Feature modelblocks (#45)

* Move to modelblocks
* Linting upgrades
* pathvars implementation

---------

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Co-authored-by: Stefan Pfenninger-Lee <stefan@pfenninger.org>

Author: 3 people

.github/ISSUE_TEMPLATE/bug_report.md

@@ -24,7 +24,7 @@ A clear and concise description of what you expected to happen.
 If applicable, add screenshots to help explain your problem.
 
 **Desktop (please complete the following information):**
- - OS: [e.g. Linux Fedora 41, Windows 10...]
+ - OS: [e.g. Linux Fedora 43, Windows 11...]
  - Version [e.g. v0.1.1]
 
 **Additional context**

.github/workflows/template-check-version.yml

@@ -49,6 +49,6 @@ jobs:
         run: |
           gh issue --repo ${{ github.repository }} \
           create --title "Template update" \
-          --body "A new version of the template has been published. Please update this project using \`copier update --skip-answered --defaults\` and review changes. If you need help, refer to the \`clio\` documentation or reach out to the calliope project team."
+          --body "A new version of the template has been published. Please update this project using \`copier update --skip-answered --defaults\` and review changes. If you need help, refer to the Modelblocks documentation or reach out to the project team."
         env:
           GH_TOKEN: ${{ secrets.GITHUB_TOKEN }}

.github/workflows/template-pr-ci.yml

@@ -12,6 +12,7 @@ repos:
       # Repo quality
       - id: check-added-large-files
         args: [--enforce-all]
+        exclude: ^pixi\.lock$
       - id: forbid-submodules
       - id: check-case-conflict
       - id: check-illegal-windows-names
@@ -37,4 +38,4 @@ repos:
     - id: codespell
 
 ci:  # https://pre-commit.ci/
-  autoupdate_schedule: monthly
+  autoupdate_schedule: quarterly

.pre-commit-config.yaml

@@ -2,6 +2,6 @@ This is the list of contributors for copyright purposes.
 
 This does not necessarily list everyone who has contributed to this software's
 code or documentation. For a full contributor list, see:
-<https://github.com/calliope-project/data-module-template/graphs/contributors>
+<https://github.com/modelblocks-org/data-module-template/graphs/contributors>
 
 Ivan Ruiz Manuel, TU Delft <i.ruizmanuel@tudelft.nl>

AUTHORS

@@ -3,8 +3,8 @@
 # https://citation-file-format.github.io/
 cff-version: 1.2.0
 message: If you use this software or data produced by it, please cite it using the metadata from this file.
-title: clio - data module template
-repository: https://github.com/calliope-project/data-module-template
+title: Modelblocks - data module template
+repository: https://github.com/modelblocks-org/data-module-template
 license: Apache-2.0
 authors:
   - given-names: Ivan

CITATION.cff

@@ -1,18 +1,48 @@
-# Data module template
+# Modelblocks data module template
 
-A template for modular data workflows using [`snakemake`](https://snakemake.readthedocs.io/en/stable/), part of the [`clio`](https://clio.readthedocs.io/) toolset.
+A template for modular data workflows using [`snakemake`](https://snakemake.readthedocs.io/en/stable/) workflows, part of the [Modelblocks](https://www.modelblocks.org/) toolset.
+
+> [!TIP]
+> Looking for general information on Modelblocks?
+> Check the [Modelblocks](https://www.modelblocks.org/) website and our [documentation and guidelines](https://modelblocks.readthedocs.io/en).
 
 ## Resources
 
-To familiarise yourself with `clio` data modules:
+To familiarise yourself with Modelblocks data modules:
 
 - Check the auto-generated minimal example. You can find it in `tests/integration/Snakefile`.
-- Read about the `clio` approach in [our documentation](https://clio.readthedocs.io/).
 - Read about `snakemake` modularisation in [their documentation](https://snakemake.readthedocs.io/en/stable/snakefiles/modularization.html#modules).
 
+## Features
+
+- Standardised layout compliant with the [snakemake workflow catalogue's](https://snakemake.github.io/snakemake-workflow-catalog/#) listing requirements, enabling them to be automatically included in their listings once published. Read more about those requirements [here](https://snakemake.github.io/snakemake-workflow-catalog/docs/catalog.html#standardized-usage-workflows).
+- Standardised input-output structure across modules:
+  - `resources/`: files needed for the module's processes.
+    - `user/`: files that should be provided by users. Document them well!
+    - `automatic/`: files that the module downloads or prepares in intermediate steps.
+  - `results/`: files generated by the module's algorithms that are relevant to the user.
+- Pre-made integration setup for your module.
+  - Continuous Integration (CI) settings, ready for [pre-commit.ci](https://pre-commit.ci/).
+  - GitHub actions to automate chores during pull requests and releases.
+  - Premade `pytest` setup.
+
+> [!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 (e.g., calling the `all:` rule) may not work, as the module may not have the necessary `resources/` to execute properly.
+> - **Please be sure to maintain the following files to ensure Modelblocks compatibility**
+>   - `INTERFACE.yaml`: a simple description of the module's input/output structure.
+>   - `config/config.yaml`: a basic functioning example of how to configure this module.
+>   - `workflow/internal/config.schema.yaml`: the module's configuration schema, used by `snakemake` for [validation](https://snakemake.readthedocs.io/en/stable/snakefiles/configuration.html).
+>   - `AUTHORS` / `CITATION.cff` / `LICENSE`: licensing and attribution of this module's code and methods.
+
+
 ## How to use this template
 
