Merge pull request #2 from NFDI4Chem/fix-mermaid-diagrams

Fix Mermaid diagrams

.cruft.json

@@ -1,18 +1,18 @@
 {
   "template": "https://github.com/linkml/linkml-project-cookiecutter",
-  "commit": "d9b85bbbdcc49163416a3e3e18e23fe2ecce501b",
+  "commit": "c81851945f83b0217a65a9190219ddf9cd4bee20",
   "checkout": null,
   "context": {
     "cookiecutter": {
-      "project_name": "NFDI4Chem_MIChI",
-      "__project_slug": "nfdi4chem_michi",
+      "project_name": "MICHI",
+      "__project_slug": "michi",
       "github_org": "NFDI4Chem",
-      "__source_path": "src/nfdi4chem_michi/schema/nfdi4chem_michi.yaml",
-      "project_description": "This is the LinkML metadata schema prototype for NFDI4Chem",
+      "__source_path": "src/michi/schema/michi.yaml",
+      "project_description": "NFDI4Chem metadata schema",
       "full_name": "Philip Strömert",
       "email": "[email protected]",
       "__author": "Philip Strömert <[email protected]>",
-      "license": "MIT",
+      "license": "GNU GPL v3.0",
       "main_schema_class": "Dataset",
       "create_python_classes": "Yes",
       "use_schemasheets": "No",

.env.public

@@ -2,7 +2,7 @@
 
 ###### schema definition variables, used by makefile
 
-LINKML_SCHEMA_NAME="nfdi4chem_michi"
+LINKML_SCHEMA_NAME="MICHI"
 LINKML_SCHEMA_AUTHOR="Philip Strömert <[email protected]>"
 LINKML_SCHEMA_DESCRIPTION="This is the LinkML metadata schema prototype for NFDI4Chem"
 LINKML_SCHEMA_SOURCE_PATH="src/nfdi4chem_michi/schema/nfdi4chem_michi.yaml"

CONTRIBUTING.md

@@ -1,9 +1,9 @@
-# Contributing to NFDI4Chem_MIChI
+# Contributing to MICHI
 
 :+1: First of all: Thank you for taking the time to contribute!
 
 The following is a set of guidelines for contributing to
-NFDI4Chem_MIChI. These guidelines are not strict rules.
+MICHI. These guidelines are not strict rules.
 Use your best judgment, and feel free to propose changes to this document
 in a pull request.
 
@@ -22,7 +22,7 @@ in a pull request.
 
 ## Code of Conduct
 
-The NFDI4Chem_MIChI team strives to create a
+The MICHI team strives to create a
 welcoming environment for editors, users and other contributors.
 Please carefully read our [Code of Conduct](CODE_OF_CONDUCT.md).
 
@@ -73,7 +73,7 @@ Please submit a [Pull Request][pulls] to submit a new term for consideration.
     - Never work on the main branch, always work on an issue/feature branch
     - Core developers can work on branches off origin rather than forks
     - Always create a PR on a branch to maximize transparency of what you are doing
-    - PRs should be reviewed and merged in a timely fashion by the NFDI4Chem_MIChI technical leads
+    - PRs should be reviewed and merged in a timely fashion by the MICHI technical leads
     - PRs that do not pass GitHub actions should never be merged
     - In the case of git conflicts, the contributor should try and resolve the conflict
     - If a PR fails a GitHub action check, the contributor should try and resolve the issue in a timely fashion
@@ -115,7 +115,7 @@ Core developers should read the material on the [LinkML site](https://linkml.io/
 [about-branches]: https://docs.github.com/en/pull-requests/collaborating-with-pull-requests/proposing-changes-to-your-work-with-pull-requests/about-branches
 [about-issues]: https://docs.github.com/en/issues/tracking-your-work-with-issues/about-issues
 [about-pulls]: https://docs.github.com/en/pull-requests/collaborating-with-pull-requests/proposing-changes-to-your-work-with-pull-requests/about-pull-requests
-[issues]: https://github.com/NFDI4Chem/NFDI4Chem_MIChI/issues/
-[pulls]: https://github.com/NFDI4Chem/NFDI4Chem_MIChI/pulls/
+[issues]: https://github.com/NFDI4Chem/MICHI/issues/
+[pulls]: https://github.com/NFDI4Chem/MICHI/pulls/
 
 We recommend also reading [GitHub Pull Requests: 10 Tips to Know](https://blog.mergify.com/github-pull-requests-10-tips-to-know/)

Makefile

@@ -170,7 +170,7 @@ examples/%.ttl: src/data/examples/%.yaml
 
 test-examples: examples/output
 
-examples/output: src/nfdi4chem_michi/schema/nfdi4chem_michi.yaml
+examples/output: src/michi/schema/michi.yaml
 	mkdir -p $@
 	$(RUN) linkml-run-examples \
 		--output-formats json \

README.md

@@ -1,20 +1,20 @@
-# NFDI4Chem_MIChI
+# MICHI
 
-This is the LinkML metadata schema prototype for NFDI4Chem
+NFDI4Chem metadata schema
 
 ## Website
 
-[https://NFDI4Chem.github.io/MIChI](https://NFDI4Chem.github.io/MIChI)
+[https://NFDI4Chem.github.io/MICHI](https://NFDI4Chem.github.io/MICHI)
 
 ## Repository Structure
 
 * [examples/](examples/) - example data
 * [project/](project/) - project files (do not edit these)
 * [src/](src/) - source files (edit these)
-  * [nfdi4chem_michi](src/nfdi4chem_michi)
-    * [schema](src/nfdi4chem_michi/schema) -- LinkML schema
+  * [michi](src/michi)
+    * [schema](src/michi/schema) -- LinkML schema
       (edit this)
-    * [datamodel](src/nfdi4chem_michi/datamodel) -- generated
+    * [datamodel](src/michi/datamodel) -- generated
       Python datamodel
 * [tests/](tests/) - Python tests
 

examples/Dataset-001.yaml

@@ -3,4 +3,5 @@
 entries:
   - id: example:Dataset001
     name: foo bar
-
+    primary_email: [email protected]
+    age_in_years: 33

examples/README.md

@@ -1,5 +1,5 @@
-# Examples of use of nfdi4chem_michi
+# Examples of use of michi
 
-This folder contains example data conforming to nfdi4chem_michi
+This folder contains example data conforming to michi
 
 The source for these is in [src/data](../src/data/examples)

mkdocs.yml

@@ -1,5 +1,5 @@
 ---
-site_name: "NFDI4Chem MIChI"
+site_name: "MICHI"
 theme:
   name: material
   # palette:
@@ -10,6 +10,8 @@ theme:
 plugins:
   - search
   - mermaid2
+  - mermaid2:
+      version: 10.9.0
 nav:
   # - Home: home.md
   - Index: index.md