chore: fix up Markdown rendering

.gitignore

@@ -1,3 +1,4 @@
+.DS_Store
 .vscode/
 
 # Byte-compiled / optimized / DLL files

docs/installation-and-developers-documentation.md

@@ -38,7 +38,7 @@ mamba install -c bioconda prymer
     poetry install
     ```
 
-# Checking the Build
+## Checking the Build
 
 Use `poetry` to test your code.
 
@@ -47,22 +47,21 @@ poetry run pytest
 ```
 
 Note that `poetry run pytest` will run `mypy` checks, `ruff` checks, `pytest` unit tests, and will provide a unit test coverage report.
-
 However, `pytest` will neither run the ruff formatter nor apply `ruff`'s automatic lint fixes, which can be done by calling `ruff` directly. 
 
 ```console
 poetry run ruff format && poetry run ruff check --fix
 ```
 
-# Building the Documentation
+## Building the Documentation
 
 Use `mkdocs` to build and serve the documentation.
 
 ```console
 poetry run mkdocs build && poetry run mkdocs serve
 ```
 
-# Creating a Release on PyPi
+## Creating a Release on PyPi
 
 1. Clone the repository recursively and ensure you are on the `main` (un-dirty) branch
 2. Checkout a new branch to prepare the library for release

prymer/offtarget/bwa.py

@@ -18,8 +18,8 @@
 Use of this module requires installation of a custom version of BWA named `bwa-aln-interactive`.
 See:
 
-    - https://github.com/fulcrumgenomics/bwa-aln-interactive
-    - https://bioconda.github.io/recipes/bwa-aln-interactive/README.html
+- [https://github.com/fulcrumgenomics/bwa-aln-interactive](https://github.com/fulcrumgenomics/bwa-aln-interactive)
+- [https://bioconda.github.io/recipes/bwa-aln-interactive/README.html](https://bioconda.github.io/recipes/bwa-aln-interactive/README.html)
 
 ## Example
 
@@ -192,7 +192,7 @@ class BwaResult:
 """The default length of the seed region"""
 
 BWA_AUX_EXTENSIONS: list[str] = [".amb", ".ann", ".bwt", ".pac", ".sa"]
-"""The file extensiosn for BWA index files"""
+"""The file extensions for BWA index files"""
 
 
 class BwaAlnInteractive(ExecutableRunner):
@@ -201,9 +201,9 @@ class BwaAlnInteractive(ExecutableRunner):
     back without waiting for a full batch of reads to be sent.
 
     See:
-        - https://github.com/fulcrumgenomics/bwa-aln-interactive
-        - https://bioconda.github.io/recipes/bwa-aln-interactive/README.html
 
+    - [https://github.com/fulcrumgenomics/bwa-aln-interactive](https://github.com/fulcrumgenomics/bwa-aln-interactive)
+    - [https://bioconda.github.io/recipes/bwa-aln-interactive/README.html](https://bioconda.github.io/recipes/bwa-aln-interactive/README.html)
 
     Attributes:
         max_hits: the maximum number of hits to report - if more than this number of seed hits