Update README.md and CONTRIBUTING.md with suggestions from review

CONTRIBUTING.md

@@ -169,7 +169,7 @@ After completing this step, try running the Local Neighborhood algorithm through
 ```bash
 snakemake --cores 1 --configfile config/config.yaml
 ```
-Make sure to run the command inside the `spras` conda environment. If installing via `pip` instead of using conda, install with the `-e .[dev]` options (the full command to run from the repo root is `python -m pip install -e .[dev] .`) so that Python picks up any changes you make and installs all optional development packages. Omitting the `-e` flag will prevent your changes from being reflected unless you force re-install, and omitting `.[dev]` will prevent pip from installing `pre-commit` and `pytest`.
+Make sure to run the command inside the `spras` conda environment. If installing via `pip` instead of using conda, install with the `-e .[dev]` options (the full command to run from the repo root is `python -m pip install -e .[dev]`) so that Python picks up any changes you make and installs all optional development packages. Omitting the `-e` flag will prevent your changes from being reflected unless you force re-install, and omitting `.[dev]` will prevent pip from installing `pre-commit` and `pytest`.
 
 As a workflow manager, Snakemake will consider the work described in the configuration file to be completed once the necessary output files have been written to the relevant output directory (`output` in the `config/config.yaml` configuration).
 That means that if you change your code and rerun the Snakemake command above, nothing may happen if the output files already exist.
@@ -223,7 +223,7 @@ Example errors include a yaml file that cannot be parsed or a local variable tha
 These tests are run automatically on every commit through the GitHub Actions.
 However, developers will benefit from setting up their environment to run the same tests locally while they modify the SPRAS source.
 
-The `pre-commit` package is installed as part of the conda environment in `environment.yml`.
+The `pre-commit` package is installed as part of the conda environment in `environment.yml`, or when installing SPRAS with `python -m pip install -e .[dev]`.
 From there, the pre-commit [quick start](https://pre-commit.com/#quick-start) guide explains two primary ways to use it locally:
 - run against all source files with `pre-commit run --all-files` to identify errors and automatically fix them when possible
 - configure `git` to run the hooks before every `git commit` so that a commit will only succeed if the tests pass, ensuring new errors are not introduced

README.md

@@ -35,7 +35,7 @@ conda activate spras
 to create a conda environment with the required packages and activate that environment.
 If you have a different version of Python already, you can install the specified versions of the required packages in your preferred manner instead of using Anaconda.
 
-SRAS can also be installed with Python's package manager `pip` by running `python -m pip install .` from the repo's root directory. This makes SPRAS more portable by allowing you to run
+SPRAS can also be installed with Python's package manager `pip` by running `python -m pip install .` from the repo's root directory. This makes SPRAS more portable by allowing you to run
 snakemake anywhere the Snakefile, data, and configuration file can be accessed. However, use caution when pip installing directly to your computer without using some form of virtual
 environment as this can alter your system's underlying python modules, which could lead to unexpected behavior.
 
@@ -67,7 +67,7 @@ The files to create these Docker images are in the `docker-wrappers` subdirector
 The Docker images are available on [DockerHub](https://hub.docker.com/orgs/reedcompbio).
 
 **Python wrapper for calling algorithms**: Wrapper functions provide an interface between the common file formats for input and output data and the algorithm-specific file formats and reconstruction commands.
-These wrappers are in the `src/` subdirectory.
+These wrappers are in the `spras/` subdirectory.
 
 **Test code**: Tests for the Docker wrappers and SPRAS code.
 The tests require the conda environment in `environment.yml` and Docker.