chore: Add pre-commit config and perform style fixes (#48)

* feat: Add pre-commit configuration file

* chore: Add codespell words whitelists

* chore: Add pre-commit deps and bump down jupyterlab

* refactor: Skip prettier for yaml

* style: Perform style fixes with pre-commit

* chore: Remove R-CMD-check action for now

* ci: Change cargo-fmt to have language of rust

.codespell-whitelist

@@ -0,0 +1 @@
+crate

.github/workflows/ci-rust.yaml

@@ -7,7 +7,7 @@ on:
       - dev
   pull_request:
 
-env: 
+env:
   CARGO_TERM_COLOR: always
 
 jobs:

.gitignore

@@ -185,4 +185,7 @@ trees/# pixi environments
 .DS_Store
 
 # Web
-*.html
+*.html
+
+# Experimental notebooks folder
+notebooks/

.pre-commit-config.yaml

@@ -0,0 +1,53 @@
+exclude: (^.pixi/|.snap)
+
+ci:
+  autoupdate_commit_msg: "chore: update pre-commit hooks"
+  autofix_commit_msg: "style: pre-commit fixes"
+
+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: "v4.6.0"
+    hooks:
+      - id: check-added-large-files
+      - id: check-case-conflict
+      - id: check-merge-conflict
+      - id: check-symlinks
+      - id: check-yaml
+      - id: debug-statements
+      - id: end-of-file-fixer
+      - id: mixed-line-ending
+      - id: trailing-whitespace
+
+  - repo: https://github.com/pre-commit/mirrors-prettier
+    rev: "v3.1.0"
+    hooks:
+      - id: prettier
+        types_or: [markdown, html, css, scss, javascript, json]
+        args: [--prose-wrap=always]
+
+  - repo: https://github.com/codespell-project/codespell
+    rev: "v2.3.0"
+    hooks:
+      - id: codespell
+        args: ["--write-changes", "--ignore-words", ".codespell-whitelist"]
+
+  - repo: local
+    hooks:
+      - id: disallow-caps
+        name: Disallow improper capitalization
+        language: pygrep
+        entry: Github
+        exclude: .pre-commit-config.yaml
+      - id: cargo-fmt
+        name: fmt
+        language: rust
+        stages: [pre-commit, pre-push, manual]
+        types: [file, rust]
+        entry: cargo fmt
+        pass_filenames: false
+
+  - repo: https://github.com/python-jsonschema/check-jsonschema
+    rev: "0.28.4"
+    hooks:
+      - id: check-dependabot
+      - id: check-github-workflows

README.md

@@ -1,6 +1,7 @@
 # Phylo2Vec
 
-This repository contains an implementation of Phylo2Vec. It is distributed under the GNU Lesser General Public License v3.0 (LGPL).
+This repository contains an implementation of Phylo2Vec. It is distributed under
+the GNU Lesser General Public License v3.0 (LGPL).
 
 [![PyPI version](https://badge.fury.io/py/phylo2vec.svg)](https://pypi.org/project/phylo2vec/)
 
@@ -10,12 +11,12 @@ Link to the paper: <https://doi.org/10.1093/sysbio/syae030>
 
 ### Dependencies
 
-* python>=3.9
-* numba==0.56.4
-* numpy==1.23.5
-* biopython==1.80.0
-* joblib>=1.2.0
-* ete3==3.1.3
+- python>=3.9
+- numba==0.56.4
+- numpy==1.23.5
+- biopython==1.80.0
+- joblib>=1.2.0
+- ete3==3.1.3
 
 ### User installation
 
@@ -27,8 +28,9 @@ pip install phylo2vec
 
 #### Manual installation
 
-* We recommend to setup an isolated enviroment, using conda, mamba or virtualenv.
-* Clone the repository and install using ```pip```:
+- We recommend to setup an isolated environment, using conda, mamba or
+  virtualenv.
+- Clone the repository and install using `pip`:
 
 ```bash
 git clone https://github.com/Neclow/phylo2vec_dev.git
@@ -39,18 +41,19 @@ pip install -e .
 
 ### Additional test dependencies
 
-* pytest==7.4.2
-* six==1.16.0
+- pytest==7.4.2
+- six==1.16.0
 
 ### Testing
 
-After installation, you can launch the test suite from outside the source directory:
+After installation, you can launch the test suite from outside the source
+directory:
 
 ```bash
 pytest phylo2vec
 ```
 
-Warning! You might need to clear your ```__pycache__``` folders beforehand:
+Warning! You might need to clear your `__pycache__` folders beforehand:
 
 ```bash
 rm -rf phylo2vec/__pycache__/
@@ -61,7 +64,8 @@ rm -rf phylo2vec/base/__pycache__/
 
 ### Conversions
 
-* The ```base``` module contains elements to convert a Newick string (```to_vector```) to a Phylo2Vec vector and vice versa (```to_newick```)
+- The `base` module contains elements to convert a Newick string (`to_vector`)
+  to a Phylo2Vec vector and vice versa (`to_newick`)
 
 Example:
 
@@ -78,8 +82,9 @@ v_converted = to_vector(newick) # array([0, 1, 2, 3, 4], dtype=int16)
 
 ### Optimization
 
-* The ```opt``` module contains methods to perform phylogenetic inference using Phylo2Vec vectors
-* TODO: include GradME from <https://github.com/Neclow/GradME>
+- The `opt` module contains methods to perform phylogenetic inference using
+  Phylo2Vec vectors
+- TODO: include GradME from <https://github.com/Neclow/GradME>
 
 Example:
 
@@ -101,6 +106,8 @@ v_opt, taxa_dict, losses = hc.fit("/path/to/your_fasta_file.fa")
 }
 ```
 
-* Preprint repository (core functions are deprecated): <https://github.com/Neclow/phylo2vec_preprint>
-* C++ version (deprecated): <https://github.com/Neclow/phylo2vec_cpp>
-* GradME: <https://github.com/Neclow/GradME> = phylo2vec + minimum evolution + gradient descent
+- Preprint repository (core functions are deprecated):
+  <https://github.com/Neclow/phylo2vec_preprint>
+- C++ version (deprecated): <https://github.com/Neclow/phylo2vec_cpp>
+- GradME: <https://github.com/Neclow/GradME> = phylo2vec + minimum evolution +
+  gradient descent