Add CLI for spatialdata_io.

[migueLib]

There was an initial commit done by @FloWuenne in the PR #72.

The commit will add :

• CLI for each of the readers to convert to SpatialData object.
• CLI for to convert generic formats to .zarr.

This commit should close issue #238 and #231 (? @LLehner, @LucaMarconato, @quentinblampey )
This commit is co-authored by: @chiarasch

[codecov-commenter]

Codecov Report

❌ Patch coverage is 85.60000% with 36 lines in your changes missing coverage. Please review.
✅ Project coverage is 50.41%. Comparing base (c4f6cf7) to head (fe30019).
⚠️ Report is 189 commits behind head on main.

Files with missing lines	Patch %	Lines
src/spatialdata_io/__main__.py	85.87%	25 Missing ⚠️
src/spatialdata_io/converters/generic_to_zarr.py	75.00%	7 Missing ⚠️
src/spatialdata_io/readers/generic.py	88.57%	4 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #239      +/-   ##
==========================================
+ Coverage   43.68%   50.41%   +6.72%     
==========================================
  Files          23       26       +3     
  Lines        2353     2644     +291     
==========================================
+ Hits         1028     1333     +305     
+ Misses       1325     1311      -14     

Files with missing lines	Coverage Δ
src/spatialdata_io/__init__.py	100.00% <100.00%> (ø)
src/spatialdata_io/experimental/__init__.py	100.00% <100.00%> (ø)
src/spatialdata_io/readers/generic.py	88.57% <88.57%> (ø)
src/spatialdata_io/converters/generic_to_zarr.py	75.00% <75.00%> (ø)
src/spatialdata_io/__main__.py	85.87% <85.87%> (ø)

... and 2 files with indirect coverage changes

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[migueLib]

Forgot to mention @melonora

[quentinblampey]

Hi, thanks again for the PR, nice work!
I made a review, but it will still need to be also reviewed by Luca

[LucaMarconato]

Thanks again @migueLib @chiarasch @LLehner @FloWuenne @quentinblampey.

I applied the changes suggested from @quentinblampey's code review and reviewed the code myself. I have:

• done some refactoring in the function to read generic files (and a bit on the CLI)
• updated the CLIs to reflect the new parameters used in visium_hd, seqfish and by adding the new macsima reader
• I added tests for the CLI, for the generic data types, and for those readers that already had a tests (Xenium, Seqfish, Macsima)
• I added a CLI section in the docs using (sphinx-click)

[LucaMarconato]

One comment:

• for the future I would consider exploring a semi-automatic way to generate the CLI and help message from existing functions and their docstrings. I could not find any click API or library that does it for click. But together with AI I made this draft. One big caveat. I don't know if this will play around nicely with sphinx-click (automatic generation of the documentation for the CLI).

import click
import inspect


def auto_click(func):
    # Get the function's signature
    sig = inspect.signature(func)

    # Create a Click command decorator
    @click.command(help=func.__doc__)
    # Add Click options based on the function's parameters
    def wrapper(*args, **kwargs):
        return func(*args, **kwargs)

    for name, param in sig.parameters.items():
        # Determine the Click option type
        param_type = (
            click.INT if param.annotation == int else
            click.FLOAT if param.annotation == float else
            click.BOOL if param.annotation == bool else
            click.STRING
        )

        # Add the option to the wrapper
        wrapper = click.option(
            f"--{name.replace('_', '-')}",
            default=param.default if param.default is not inspect.Parameter.empty else None,
            type=param_type,
            show_default=True,
            help=f"{param.name} (type: {param.annotation.__name__})"
        )(wrapper)

    return wrapper


# Example function
@auto_click
def example_function(param1: int = 10, param2: str = "default"):
    """Example function docstring."""
    print(f"param1: {param1}, param2: {param2}")


if __name__ == "__main__":
    example_function()

Starting from this we could consider simplify the code and in this way reduce the maintenance burden (otherwise every time we modify/add/remove readers, or change their docstrings, we need to manually update the CLI).

Anyway, it's very good to have a working version for all techs that we can merge already. Thanks again!

[LucaMarconato]

@HelenaLC we are going to merge this soon (I promised you I would have tagged you when the CLI would have been ready and documented). CC @vjcitn