refactor: 4th use environment vars instead of about.yaml

[noelmcloughlin]

This PR refactors how schema definition is passed to makefile.

• Move variables from about.yaml to .env.public
• Delete about.yaml and utils/ directory as not needed anymore
• Update Makefile to use environment variables from `.env.public.
• Run check-config as part of make setup to validate include .env.public worked

See #57 (comment)

[pkalita-lbl]

I made this as a comment in #57 before I looked at this PR, but I wonder if this is also a good opportunity to use a standard .env filename instead of config.env. Would be curious to get other LinkML developers' thoughts.

[noelmcloughlin]

I'd agree with that in this PR, good suggestion. There is some open tooling which looks for a '.env' file, and auto loads environment vars if found. Chezmoi is one example, another called 'dotenv' I think. So it may be an official standard😊

There may also be value in using a standardized interface called '.config/' directory but I need to think about that. Its official standard for home directories, but I'm not 100% sure it's a standard for git repos.

[noelmcloughlin]

According to google search, .env may be best. There is also a .dotenv competing standard maybe, but I'd vote for .env

[noelmcloughlin]

@pkalita-lbl Looks like .env may not be best choice, see https://configu.com/blog/dotenv-managing-environment-variables-in-node-python-php-and-more/#NoCommit

[noelmcloughlin]

Maybe .env.public is semantic alternative?

prisma/prisma#15681 (comment)

[noelmcloughlin]

@pkalita-lbl we can go ahead with .env.public for now. PR is ready now.

[pkalita-lbl]

Great stuff!

[zmughal]

Just a note, when using a .env-style file in combination with GNU Make include, it must follow GNU Make syntax. If that file is meant to be sourced by sh(1), then it must use only a common subset of that syntax (but that's not being done here).

Specifically, GNU Make retains any quotes as literal quotes whereas sh(1) does its own quoting. So any further use of these variables with functions (such as $(dir ...)) will be impacted such as with the SOURCE_SCHEMA_DIR variable which will start with a " character and end with a /. I have a fix for this as follows:

diff --git a/Makefile b/Makefile
index 26adc0a..cf84f7e 100644
--- a/Makefile
+++ b/Makefile
@@ -6,6 +6,10 @@ SHELL := bash
 .SUFFIXES:
 .SECONDARY:

+# define temporary variable for $(call ...)
+1 :=
+unquote = $(patsubst "%,%,$(patsubst %",%,$(1)))
+
 # environment variables
 .EXPORT_ALL_VARIABLES:
 ifdef LINKML_ENVIRONMENT_FILENAME
@@ -16,8 +20,8 @@ endif

 RUN = poetry run
 SCHEMA_NAME = $(LINKML_SCHEMA_NAME)
-SOURCE_SCHEMA_PATH = $(LINKML_SCHEMA_SOURCE_PATH)
-SOURCE_SCHEMA_DIR = $(dir $(SOURCE_SCHEMA_PATH))
+SOURCE_SCHEMA_PATH = $(call unquote,$(LINKML_SCHEMA_SOURCE_PATH))
+SOURCE_SCHEMA_DIR = $(patsubst %/,%,$(dir $(SOURCE_SCHEMA_PATH)))
 SRC = src
 DEST = project
 PYMODEL = $(SRC)/$(SCHEMA_NAME)/datamodel

I can make a PR for this.

The other solution is not use quotes on some of the variables (LINKML_SCHEMA_SOURCE_PATH, LINKML_SCHEMA_GOOGLE_SHEET_TABS), but that might confuse users as some variables don't follow the same pattern as others. Though this is already the case with the LINKML_GENERATORS_CONFIG_YAML variable and I suppose the other *_ARGS variables.