Move docs hosting from Read the Docs to GitHub Pages

.readthedocs.yml pointed at docs/requirements.txt, which was deleted
in #1009, and used the deprecated top-level python.version config
format, so RTD builds were failing outright. Rather than fix the RTD
config, build and deploy the Sphinx docs via GitHub Actions to GitHub
Pages (which the repo already had pages configured for), and drop the
stale codecov and readthedocs badges from the README.

Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>

Author: aarmey

.github/workflows/docs.yml

@@ -0,0 +1,44 @@
+name: Docs
+
+on:
+  push:
+    branches: [master]
+  workflow_dispatch:
+
+permissions:
+  contents: read
+  pages: write
+  id-token: write
+
+concurrency:
+  group: pages
+  cancel-in-progress: true
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v7
+      - name: Setup submodule
+        run: git submodule update --init --recursive
+      - name: Install uv
+        uses: astral-sh/setup-uv@v10.0.1
+        with:
+          enable-cache: true
+      - name: Install dependencies
+        run: uv sync --extra docs
+      - name: Build docs
+        run: uv run sphinx-build -b html docs docs/_build/html
+      - uses: actions/upload-pages-artifact@v3
+        with:
+          path: docs/_build/html
+
+  deploy:
+    needs: build
+    runs-on: ubuntu-latest
+    environment:
+      name: github-pages
+      url: ${{ steps.deployment.outputs.page_url }}
+    steps:
+      - id: deployment
+        uses: actions/deploy-pages@v4

.gitignore

@@ -23,4 +23,5 @@ spell.txt
 .vscode
 lineage/data/taxol
 output/
+docs/_build/
 

.readthedocs.yml

@@ -2,13 +2,6 @@
 tHMM
 ====
 
-.. image:: https://codecov.io/gh/meyer-lab/tHMM/branch/master/graph/badge.svg
-        :target: https://codecov.io/gh/meyer-lab/tHMM
-
-.. image:: https://readthedocs.org/projects/tHMM/badge/?version=latest
-        :target: https://lineage-growth.readthedocs.io/
-
-
 ``tHMM`` is a Python3 package for clustering, visualizing, and analyzing data in the form of lineage trees. This work is now published in Communications Biology https://www.nature.com/articles/s42003-022-04208-9
 
 
@@ -41,7 +34,7 @@ Install the environment and dependencies by running:
 Documentation
 -------------
 
-Please find the documentation at https://thmm.readthedocs.io.
+Please find the documentation at https://meyer-lab.github.io/tHMM/.
 
 License
 -------