pre-commit setup & code changes

.github/CODE_OF_CONDUCT.md

@@ -18,6 +18,6 @@ This code of conduct applies to all communication: this includes IRC, the mailin
   - Unwelcome sexual attention.
   - Advocating for, or encouraging, any of the above behaviour.
   - Repeated harassment of others. In general, if someone asks you to stop, then stop.
-- When we disagree, we try to understand why. Disagreements, both social and technical, happen all the time and GPJax is no exception. It is important that we resolve disagreements and differing views constructively. Remember that we're different. The strength of GPJax comes from its varied community, people from a wide range of backgrounds. Different people have different perspectives on issues. Being unable to understand why someone holds a viewpoint doesn't mean that they're wrong. Don't forget that it is human to err and blaming each other doesn't get us anywhere, rather offer to help resolving issues and to help learn from mistakes. 
+- When we disagree, we try to understand why. Disagreements, both social and technical, happen all the time and GPJax is no exception. It is important that we resolve disagreements and differing views constructively. Remember that we're different. The strength of GPJax comes from its varied community, people from a wide range of backgrounds. Different people have different perspectives on issues. Being unable to understand why someone holds a viewpoint doesn't mean that they're wrong. Don't forget that it is human to err and blaming each other doesn't get us anywhere, rather offer to help resolving issues and to help learn from mistakes.
 
-Text adapted from the [Speak Up! project](http://web.archive.org/web/20141109123859/http://speakup.io/coc.html) and [Django](https://www.djangoproject.com/conduct/)
+Text adapted from the [Speak Up! project](http://web.archive.org/web/20141109123859/http://speakup.io/coc.html) and [Django](https://www.djangoproject.com/conduct/)

.github/dependabot.yml

@@ -18,4 +18,4 @@ updates:
       interval: weekly
     versioning-strategy: lockfile-only
     allow:
-      - dependency-type: "all"
+      - dependency-type: "all"

.github/pull_request_template.md

@@ -17,4 +17,3 @@
 Please describe your changes here. If this fixes a bug, please link to the issue, if possible.
 
 Issue Number: N/A
-

.github/release-drafter.yml

@@ -25,4 +25,4 @@ categories:
       - "build"
 template: |
   ## Changes
-  $CHANGES
+  $CHANGES

.pre-commit-config.yaml

@@ -1,4 +1,29 @@
+minimum_pre_commit_version: 2.15.0
+ci:
+  autofix_prs: false
 repos:
+  - repo: https://github.com/psf/black
+    rev: 23.3.0
+    hooks:
+    - id: black
+      language_version: python3.8
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.4.0
+    hooks:
+      - id: trailing-whitespace
+      - id: end-of-file-fixer
+        exclude_types: [json, binary]
+  - repo: https://github.com/codespell-project/codespell
+    rev: v2.2.2
+    hooks:
+    -   id: codespell
+        types_or: [python, markdown]
+        additional_dependencies: [tomli]
+  - repo: https://github.com/PyCQA/isort
+    rev: 5.12.0
+    hooks:
+    -   id: isort
+        exclude: examples/
   - repo: local
     hooks:
       - id: commitizen
@@ -17,13 +42,8 @@ repos:
       - id: ruff
         name: ruff
         entry: ruff
-        args: ["--fixable=ERA001,F401,F841,T201,T203"]
+        args: ["--exit-non-zero-on-fix"]
         require_serial: true
         language: system
         types: [python]
-      - id: black
-        name: black
-        entry: black
-        require_serial: true
-        language: system
-        types: [python]
+        exclude: examples/

.readthedocs.yml

@@ -17,4 +17,4 @@ build:
       - poetry install --with docs
 
 sphinx:
-  configuration: docs/conf.py
+  configuration: docs/conf.py

CITATION.bib

@@ -26,4 +26,4 @@
   title: "GPJax: A Gaussian Process Framework in JAX"
   issue: 75
   volume: 7
-  year: 2022
+  year: 2022

README.md

@@ -59,7 +59,7 @@ process modelling.
 > - [**Deep Kernel Regression**](https://gpjax.readthedocs.io/en/latest/examples/haiku.html)
 
 ## Guides for customisation
-> 
+>
 > - [**Custom kernels**](https://gpjax.readthedocs.io/en/latest/examples/kernels.html#Custom-Kernel)
 > - [**UCI regression**](https://gpjax.readthedocs.io/en/latest/examples/yacht.html)
 
@@ -161,7 +161,7 @@ pip install gpjax
 ## Development version
 > **Warning**
 >
-> This version is possibly unstable and may contain bugs. 
+> This version is possibly unstable and may contain bugs.
 
 Clone a copy of the repository to your local machine and run the setup
 configuration in development mode.

docs/Makefile

@@ -13,4 +13,4 @@ help:
 .PHONY: help Makefile
 
 %: Makefile
-	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)

docs/README.md

@@ -29,14 +29,14 @@ highly desirable.
 
 We are making an active effort within GPJax to improve our documentation. If you
 spot any areas where there is missing information within the existing
-documentation, then please either raise an issue or 
+documentation, then please either raise an issue or
 [create a pull request](https://gpjax.readthedocs.io/en/latest/contributing.html).
 
 ## An example docstring
 
-An example docstring that adheres the principles of GPJax is given below. 
-The docstring contains a simple, snappy introduction with links to auxillary 
-components. More detail is then provided in the form of a mathematical 
+An example docstring that adheres the principles of GPJax is given below.
+The docstring contains a simple, snappy introduction with links to auxillary
+components. More detail is then provided in the form of a mathematical
 description and a code example. The docstring is concluded with a description
 of the objects attributes with corresponding types.
 
@@ -76,5 +76,5 @@ class Prior(AbstractPrior):
 
 ### Documentation syntax
 
-A helpful cheatsheet for writing restructured text can be found 
+A helpful cheatsheet for writing restructured text can be found
 [here](https://github.com/ralsina/rst-cheatsheet/blob/master/rst-cheatsheet.rst).

docs/_static/css/gpjax_theme.css

@@ -1,3 +1,3 @@
 nav .bd-links a:hover{
     color: #B5121B
-}
+}