Merge branch 'main' into main

Author: yibeichan

.gitignore

@@ -135,7 +135,6 @@ dmypy.json
 # Pycharm
 .idea/
 
-# Serena IDE configuration
 .serena/
 
 # Internal documentation

.pre-commit-config.yaml

@@ -6,7 +6,7 @@ exclude: ".*\\.csv$"
 
 repos:
 -   repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v5.0.0
+    rev: v6.0.0
     hooks:
     -   id: trailing-whitespace
     -   id: end-of-file-fixer
@@ -35,7 +35,7 @@ repos:
 
 # Format TOML files
 -   repo: https://github.com/macisamuele/language-formatters-pre-commit-hooks
-    rev: v2.14.0
+    rev: v2.15.0
     hooks:
     -   id: pretty-format-toml
         args: [--autofix, --indent, '4']
@@ -47,7 +47,7 @@ repos:
 # flake8-functions checks functions quality: https://pypi.org/project/flake8-functions/
 # flake8-bugbear detects some common bugs: https://github.com/PyCQA/flake8-bugbear
 -   repo: https://github.com/pyCQA/flake8
-    rev: 7.1.2
+    rev: 7.3.0
     hooks:
     -   id: flake8
         args: [--config, .flake8, --verbose, reproschema]

README.md

@@ -19,6 +19,11 @@ git clone https://github.com/<your github>/reproschema-py.git
 cd reproschema-py
 pip install -e .
 ```
+#### Notes on the reproschema model
+This repository uses the `pydantic` representation of the `reproschema` model, defined in [model.py](https://github.com/ReproNim/reproschema-py/blob/main/reproschema/models/model.py).
+The `pydantic` model is automatically generated from the LinkML model maintained in the [ReproNim/reproschema repository](https://github.com/ReproNim/reproschema).
+**All changes to the model should be made in the LinkML source in that repository.**
+
 #### Style
 This repo uses pre-commit to check styling.
 - Install pre-commit with pip: `pip install pre-commit`