Update documentation and add pre-commit tooling

.all-contributorsrc

@@ -1,7 +1,5 @@
 {
-  "files": [
-    "README.md"
-  ],
+  "files": ["README.md", "docs/contributing.md"],
   "imageSize": 100,
   "commit": false,
   "commitType": "docs",
@@ -12,38 +10,28 @@
       "name": "Laura Gomez Navarro",
       "avatar_url": "https://avatars.githubusercontent.com/u/20359692?v=4",
       "profile": "https://github.com/LauraGomezNavarro",
-      "contributions": [
-        "code"
-      ]
+      "contributions": ["code"]
     },
     {
       "login": "jimena-medinarubio",
       "name": "Jimena Medina",
       "avatar_url": "https://avatars.githubusercontent.com/u/101462540?v=4",
       "profile": "https://github.com/jimena-medinarubio",
-      "contributions": [
-        "code"
-      ]
+      "contributions": ["code"]
     },
     {
       "login": "sruehs",
       "name": "sruehs",
       "avatar_url": "https://avatars.githubusercontent.com/u/33282992?v=4",
       "profile": "https://github.com/sruehs",
-      "contributions": [
-        "ideas",
-        "code",
-        "projectManagement"
-      ]
+      "contributions": ["ideas", "code", "projectManagement"]
     },
     {
       "login": "dicaearchus",
       "name": "Bas Altena",
       "avatar_url": "https://avatars.githubusercontent.com/u/64000582?v=4",
       "profile": "https://www.uu.nl/staff/BAltena",
-      "contributions": [
-        "code"
-      ]
+      "contributions": ["code"]
     }
   ],
   "contributorsPerLine": 7,

.github/CONTRIBUTING.md

@@ -0,0 +1 @@
+See https://lagrangian-diags.readthedocs.io/en/latest/contributing/index.html

.gitignore

@@ -1,8 +1,9 @@
 # Data
 Simulations/out-*
+docs/_build
 
 # Jupyter Notebook
 .ipynb_checkpoints
 
 *.pyc
-
+.DS_Store

.pre-commit-config.yaml

@@ -0,0 +1,42 @@
+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v5.0.0
+    hooks:
+      - id: trailing-whitespace
+      - id: end-of-file-fixer
+        exclude: '.*\.zarr'
+
+      - id: check-yaml
+      - id: check-ast
+      - id: check-json
+        types: [text]
+        files: \.(json|ipynb)$
+  # - repo: https://github.com/astral-sh/ruff-pre-commit
+  #   rev: v0.7.0
+  #   hooks:
+  #     - id: ruff
+  #       args: [--fix, --show-fixes]
+  #       types_or: [python]
+  #     - id: ruff
+  #       name: ruff (isort jupyter)
+  #       args: [--select, I, --fix]
+  #       types_or: [jupyter]
+  #     - id: ruff-format
+  #       types_or: [python, jupyter]
+  - repo: https://github.com/rbubley/mirrors-prettier # Update mirror as official mirror is deprecated
+    rev: v3.3.3
+    hooks:
+      - id: prettier
+
+  # Ruff doesn't have full coverage of pydoclint https://github.com/astral-sh/ruff/issues/12434
+  - repo: https://github.com/PyCQA/flake8
+    rev: 7.1.1
+    hooks:
+      - id: flake8
+        name: pydoclint
+        files: "none"
+        # files: parcels/fieldset.py # put here instead of in config file due to https://github.com/pre-commit/pre-commit-hooks/issues/112#issuecomment-215613842
+        args:
+          - --select=DOC103 # TODO: Expand coverage to other codes
+        additional_dependencies:
+          - pydoclint[flake8]

.readthedocs.yaml

@@ -12,4 +12,4 @@ sphinx:
   configuration: docs/conf.py
 
 conda:
-  environment: docs/environment_docs.yml
+  environment: docs/environment_docs.yml