Please release `pydot` 2.x for Python 3.13

[mr-c]

cwltool needs a pre-3.0 version due to backwards incompatible changes that there are still no upstream fixes for common-workflow-language/cwltool#2019 (comment)

conda-forge/cwltool-feedstock#166

[leycec]

I am not @ferdnyc, but I can say that packaging older versions of pure-Python packages for conda-forge is... non-trivial. Anyone who wants to try doing that should definitely read this first.

It's not impossible – but it's sufficiently non-trivial that it might never happen. It would probably be preferable for either:

• PyDot to simply be fixed. Fix pydot tests common-workflow-language/cwltool#2019 looks suspiciously like a PyDot bug, honestly.
• cwltool to monkey-patch what PyDot is doing. A simple regex would suffice to strip the double quotes from erroneous strings like file:"///<your_path>/three_step_color.cwl#string_output" into valid strings like file:///<your_path>/three_step_color.cwl#string_output.

It is what it is. 😭

[ferdnyc]

I added some commentary at common-workflow-language/cwltool#2019 (comment) -- but what I can say is that if Pydot 3.x is doing something wrong, certainly we'll fix it. But the fact that it's doing something different is consistent with the fact that it's a major version increment, which permits incompatible changes.

The way Pydot is being used by cwltool may need to be adjusted, and I'm happy to help sort out what changes may need to be made. But unless Pydot 3.x's behavior is incorrect (which is not the same thing as "doesn't match 2.x behavior" or "doesn't output what cwltool expects based on 2.x"), it's unlikely the behavior will be "fixed" back to a more-broken state.

[ferdnyc]

Obligatory xkcd 😉

[ferdnyc]

common-workflow-language/cwltool#2019 has now been merged, am I correct in thinking that means cwltool can now use Pydot 3.x instead of having to pin it at version 2.0? Which in turn means that this request is no longer needed?