Merge pull request #97 from khanlab/doc-updates

Fix spelling & grammar in documentation

docs/contributing/contributing.md

@@ -1,20 +1,20 @@
 # Contributing to SCATTR
 
-SCATTR python package dependencies are managed with Poetry (`v1.2.0+`), which
-you will need installed on your machine. You can find installation instructions 
-on the [Poetry website](https://python-poetry.org/docs/master/#installation).
+SCATTR python package dependencies are managed with Poetry, which
+will need to be installed on your machine. Installation instructions can be
+found on the 
+[Poetry website](https://python-poetry.org/docs/master/#installation).
 
 SCATTR also has a few dependencies outside of python, including popular 
 neuroimaging packages like `ANTs`, `Freesurfer`, `MRtrix3`, and others. We 
 **strongly** recommend using SCATTR with the `--use-singularity` flag, which 
-will pull and use the required containers, unless you are comfortable using
+will pull and use the required containers, unless you are comfortable 
 installing and using all of these tools yourself.
 
-_Note: These instructions are only recommended if you are making changes to the
-SCATTR codebase and committing these back to the repository, or if you are 
+_Note: These instructions are only recommended if you are making changes to 
+the SCATTR codebase and committing these back to the repository or if you are 
 using Snakemake's cluster execution profiles. If not, it is easier to run 
-SCATTR using the packaged singularity container (e.g. 
-`docker://khanlab/scattr:latest`)._
+SCATTR using the packaged container (e.g. `docker://khanlab/scattr:latest`)._
 
 ## Setup the development environment
 
@@ -54,10 +54,9 @@ You can see what commands are available by running:
 poetry run poe 
 ```
 
-We use a a few tools, including `black`, `flake8`, `isort`, `snakefmt`, and 
-`yamlfix` to ensure formatting and style of our codebase is consistent. There 
-are two task runners you can use to check and fix your code, which can be 
-invoked with:
+We use a few tools, including `ruff`, `snakefmt`, and `yamlfix` to ensure 
+formatting and style of our codebase is consistent. There are two task runners 
+you can use to check and fix your code, which can be invoked with:
 
 ```
 poetry run poe quality-check
@@ -68,6 +67,7 @@ _Note: If you are in a poetry shell, you do not need to prepend `poetry run` to
 the command._
 
 ## Dry-run / testing your workflow
+
 Using Snakemake\'s dry-run option (`--dry-run`/`-n`) is an easy way to verify
 any changes made to the workflow are working direcctly. The `test/data` folder 
 contains a _fake_ BIDS dataset (i.e. dataset with zero-sized files) that is 

docs/getting_started/docker.md

@@ -1,8 +1,9 @@
 # Running SCATTR with Docker on Windows
 
-_Note, these instructions you have Docker installed already on a Windows system.
-Docker can also be run on Linux or MacOS with similar commands, but here, we 
-will assume the default Windows CLI is being used._
+_Note, these instructions assume you have Docker installed already on a 
+Windows system. Docker can also be run on Linux or MacOS with similar 
+commands, but here, we will assume the default Windows CLI is being 
+used._
 
 ## First time setup
 
@@ -17,7 +18,7 @@ cd c:\Users\username\Downloads
 ```
 
 Pull the container (this will take some time and storage space, but like an 
-installation, it only needs to be done once and can be then be run on many 
+installation, it only needs to be done once and can then be run on many 
 datasets). The example below pulls the latest versioned container (replace 
 `latest` with `vX.X.X` for a specific version).
 
@@ -49,7 +50,7 @@ docker run -it --rm khanlab_scattr_latest.sif --help-snakemake
 We will use the `test` folder found from the 
 [Github repository](https://github.com/khanlab/scattr/tree/main/test/) via
 `git clone` to the previously mentioned folder to demonstrate an example of 
-how to run SCATTR
+how to run SCATTR.
 
 ```
 docker run -it --rm -v c:\Users\username\Downloads\scattr\test:\test khanlab_scattr_latest.sif /test/data/bids /test/data/derivatives participant --fs-license /test/fs_license --force-output -n

docs/getting_started/installation.md

@@ -16,7 +16,7 @@ and DWI derivatives (which can be stored separately).
 
 ## Docker on Windows / Mac (Intel) / Linux
 
-The SCATTR BIDS App is available on DuckerHub as versioned releases.
+The SCATTR BIDS App is available on DockerHub as versioned releases.
 Instructions can be found in the [Docker](https://scattr.readthedocs.io/en/stable/getting_started/docker.html) documentation page.
 
 ### Pros

docs/getting_started/singularity.md

@@ -1,7 +1,7 @@
 # Running SCATTR with Singularity
 
 ## Pre-requisites
-1. Singularity / Apptainer is is installed on your system. For more info, see
+1. Singularity / Apptainer is installed on your system. For more info, see
 the detailed [Apptainer install instructions](https://apptainer.org/docs/admin/main/installation.html#install-from-pre-built-packages).
 1. The following command-line tools are installed:
     * wget
@@ -10,7 +10,7 @@ the detailed [Apptainer install instructions](https://apptainer.org/docs/admin/m
     * in your working folder to store the container (~20GB)
     * for SCATTR outputs (~40GB per subject using default parameters)
 1. Sufficient CPU and memory - the more you have, the faster it will run and 
-the more streamlines that can be estimated. We recommand at least 8 CPU cores 
+the more streamlines that can be estimated. We recommend at least 8 CPU cores 
 and 64GB memory if using default parameters.
 
 ## First time setup