Fix code block indents and pyspi stylization

Author: anniegbryant

docs/source/conf.py

@@ -2,12 +2,12 @@
 
 # -- Project information
 
-project = 'PySPI'
+project = 'pyspi'
 copyright = '2022, Oliver M. Cliff'
 author = 'Oliver M. Cliff'
 
-release = '0.3'
-version = '0.3.0'
+release = '0.4'
+version = '0.4.0'
 
 # -- General configuration
 

docs/source/faq.rst

@@ -19,7 +19,7 @@ One user reported the following error when installing `pyspi` on a MacBook Air a
    OSError: [Errno 0] JVM DLL not found /Library/Java/JavaVirtualMachines/jdk-19.jdk/Contents/Home/lib/libjli.dylib
 
 
-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>`_. This issue can arise from the version of OpenJDK identified as the system default
+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.
 
 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:
 
@@ -33,48 +33,57 @@ Install homebrew if you don't already have it:
 Install `jenv` as your Java version manager:
 
 .. code-block:: 
+
     $ brew install jenv
 
 
 Add `jenv` to your shell's configuration file (e.g. `.bashrc` if you use `bash`):
 
 .. code-block:: 
+
     $ export PATH="$HOME/.jenv/bin:$PATH"
     $ eval "$(jenv init -)"
 
 Source your shell's configuration file:
 
 .. code-block:: 
+
     $ source ~/.bashrc # If you use bash
 
 Confirm proper installation of `jEnv`:
 
 .. code-block::
+
     $ jenv doctor
 
 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:
 
 .. code-block:: 
+
     $ brew install AdoptOpenJDK/openjdk/adoptopenjdk11
 
 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:
 
 .. code-block:: 
+
     $ /usr/libexec/java_home -V
 
 This will list all your installed java JDK versions. Locate the one for `AdoptOpenJDK` version 11 and paste the path:
 
 .. code-block::
+
     $ jenv add <path_to_adopt_open_jdk_11>
 
 Confirm `AdoptOpenJDK` version 11 was added to `jEnv`:
 
 .. code-block:: 
+
     $ jenv versions
 
 You can set `AdoptOpenJDK` version 11 as your global Java version with the following:
 
 .. code-block:: 
+
     $ jenv global <AdoptOpenJDK version>
     $ # example:
     $ jenv global 11.0

docs/source/index.rst

@@ -1,4 +1,4 @@
-Welcome to PySPI's documentation!
+Welcome to pyspi's documentation!
 ===================================
 
 **pyspi** (/pie'spy/) is a Python library for simultaneously evaluating hundreds of pairwise interactions directly from multivariate time-series data.