- changing the menu

Author: emattei

.editorconfig

@@ -0,0 +1,15 @@
+root = true
+
+[*]
+charset = utf-8
+end_of_line = lf
+insert_final_newline = true
+indent_style = space
+indent_size = 2
+trim_trailing_whitespace = true
+
+[*.py]
+indent_size = 4
+
+[Makefile]
+indent_style = tab

.gitattributes

@@ -0,0 +1 @@
+* text=auto eol=lf

.pre-commit-config.yaml

@@ -0,0 +1,30 @@
+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v5.0.0
+    hooks:
+      - id: trailing-whitespace
+      - id: end-of-file-fixer
+      - id: mixed-line-ending
+        args: [--fix=lf]
+      - id: check-yaml
+      - id: check-toml
+      - id: check-json
+      - id: check-merge-conflict
+      - id: detect-private-key
+      - id: check-added-large-files
+      - id: no-commit-to-branch
+        args: [--branch, main]
+
+  - repo: https://github.com/igorshubovych/markdownlint-cli
+    rev: v0.43.0
+    hooks:
+      - id: markdownlint
+        args: [--disable, MD013]
+
+  - repo: local
+    hooks:
+      - id: forbid-tabs
+        name: forbid-tabs
+        entry: '\t'
+        language: pygrep
+        types: [text]

README.md

@@ -90,6 +90,14 @@ tests/                     Python and R tests
 
 ## Development
 
+Install pre-commit hooks:
+
+```bash
+python -m pip install pre-commit
+pre-commit install
+pre-commit run --all-files
+```
+
 Run Python tests:
 
 ```bash

_pkgdown.yml

@@ -4,7 +4,7 @@ template:
 
 navbar:
   structure:
-    left: [reference]
+    left: [home, reference]
 
 reference:
   - title: Normalization

docs/python/index.md

@@ -0,0 +1,7 @@
+# Python API
+
+This section contains reference docs generated from Python docstrings.
+
+Available modules:
+
+- `crispr_analysis_utils.normalization`

docs/python/normalization.md

@@ -0,0 +1,3 @@
+# Normalization
+
+::: crispr_analysis_utils.normalization

docs/python/reference.md

@@ -2,6 +2,8 @@
 
 The full R reference is published under `/r/` via pkgdown.
 
+Reference index: `/r/reference/`
+
 Build it locally after the MkDocs site:
 
 ```r

docs/r-api.md

@@ -30,6 +30,7 @@ nav:
   - Home: index.md
   - Getting started: getting-started.md
   - Python API:
-      - Reference: python/reference.md
+      - Overview: python/index.md
+      - Normalization: python/normalization.md
   - R API: r-api.md
   - Contributing: contributing.md