Docs + Schema Fixes

.gitignore

@@ -44,6 +44,15 @@ docs/*
 !docs/development.md
 !docs/quickstart.md
 !docs/index.md
+# Allow generated documentation files
+!docs/*.md
+!docs/**/*.md
+# Allow subdirectories with markdown files
+!docs/*/
+!docs/*/*.md
+# Allow CSV exports
+!docs/csv/
+!docs/csv/*.csv
 # Also ignore these specific doc directories
 docs/_build/
 docs/site/

.readthedocs.yaml

@@ -0,0 +1,14 @@
+version: 2
+
+build:
+  os: ubuntu-22.04
+  tools:
+    python: "3.11"
+  commands:
+    - pip install -r requirements.txt
+    - rm -rf _build _readthedocs
+    - python -m sphinx -b html -d "${READTHEDOCS_OUTPUT}/.doctrees" . "${READTHEDOCS_OUTPUT}/html"
+
+python:
+  install:
+    - requirements: requirements.txt

Makefile

@@ -109,17 +109,9 @@ format:
 # ---
 #
 # check we are up to date
-check: cruft-check
-cruft-check:
-	cruft check
-cruft-diff:
-	cruft diff
+check: update-linkml
 
-update: update-template update-linkml
-update-template:
-	cruft update
-
-# todo: consider pinning to template
+update: update-linkml
 update-linkml:
 	poetry add -D linkml@latest
 
@@ -130,7 +122,6 @@ create-data-harmonizer:
 all: site
 site: gen-project gendoc
 %.yaml: gen-project
-deploy: all mkd-gh-deploy
 
 compile-sheets:
 	$(RUN) sheets2linkml --gsheet-id $(SHEET_ID) $(SHEET_TABS) > $(SHEET_MODULE_PATH).tmp && mv $(SHEET_MODULE_PATH).tmp $(SHEET_MODULE_PATH)
@@ -185,18 +176,13 @@ mkd-%:
 git-init-add: git-init git-add git-commit git-status
 git-init:
 	git init
-git-add: .cruft.json
+git-add:
 	git add .
 git-commit:
 	git commit -m 'chore: make setup was run' -a
 git-status:
 	git status
 
-# only necessary if setting up via cookiecutter
-.cruft.json:
-	echo "creating a stub for .cruft.json. IMPORTANT: setup via cruft not cookiecutter recommended!" ; \
-	touch $@
-
 check-config:
 ifndef LINKML_SCHEMA_NAME
 	$(error **Project not configured**:\n\n - See '.env.public'\n\n)

_build/html/.buildinfo

@@ -0,0 +1,4 @@
+# Sphinx build info version 1
+# This file records the configuration used when building these files. When it is not found, a full rebuild will be done.
+config: f51bb1e327b6630e90dc860f99dd7540
+tags: 645f666f9bcd5a90fca523b33c5a78b7