Fix documention build on RTD

Added post_create_environment job to generate requirements.txt using uv,
and updated python install method to use the generated requirements file.

Signed-off-by: John Strunk <jstrunk@redhat.com>

Author: JohnStrunk

.readthedocs.yml

@@ -5,10 +5,15 @@
 
 # Required
 version: 2
-build: 
+build:
   os: ubuntu-22.04  # <- add this line
   tools:
     python: "3.10"
+  jobs:
+    post_create_environment:
+      # Use uv to create a requirements file that RTD can install
+      - pip install uv
+      - uv export --format requirements.txt --only-group docs -o requirements.txt
 
 # Build documentation in the docs/ directory with Sphinx
 sphinx:
@@ -24,12 +29,8 @@ formats: all
 # Optionally set the version of Python and requirements required to build your docs
 python:
    install:
-      - method: pip
-        path: .
-        extra_requirements:
-            - dev
-      - method: setuptools
-        path: .
+      # Install the requirements file created during the post_create_environment job
+      - requirements: requirements.txt
 
 #   build: 
 #     os: ubuntu-22.04

Makefile

@@ -124,12 +124,20 @@ test-api:
 # 	@ bash -c 'tox -e ALL'
 
 
+#
+# UV installation
+#
+.PHONY: uv
+uv:
+	@ command -v uv >/dev/null 2>&1 || { echo "Installing uv..."; pip install --user uv; }
+
 #
 # Documentation
 #
 .PHONY: docs docs-view
-docs:
-	@ bash -c 'cd docs/ && rm -rf build/ && make html;'
+docs: uv
+	-rm -rf docs/build
+	uv run --only-group docs make -C docs html
 
 docs-view: docs
 	@ bash -c 'open docs/build/html/index.html'
@@ -184,4 +192,4 @@ docker-run-database:
 docker-run-rabbitmq:
 	@ - docker stop augur_rabbitmq
 	@ - docker rm augur_rabbitmq
-	docker run -p 5434:5432 --name augur_rabbitmq augurlabs/augur:rabbitmq
+	docker run -p 5434:5432 --name augur_rabbitmq augurlabs/augur:rabbitmq

pyproject.toml

@@ -88,7 +88,6 @@ dependencies = [
     "tornado==6.4.1",
     "typing-extensions==4.7.1",
     "Werkzeug~=2.0.0",
-    "wheel",
     "xgboost==1.4.2",
     "xlrd==2.0.1",
     "xlsxwriter==1.3.7",
@@ -100,11 +99,17 @@ dev = [
     "pytest==6.2.5",
     "toml>=0.10.2",
     "ipdb==0.13.9",
+    {include-group = "docs"},
+]
+docs = [
+    "docutils==0.20.1",
+    # setuptools is needed for pkg_resources due to sphinxcontrib-redoc
+    # See: https://github.com/sphinx-contrib/redoc/issues/47
+    "setuptools",
     "sphinx==7.2.6",
     "sphinx_rtd_theme==2.0.0",
     "sphinxcontrib-openapi==0.8.3",
     "sphinxcontrib-redoc==1.6.0",
-    "docutils==0.20.1"
 ]
 
 [project.scripts]