-We recommend using [`pixi`](https://pixi.sh/) as your package manager. Once installed, do the following:
+We require [`pixi`](https://pixi.sh/) as a package manager. Once installed, do the following:
 
 1. Install the templater tool [`copier`](https://copier.readthedocs.io/en/stable/).
 
@@ -25,16 +55,17 @@ We recommend using [`pixi`](https://pixi.sh/) as your package manager. Once inst
    We recommend you use the module name as the directory name.
 
    ```shell
-   copier copy https://github.com/calliope-project/data-module-template.git ./path/to/<module_name>
+   copier copy https://github.com/modelblocks-org/data-module-template.git ./<module_name>
    ```
 
-   If your terminal does not have access to `copier` then you may need to update your `PATH` variable to include `~/.pixi/bin`.
+   > [!TIP]
+   > If your terminal does not have access to `copier` then you may need to update your `PATH` variable to include `~/.pixi/bin`.
 
 3. Answer some questions so can we pre-fill licensing, citation files, etc...
 4. Initialise the `pixi` project environment of your new module.
 
    ```shell
-   cd ./path/to/<module_name> # navigate to the new project
+   cd ./<module_name> # navigate to the new project
    pixi install --all  # install the project environment
    ```
 
@@ -44,30 +75,3 @@ We recommend using [`pixi`](https://pixi.sh/) as your package manager. Once inst
    cd tests/integration  # go to the integration test...
    pixi run snakemake --use-conda  # run it!
    ```
-
-## Features
-
-- Standardised layout compliant with the [snakemake workflow catalogue's](https://snakemake.github.io/snakemake-workflow-catalog/#) listing requirements, enabling them to be automatically included in their listings once published. Read more about those requirements [here](https://snakemake.github.io/snakemake-workflow-catalog/docs/catalog.html#standardized-usage-workflows).
-- Standardised input/output structure across modules:
-  - `resources/`: files needed for the module's processes.
-    - `user/`: files that should be provided by users. Document them well!
-    - `automatic/`: files that the module downloads or prepares in intermediate steps.
-  - `results/`: files generated by the module's algorithms that are relevant to the user.
-- Pre-made integration setup for your module.
-  - Continuous Integration (CI) settings, ready for [pre-commit.ci](https://pre-commit.ci/).
-  - GitHub actions to automate chores during pull requests and releases.
-  - Premade `pytest` setup.
-
-> [!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 (e.g., calling the `all:` rule) may not work, as the module may not have the necessary `resources/` to execute properly.
-> - **Please be sure to maintain the following files to ensure `clio` compatibility**
->   - These are:
->     - `INTERFACE.yaml`: a simple description of the module's input/output structure.
->     - `config/config.yaml`: a basic functioning example of how to configure this module.
->     - `workflow/internal/config.schema.yaml`: the module's configuration schema, used by `snakemake` for [validation](https://snakemake.readthedocs.io/en/stable/snakefiles/configuration.html).
->     - `AUTHORS` / `CITATION.cff` / `LICENSE`: licensing and attribution of this module's code and methods.

README.md

@@ -21,8 +21,8 @@ _exclude:
 _skip_if_exists:
   # Respect user changes, except for a few standard files.
   - config/**
-  - docs/**
   - resources/**
+  - figures/**
   - results/**
   - tests/**
   - workflow/**
@@ -32,7 +32,7 @@ _skip_if_exists:
   - INTERFACE.yaml
   # Special cases: these files should not be user-modified, even though they are in user-modifiable directories
   - "!config/README.md"
-  - "!tests/clio_test.py"
+  - "!tests/integration_test.py"
 _templates_suffix: .jinja
 _answers_file: .copier-answers.yml
 
@@ -67,12 +67,12 @@ github_org:
   type: str
   help: >-
     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').
+    this module will be created (e.g., 'modelblocks-org' in 'github.com/modelblocks-org').
   validator: >-
     {% 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"
+  default: "modelblocks-org"
 license:
   type: str
   help: "Please choose a license."

copier.yaml

@@ -1,3 +1,4 @@
 [mypy]
 disable_error_code = import-untyped
 exclude = (^|/)\.(snakemake|pixi)(/|$)
+exclude_gitignore = True