Add --version to every entry point

[JAlvarezJarreta]

It turns out Python's argument parser has a quick workaround for this, so it was pretty quick to update all our entry points.

[vsitnik]

why not a single entry point instead?

[JAlvarezJarreta]

why not a single entry point instead?

I felt this was more the standard approach for every tool we use, even for tool suites such as bcftools. When checking how this should be done for Python libraries, the official answers are either use the python -c "import ..." approach we already have, or get it via pip, and both have their issues, as we know.

It is also only adding two lines of code, and we could even reduce it to one if we move the logic into ensembl.utils. Happy with what the majority decides, as I have no strong feelings for any solution.

[ens-LCampbell]

Looks good to me, thanks Jorge. Tested some entry points too and looks fine !

[ens-LCampbell]

Side note, is there currently way quick way to list or find all genomio entry points available ? Would it be useful to add such a functionality and a single entry point cmd to list all (+ maybe add current library version as well) ?

[JAlvarezJarreta]

Side note, is there currently way quick way to list or find all genomio entry points available ? Would it be useful to add such a functionality and a single entry point cmd to list all (+ maybe add current library version as well) ?

The only way I can think of is looking at pyproject.toml. After some digging, there is a programmatic way to obtain them in Python:

from importlib.metadata import entry_points
genomio_scripts = [
    script.name for script in entry_points(group='console_scripts') if script.module.startswith("ensembl.io.genomio")
]
print("\n".join(genomio_scripts))

What I have found more frequently is that every entry point has its entry in the documentation. Something we should consider if we want to avoid having the auxiliary script you are mentioning (or have both).

[Dishalodha]

Looks good, a nice way of using version with the parser