Sprint improvements (#29)

irm-codebase · web-flow · commit 0fb095f4f2f1 · 2025-07-28T12:46:57.000+02:00
* sync pixi.toml

* remove mkdocs files

* Integration test a single core

* lint main workflow and integration workflow

* tell mypy to ignore .pixi and .snakemake folders

* Ensure json 2012 draft compatibility

* Add example of local file inclusion to main snakefile

* Ignore pixi environment folder
diff --git a/.github/workflows/template-pr-ci.yml b/.github/workflows/template-pr-ci.yml
@@ -22,7 +22,9 @@ jobs:
         continue-on-error: true
       - name: Run snakemake linting
         id: linting
-        run: pixi run snakemake --lint
+        run: |
+          pixi run snakemake --lint --snakefile workflow/Snakefile
+          pixi run snakemake --lint --snakefile tests/integration/Snakefile
         continue-on-error: true
       - name: Save integration logs
         if: ${{ always() }}
diff --git a/README.md b/README.md
@@ -47,7 +47,8 @@ We recommend using [`pixi`](https://pixi.sh/) as your package manager. Once inst
 
 ## Features
 
-- Standardised layout compliant with the [snakemake workflow catalogue's](https://snakemake.github.io/snakemake-workflow-catalog/#) listing requirements.
+- 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.
@@ -56,7 +57,6 @@ We recommend using [`pixi`](https://pixi.sh/) as your package manager. Once inst
   - 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.
-- Documentation setup, ready for [Read the Docs](https://about.readthedocs.com/) or [Github Pages](https://pages.github.com/).
 
 > [!IMPORTANT]
 >
diff --git a/copier.yaml b/copier.yaml
@@ -30,8 +30,7 @@ _skip_if_exists:
   - AUTHORS
   - CITATION.cff
   - INTERFACE.yaml
-  - mkdocs.yaml
-  - pixi.toml
+  # Special cases: these files should not be user-modified, even though they are in user-modifiable directories
   - "!config/README.md"
   - "!tests/clio_test.py"
 _templates_suffix: .jinja
diff --git a/mypy.ini b/mypy.ini
@@ -1,2 +1,3 @@
 [mypy]
 disable_error_code = import-untyped
+exclude = (^|/)\.(snakemake|pixi)(/|$)
diff --git a/template/.gitignore.jinja b/template/.gitignore.jinja
@@ -11,6 +11,9 @@
 __pycache__
 *.pyc
 
+### Environments
+.pixi/
+
 ### Snakemake
 .snakemake/
 gurobi.log
diff --git a/template/.readthedocs.yaml b/template/.readthedocs.yaml
diff --git a/template/mkdocs.yaml.jinja b/template/mkdocs.yaml.jinja
diff --git a/template/mypy.ini.jinja b/template/mypy.ini.jinja
@@ -1,2 +1,3 @@
 [mypy]
 disable_error_code = import-untyped
+exclude = (^|/)\.(snakemake|pixi)(/|$)
diff --git a/template/pixi.toml.jinja b/template/pixi.toml.jinja
@@ -13,6 +13,7 @@ clio-tools = ">=2025.03.03"
 conda = ">=25.0.0"
 ipdb = ">=0.13.13"
 ipykernel = ">=6.29.5"
+jsonschema = ">=4.0.0"
 mypy = ">=1.15.0"
 pytest = ">=8.3.5"
 python = ">=3.12"
@@ -22,16 +23,3 @@ snakemake-minimal = ">=8.29.0"
 
 [tasks]
 test-integration = {cmd = "pytest tests/clio_test.py"}
-
-[feature.docs.dependencies]
-mkdocs-material = ">=9.6.7"
-
-[feature.docs.pypi-dependencies]
-mkdocs-mermaid2-plugin = ">=1.2.1"
-
-[feature.docs.tasks]
-serve-docs = {cmd = "mkdocs serve"}
-build-docs = {cmd = "mkdocs build"}
-
-[environments]
-docs = ["docs"]
diff --git a/template/tests/clio_test.py.jinja b/template/tests/clio_test.py.jinja
@@ -40,15 +40,15 @@ def test_standard_file_existance(module_path, file):
 def test_snakemake_all_failure(module_path):
     """The snakemake 'all' rule should return an error by default."""
     process = subprocess.run(
-        "snakemake --cores 4", shell=True, cwd=module_path, capture_output=True
+        "snakemake --cores 1", shell=True, cwd=module_path, capture_output=True
     )
     assert "INVALID (missing locally)" in str(process.stderr)
 
 
 def test_snakemake_integration_testing(module_path):
     """Run a light-weight test simulating someone using this module."""
     assert subprocess.run(
-        "snakemake --use-conda --cores 4",
+        "snakemake --use-conda --cores 1",
         shell=True,
         check=True,
         cwd=module_path / "tests/integration",
diff --git a/template/workflow/Snakefile b/template/workflow/Snakefile
@@ -21,6 +21,10 @@ with open(workflow.source_path("internal/settings.yaml"), "r") as f:
 include: "rules/automatic.smk"
 include: "rules/dummy.smk"
 
+# Add additional files to be delivered alongside the workflow here.
+# This is needed e.g. for python code files that are never
+# explicitly used as a script or input in a snakemake rule.
+# e.g.: workflow.source_path("scripts/_utils.py")
 
 rule all:
     message:
diff --git a/tests/template_test.py b/tests/template_test.py
@@ -35,11 +35,6 @@ def pixi_built(template_project):
     return template_project
 
 
-def test_mkdocs_build(pixi_built):
-    """The template's mkdocs should build without issues."""
-    assert subprocess.run("pixi run build-docs", shell=True, check=True, cwd=pixi_built)
-
-
 def test_pytest(pixi_built):
     """The template's tests should pass by default."""
     assert subprocess.run(

Original file line number	Diff line number	Diff line change
`@@ -1,2 +1,3 @@`
`1`	`1`	`[mypy]`
`2`	`2`	`disable_error_code = import-untyped`
	`3`	`+exclude = (^\|/)\.(snakemake\|pixi)(/\|$)`