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Merge pull request #20 from anniegbryant/docs_dev
Start Issues and FAQ page for docs
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‎docs/source/conf.py

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# -- Project information
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project = 'PySPI'
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project = 'pyspi'
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copyright = '2022, Oliver M. Cliff'
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author = 'Oliver M. Cliff'
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release = '0.3'
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version = '0.3.0'
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release = '0.4'
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version = '0.4.0'
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# -- General configuration
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‎docs/source/faq.rst

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Issues & FAQ
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===================================
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FAQ
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########
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Issues
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########
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Java JVM DLL not found (specific to Mac)
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**********************
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One user reported the following error when installing `pyspi` on a MacBook Air an M2 chip and Catalina OS:
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.. code-block::
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OSError: [Errno 0] JVM DLL not found /Library/Java/JavaVirtualMachines/jdk-19.jdk/Contents/Home/lib/libjli.dylib
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This issue is similar to those reported `here <https://stackoverflow.com/questions/71504214/jvm-dll-not-found-but-i-can-clearly-see-the-file>`_ and `here <https://github.com/jpype-project/jpype/issues/994>`_; it can arise from the version of OpenJDK identified as the system default. Some Java versions don't include all of the binary (DLL) files that `pyspi` looks for.
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We recommend following this `helpful tutorial <https://blog.bigoodyssey.com/how-to-manage-multiple-java-version-in-macos-e5421345f6d0>`_ by Chamika Kasun to install `AdoptOpenJDK <https://adoptopenjdk.net/index.html>`_. In a nutshell, here are the steps you should run:
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Install homebrew if you don't already have it:
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$ /bin/bash -c "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/HEAD/install.sh)"
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Install `jenv` as your Java version manager:
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$ brew install jenv
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Add `jenv` to your shell's configuration file (e.g. `.bashrc` if you use `bash`):
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$ export PATH="$HOME/.jenv/bin:$PATH"
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$ eval "$(jenv init -)"
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Source your shell's configuration file:
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$ source ~/.bashrc # If you use bash
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Confirm proper installation of `jEnv`:
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$ jenv doctor
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Even if this returns some errors, as long as you see `Jenv is correctly loaded`, you're all set. We recommend using `AdoptOpenJDK` version 11, which you can install with the following command:
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$ brew install AdoptOpenJDK/openjdk/adoptopenjdk11
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Now, you will need to add your `AdoptOpenJDK` path to your `jEnv` environments. First, you can find where your jdk files are installed with the following command:
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$ /usr/libexec/java_home -V
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This will list all your installed java JDK versions. Locate the one for `AdoptOpenJDK` version 11 and paste the path:
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$ jenv add <path_to_adopt_open_jdk_11>
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Confirm `AdoptOpenJDK` version 11 was added to `jEnv`:
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$ jenv versions
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You can set `AdoptOpenJDK` version 11 as your global Java version with the following:
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$ jenv global <AdoptOpenJDK version>
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$ # example:
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$ jenv global 11.0

‎docs/source/index.rst

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Welcome to PySPI's documentation!
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Welcome to pyspi's documentation!
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===================================
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**PySPI** (/pie'spy/) is a Python library for simultaneously evaluating hundreds of pairwise interactions directly from multivariate time-series data.
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**pyspi** (/pie'spy/) is a Python library for simultaneously evaluating hundreds of pairwise interactions directly from multivariate time-series data.
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It provides easy access to over 250 methods for evaluating the relationship between pairs of time series, from simple statistics (like correlation coefficients) to advanced multi-step algorithms (like Granger causality).
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.. toctree::
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installation
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usage
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advanced
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api
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api
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faq

‎docs/source/installation.rst

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Installation
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===================================
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Pre-installation
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----------------
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The code requires GNU's `Octave <https://www.gnu.org/software/octave/index>`_ by default, which is freely available on all popular operating systems.
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See the `installation instructions <https://wiki.octave.org/Category:Installation>`_ to find out how to install Octave on your system.
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.. note::
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You can safely install `pyspi` without first installing Octave but you will not have access to the `Integrated Information Theory` statistics, see :ref:`Using the toolkit without Octave`.
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While you can also install `pyspi` outside of a `conda <https://docs.conda.io/projects/conda/en/latest/index.html>`_ environment, it depends on a lot of user packages that may make managing dependencies quite difficult.
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So, we would also recommend installing `pyspi` in a conda environment.
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After `installing conda <https://docs.conda.io/projects/conda/en/latest/user-guide/install/index.html>`_, create a new environment for using the toolkit:
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.. code-block:: console
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$ conda create -n pyspi python=3.9.0
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$ conda activate pyspi
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Installation
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------------
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Next, download or clone the `latest version <https://github.com/olivercliff/pyspi>`_ from GitHub, unpack and install:
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.. code-block:: console
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$ git clone https://github.com/olivercliff/pyspi.git
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$ cd pyspi
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$ pip install .
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You can confirm that `pyspi` and dependencies installed properly with the following command:
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.. code-block:: console
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$ setup.py test

‎docs/source/usage.rst

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Usage
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=====
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Pre-installation
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----------------
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The code requires GNU's `Octave <https://www.gnu.org/software/octave/index>`_ by default, which is freely available on all popular operating systems.
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See the `installation instructions <https://wiki.octave.org/Category:Installation>`_ to find out how to install Octave on your system.
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.. note::
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You can safely install `PySPI` without first installing Octave but you will not have access to the `Integrated Information Theory` statistics, see :ref:`Using the toolkit without Octave`.
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While you can also install `PySPI` outside of a `conda <https://docs.conda.io/projects/conda/en/latest/index.html>`_ environment, it depends on a lot of user packages that may make managing dependencies quite difficult.
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So, we would also recommend installing `PySPI` in a conda environment.
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After `installing conda <https://docs.conda.io/projects/conda/en/latest/user-guide/install/index.html>`_, create a new environment for using the toolkit:
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$ conda create -n pyspi python=3.9.0
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$ conda activate pyspi
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Installation
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------------
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Next, download or clone the `latest version <https://github.com/olivercliff/pyspi>`_ from GitHub, unpack and install:
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$ git clone https://github.com/olivercliff/pyspi.git
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$ cd pyspi
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$ pip install .
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Getting Started
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---------------

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