PR fixes: no pixi shell use, remove unused mkdocs plugin, fix github …

…username

README.md

@@ -37,9 +37,7 @@ We recommend using [`pixi`](https://pixi.sh/) as your package manager. Once inst
 5. Extra: run the auto-generated example module!
 
     ```shell
-    pixi shell    # activate your project's environment
-    cd tests/integration/  # navigate to the integration example...
-    snakemake --use-conda  # run the example!
+    pixi run snakemake --snakefile=tests/integration/Snakefile --use-conda
     ```
 
 ## Features
@@ -54,14 +52,15 @@ We recommend using [`pixi`](https://pixi.sh/) as your package manager. Once inst
     - Premade `pytest` setup.
 - Auto-generated documentation, ready for [Read the Docs](https://about.readthedocs.com/).
 
-## IMPORTANT
-
-A few things to be aware of.
-
-- **Modules do not work like regular snakemake workflows**
-    - The primary way to test them should be external (calling `module:`, passing resources, and requesting results). Check the pre-made example in `tests/integration` for more info.
-    - Internal access (calling the `all:` rule) will not work, as the module will not have the necessary `resources/` to execute properly.
-- **Please respect the 'specification' section of the documentation**
-    - `docs/hooks/clio_standard.py` will auto-generate documentation for you as long as certain files (e.g., `INTERFACE.yaml`, `CITATION.yaml`) are filled correctly.
-    - Please **do not modify this file** to ensure all data modules have a similar 'specification' section.
-    - If you wish to extend the documentation, feel free to add other sections.
+> [!IMPORTANT]
+>
+> A few things to be aware of.
+>
+> - **Modules do not work like regular snakemake workflows**
+>     - The primary way to test them should be external (calling `module:`, passing resources, and requesting results). Check the pre-made example in `tests/integration` for more info.
+>     - Internal access (calling the `all:` rule) will not work, as the module will not have the necessary `resources/` to execute properly.
+> - **Please respect the 'specification' section of the documentation**
+>     - `docs/hooks/clio_standard.py` will auto-generate documentation for you as long as certain files (e.g., `INTERFACE.yaml`, `CITATION.yaml`) are filled correctly.
+>     - Please **do not modify this file** to ensure all data modules have a similar 'specification' section.
+>     - If you wish to extend the documentation, feel free to add other sections.
+>

copier.yaml

@@ -50,7 +50,7 @@ github_org:
     Please provide the name of the github account or organisation where
     this module will be created (e.g., 'calliope-project' in 'github.com/calliope-project').
   validator: >-
-    {% if not (github_org | regex_search('^[a-z][a-z0-9_-]*$')) %}
+    {% if not (github_org | regex_search('^[a-zA-Z0-9][a-zA-Z0-9-]*$')) %}
     "Only lowercase letters, digits, hyphens and underscores are valid."
     {% endif %}
   default: "calliope-project"

template/{{ module_short_name }}/mkdocs.yaml.jinja

@@ -42,8 +42,6 @@ theme:
       accent: pink
 markdown_extensions:
   - admonition
-  - pymdownx.tasklist:
-      custom_checkbox: true
   - pymdownx.arithmatex:
       generic: true
   - pymdownx.betterem:

template/{{ module_short_name }}/tests/clio_test.py.jinja

@@ -1,4 +1,8 @@
-"""Set of standard clio tests."""
+"""Set of standard clio tests.
+
+DO NOT MANUALLY MODIFY THIS FILE!
+It should be updated through our templating functions.
+"""
 
 import subprocess
 from pathlib import Path

template/{{ module_short_name }}/workflow/Snakefile

@@ -6,7 +6,7 @@ min_version("8.10")
 
 
 # Load the example configuration. This will be overridden by users.
-configfile: "config/example.yaml"
+configfile: workflow.source_path("config/example.yaml")
 
 
 # Validate the configuration using the schema file.