Merge branch 'main' into doc

.flake8

@@ -0,0 +1,4 @@
+[flake8]
+max-line-length=79
+exclude =
+    scripts/editProperties.py

.github/workflows/validate_and_release.yml

@@ -46,12 +46,32 @@ jobs:
       uses: actions/setup-python@v5
       with:
         python-version: 3.12
-
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip setuptools
+        pip install linkml astor pre-commit
+        pip install git+https://github.com/ReproNim/reproschema-py.git
+    - name: Generate pydantic  using linml and fixing it with reproschema specific script
+      run: |
+        gen-pydantic --pydantic-version 2 linkml-schema/reproschema.yaml > reproschema_model.py
+        python scripts/fix_pydantic.py reproschema_model.py
+        pre-commit run --files reproschema_model.py || true
+    - name: Generate jsonld format using linkml
+      run: |
+        gen-jsonld --context https://raw.githubusercontent.com/ReproNim/reproschema/main/contexts/reproschema linkml-schema/reproschema.yaml > reproschema.jsonld
+    - name: Generate n-triples and turtle formats using reproschema
+      run: |
+        reproschema convert --format n-triples reproschema.jsonld > reproschema.nt
+        reproschema convert --format turtle reproschema.jsonld > reproschema.ttl
     - name: Make a release
       run: |
         echo "Making a release ${{ inputs.version }}"
         mkdir releases/${{ inputs.version }}
-        cp contexts/reproschema releases/${{ inputs.version }}/base
+        cp contexts/reproschema releases/${{ inputs.version }}/reproschema
+        mv reproschema_model.py releases/${{ inputs.version }}/reproschema_model.py
+        mv reproschema.jsonld releases/${{ inputs.version }}/reproschema.jsonld
+        mv reproschema.nt releases/${{ inputs.version }}/reproschema.nt
+        mv reproschema.ttl releases/${{ inputs.version }}/reproschema.ttl
     #     python scripts/makeRelease.py ${{ inputs.version }}
 
     -   name: Open pull requests to add files

.gitmodules

@@ -0,0 +1,4 @@
+[submodule "library"]
+	path = library
+	url = https://github.com/ReproNim/reproschema-library.git
+	datalad-url = https://github.com/ReproNim/reproschema-library.git

.pre-commit-config.yaml

@@ -11,11 +11,29 @@ repos:
     -   id: check-ast
     -   id: check-added-large-files
     -   id: check-merge-conflict
+
+# Sorts Python imports alphabetically and by section with `isort`.
+-   repo: https://github.com/pycqa/isort
+    rev: 5.13.2
+    hooks:
+    -   id: isort
+        args: [--settings-path, pyproject.toml]
+
 -   repo: https://github.com/psf/black
     rev: 24.3.0
     hooks:
     -   id: black
+
 -   repo: https://github.com/codespell-project/codespell
     rev: v2.2.6
     hooks:
     -   id: codespell
+        args: [--toml, pyproject.toml]
+        additional_dependencies: [tomli]
+
+-   repo: https://github.com/pyCQA/flake8
+    rev: 7.1.0
+    hooks:
+    -   id: flake8
+        args: [--config, .flake8, --verbose]
+        additional_dependencies: [flake8-bugbear]

docs/FAQ.md

@@ -40,7 +40,6 @@ you can explore them on [schema.repronim.org/](https://schema.repronim.org/rl/).
 
 The ReproSchema is also used to develop a checklist to [improve methods and results reporting in neuroimaging](https://github.com/ohbm/cobidas).
 
-
 ## Linked data and semantic web
 
 ## What is the semantic web?

docs/library.md

@@ -0,0 +1,14 @@
+---
+hide:
+    - toc
+---
+# Reproschema library
+
+At the moment, all the assessments that support this standard are listed in [this folder](https://github.com/ReproNim/reproschema-library/tree/master/activities) of the [reproschema-library repository](https://github.com/ReproNim/reproschema-library).
+
+For convenience we are listing them in the table below.
+
+If you want to see those different tools in action using our user interface,
+you can explore them on [schema.repronim.org/](https://schema.repronim.org/rl/).
+
+{{ MACROS___library_table() }}

docs/project-structure.md

@@ -51,8 +51,7 @@ questionnaire for your next participant or patient. Also you can mix and match
 items from this library, knowing that the information is tracked in your protocol.
 
 All assessments are listed in [the `activity` folder](https://github.com/ReproNim/reproschema-library/tree/master/activities)
-and are served [here](https://schema.repronim.org/rl/) if you want to visualize
-them.
+and are served [here](https://schema.repronim.org/rl/) if you want to visualize them.
 
 -   **Standard Alignment:** Each element in the library aligns with the ReproSchema framework, ensuring uniformity in terms and structure and upholding validation protocols for consistency across the ecosystem.
 -   **Research Protocol Integration:** Researchers can utilize these assessments in various combinations to align with specific protocol needs, customizing their application per study objectives. This process can be integrated using the reproschema-protocol-cookiecutter for constructing user interfaces.

linkml-schema/reproschema.yaml

@@ -55,7 +55,7 @@ slots:
     slot_uri: schema:associatedMedia
   audio:
     title: audio
-    description: TODO
+    description: An audio object.
     slot_uri: schema:audio
     any_of:
     - range: uri
@@ -101,12 +101,8 @@ slots:
   contentUrl:
     slot_uri: schema:contentUrl
     range: uriorcurie
-  creator:
-    slot_uri: schema:creator
-    range: Person
   cronTable:
     title: cronTable
-    description: TODO not described in reproschema
     slot_uri: reproschema:cronTable
   datumType:
     title: datumType
@@ -264,7 +260,7 @@ slots:
     range: OverrideProperty
   preamble:
     title: Preamble
-    description: The preamble for an assessment
+    description: The preamble for an assessment.
     slot_uri: reproschema:preamble
     multivalued: true
     range: langString
@@ -326,7 +322,7 @@ slots:
     range: datetime
     slot_uri: prov:startedAtTime
   subject_id:
-    slot_uri: nidm:subject_id #TODO check this @type:rdf:Property
+    slot_uri: nidm:subject_id
     range: string
   ui:
     title: UI
@@ -502,7 +498,7 @@ classes:
     class_uri: rdf:langString
   MediaObject:
     title: Media Object
-    description: Add description #TODO
+    description: A media object, such as an image, video, audio, or text object embedded in a web page or a downloadable dataset.
     is_a: Thing
     class_uri: schema:MediaObject
     slots:
@@ -542,7 +538,7 @@ classes:
       - id
       - subject_id
     class_uri: reproschema:Participant
-  Protocol: # TODO multiple types
+  Protocol:
     title: Protocol
     description: A representation of a study which comprises one or more assessments.
     is_a: Thing
@@ -555,6 +551,7 @@ classes:
     - description
     - landingPage
     - messages
+    - preamble
     - prefLabel
     - schemaVersion
     - ui
@@ -596,7 +593,7 @@ classes:
     - unitOptions
     - valueType
     class_uri: reproschema:ResponseOption
-  SoftwareAgent: # TODO multiple types
+  SoftwareAgent:
     title: Software Agent
     description:
       Captures information about some action that took place. It also links to information
@@ -616,9 +613,8 @@ classes:
       - category
     class_uri: schema:Thing
   UI:
-    title: todo
-    description:
-    - todo
+    title: UI properties
+    description: A group of properties related to UI.
     slots:
       - order
       - addProperties

macros/__init__.py

@@ -0,0 +1,9 @@
+from .macros import (
+    library_table,
+)
+from .main import define_env
+
+__all__ = [
+    "define_env",
+    "library_table",
+]