Spurious error when running `make setup` for the first time

[vladistan]

Describe the bug

This is a minor book, but can confuse some first time users

After using coockie-cutter to create a new project and running make setup I get the following error:

warning: in the working copy of 'CONTRIBUTING.md', CRLF will be replaced by LF the next time Git touches it
Command not found: gen-project
Command not found: gen-doc
make: *** [gen-project] Error 1
make: *** [gendoc] Error 1
Updating dependencies
Resolving dependencies... (6.5s)

Package operations: 119 installs, 1 update, 0 removals

  - Installing six (1.16.0)

Looks like make is trying to run gen-project and gen-doc before poetry. Running make setup second time makes this problem going away.

Version of LinkML you are using

1.8.4

Template commit id: 21dc84

Please provide a schema (and if applicable, a data file) that replicates the issue

It uses default schema, steps to replicate are:

1. Install poetry
2. Install pipx
3. Install cruft
   pipx install cruft
4. Run cruft to create the project cruft create https://github.com/linkml/linkml-project-cookiecutter enter default answers to all questions

[vladistan]

After a bit of investigation I found out that my dotfiles set this variable on login

MAKEFLAGS=' -j48

This explains the error, looks like Makefile dependencies are not completely specified.

We should either fix this or provide a note in the README that make setup is not compatible with parallel make

[amc-corey-cox]

I have had problems with gen-proj due to tests failing, due to cookie-cutter having no tests. This may be related. I'll be looking into this over the next few weeks.

Chris Mungall suggests this for how to make tests for cookie-cutter:
https://github.com/monarch-initiative/dragon-ai-cookiecutter/blob/main/examples/Makefile

[amc-corey-cox]

Your right that the low-hanging fruit is to just update the README.md to say that make setup is not compatible with parallel make but we also want to see if we can make that work. There isn't any reason we should avoid parallel make generally.