From 0f9e77689b72ee5bc87607fee5962aabd86e85a3 Mon Sep 17 00:00:00 2001
From: handwerkerd <dan.handwerker@gmail.com>
Date: Mon, 22 Jul 2024 15:45:41 -0400
Subject: [PATCH 1/3] install instructions

---
 docs/installation.rst | 48 +++++++++++++++++++++++++++----------------
 1 file changed, 30 insertions(+), 18 deletions(-)

diff --git a/docs/installation.rst b/docs/installation.rst
index 9ff6bd4ab..a8f9ad619 100644
--- a/docs/installation.rst
+++ b/docs/installation.rst
@@ -2,35 +2,47 @@
 Installation
 ############
 
-You'll need to set up a working development environment to use ``tedana``.
-To set up a local environment, you will need Python >=3.8 and the following
-packages will need to be installed:
+You'll need to install ``tedana`` in your python environment.
+If you already have a python environment and you want to add tedana, type:
 
-- nilearn
-- nibabel
-- numpy
-- scikit-learn
-- scipy
-- mapca
+.. code-block:: bash
+
+  pip install tedana
 
-After installing relevant dependencies, you can then install ``tedana`` with:
+You can use a program like `conda`_ to create an environment for ``tedana`` with:
 
 .. code-block:: bash
 
+  conda create -n tedenv python=3.12 pip
+  conda activate tedenv
   pip install tedana
 
-In addition to the Python package, installing ``tedana`` will add the ``tedana``
-and ``t2smap`` workflow CLIs to your path.
-You can confirm that ``tedana`` has successfully installed by launching a Python instance and running:
+The above will create a python environment for tedana called ``tedenv``,
+and you can enter that environment with ``conda activate tedenv``.
 
-.. code-block:: python
+With either of the above methods, `pip` will install python and all its dependencies.
+tedana's `dependencies are listed here`_.
 
-  import tedana
 
-You can check that it is available through the command line interface (CLI) with:
+Once ``tedana`` is installed, there are two ways to run it.
+You can run ``tedana``, ``ica_reclassify``, and ``t2smap`` from the command line interface (CLI).
+You can see the options for any of these commands using ``--help`` (i.e. ``tedana --help``).
 
-.. code-block:: bash
+You can also import these commands to run within python using:
 
-  tedana --help
+.. code-block:: python
+
+  from tedana.workflows import ica_reclassify_workflow, t2smap_workflow, tedana_workflow
+
+API instructions for running these `commands in python are here`_.
 
 If no error occurs, ``tedana`` has correctly installed in your environment!
+
+If you are having trouble solving errors,
+`here are places the tedana community monitors`_ to offer support.
+
+
+.. _commands in python are here: https://tedana.readthedocs.io/en/stable/api.html#module-tedana.workflows
+.. _conda: https://www.anaconda.com/download
+.. _dependencies are listed here: https://github.com/ME-ICA/tedana/blob/main/pyproject.toml
+.. _here are places the tedana community monitors: https://tedana.readthedocs.io/en/stable/support.html

From 887f7803b855f2b324b625b0bc3eccdc4444d09c Mon Sep 17 00:00:00 2001
From: Dan Handwerker <7406227+handwerkerd@users.noreply.github.com>
Date: Tue, 23 Jul 2024 10:02:48 -0400
Subject: [PATCH 2/3] Update docs/installation.rst

Co-authored-by: Taylor Salo <tsalo90@gmail.com>
---
 docs/installation.rst | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/docs/installation.rst b/docs/installation.rst
index a8f9ad619..f96d1ee8d 100644
--- a/docs/installation.rst
+++ b/docs/installation.rst
@@ -9,7 +9,11 @@ If you already have a python environment and you want to add tedana, type:
 
   pip install tedana
 
-You can use a program like `conda`_ to create an environment for ``tedana`` with:
+As long as your python environment contains a compatible version of python, this should work.
+
+If you want more control over your environment to ensure that every python dependency
+is optimized for tedana, 
+you can use a program like `conda`_ to create an environment specifically for ``tedana`` with:
 
 .. code-block:: bash
 

From 8279d6da890bcccbe731ea758e039156902e787c Mon Sep 17 00:00:00 2001
From: Dan Handwerker <7406227+handwerkerd@users.noreply.github.com>
Date: Tue, 23 Jul 2024 22:17:52 -0400
Subject: [PATCH 3/3] Update docs/installation.rst
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

Co-authored-by: Eneko Uruñuela <e.urunuela@icloud.com>
---
 docs/installation.rst | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/docs/installation.rst b/docs/installation.rst
index f96d1ee8d..830fa58ff 100644
--- a/docs/installation.rst
+++ b/docs/installation.rst
@@ -24,7 +24,7 @@ you can use a program like `conda`_ to create an environment specifically for ``
 The above will create a python environment for tedana called ``tedenv``,
 and you can enter that environment with ``conda activate tedenv``.
 
-With either of the above methods, `pip` will install python and all its dependencies.
+With either of the above methods, `pip` will install tedana and all its dependencies.
 tedana's `dependencies are listed here`_.