From 4004bbf60b82a08fe4d0d47bf06ede492cc25c5e Mon Sep 17 00:00:00 2001
From: noelmcloughlin <noel.mcloughlin@gmail.com>
Date: Thu, 9 Feb 2023 00:25:41 +0000
Subject: [PATCH 1/3] feat: support gen-xxx environment variables

---
 README.md                              |  7 +++++++
 {{cookiecutter.project_name}}/Makefile | 24 ++++++++++++++++++------
 2 files changed, 25 insertions(+), 6 deletions(-)

diff --git a/README.md b/README.md
index 00d773e..946121b 100644
--- a/README.md
+++ b/README.md
@@ -91,6 +91,13 @@ See [linkml/linkml-project-cookiecutter](https://github.com/linkml/linkml-projec
 
 ### Step 4: Setup the LinkML project
 
+Optionally set project generation environment variables, skip if unsure.
+
+```
+export LINKML_COOKIECUTTER_GEN_DOC_ARGS=--no-mergeimports   # custom arg
+export LINKML_COOKIECUTTER_GEN_PROJECT_ARGS=--mergeimports  # default arg
+```
+
 Change to the folder your generated project is in
 
 ```bash
diff --git a/{{cookiecutter.project_name}}/Makefile b/{{cookiecutter.project_name}}/Makefile
index fbf6b84..bc31e88 100644
--- a/{{cookiecutter.project_name}}/Makefile
+++ b/{{cookiecutter.project_name}}/Makefile
@@ -21,6 +21,18 @@ SHEET_ID = $(shell sh ./utils/get-value.sh google_sheet_id)
 SHEET_TABS = $(shell sh ./utils/get-value.sh google_sheet_tabs)
 SHEET_MODULE_PATH = $(SOURCE_SCHEMA_DIR)/$(SHEET_MODULE).yaml
 
+# environment variables
+GEN_PARGS =
+ifdef LINKML_COOKIECUTTER_GEN_PROJECT_ARGS
+GEN_PARGS = ${LINKML_COOKIECUTTER_GEN_PROJECT_ARGS}
+endif
+
+GEN_DARGS =
+ifdef LINKML_COOKIECUTTER_GEN_DOC_ARGS
+GEN_DARGS = ${LINKML_COOKIECUTTER_GEN_DOC_ARGS}
+endif
+
+
 # basename of a YAML file in model/
 .PHONY: all clean
 
@@ -91,27 +103,27 @@ gen-examples:
 # generates all project files
 {% if cookiecutter.use_schemasheets == "Yes"  %}
 gen-project: $(PYMODEL) compile-sheets
-	$(RUN) gen-project -d $(DEST) $(SOURCE_SCHEMA_PATH) && mv $(DEST)/*.py $(PYMODEL)
+	$(RUN) gen-project ${GEN_PARGS} -d $(DEST) $(SOURCE_SCHEMA_PATH) && mv $(DEST)/*.py $(PYMODEL)
 {% else %}
 gen-project: $(PYMODEL)
-	$(RUN) gen-project -d $(DEST) $(SOURCE_SCHEMA_PATH) && mv $(DEST)/*.py $(PYMODEL)
+	$(RUN) gen-project ${GEN_PARGS} -d $(DEST) $(SOURCE_SCHEMA_PATH) && mv $(DEST)/*.py $(PYMODEL)
 {% endif %}
 
 test: test-schema test-python
 test-schema:
-	$(RUN) gen-project -d tmp $(SOURCE_SCHEMA_PATH) 
+	$(RUN) gen-project ${GEN_PARGS} -d tmp $(SOURCE_SCHEMA_PATH)
 
 test-python:
 	$(RUN) python -m unittest discover
 
 lint:
-	$(RUN) linkml-lint $(SOURCE_SCHEMA_PATH) 
+	$(RUN) linkml-lint $(SOURCE_SCHEMA_PATH)
 
 check-config:
 	@(grep my-datamodel about.yaml > /dev/null && printf "\n**Project not configured**:\n\n  - Remember to edit 'about.yaml'\n\n" || exit 0)
 
 convert-examples-to-%:
-	$(patsubst %, $(RUN) linkml-convert  % -s $(SOURCE_SCHEMA_PATH) -C Person, $(shell find src/data/examples -name "*.yaml")) 
+	$(patsubst %, $(RUN) linkml-convert  % -s $(SOURCE_SCHEMA_PATH) -C Person, $(shell find src/data/examples -name "*.yaml"))
 
 examples/%.yaml: src/data/examples/%.yaml
 	$(RUN) linkml-convert -s $(SOURCE_SCHEMA_PATH) -C Person $< -o $@
@@ -133,7 +145,7 @@ $(DOCDIR):
 
 gendoc: $(DOCDIR)
 	cp $(SRC)/docs/*md $(DOCDIR) ; \
-	$(RUN) gen-doc -d $(DOCDIR) $(SOURCE_SCHEMA_PATH)
+	$(RUN) gen-doc ${GEN_DOC_ARGS} -d $(DOCDIR) $(SOURCE_SCHEMA_PATH)
 
 testdoc: gendoc serve
 

From ecab9b24c71e7286107a43f22edb13db0d0bba3c Mon Sep 17 00:00:00 2001
From: noelmcloughlin <noel.mcloughlin@gmail.com>
Date: Thu, 9 Feb 2023 00:47:01 +0000
Subject: [PATCH 2/3] fix: corrected varname

---
 {{cookiecutter.project_name}}/Makefile | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/{{cookiecutter.project_name}}/Makefile b/{{cookiecutter.project_name}}/Makefile
index bc31e88..737e26e 100644
--- a/{{cookiecutter.project_name}}/Makefile
+++ b/{{cookiecutter.project_name}}/Makefile
@@ -145,7 +145,7 @@ $(DOCDIR):
 
 gendoc: $(DOCDIR)
 	cp $(SRC)/docs/*md $(DOCDIR) ; \
-	$(RUN) gen-doc ${GEN_DOC_ARGS} -d $(DOCDIR) $(SOURCE_SCHEMA_PATH)
+	$(RUN) gen-doc ${GEN_DARGS} -d $(DOCDIR) $(SOURCE_SCHEMA_PATH)
 
 testdoc: gendoc serve
 

From b0ffbabf3c3f81cf3cd61688798f8ba4de726337 Mon Sep 17 00:00:00 2001
From: noelmcloughlin <noel.mcloughlin@gmail.com>
Date: Sat, 11 Feb 2023 19:08:04 +0000
Subject: [PATCH 3/3] doc: minor update

---
 README.md | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/README.md b/README.md
index 946121b..26552c7 100644
--- a/README.md
+++ b/README.md
@@ -91,11 +91,11 @@ See [linkml/linkml-project-cookiecutter](https://github.com/linkml/linkml-projec
 
 ### Step 4: Setup the LinkML project
 
-Optionally set project generation environment variables, skip if unsure.
+Optionally set project generation environment variables (see `gen-doc --help` and `gen-project --help`):
 
 ```
-export LINKML_COOKIECUTTER_GEN_DOC_ARGS=--no-mergeimports   # custom arg
-export LINKML_COOKIECUTTER_GEN_PROJECT_ARGS=--mergeimports  # default arg
+export LINKML_COOKIECUTTER_GEN_DOC_ARGS=--no-mergeimports      # example
+export LINKML_COOKIECUTTER_GEN_PROJECT_ARGS=--no-mergeimports  # example
 ```
 
 Change to the folder your generated project is in