Merge pull request #91 from berkeleybop/copier-migration

replace cookiecutter wtih copier where applicable

Author: sierra-moxon

best_practice/index.md

@@ -26,8 +26,11 @@ If there is anything you don't understand, **ask on slack**!
    - make a PR for your branch - mark as draft if not ready
 - Make repos public by default
 - Use standard repo layouts
-   - choose a cookiecutter
-       - [monarch-project-template](https://github.com/monarch-initiative/monarch-project-template) for code-oriented projects
+   - choose a copier template
+       - [monarch-project-copier](https://github.com/monarch-initiative/monarch-project-copier) for code-oriented projects
+       - AI GUI projects using [`nicegui-app-copier`](https://github.com/knowledge-Graph-Hub/nicegui-app-copier)
+       - AI GitHub integrations using [`github-ai-integrations`](https://github.com/ai4curation/github-ai-integrations)
+       - LinkML projects using [linkml-project-copier](https://github.com/linkml/linkml-project-copier)
    - don't reinvent
    - look at exemplars
 - Include standard files:
@@ -146,7 +149,11 @@ If there is anything you don't understand, **ask on slack**!
    - [kgx](https://github.com/biolink/kgx/)
    - [linkml](https://github.com/linkml/linkml)
    - [OAK](https://github.com/INCATools/ontology-access-kit)
-   - Or better: monarch project cookiecutter
+   - Or better: [monarch](https://github.com/monarch-initiative/monarch-project-copier)
+       - [LinkML project copier](https://github.com/linkml/linkml-project-copier) template
+       - AI GUI projects using [`nicegui-app-copier`](https://github.com/knowledge-Graph-Hub/nicegui-app-copier)
+       - AI GitHub integrations using [`github-ai-integrations`](https://github.com/ai4curation/github-ai-integrations)
+       - LinkML projects using [linkml-project-copier](https://github.com/linkml/linkml-project-copier)
 - Include a README.md
    - provide sufficient context
    - don't boil the ocean - put reference material in a separate reference guide
@@ -188,7 +195,7 @@ If there is anything you don't understand, **ask on slack**!
 ### Schema/Standards-centric Repos, Data and metadata repos
 
 - Use [LinkML](https://github.com/linkml/linkml)
-- Create repo from [LinkML template](https://github.com/linkml/linkml-template)
+- Create repo from [LinkML template](https://github.com/linkml/linkml-project-copier)
 - Examples:
    - NMDC
    - MIxS
@@ -383,8 +390,9 @@ If there is anything you don't understand, **ask on slack**!
    - double up: unit tests can serve as examples and vice versa
    - See linkml-run-examples framework
 - Use existing templates
-   - [monarch-project-template](https://github.com/monarch-initiative/monarch-project-template) for code-oriented projects
-   - linkml cookiecutter for schema projects
+   - [monarch-project-copier](https://github.com/monarch-initiative/monarch-project-copier) for code-oriented projects
+   - [linkml-project-copier](https://github.com/linkml/linkml-project-copier) for schema projects
+   - [AI agent GUi copier template](https://github.com/knowledge-Graph-Hub/nicegui-app-copier)
    - ODK for ontology projects
    - kghub template for KG projects
 - use Markdown as default
@@ -678,8 +686,10 @@ If there is anything you don't understand, **ask on slack**!
 - Mappings (ontology or otherwise)
    - SSSOM with skos predicates
 - Cookiecutters for starting a new project.
-  - General-purpose projects using [`monarch-project-template`](https://github.com/monarch-initiative/monarch-project-template)
-  - LinkML based projects using [`linkml-project-cookiecutter`](https://github.com/linkml/linkml-project-cookiecutter)
+  - General-purpose projects using [`monarch-project-template`](https://github.com/monarch-initiative/monarch-project-copier)
+  - AI GUI projects using [`nicegui-app-copier`](https://github.com/knowledge-Graph-Hub/nicegui-app-copier)
+  - AI GitHub integrations using [`github-ai-integrations`](https://github.com/ai4curation/github-ai-integrations)
+  - LinkML based projects using [`linkml-project-copier`](https://github.com/linkml/linkml-project-copier)
   - Ontology Access Kit (`oaklib`) plugin projects using [`oakx-plugin-cookiecutter](https://github.com/INCATools/oakx-plugin-cookiecutter)
 - KGs
    - biolink