diff --git a/docs/cli.rst b/docs/cli.rst new file mode 100644 index 000000000..7a1f9db18 --- /dev/null +++ b/docs/cli.rst @@ -0,0 +1,14 @@ +====================== +Command Line Interface +====================== + +.. code-block:: bash + + cubids --help + +This will print the instructions for using the command line interface in your command line. + +.. argparse:: + :ref: cubids.cli._get_parser + :prog: cubids + :func: _get_parser diff --git a/docs/glossary.rst b/docs/glossary.rst index 47c566960..8a2b3a4f3 100644 --- a/docs/glossary.rst +++ b/docs/glossary.rst @@ -1,5 +1,8 @@ .. include:: links.rst +Glossary +======== + .. glossary:: Key Group @@ -32,6 +35,6 @@ References -========== +---------- .. footbibliography:: diff --git a/docs/index.rst b/docs/index.rst index fc9e9981a..0b4ba8858 100644 --- a/docs/index.rst +++ b/docs/index.rst @@ -9,8 +9,9 @@ Contents :maxdepth: 2 about - usage installation + usage + cli example examples ../CONTRIBUTING diff --git a/docs/usage.rst b/docs/usage.rst index be6496131..f86b4e386 100644 --- a/docs/usage.rst +++ b/docs/usage.rst @@ -1,6 +1,6 @@ -================== -Commands & Actions -================== +======================== +General Usage Guidelines +======================== Before we implement a ``CuBIDS`` workflow, let's define the terminology and take a look at some of the commands available in the software. @@ -226,25 +226,9 @@ Applying these changes we would see: :header-rows: 1 -Command line tools ------------------- - -With that brief introduction done, we can introduce the full gamut of ``CuBIDS`` command line tools: - -.. code-block:: bash - - cubids --help - -This will print the instructions for using the command line interface in your command line. - -.. argparse:: - :ref: cubids.cli._get_parser - :prog: cubids - :func: _get_parser - - Customizable configuration ---------------------------- +-------------------------- + ``CuBIDS`` also features an optional, customizable, MRI image type-specific configuration file. This file can be passed as an argument to ``cubids group`` and ``cubids apply`` using the ``--config`` flag and allows users to customize grouping settings based on