Ghislain Vaillant

Provide a pre-commit hook for `hatch fmt`

4

I am using Hatch for project management in my Python projects, and recently adopted `hatch fmt` instead of directly calling Ruff previously. I also use `pre-commit` in my CI workflows...

Provide better documentation for SPM standalone setup

10

### Discussed in https://github.com/aramis-lab/clinica/discussions/819 Originally posted by **AudreyDuran** November 28, 2022 Hi, I am trying to run `t1-volume` pipeline with SPM12 standalone and clinica v0.7.2, on a custom dataset. Here...

Build failures on Windows for conda-forge package

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**When did the error occur?** [ ] CMake configuration (cmake / ccmake) [x] Compilation (make) [ ] Installation (make install) **Build environment** - OS: Windows - Type of system: conda-forge...

TypeError: Cannot coerce {'mandatory': True} into <class 'str'>

5

This snippet used to work with version 0.22: ```python from pydra.engine import Worflow from pydra.engine.specs import BaseSpec, SpecInfo input_spec = SpecInfo(name="Input", fields=[("T1w", str, {"mandatory": True})], bases=(BaseSpec,)) workflow = Workflow(name="foo", input_spec=input_spec)...

TypeError: TypeParser doesn't know how to handle args ((<class 'pathlib.Path'>, <class 'NoneType'>)) for <class 'types.UnionType'>

3

The following task definition: ```python @task @annotate({"return": {"smoothed_image": Path}}) def smooth_image(input_image: Path, smoothed_image: Path | None) -> Path: ... ``` triggers an error: `TypeError: TypeParser doesn't know how to handle...

FileNotFoundError triggered when running a task with a splitter

15

I defined and ran the following workflow: ```python from pathlib import Path from pydra import Submitter, Workflow from pydra.mark import annotate, task # Producer of T1w images @task @annotate({"return": {"t1w_images":...

WIP: Static checking with mypy

2

*Work in progress* See methodology [here](https://mypy.readthedocs.io/en/stable/existing_code.html#introduce-stricter-options).

Shortcut for equal-separated option value pairs

1

Certain CLI parsers, such as FSL's Eddy, implement a rigid formulation where only equal-separated options (`--long-option=value`) are accepted and space-separated ones (`--long-option value`) are rejected. Pydra implements space-separated options, which...

AttributeError: 'Input' object has no attribute 'files_hash' with split and combine

4

I am trying to split a simple workflow consisting of 3 sequential steps (bias correction, registration and resampling) on multiple T1w images in a BIDS dataset. The code is provided...