cameo install_dir BINARY_DIR)
+  set(cameo_DIR ${BINARY_DIR})
+  list(APPEND DEPENDENT_PACKAGES cameo)
+  #set(cameo_DIR ${install_dir})
+endif(NOT cameo_FOUND)
+
+
+ExternalProject_Add(cameopython
+  SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/src/
+  DEPENDS  ${DEPENDENT_PACKAGES}
+  CMAKE_ARGS  -DCMAKE_INSTALL_PREFIX=${CMAKE_INSTALL_PREFIX} -DCMAKE_PREFIX_PATH=${CMAKE_PREFIX_PATH}  -Dpybind11_DIR=${pybind11_DIR} #pybind is fake-installed in the build
+  #INSTALL_DIR ${CMAKE_INSTALL_PREFIX}
+  )
+
+
+if(TESTING)
+enable_testing()
+
+list(APPEND CMAKE_PREFIX_PATH ${CMAKE_INSTALL_PREFIX}/${CMAKE_INSTALL_LIBDIR})
+ExternalProject_Add(testing
+  SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/test/
+  DEPENDS ${DEPENDENT_PACKAGES}
+  CMAKE_ARGS -DCMAKE_PREFIX_PATH=${CMAKE_PREFIX_PATH} 
+  INSTALL_COMMAND ""
+  )
+endif(TESTING)
+
+#if(CAMEOPYTHON_TESTS)
+#  message("TESTS have been enabled")
+#  enable_testing()
+#  
+#  add_subdirectory(test)
+#endif(CAMEOPYTHON_TESTS)
+#unset(CAMEOPYTHON_TESTS CACHE)  # this removes the value from the CACHE, this is a trick to get the test compiled when running cmake --build . the second time
+
+#ExternalProject_Add_StepDependencies(cameopython build cameocpp)
+

LICENSE

+                      EUROPEAN UNION PUBLIC LICENCE v. 1.2
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+
+Appendix
+
+‘Compatible Licences’ according to Article 5 EUPL are:
+
+- GNU General Public License (GPL) v. 2, v. 3
+- GNU Affero General Public License (AGPL) v. 3
+- Open Software License (OSL) v. 2.1, v. 3.0
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+- GNU Lesser General Public Licence (LGPL) v. 2.1, v. 3
+- Creative Commons Attribution-ShareAlike v. 3.0 Unported (CC BY-SA 3.0) for
+  works other than software
+- European Union Public Licence (EUPL) v. 1.1, v. 1.2
+- Québec Free and Open-Source Licence — Reciprocity (LiLiQ-R) or Strong
+  Reciprocity (LiLiQ-R+).
+
+The European Commission may update this Appendix to later versions of the above
+licences without producing a new version of the EUPL, as long as they provide
+the rights granted in Article 2 of this Licence and protect the covered Source
+Code from exclusive appropriation.
+
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+EUPL version.

README.md

 # cameo-python
 
-Python API for Cameo.
\ No newline at end of file
+This library provides the Python API for Cameo.
+
+ 
+## Compilation dependencies
+   - cmake
+The API is obtained using pybind11 and the C++ Cameo API.
+   - [pybind11](https://github.com/pybind/pybind11)
+
+Testing is performed using the doctest framework:
+   - [doctest](https://github.com/onqtam/doctest)
+   
+These packages can either be installed on the system (see exact name of the packages below), or be downloaded from GitHub and compiled from source if not found on the system.
+
+### CENTOS 8
+```yum install -y cmake pybind11-devel```
+
+For testing:
+```yum install -y doctest-devel```
+
+### Ubuntu 18
+```sudo apt install python3-pybind11 libzmq3-dev```
+
+For testing:
+```sudo apt install doctest-dev```
+
+## How to compile and install
+You can run the `build.sh` script.
+
+Don't forget to set your LD_LIBRARY_PATH to `/usr/local/lib64/`
+
+Developers can follow the instructions [here](doc/DEVEL.md)

build.sh

+#!/bin/bash
+
+usage(){
+    echo "`basename $0` [INSTALL_PREFIX] [CMAKE_PREFIX_PATH]" 
+}
+
+
+case $1 in
+    dev|DEV|devel|DEVEL)
+	DEV=true
+	INSTALL_PREFIX=${2:-/tmp/devel}
+	echo "[INFO] Development mode: installation directory is $INSTALL_PREFIX"
+	ARGS="-DCMAKE_INSTALL_PREFIX=${INSTALL_PREFIX} -DCMAKE_PREFIX_PATH=$3"
+	;;
+    "")
+	;;
+    *)
+	INSTALL_PREFIX=$1
+	ARGS="-DCMAKE_INSTALL_PREFIX=${INSTALL_PREFIX} -DCMAKE_PREFIX_PATH=$2"
+	;;
+esac
+
+
+# to force recompilation:
+# cmake --build . --target cameo-api-cpp --clean-first
+mkdir -p build/ 
+cd build/
+cmake .. $ARGS
+# compile without the tests, because they need the rest to be compiled first
+cmake --build . || {
+    echo "[ERROR]" >> /dev/stderr
+    exit 1
+}
+    
+# if [ -n "$DEV" ];then
+#     echo "Enabling testing"
+#     # now enable the tests 
+#     cmake  -DCAMEOPYTHON_TESTS=ON $ARGS ..
+#     cmake --build .  || exit 1
+# fi

