## pyenv

Pyenv is a platform to install and manage different versions of Python, isolated from the default Python version. Its advantage compared to the other options, like Anaconda, is its simplicity and smallness. Currently, to build BornAgain libraries for different versions of Python, we use the `pyenv` platform.

#### Installation

##### Linux

Obtain the installer from https://github.com/pyenv/pyenv-installer. To install `pyenv`, use

    curl https://pyenv.run | bash

By default, `pyenv` is installed in `$HOME/.pyenv`.

The dependencies must be installed before building Python; see https://github.com/pyenv/pyenv/wiki#suggested-build-environment:

    sudo apt install build-essential libssl-dev zlib1g-dev \
    libbz2-dev libreadline-dev libsqlite3-dev curl \
    libncursesw5-dev xz-utils tk-dev libxml2-dev libxmlsec1-dev libffi-dev liblzma-dev

##### MacOS

Install `pyenv` via `homebrew`:

    brew install pyenv

The rest of the `pyenv` instructions are like those for Linux.

##### Windows

On MS-Windows, pyenv-win should be used.

The available Python versions are distributed as binary, therefore one must choose the version from a given list.

The Python environments are installed by default under `%USERPROFILE%\.pyenv\pyenv-win\versions`.

To obtain the `pyenv` root, enter the following in `cmd`:

    echo %PYENV_ROOT%

#### Using pyenv

Obtain a list of available Python versions

    pyenv install --list

Obtain a list of available Python versions

    pyenv install --list

Install a Python version To install a certain version, say 3.10, use:

    pyenv install 3.10

List installed versions

    pyenv versions

Obtain the `pyenv` root folder where all versions are stored

    pyenv root

Obtain the path to the current version of Python in pyenv

    pyenv which python3

Install Python packages for a certain version of Python

If the path to the Python executable is, for instance, `$HOME/.pyenv/versions/3.10.12/bin/python3`, then to install `numpy` for this specific Python version, one should use

    $HOME/.pyenv/versions/3.10.12/bin/python3 -m pip install numpy

#### Build BornAgain with a specific Python version

To build BornAgain with a specific Python version, the path to the Python platform should be included in `CMAKE_PREFIX_PATH` variable; for instance, if Python 3.10.12 is installed in `$HOME/.pyenv/versions/3.10.12` folder, then `CMAKE_PREFIX_PATH` should include this path.

- Introduction
  - Functionality overview
  - Architectural overview

- Install or build
  - Install Python
    - Python on Linux
    - Python on Windows
    - Python on Mac
    - Python modules
  - Install BornAgain
    - Linux
    - Windows
    - MacOS
    - Development snapshot
  - Build BornAgain
    - Unix
      - Install third-party software
      - Get the source
      - Build and install BornAgain
      - Run a first simulation
    - Windows

- Graphical user interface
  - Quick Start
  - GUI overview
  - Fitting in the GUI

- Python scripting
  - Run a script
  - Understand the syntax
  - Fitting
  - Upgrading

- Reference
  - Simulation model
    - Simulation classes
      - Specular
        - Example
      - Scattering
        - Examples
          - GISAS
          - without DWBA terms
          - with specular peak
          - SAS
          - Polarized SANS
          - Monte-Carlo
      - Off-specular
        - Off-specular
      - Depth probe
        - Examples
          - Thin film
          - Transmitted modulus
          - Resonator
    - Common settings
      - Background
      - Options
        - Monte-Carlo
        - # threads
        - Average materials
        - Include specular
      - Progress monitor
  - Instrument model
    - Beam
      - Footprint
      - Beam divergence
    - Scan
      - TOF reflectometry
      - TOF resolution
      - Beam Angular Spread
      - Beam Wavelength Spread
    - Detectors
      - SphericalDetector
      - 2d detector resolution
      - Offspec detector
    - Neutron polarization
      - Spin asymmetry example
    - Examples
      - 2D detector resolution
      - Neutron polarization
        - Magnetic layer
        - Ditto, realistic instrument
        - Polarized scattering
  - Sample model
    - Materials
      - Magnetization
    - Sample
      - Layer
      - LayerStack
      - Layout
    - Roughness
      - Interface model
      - Transient
      - Cross-correlation
      - Examples
        - GISAS
        - Reflectivity
    - Particles
      - Form factor
        - Hard particles
          - Bipyramid4
          - Box
          - CantellatedCube
          - Cone
          - Cylinder
          - Dodecahedron
          - EllipsoidalCylinder
          - HemiEllipsoid
          - HorizontalCylinder
          - Icosahedron
          - PlatonicOctahedron
          - PlatonicTetrahedron
          - Prism3
          - Prism6
          - Pyramid2
          - Pyramid3
          - Pyramid4
          - Pyramid6
          - Sphere
          - SphericalSegment
          - Spheroid
          - SpheroidalSegment
          - TruncatedCube
        - Ripples
          - Bar ripple
          - Cosine ripple
          - Sawtooth ripple
        - Soft particles
          - FuzzySphere
          - Gauss
        - Custom formfactor
      - Composite particles
        - Core and shell
        - Compound particle
        - Mesocrystal
      - Examples
        - Compound particle
        - Core and shell
        - Crossing an interface
        - Mesocrystal
        - Rotation example
        - Dense cylinders
        - Dense hemispheres
        - Uncorrelated mixture
        - Polydispersity
    - Particle assemblies
      - Grating
        - 1D lattice
        - Cosine ripples in a lattice
        - Triangular ripples in a lattice
      - 2D lattice
        - Square lattice
        - Lattice orientation distribution
        - Finite square lattice
        - Lattice with basis
        - Multi-layer lattice
        - Position variance
      - Radial paracrystal
      - 2D paracrystal
      - Others
        - Size-distribution model: decoupling approximation
        - Size-distribution model: local monodisperse approximation
        - Size-distribution model: size-spacing coupling approximation
  - Model modifiers
    - Rotation
    - Distributions
  - Data types
    - Class Datafield
      - Export
      - Find intensity peaks
    - SLD profile
      - SLD profile with rough interfaces
      - SLD profile with a sliced particle layer
  - Plotting
    - Functions
    - Configuration
    - Heat map
    - LaTeX markup
    - Export
    - Plot axes in different units
  - Fitting
    - Data import
      - TIFF
    - Minimizer settings
    - Multiple datasets
    - Examples
      - Fitting with masks
      - Custom objective function
      - Fitting along slices
      - GISAS 2D fits
      - Experiment at GALAXI
      - Find background
      - Minimizer settings
      - Bayesian Sampling
      - Consecutive fitting
      - Considering uncertainties
      - External minimizer
      - External minimizer: plotting
      - Simultaneous fit of two datasets
      - Spin asymmetry fit example
      - Reflectometry: Fit Pt layer
      - Reflectometry: Fit honeycomb

- Literature
  - Babonneau2010
  - Babonneau2013
  - Croset2021
  - Lazzari2002
  - Lazzari2006
  - Pospelov2020
  - Renaud2009
  - Sears1992
  - Wuttke2021

- How to
  - Get announcements
  - Solve known problems
    - Set Python environmental variables under Windows
  - Request help or report bugs
  - Cite BornAgain

- Developers' corner
  - Configure
    - Build
    - Pyenv
  - Develop
    - Manual checks
    - Debug
    - Webdoc
    - Code analyses
  - Release
    - Manual GUI test