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Copy file name to clipboardExpand all lines: README.md
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@@ -12,7 +12,7 @@ Use BOBE if:
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-**You need Bayesian evidence estimates and/or posterior samples efficiently**
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BOBE works best for problems with up to 15-20 parameters, although this can vary based on the specific problem and likelihood structure.
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It has been tested to work well upto 30 dimensions for simple multivariate Gaussian likelihoods and upto 16 dimensions for cosmological likelihoods (LCDM + curvature) with the Planck Camspec likelihood).
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It has been tested to work well upto 30 dimensions for simple multivariate Gaussian likelihoods and upto 16 dimensions for cosmological likelihoods (LCDM + curvature) with the Planck Camspec likelihood.
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BOBE may not be necessary if your likelihood already evaluates in milliseconds, as the overhead of training the GP surrogate and running Bayesian optimisation
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may not be worth the speedup. For such cases, there is generally no need to go beyond standard MCMC/nested sampling tools.
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@@ -42,37 +42,41 @@ See `pyproject.toml` and the [documentation](https://BOBE.readthedocs.io/en/) fo
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## Installation
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### From source
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### From PyPI (Recommended)
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```bash
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git clone https://github.com/Ameek94/BOBE.git
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cd BOBE
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python -m pip install .
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```
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For an editable (dev) install do
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BOBE is available on PyPI and can be installed with pip:
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```bash
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python -m pip install -e .
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pip install BOBE
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```
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from the package directory.
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### Optional Dependencies
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BOBE has several optional dependencies for extended functionality. When installing from source, you can install them as follows:
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BOBE has several optional dependencies for extended functionality:
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-**Cosmology Suite**: Install with `pip install -e '.[cosmo]'`
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-**Cosmology Suite**: Install with `pip install BOBE[cosmo]`
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- This will install Cobaya, needed for several cosmological likelihoods. You will still need to download and install the data for some likelihoods - see the [Cobaya documentation](https://cobaya.readthedocs.io/en/latest/) for more details.
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- It will also install mpi4py (you will need to have an MPI implementation such as openmpi or mpich). Enables parallel likelihood evaluation and GP fitting across multiple processes using mpi4py.
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-**Cobaya Only**: Install with `pip install -e '.[cobaya]'`
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-**Cobaya Only**: Install with `pip install BOBE[cobaya]`
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-**MPI Only**: Install with `pip install -e '.[mpi]'`
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-**MPI Only**: Install with `pip install BOBE[mpi]`
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-**Neural Networks**: Install with `pip install BOBE[nn]`
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-**All Optional Dependencies**: Install with `pip install -e '.[all]'`
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-**All Optional Dependencies**: Install with `pip install BOBE[all]`
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### From Source (Development)
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For development or to use the latest unreleased features:
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```bash
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git clone https://github.com/Ameek94/BOBE.git
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cd BOBE
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pip install -e .
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```
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**Note:** The `-e` flag installs in editable mode. For a regular install, use `pip install '.[extra]'`instead (replace extra with name of dependency).
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Optional dependencies can be installed with `pip install -e '.[extra]'` (replace `extra` with the desired dependency name).
Copy file name to clipboardExpand all lines: docs/source/installation.rst
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@@ -53,8 +53,41 @@ Core Dependencies
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Installation Methods
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--------------------
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From Source (Recommended)
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~~~~~~~~~~~~~~~~~~~~~~~~~~
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From PyPI (Recommended)
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~~~~~~~~~~~~~~~~~~~~~~~
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BOBE is available on PyPI and can be installed with pip:
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.. code-block:: bash
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pip install BOBE
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Optional Dependencies
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~~~~~~~~~~~~~~~~~~~~~
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BOBE has several optional dependencies for extended functionality:
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.. code-block:: bash
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# For cosmological likelihoods through Cobaya + MPI support
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pip install BOBE[cosmo]
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# For Cobaya only
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pip install BOBE[cobaya]
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# For MPI support only
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pip install BOBE[mpi]
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# For neural network classifiers
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pip install BOBE[nn]
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# For all optional dependencies
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pip install BOBE[all]
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From Source (Development)
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~~~~~~~~~~~~~~~~~~~~~~~~~
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For development or to use the latest unreleased features:
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1. Clone the repository:
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@@ -63,34 +96,21 @@ From Source (Recommended)
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git clone https://github.com/Ameek94/BOBE.git
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cd BOBE
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2. Install the package:
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2. Install in editable mode:
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.. code-block:: bash
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# For regular install
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pip install .
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# For development mode
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pip install -e .
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3. (Optional) Install with additional features:
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.. code-block:: bash
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# For cosmological likelihoods through Cobaya
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pip install -e '.[cobaya]'
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# For MPI support
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pip install -e '.[mpi]'
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# For neural network classifiers
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pip install -e '.[nn]'
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# For all optional dependencies
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pip install -e '.[all]'
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.. note::
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The ``-e`` flag installs in editable mode. For a regular install, use ``pip install '.[extra]'`` instead (replace extra with desired optional dependency).
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pip install -e '.[cosmo]'# Cobaya + MPI
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pip install -e '.[cobaya]'# Cobaya only
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pip install -e '.[mpi]'# MPI only
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pip install -e '.[nn]'# Neural networks
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pip install -e '.[all]'# Everything
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Virtual Environment Setup
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--------------------------
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conda create -n BOBE python=3.12
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conda activate BOBE
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pip install -e .
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pip install BOBE
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Using venv
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~~~~~~~~~~
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python -m venv BOBE_env
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source BOBE_env/bin/activate
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pip install -e .
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pip install BOBE
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GPU/TPU Support
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---------------
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.. code-block:: bash
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git clone https://github.com/Ameek94/BOBE.git
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cd BOBE
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# Create environment from the minimal essential packages
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