Added docs dependencies and cruft update

.cruft.json

@@ -1,6 +1,6 @@
 {
   "template": "https://github.com/monarch-initiative/monarch-project-template/",
-  "commit": "e5f758215fa58b92093e71b632f804569fde9dba",
+  "commit": "9d4f915d4a4cd1a9d8206506db1e261bc397de9c",
   "checkout": null,
   "context": {
     "cookiecutter": {

.github/workflows/deploy-docs.yml

@@ -40,4 +40,4 @@ jobs:
         branch: gh-pages
         force: true
         folder: gh-pages
-        token: ${{ secrets.GH_TOKEN }}
+        token: ${{ secrets.GH_TOKEN }}

docs/conf.py

@@ -3,10 +3,10 @@
 # https://www.sphinx-doc.org/en/master/usage/configuration.html
 
 import os
-import re
-import sys
 from datetime import date
+
 from curate_gpt import __version__
+
 # -- Project information -----------------------------------------------------
 # https://www.sphinx-doc.org/en/master/usage/configuration.html#project-information
 

pyproject.toml

@@ -60,6 +60,15 @@ sphinx-click = {version = ">=4.3.0", extras = ["docs"]}
 sphinx-automodapi = {version = "*", extras = ["docs"]}
 myst-parser = {version = ">=0.18.1", extras = ["docs"]}
 
+[tool.poetry.group.docs]
+optional = true
+
+[tool.poetry.group.docs.dependencies]
+sphinx = {version = ">=6.1.3"}
+sphinx-rtd-theme = {version = ">=1.0.0"}
+sphinx-autodoc-typehints = {version = ">=1.2.0"}
+sphinx-click = {version = ">=4.3.0"}
+myst-parser = {version = ">=0.18.1"}
 
 [tool.poetry.scripts]
 curategpt = "curate_gpt.cli:main"

tox.ini

@@ -38,8 +38,8 @@ deps =
     ruff
 skip_install = true
 commands =
-    black src/ tests/
-    ruff --fix src/ tests/
+    black src/ tests/ --exclude "/(tests/input|tests/output)/"
+    ruff --fix src/ tests/ --exclude tests/input --exclude tests/output
 description = Run linters.
 
 # This is used for QC checks.
@@ -49,8 +49,8 @@ deps =
     ruff
 skip_install = true
 commands =
-    black --check --diff src/ tests/
-    ruff check src/ tests/
+    black --check --diff src/ tests/ --exclude "/(tests/input|tests/output)/"
+    ruff check src/ tests/ --exclude tests/input --exclude tests/output
 description = Run linters.
 
 [testenv:doclint]
@@ -67,7 +67,7 @@ skip_install = true
 deps =
     codespell
     tomli  # required for getting config from pyproject.toml
-commands = codespell src/ tests/
+commands = codespell src/ tests/ -S tests/input/,tests/output/
 
 [testenv:codespell-write]
 description = Run spell checker and write corrections.