Merge pull request #500 from ReproNim/release-prep

preparation for release 1.0.0

.flake8

@@ -1,4 +1,2 @@
 [flake8]
 max-line-length=79
-exclude =
-    scripts/editProperties.py

.github/workflows/publishdocs.yaml

@@ -12,6 +12,19 @@ jobs:
       - name: Checkout
         uses: actions/checkout@v4
 
+      - name: Set up Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: 3.9
+
+      - name: Install the required python packages
+        run: python -m pip install linkml
+
+      - name: Generating docs
+        run: |
+          gen-doc -d docs/schema/doc-linkml-autogen linkml-schema/reproschema.yaml
+          gen-erdiagram linkml-schema/reproschema.yaml > docs/schema/erdiagram-autogen.md
+
       - name: Deploy docs
         uses: mhausenblas/mkdocs-deploy-gh-pages@master
         env:

.github/workflows/validate_and_release.yml

@@ -72,7 +72,6 @@ jobs:
         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
         uses: peter-evans/create-pull-request@v6

.gitignore

@@ -6,8 +6,12 @@ __pycache__
 
 .idea/
 
-node_modules
 local_data
 
+# ignore linkml auto generated doc
+docs/schema/doc-linkml-autogen
+docs/schema/erdiagram-autogen.md
+
+node_modules
 package-lock.json
 package.json

.pre-commit-config.yaml

@@ -7,6 +7,11 @@ repos:
     -   id: trailing-whitespace
     -   id: end-of-file-fixer
     -   id: check-yaml
+        exclude: |
+            (?x)^(
+                docs/specification/.*
+                | mkdocs.yml
+            )$
     -   id: check-json
     -   id: check-ast
     -   id: check-added-large-files

README.md

@@ -19,37 +19,49 @@ This repository contains:
 - a example of [a protocol based on the reproschema](./examples)
 - the [documentation](./docs)
 
+## Developing ReproSchema
 
-## Licenses
+### Updating the schema
 
-### Code
+As of release 1.0.0, a linked data modeling language, [LinkML](https://linkml.io/linkml/), is used to create
+a [YAML file](linkml-schema/reproschema.yaml) with the schema.
 
-The content of this repository is distributed under the [Apache 2.0 license](./LICENSE).
+The [context file](contexts/reproschema) was automatically generated using LinkML,
+and then manually curated in order to support all the reproschema feature.
 
-### Documentation
+#### Style
 
-<a rel="license" href="http://creativecommons.org/licenses/by/4.0/"><img alt="Creative Commons License" style="border-width:0" src="https://i.creativecommons.org/l/by/4.0/88x31.png" /></a><br />The corresponding documentation is licensed under a <a rel="license" href="http://creativecommons.org/licenses/by/4.0/">Creative Commons Attribution 4.0 International License</a>.
+This repo uses pre-commit to check styling.
+- Install pre-commit with pip: `pip install pre-commit`
+- In order to use it with the repository, you have to run `run pre-commit install` in the root directory the first time you use it.
 
-## Contributors
 
-https://github.com/ReproNim/reproschema/graphs/contributors
+### Release
+Upon release, there are additional formats, `jsonsld`, `turtle`, `n-triples`
+and `pydantic` that are created using `LinkML` tools, `reproschema-py`,
+and [reproschema-specific script](./scripts/fix_pydantic.py) to "fix" the `pydantic` format.
+The entire process is automated in the GitHub Action Workflow:
+[Validate and Release](.github/workflows/validate_and_release.yml).
+This workflow must be manually triggered by the core developers once a new release is ready.
+All the releases can be found in [releases directory](./releases).
+
+### Updating model in reproschema-py
+Another GitHub Action Workflow: [ Create Pull Request to reproschema-py](.github/workflows/push_reproschema_py.yml)
+is responsible for creating pull request to the `reproschema-py` Python library with
+the new version of pydantic model and context.
+The workflow is currently also triggered manually by the core developers.
 
-### Developer notes
-To run the Python scripts in the scripts directory, you will need to install the
-following libraries via pip
 
-- reproschema (makeRelease.py)
-- pytablewriter (editProperties.py)
+## Licenses
+
+### Code
 
-To make a new release:
+The content of this repository is distributed under the [Apache 2.0 license](./LICENSE).
 
-```bash
-python scripts/makeRelease.py <version>
-python scripts/editProperties.py <version>
-```
+### Documentation
 
-In addition, this repo uses pre-commit to check styling.
+<a rel="license" href="http://creativecommons.org/licenses/by/4.0/"><img alt="Creative Commons License" style="border-width:0" src="https://i.creativecommons.org/l/by/4.0/88x31.png" /></a><br />The corresponding documentation is licensed under a <a rel="license" href="http://creativecommons.org/licenses/by/4.0/">Creative Commons Attribution 4.0 International License</a>.
 
-Install: `pip install pre-commit`
+## Contributors
 
-Use: run `pre-commit install` in the root directory of the repo.
+https://github.com/ReproNim/reproschema/graphs/contributors

docs/index.md

@@ -17,7 +17,7 @@ things are to use the ReproSchema but some "big picture" conceptual understandin
 could save you from a lot of confusion. 😉
 
 -   Not sure how the project is organized? Check out the [project structure](./project-structure.md) page.
--   Want more details on how the `Reproschema` itself is structured: check out our [schema page](./schema.md)
+-   Want more details on how the `Reproschema` itself is structured: check out our [schema page](./schema/schema.md)
 
 <!-- - If you want to use the schema to create your own questionnaire: check out our
 

docs/project-structure.md

@@ -37,7 +37,7 @@ The ReproSchema is like a blueprint for research projects, ensuring everyone col
 
 There is also an [`example`](https://github.com/ReproNim/reproschema/tree/master/examples)
 schema that can help give you a quick overview of what the protocol and activity
-for a study might look like. For more details see the [schema section](./schema.md).
+for a study might look like. For more details see the [schema section](./schema/schema.md).
 
 ## [reproschema-library](https://github.com/ReproNim/reproschema-library)