Merge pull request #18 from ryanharvey1/add-docs

Add autogenerated docs

.github/workflows/deploy-docs.yml

@@ -0,0 +1,26 @@
+name: Deploy docs
+on: [push, pull_request]
+jobs:
+  build:
+    name: Deploy docs
+    runs-on: ubuntu-latest
+    steps:
+      - name: Download source
+        uses: actions/checkout@v3
+      - name: Install Crystal
+        uses: oprypin/install-crystal@v1
+      - name: Install Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: '3.x'
+      - name: Install Python libs
+        run: pip install .
+      - name: Install Crystal libs
+        run: |
+          shards init
+          shards install
+      - name: Build site
+        run: mkdocs build
+      - name: Deploy to gh-pages
+        if: github.event_name == 'push' && github.ref == 'refs/heads/main'
+        run: mkdocs gh-deploy --force

README.md

@@ -4,7 +4,7 @@ Analysis of neuroelectrophysiology data in Python.
 
 Overview
 ========
-neuro_py is a Python package for analysis of neuroelectrophysiology data. It is built on top of the [nelpy](https://github.com/nelpy/nelpy) package, which provides core data objects. neuro_py provides a set of functions for analysis of freely moving electrophysisology, including behavior tracking utilities, neural ensemble detection, peri-event analyses, robust batch analysis tools, and more. 
+neuro_py is a Python package for analysis of neuroelectrophysiology data. It is built on top of the [nelpy](https://github.com/nelpy/nelpy) package, which provides core data objects. neuro_py provides a set of functions for analysis of freely moving electrophysiology, including behavior tracking utilities, neural ensemble detection, peri-event analyses, robust batch analysis tools, and more. 
 
 Tutorials are [here](https://github.com/ryanharvey1/neuro_py/tree/master/tutorials) and more will be added. 
 

docs/gen_ref_pages.py

@@ -0,0 +1,40 @@
+"""Generate the code reference pages."""
+from pathlib import Path
+
+import mkdocs_gen_files
+
+
+nav = mkdocs_gen_files.Nav()
+mod_symbol = ''
+
+root = Path(__file__).parent.parent
+src = root
+
+for path in sorted(src.rglob("*.py")):
+    if path.relative_to(src).parts[0] != "neuro_py":
+        continue
+    module_path = path.relative_to(src).with_suffix("")
+    doc_path = path.relative_to(src).with_suffix(".md")
+    full_doc_path = Path("reference", doc_path)
+
+    parts = tuple(module_path.parts)
+
+    if parts[-1] == "__init__":
+        parts = parts[:-1]
+        doc_path = doc_path.with_name("index.md")
+        full_doc_path = full_doc_path.with_name("index.md")
+    elif parts[-1] == "__main__":
+        continue
+
+    nav_parts = [f"{mod_symbol} {part}" for part in parts]
+    print(nav_parts)
+    nav[tuple(nav_parts)[-2:]] = doc_path.as_posix()
+
+    with mkdocs_gen_files.open(full_doc_path, "w") as fd:
+        identifier = ".".join(parts)
+        print(f"---\ntitle: {identifier}\n---\n\n::: {identifier}", file=fd)
+
+    mkdocs_gen_files.set_edit_path(full_doc_path, path.relative_to(root))
+
+with mkdocs_gen_files.open("reference/SUMMARY.md", "w") as nav_file:
+    nav_file.writelines(nav.build_literate_nav())

docs/index.md

@@ -0,0 +1 @@
+# neuro-py

docs/stylesheets/extra.css

@@ -0,0 +1,36 @@
+:root {
+  --md-code-font: "Roboto Mono";
+  --md-default-fg-color: #111;
+  --md-default-fg-color--light: #000000d0;
+  --md-default-fg-color--lighter: #00000052;
+  --md-default-fg-color--lightest: #00000012;
+  --md-accent-fg-color: #38195A;
+  --md-accent-fg-color--hover: #E4AF68;
+  --md-accent-fg-color--transparent: #38195a1a;
+
+  --md-default-bg-color: #fff;
+  --md-default-bg-color--light: #ffffffb3;
+  --md-default-bg-color--lighter: #ffffff4d;
+  --md-default-bg-color--lightest: #ffffff1f;
+  --md-accent-bg-color: #fff;
+  --md-accent-bg-color--light: #ffffffb3;
+}
+
+[data-md-color-scheme="slate"] {
+  --md-hue: 210;
+}
+
+/* Indentation for API Reference. */
+.md-content div.doc-contents:not(.first) {
+  padding-left: 25px;
+  border-left: .05rem solid var(--md-typeset-table-color);
+}
+
+/* Gradient banner */
+.md-header {
+  background: linear-gradient(145deg, rgba(229,119,39,1) 3%, rgba(144,3,12,1) 31%, rgba(133,59,96,1) 51%, rgba(31,67,103,1) 79%, rgba(31,99,120,1) 94%, rgba(32,135,139,1) 100%);
+}
+
+.md-tabs {
+  background: none;
+}

mkdocs.yml

@@ -0,0 +1,73 @@
+site_name: "neuro_py"
+repo_name: ryanharvey1/neuro_py
+repo_url: https://github.com/ryanharvey1/neuro_py
+edit_uri: edit/main/docs/
+
+extra_css:
+  - stylesheets/extra.css
+
+theme:
+  name: "material"
+  font:
+    text: Roboto
+    code: Roboto Mono
+  palette:
+  - media: "(prefers-color-scheme: dark)"
+    toggle:
+      icon: material/brightness-auto
+      name: Switch to light mode
+  - media: "(prefers-color-scheme: light)"
+    scheme: light
+    primary: custom
+    accent: custom
+    toggle:
+      icon: material/weather-sunny
+      name: Switch to dark mode
+  - media: "(prefers-color-scheme: dark)"
+    scheme: slate
+    primary: indigo
+    accent: blue
+    toggle:
+      icon: material/weather-night
+      name: Switch to system preference
+  features:
+  - announce.dismiss
+  - content.action.edit
+  - content.action.view
+  - content.code.annotate
+  - content.code.copy
+  - content.tooltips
+  - content.tabs.link
+  - navigation.footer
+  - navigation.indexes
+  - navigation.instant.prefetch
+  - navigation.instant.preview
+  - navigation.instant.progress
+  - navigation.path
+  - navigation.sections
+  - navigation.tabs
+  - navigation.tabs.sticky
+  - navigation.top
+  - navigation.tracking
+  - search.highlight
+  - search.suggest
+  - toc.follow
+
+plugins:
+- search
+- gen-files:
+    scripts:
+    - docs/gen_ref_pages.py
+- literate-nav:
+    nav_file: SUMMARY.md
+- section-index
+- mkdocstrings:
+    handlers:
+      python:
+        options:
+          docstring_style: numpy
+
+
+nav:
+- Home: index.md
+- API Reference: reference/

neuro_py/behavior/cheeseboard.py

@@ -47,7 +47,3 @@ def plot_grid_with_circle_and_random_dots():
     plt.gca().set_aspect("equal", adjustable="box")
     plt.axis("off")
     plt.show()
-
-
-if __name__ == "__main__":
-    plot_grid_with_circle_and_random_dots()