Merge branch 'main' into issue120-just

.github/workflows/codespell.yml

@@ -20,3 +20,5 @@ jobs:
         uses: actions/checkout@v3
       - name: Codespell
         uses: codespell-project/actions-codespell@v2
+        with:
+          skip: '*.js'

README.md

@@ -18,20 +18,20 @@ The following are required and recommended tools for using this cookiecutter and
 
   * **Poetry**
 
-    Poetry is a Python project management tool. You will use it in your generated project to manage dependencies and build distribution files. If you have pipx installed you can install Poetry by running: 
+    Poetry is a Python project management tool. You will use it in your generated project to manage dependencies and build distribution files. If you have pipx installed ([alternative installation methods](https://python-poetry.org/docs/#installation) are available) you can install Poetry by running:
      ```shell
      pipx install poetry
      ```
-     For other installation methods see: https://python-poetry.org/docs/#installation
 
-  * **Poetry behind firewalls**
+    This project manages project-level configuration. User-level [configuration](https://python-poetry.org/docs/configuration/), if needed, is your responsibility.
 
-    In sandboxed environments (proxy or internal repositories), you must configure poetry source in `~/.config/pypoetry/pyproject.toml` to allow software installation, illustrated below:
+  * **Poetry private repository**
+
+    Sandboxed environments have private pypi repositories. Poetry supports project-level [repository](https://python-poetry.org/docs/repositories/), but it is recommended to configure [this plugin](https://pypi.org/project/poetry-plugin-pypi-mirror) to persist repository across all poetry projects (and avoid cookiecutter failure):
     ```shell
-    [[tool.poetry.source]]
-    name = "myproxy"
-    url = "https://repo.example.com/repository/pypi-all/simple"
-    priority = "default"
+    pip3 install poetry-plugin-pypi-mirror --user
+    # example, add line to `~/.profile` for persistence
+    export POETRY_PYPI_MIRROR_URL = "https://pypi-proxy.myorg.com/repository/pypi-all/simple"
     ```
 
   * **Poetry Dynamic Versioning Plugin**: 
@@ -121,11 +121,6 @@ Optionally customize your project if needed:
 
 * pass arguments to linkml generators via 'config.yaml' configuration file;
 * pass supported environment variables via '.env.public' configuration file;
-* configure proxy server via project configuration file (as illustrated):
-  ```bash
-  git init
-  poetry source add --priority=default myproxy https://repo.example.com/repository/pypi-all/simple
-  ```
 
 Setup your project
 ```bash

cookiecutter.json

@@ -17,5 +17,9 @@
     "google_sheet_id": "1wVoaiFg47aT9YWNeRfTZ8tYHN8s8PAuDx5i2HUcDpvQ",
     "google_sheet_tabs": "personinfo enums",
     "__google_sheet_module": "{{ cookiecutter.google_sheet_tabs|lower()|replace(' ', '_')|replace('-', '_') }}",
-    "github_token_for_pypi_deployment": "PYPI_PASSWORD"
+    "github_token_for_pypi_deployment": "PYPI_PASSWORD",
+    "_copy_without_render": [
+        "src/docs/js/*",
+        "src/docs/javascript/*"
+    ]
 }

{{cookiecutter.project_name}}/.gitignore

@@ -1,7 +1,7 @@
 /docs/
 /project/docs/
 /tmp/
-
+.idea/  # PyCharm files
 # Byte-compiled / optimized / DLL files
 __pycache__/
 *.py[cod]

{{cookiecutter.project_name}}/mkdocs.yml

@@ -9,6 +9,9 @@ theme:
     - content.tabs.link
 plugins:
   - search
+  - mermaid2
+  - mknotebooks:
+      execute: false
   - mermaid2:
       version: 11.4.1
       # if you want/have to use a local copy of the mermaid.js library, uncomment the next line

{{cookiecutter.project_name}}/pyproject.toml

@@ -21,6 +21,8 @@ linkml = "^1.3.5"
 mkdocs-material = "^8.2.8"
 mkdocs-mermaid2-plugin = "^1.1.1"
 schemasheets = "^0.1.14"
+jupyter = "^1.0.0"
+mknotebooks = "*"
 
 [build-system]
 requires = ["poetry-core>=1.0.0", "poetry-dynamic-versioning"]