Migrate from Jupyter Book to Sphinx (#5)

* Update content

* Fix dependencies

* Migrate to Sphinx

.github/workflows/gh-pages.yml

@@ -1,4 +1,4 @@
-name: Publish to GitHub Pages
+name: docs
 on:
   push:
     branches:
@@ -12,18 +12,17 @@ jobs:
       - name: Set up Python
         uses: actions/setup-python@v5
         with:
-          python-version: 3.11
+          python-version: 3.9
           cache: "pip"
       - name: Install Dependencies
         run: |
-          if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
           if [ -f pyproject.toml ]; then pip install ".[docs]"; fi
-      - name: Build Juputer Book Documentation
+      - name: Build Sphinx Documentation
         run: |
-          jupyter-book build . --config docs/_config.yml --toc docs/_toc.yml
+          sphinx-build docs _build/html -b html
       - name: Upload artifact
         uses: actions/upload-pages-artifact@v3
-        if: github.ref == 'refs/heads/main' && job.status == 'success'
+        if: job.status == 'success'
         with:
           path: "_build/html"
 

README.md

@@ -1,4 +1,4 @@
-# Mobilyze: Mobility Analysis
+# Mobilyze: Mobility Data Analysis
 
 ![Development Status](https://img.shields.io/badge/status-in%20development-orange)
 [![pre-commit.ci status](https://results.pre-commit.ci/badge/github/datapartnership/mobilyze/main.svg)](https://results.pre-commit.ci/latest/github/datapartnership/mobilyze/main)

docs/README.md

@@ -0,0 +1 @@
+../README.md

docs/_toc.yml

@@ -2,9 +2,9 @@ format: jb-book
 root: README
 
 parts:
-  - caption: Literature Review & Methodology
+  - caption: API Reference
     chapters:
-      - file: docs/methodology
+      - file: api/mobilyze
   - caption: Tutorials
     chapters:
       - file: notebooks/tessellate.ipynb

docs/conf.py

@@ -0,0 +1,78 @@
+###############################################################################
+# Auto-generated by `jupyter-book config`
+# If you wish to continue using _config.yml, make edits to that file and
+# re-generate this one.
+###############################################################################
+apidoc_module_dir = "../src"
+author = "Development Data Group"
+bibtex_bibfiles = ["bibliography.bib"]
+comments_config = {"hypothesis": False, "utterances": False}
+copyright = "2024"
+exclude_patterns = ["**.ipynb_checkpoints", ".DS_Store", "Thumbs.db", "_build"]
+extensions = [
+    "sphinx_togglebutton",
+    "sphinx_copybutton",
+    "myst_nb",
+    "jupyter_book",
+    "sphinx_thebe",
+    "sphinx_comments",
+    "sphinx_external_toc",
+    "sphinx.ext.intersphinx",
+    "sphinx_design",
+    "sphinx_book_theme",
+    "sphinxcontrib.bibtex",
+    "sphinx_jupyterbook_latex",
+    "sphinx.ext.napoleon",
+    "sphinxcontrib.apidoc",
+]
+external_toc_exclude_missing = False
+external_toc_path = "_toc.yml"
+extra_extensions = ["sphinxcontrib.apidoc"]
+html_baseurl = "https://datapartnership.github.io/mobilyze"
+html_favicon = "images/favicon.ico"
+html_last_updated_fmt = "%b %d, %Y"
+html_logo = "images/logo.png"
+html_show_copyright = False
+html_sourcelink_suffix = ""
+html_theme = "sphinx_book_theme"
+html_theme_options = {
+    "search_bar_text": "Search this book...",
+    "launch_buttons": {
+        "notebook_interface": "classic",
+        "binderhub_url": "",
+        "jupyterhub_url": "",
+        "thebe": False,
+        "colab_url": "",
+    },
+    "path_to_docs": "",
+    "repository_url": "https://github.com/datapartnership/mobilyze",
+    "repository_branch": "main",
+    "extra_footer": "",
+    "home_page_in_toc": False,
+    "announcement": "",
+    "use_repository_button": True,
+    "use_edit_page_button": True,
+    "use_issues_button": True,
+}
+html_title = ""
+latex_engine = "pdflatex"
+myst_enable_extensions = [
+    "colon_fence",
+    "dollarmath",
+    "linkify",
+    "substitution",
+    "tasklist",
+]
+myst_url_schemes = ["mailto", "http", "https"]
+nb_execution_allow_errors = False
+nb_execution_cache_path = ""
+nb_execution_excludepatterns = []
+nb_execution_in_temp = False
+nb_execution_mode = "off"
+nb_execution_timeout = 30
+nb_output_stderr = "show"
+numfig = True
+pygments_style = "sphinx"
+suppress_warnings = ["myst.domains"]
+use_jupyterbook_latex = True
+use_multitoc_numbering = True

docs/notebooks

@@ -0,0 +1 @@
+../notebooks

notebooks/tessellate.ipynb

@@ -34,11 +34,7 @@
     "import geopandas as gpd\n",
     "import matplotlib.pyplot as plt\n",
     "\n",
-    "from mobilyze.tessellation import tessellate\n",
-    "\n",
-    "%load_ext autoreload\n",
-    "%autoreload 2\n",
-    "%matplotlib inline"
+    "from mobilyze.tessellation import tessellate"
    ]
   },
   {

pyproject.toml

@@ -22,11 +22,11 @@ dynamic = ["version"]
 requires-python = ">=3.8,<3.10"
 dependencies = [
 	"bokeh", 
+	"dask_geopandas",
 	"dask",
 	"datashader",
 	"h3>=3,<4",
 	"holoviews", 
-	"humanize",
 	"mobilkit>=0.2.8",
 	"numpy<2",
 	"palettable>=3.3.3",
@@ -37,6 +37,7 @@ dependencies = [
 docs = [
 	"docutils==0.17.1",    # https://jupyterbook.org/en/stable/content/citations.html?highlight=docutils#citations-and-bibliographies
 	"jupyter-book>=1,<2",
+	"sphinxcontrib-apidoc>=0.4.0,<1",
 ]
 
 [project.urls]