TODO: explain what is PyFUGE

Then you can try to run an evolution with:

from pyfuge.evo.examples import evo_cancer
evo_cancer.run()

• CMake version >= 3.1
• Git
• vcpkg
• Python >= 3.4 (tested with 3.6.5)
• To build sources on Windows you will need
  • VS Community with (you can choose which components to install using Visual Studio Installer)
    • CMake support
    • VC compiler
    • Windows 8.1 SDK

Note: the following instructions assume a 64bits GNU/Linux machine or a 64bits Windows machine

On Windows make sure to open an admin cmd console.

1. Download vcpkg:

• git clone --recursive it somewhere. It does not matter where
• cd vcpkg
• execute bootstrap-vcpkg.{sh,bat}
• set VCPKG_ROOT environment variable
  • Windows: set VCPKG_ROOT=X:\path\to\vcpkg
  • Linux: export VCPKG_ROOT=/path/to/vcpkg

2. Install vcpkg dependencies

• On Windows

cd %VCPKG_ROOT%
.\vcpkg.exe install Eigen3:x64-windows
.\vcpkg.exe install Catch2:x64-windows
# .\vcpkg.exe install pybind11:x64-windows (don't work on Linux for now, use git submodule instead)

• On Linux

cd $VCPKG_ROOT
./vcpkg install Eigen3
./vcpkg install Catch2
#./vcpkg install pybind11 (don't work on Linux for now)

3. Create a virtualenv and activate it

• On Windows

python -m venv myvenv
.\myenv\Scripts\activate

• On Linux: TODO

4. Clone this repository

git clone --recursive $this_repo$
cd PyFUGE

5. Build the sources

• On Windows or Linux

cd PyFUGE
python setup.py build

• activate the virtualenv
• export the VCPKG_ROOT environment variable

cd PyFUGE/pyfuge/py_fiseval/FISEval
mkdir build
cd build
cmake "-DCMAKE_TOOLCHAIN_FILE=${VCPKG_ROOT}/scripts/buildsystems/vcpkg.cmake" -DCMAKE_BUILD_TYPE=Debug ..
cmake --build .
./run_tests --success

Note: at the moment tests are only compile on debug mode.

Note you must increment the version every time you upload to (test)PyPI

Note you must repeat these instructions for every Python version you want to support. At the moment, PyFUGE should compile on Python >= 3.4

Start by getting the sources as described above.

Then in the project root folder, create the binary wheel:

python setup.py build
python setup.py sdist bdist_wheel

Upload the binary to TestPyPI:

pip install twine
twine upload --repository-url https://test.pypi.org/legacy/ dist/*

Done ! Building a binary wheel on Windows is pretty straightforward you only need to do this once to target all Windows for a given platform (e.g. 64 bits)

As the linux ecosystem is vary diverse, an initiative called manylinux aims to target almost every linux systems when building Python package using C extensions.

Note you still can run but you will obtain a wheel that might not work on other Linux systems and that will be refused by PyPI when trying to upload it. (for the latter you still can rename it to manylinux but this does not solve the problem...)

python setup.py build
python setup.py sdist bdist_wheel

Steps to build a manylinux wheel:

1. Get the project sources and follow the requirements above
2. Make sure to install the vcpkg libs before going further. You must install the libs on the host machine, it will fail inside the container.
3. Install Docker and run docker run -it --rm -v /path/to/PyFUGE:/PyFUGE -v ${VCPKG_ROOT}:/vcpkg quay.io/pypa/manylinux1_x86_64 /bin/bash. Note for an unknown reason it seems to fail on Arch Linux, had to use a Ubuntu 16.04 VM.

You will enter into a shell inside the container. The following commands are meant to be executed inside this container. _

export VCPKG_ROOT=/vcpkg
export PATH=/opt/python/cp36-cp36m/bin:$PATH
cd /PyFUGE
python install cmake twine
python setup.py build
python setup.py sdist bdist_wheel

# then we must fix the wheel using auditwheel
auditwheel repair dist/xxx-linux-x86_64.whl

twine upload --repository-url https://test.pypi.org/legacy/ dist/wheelhouse/*

# create an new virtualenv with a Python version that matches one of the wheel you uploaded
pip install --index-url https://test.pypi.org/simple/ --extra-index-url https://pypi.org/simple pyfuge==XXX_VERSION