Merge remote-tracking branch 'origin/pre-commit-ci-update-config' into pre-commit-ci-update-config

Author: tobiasraabe

.github/workflows/publish-to-pypi.yml

@@ -67,7 +67,7 @@ jobs:
         name: python-package-distributions
         path: dist/
     - name: Sign the dists with Sigstore
-      uses: sigstore/gh-action-sigstore-python@v3.0.0
+      uses: sigstore/gh-action-sigstore-python@v3.0.1
       with:
         inputs: >-
           ./dist/*.tar.gz

.pre-commit-config.yaml

@@ -28,7 +28,7 @@ repos:
     -   id: python-no-log-warn
     -   id: text-unicode-replacement-char
 -   repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.12.0
+    rev: v0.12.4
     hooks:
       - id: ruff-format
       - id: ruff

CHANGELOG.md

@@ -5,6 +5,11 @@ chronological order. Releases follow [semantic versioning](https://semver.org/)
 releases are available on [PyPI](https://pypi.org/project/pytask) and
 [Anaconda.org](https://anaconda.org/conda-forge/pytask).
 
+## 0.5.5 - 2025-07-25
+
+- {pull}`692` documents how to use pytask with workspaces.
+- {pull}`694` fixes {issue}`693` so that missing dependencies are detected in some cases. Thanks to {user}`timmens` for the report!
+
 ## 0.5.4 - 2025-06-08
 
 - {pull}`676` ensures compatibility with click >8.2.0.

docs/source/how_to_guides/bp_structure_of_a_research_project.md

@@ -23,6 +23,10 @@ As an example, look at two repositories from a COVID-19 forecasting project.
 - [sid](https://github.com/covid-19-impact-lab/sid) contains the code for the
   epidemiological model which is applied in the research project.
 
+```{seealso}
+Nowadays, consider using [workspaces](using_workspaces.md) instead of separate repositories.
+```
+
 Separating the model code from the research project provided several benefits.
 
 - The model code is isolated and has its own test suite. Assessing and ensuring the code

docs/source/how_to_guides/index.md

@@ -23,6 +23,7 @@ provisional_nodes_and_task_generators
 writing_custom_nodes
 extending_pytask
 the_data_catalog
+using_workspaces
 ```
 
 ## Best Practice Guides

docs/source/how_to_guides/using_workspaces.md

@@ -0,0 +1,52 @@
+# Using workspaces
+
+There are situations where you want to structure your project as a multi-package
+workspace. Reasons are
+
+- You are developing a scientific package alongside the project that you want to publish
+  later.
+- The code for dealing with the dataset should be reused in other projects.
+- You want to strictly separate the pytask tasks from the remaining code to be able to
+  switch to another build system.
+
+In those instances, a workspace might be the right choice.
+
+```text
+project
+├── packages
+│   ├── data
+│   │   ├── pyproject.toml
+│   │   └── src
+│   │       └── data
+│   │           ├── __init__.py
+│   │           └── ...
+│   ├── analysis
+│   │   ├── pyproject.toml
+│   │   └── src
+│   │       └── analysis
+│   │           ├── __init__.py
+│   │           └── ...
+│   └── tasks
+│       ├── pyproject.toml
+│       └── src
+│           └── tasks
+│               ├── __init__.py
+│               └── ...
+│
+├── pyproject.toml
+├── README.md
+├── ...
+```
+
+## Using workspaces with uv
+
+uv provides excellent support for workspaces which you can read more about in the
+[uv documentation](https://docs.astral.sh/uv/concepts/projects/workspaces).
+
+## Using workspaces with pixi
+
+pixi is still working on a native workspace experience, but there are workarounds.
+
+- [https://pixi.sh/latest/build/workspace/](https://pixi.sh/latest/build/workspace/)
+- [https://github.com/prefix-dev/pixi/discussions/387](https://github.com/prefix-dev/pixi/discussions/387)
+- [https://github.com/Andre-Medina/python-pixi-mono-template](https://github.com/Andre-Medina/python-pixi-mono-template)

docs/source/tutorials/set_up_a_project.md

@@ -6,6 +6,12 @@ tutorial explains the minimal setup.
 If you want to use pytask with a collection of scripts, you can skip this lesson and
 move to the next section of the tutorials.
 
+```{seealso}
+In case you are thinking about developing multiple packages in the project that should be separated (one for dealing with the data, one for the analysis and a package for the pytask tasks), consider using a [workspace](../how_to_guides/using_workspaces.md).
+```
+
+## The directory structure
+
 The following directory tree gives an overview of the project's different parts.
 
 ```text
@@ -83,6 +89,10 @@ version = "0.1.0"
 requires-python = ">=3.9"
 dependencies = ["pytask"]
 
+[build-system]
+requires = ["uv_build"]
+build-backend = "uv_build"
+
 [tool.pytask.ini_options]
 paths = ["src/my_project"]
 ```
@@ -104,6 +114,10 @@ requires-python = ">=3.9"
 channels = ["conda-forge"]
 platforms = ["linux-64", "osx-64", "osx-arm64", "win-64"]
 
+[build-system]
+requires = ["hatchling"]
+build-backend = "hatchling.build"
+
 [dependencies]
 pytask = "*"
 python = ">=3.9"
@@ -120,16 +134,16 @@ paths = ["src/my_project"]
 Create a `pyproject.toml` file for project configuration:
 
 ```toml
-[build-system]
-requires = ["hatchling"]
-build-backend = "hatchling.build"
-
 [project]
 name = "my_project"
 version = "0.1.0"
 requires-python = ">=3.9"
 dependencies = ["pytask"]
 
+[build-system]
+requires = ["hatchling"]
+build-backend = "hatchling.build"
+
 [tool.pytask.ini_options]
 paths = ["src/my_project"]
 ```
@@ -162,15 +176,15 @@ dependencies:
 And a `pyproject.toml` file for project configuration:
 
 ```toml
-[build-system]
-requires = ["hatchling"]
-build-backend = "hatchling.build"
-
 [project]
 name = "my_project"
 version = "0.1.0"
 requires-python = ">=3.9"
 
+[build-system]
+requires = ["hatchling"]
+build-backend = "hatchling"
+
 [tool.pytask.ini_options]
 paths = ["src/my_project"]
 ```

src/_pytask/execute.py

@@ -162,7 +162,6 @@ def pytask_execute_task_setup(session: Session, task: PTask) -> None:  # noqa: C
             has_changed = has_node_changed(task=task, node=node, state=node_state)
             if has_changed:
                 needs_to_be_executed = True
-                break
 
     if not needs_to_be_executed:
         collect_provisional_products(session, task)

tests/test_execute.py

@@ -637,6 +637,9 @@ def task2() -> None: pass
     assert result.exit_code == ExitCode.OK
 
 
+@pytest.mark.xfail(
+    sys.platform == "linux" and sys.version_info[:2] == (3, 9), reason="flakey"
+)
 def test_pytask_on_a_module_that_uses_the_functional_api(tmp_path):
     source = """
     from pytask import task, ExitCode, build