doc/DEVEL.md

+You can build the project with the aid of the build.sh script.
+
+If you want to install it in a non-standard path (MY_INSTALL_PATH) and enable the testing:
+```
+./build.sh dev MY_INSTALL_PATH
+```
+otherwise:
+```./build.sh```
+
+By default MY_INSTALL_PATH is `/tmp/devel/`
+
+If you are using a non-standard path, the following environmental variables should then be set.
+```
+#!/bin/bash
+export CMAKE_INSTALL_PREFIX=MY_INSTALL_PATH
+export PYTHONPATH=${PYTHONPATH}:${CMAKE_INSTALL_PREFIX}/lib64/python3.6/site-packages/
+export LD_LIBRARY_PATH=${LD_LIBRARY_PATH} ${CMAKE_INSTALL_PREFIX}/lib64
+```
+Example for the fish shell:
+```
+#!/bin/fish
+set -lx CMAKE_INSTALL_PREFIX /tmp/devel/
+set -lx PYTHONPATH $PYTHONPATH $CMAKE_INSTALL_PREFIX/lib64/python3.6/site-packages/
+set -lx LD_LIBRARY_PATH ${CMAKE_INSTALL_PREFIX}/lib64/
+```
+
+# Testing
+For testing you need CAMEO to be installed in order to run the cameo_server
+
+In order to run the tests, just type
+```./test.sh```
+from the source directory root.
+
+### CENTOS
+The java.library.path is the LD_LIBRARY_PATH + [/usr/java/packages/lib, /usr/lib64, /lib64, /lib, /usr/lib]
+Point the LD_LIBRARY_PATH to the place where the libjzmq.so is stored
+
+```
+fish
+set -x LD_LIBRARY_PATH /usr/share/java/ /usr/local/lib/
+/usr/lib/jvm/java-14-openjdk-14.0.1.7-2.rolling.el8.x86_64/bin/java -jar "/usr/local/share/java/cameo-server.jar" test/cameo_config.xml
+
+# list the test cases:
+cmo -e tcp://localhost:2000 exec testA --list-test-cases --verbose
+
+cmo -e tcp://localhost:2000 exec testA -s --test-case=self
+cmo -e tcp://localhost:2000 exec testA -s --test-case=instance
+cmo -e tcp://localhost:2000 exec testA -s --test-case=requester --subcase-exclude=python
+
+ctest --output-on-failure
+```
+
+# Testing Ubuntu
+```
+bash
+export LD_LIBRARY_PATH=/usr/share/java/:/usr/lib/x86_64-linux-gnu/jni
+cameo-server test/cameo_config.xml
+```
+
+
+
+cmake .. -DopenPMD_USE_PYTHON=OFF -DopenPMD_INSTALL=OFF -DopenPMD_USE_INTERNAL_CATCH=ON -DBUILD_TESTING=OFF -DBUILD_EXAMPLES=OFF -DBUILD_CLI_TOOLS=ON
+
+
+
+
+
+ cmake .. -DCMAKE_INSTALL_PREFIX=/tmp/devel3 -Dcameo_DIR=/tmp/devel2/lib64/cmake/

doc/TODO

+
+
+## TODO
+ - [X] Add licence file
+ - [X] Add copyright comment in all the files
+ - [ ] Add reference to thirdparty libraries in the README
+   - [X] doctest
+   - [X] pybind11 
+ - [ ] Test installation
+ - [ ] Add the binding for the ostream << operation
+ - [ ] Implement WaitFor for Instance class
+

setup.py

+import os
+import re
+import sys
+import platform
+import subprocess
+
+from setuptools import setup, Extension
+from setuptools.command.build_ext import build_ext
+from distutils.version import LooseVersion
+
+
+class CMakeExtension(Extension):
+    def __init__(self, name, sourcedir=''):
+        Extension.__init__(self, name, sources=[])
+        self.sourcedir = os.path.abspath(sourcedir)
+
+
+class CMakeBuild(build_ext):
+    def run(self):
+        try:
+            out = subprocess.check_output(['cmake', '--version'])
+        except OSError:
+            raise RuntimeError(
+                "CMake 3.7.2+ must be installed to build the following " +
+                "extensions: " +
+                ", ".join(e.name for e in self.extensions))
+
+        cmake_version = LooseVersion(re.search(
+            r'version\s*([\d.]+)',
+            out.decode()
+        ).group(1))
+        if cmake_version < '3.7.2':
+            raise RuntimeError("CMake >= 3.7.2 is required")
+
+        for ext in self.extensions:
+            self.build_extension(ext)
+
+    def build_extension(self, ext):