refactor: modo -> modos [BREAKING] (#10)

* refactor: modo -> modos [BREAKING]

* chore: regen

* fix: missing refactors

* chore(deps): update poetry lock

CONTRIBUTING.md

@@ -1,9 +1,9 @@
-# Contributing to modo-schema
+# Contributing to modos-schema
 
 :+1: First of all: Thank you for taking the time to contribute!
 
 The following is a set of guidelines for contributing to
-modo-schema. These guidelines are not strict rules.
+modos-schema. 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 modo-schema team strives to create a
+The modos-schema team strives to create a
 welcoming environment for editors, users and other contributors.
 Please carefully read our [Code of Conduct](CODE_OF_CONDUCT.md).
 
@@ -70,7 +70,7 @@ 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 modo-schema technical leads
+    - PRs should be reviewed and merged in a timely fashion by the modos-schema 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
@@ -112,7 +112,7 @@ 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/sdsc-ordes/modo-schema/issues/
-[pulls]: https://github.com/sdsc-ordes/modo-schema/pulls/
+[issues]: https://github.com/sdsc-ordes/modos-schema/issues/
+[pulls]: https://github.com/sdsc-ordes/modos-schema/pulls/
 
 We recommend also reading [GitHub Pull Requests: 10 Tips to Know](https://blog.mergify.com/github-pull-requests-10-tips-to-know/)

Makefile

@@ -132,7 +132,7 @@ examples/%.ttl: src/data/examples/%.yaml
 
 test-examples: examples/output
 
-examples/output: src/modo_schema/schema/modo_schema.yaml
+examples/output: src/modos_schema/schema/modos_schema.yaml
 	mkdir -p $@
 	$(RUN) linkml-run-examples \
 		--output-formats json \

NOTICE

@@ -1,4 +1,4 @@
-modo-schema
+modos-schema
 Copyright 2024 - Swiss Data Science Center (SDSC)
 A partnership between École Polytechnique Fédérale de Lausanne (EPFL) and
 Eidgenössische Technische Hochschule Zürich (ETHZ).

README.md

@@ -1,6 +1,6 @@
-# modo-schema
+# modos-schema
 
-Metadata schema for the SMOC Multi-Omics Digital Object.
+Metadata schema for the SMOC Multi-Omics Digital Object System.
 
 ```mermaid
 erDiagram
@@ -70,17 +70,17 @@ ReferenceGenome ||--}o ReferenceSequence : "has_sequence"
 
 ## Website
 
-[https://sdsc-ordes.github.io/modo-schema](https://sdsc-ordes.github.io/modo-schema)
+[https://sdsc-ordes.github.io/modos-schema](https://sdsc-ordes.github.io/modos-schema)
 
 ## Repository Structure
 
 * [examples/](examples/) - example data
 * [project/](project/) - project files (do not edit these)
 * [src/](src/) - source files (edit these)
-  * [modo_schema](src/modo_schema)
-    * [schema](src/modo_schema/schema) -- LinkML schema
+  * [modos_schema](src/modos_schema)
+    * [schema](src/modos_schema/schema) -- LinkML schema
       (edit this)
-    * [datamodel](src/modo_schema/datamodel) -- generated
+    * [datamodel](src/modos_schema/datamodel) -- generated
       Python datamodel
 * [tests/](tests/) - Python tests
 

about.yaml

@@ -1,5 +1,5 @@
 ---
-name: modo_schema
+name: modos_schema
 author: SDSC-ORD
-description: Metadata schema for the SMOC Multi-Omics Digital Object
-source_schema_path: src/modo_schema/schema/modo_schema.yaml
+description: Metadata schema for the SMOC Multi-Omics Digital Object System
+source_schema_path: src/modos_schema/schema/modos_schema.yaml

examples/README.md

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

mkdocs.yml

@@ -1,5 +1,5 @@
 ---
-site_name: "modo-schema"
+site_name: "modos-schema"
 theme:
   name: material
   # palette:
@@ -14,8 +14,8 @@ nav:
   # - Home: home.md
   - Index: index.md
   - About: about.md
-site_url: https://sdsc-ordes.github.io/modo-schema
-repo_url: https://github.com/sdsc-ordes/modo-schema
+site_url: https://sdsc-ordes.github.io/modos-schema
+repo_url: https://github.com/sdsc-ordes/modos-schema
 
 # Uncomment this block to enable use of Google Analytics.
 # Replace the property value with your own ID.