Toots for cthoyt@scholar.social account

Written by Charles Tapley Hoyt on 2025-01-31 at 10:40

every time I run mypy and wait for it to finish, I wonder if 2025 will be the year of a red knot announcement/release from @charliermarsh and Astral

I already have a placeholder issue on my cookiecutter template repo: https://github.com/cthoyt/cookiecutter-snekpack/issues/12

[#]python #typing #typeannotations #mypy #ruff #uv

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Written by Charles Tapley Hoyt on 2025-01-28 at 14:33

@ORCID_Org your sign-in workflow with Google hasn't been working for me for a few days

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Written by Charles Tapley Hoyt on 2025-01-27 at 15:51

thank you @petrichor for helping with my PR on @pandoc 🙏

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Written by Charles Tapley Hoyt on 2025-01-18 at 11:25

@opencitations is there a PMID-PMID dump available yet?

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Written by Charles Tapley Hoyt on 2024-11-28 at 16:21

Earlier this week, I made small but meaningful PR to an open source project I use daily, but actually doesn't have much code churn. I put a lot of effort to write a good and descriptive issue, and a readable diff for the PR itself.

It got merged a day later, and the maintainer invited me to stop by for some nice drinks if I'm ever in their neighborhood in the Italian Alps.

This is how open source should look ^

[#]opensource #github #python

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Written by Charles Tapley Hoyt on 2024-11-14 at 19:59

I'm trying to use mypy inside tox with tox-uv, but mypy's --install-types flag hardcodes the usage of pip. When you're using tox-uv, pip is no longer installed in the environment because uv does the heavy lifting with uv pip install as a faster alternative to pip install

Here's my attempt at making mypy more configurable so it can install types using uv:

https://github.com/python/mypy/compare/master...cthoyt:mypy:uv-installer

[#]python #packaging #typing #uv #mypy #tox #virtualenv

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Written by Charles Tapley Hoyt on 2024-11-05 at 08:09

Finally got my Python cookiecutter template to use uv instead of twine in https://github.com/cthoyt/cookiecutter-snekpack/pull/35!

I also upgraded it to use keyring instead of the .pypirc file, which is much more secure

Now, all that's left is to wait for Astral to finish their build backend to replace setuptools, and my packages will have a full uv stack 🌞

[#]python #packaging #uv #astral

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Written by Charles Tapley Hoyt on 2024-11-02 at 14:19

Does anyone know if @readthedocs is working towards supporting PEP-0735 dependency groups?

I'm still using extra_requirements in my readthedocs.yml (c.f., https://docs.readthedocs.io/en/stable/config-file/v2.html#packages) but want to switch over for my documentation requirements!

[#]python #packaging

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Written by Charles Tapley Hoyt on 2024-10-17 at 15:56

"people write down [database] migrations but those are lies" - Scott

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Written by Charles Tapley Hoyt on 2024-10-16 at 10:31

Every time an external contributor makes a PR to a curation project that requires an explanation of how to fix it, that's an opportunity to write more curation guides.

[#]openscience #opendata #opencode #biocuration

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Written by Charles Tapley Hoyt on 2024-10-11 at 14:17

also what does it say that there are so many authors on this list and none of them ever asked, does this work?

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Written by Charles Tapley Hoyt on 2024-10-11 at 11:46

the idea in https://www.nature.com/articles/s43856-024-00625-5 is interesting, but the code (https://doi.org/10.5522/04/25541392.v1) can't be rerun

At least they posted it. It's a start, but it's the same as a recipe for a cookbook that tells you to add in some secret spices, and you're wondering "which ones?"

[#]reproducibilitycrisis #incentivescrisis

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Written by Charles Tapley Hoyt on 2024-10-09 at 14:47

excited for uv to replace setuptools following https://github.com/astral-sh/uv/pull/7901 and https://github.com/astral-sh/uv/pull/7976

ty @charliermarsh and crew. Does Astral have a mastodon handle?

[#]uv #packaging #python #pythonuv

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Written by Charles Tapley Hoyt on 2024-09-25 at 19:59

things aren't going well. Haskell is winning.

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Written by Charles Tapley Hoyt on 2024-09-25 at 16:57

uv adds a "publish" command, adding twine to the list of tools it supersedes

https://github.com/astral-sh/uv/pull/7475

[#]python #tooling #packaging

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Written by Charles Tapley Hoyt on 2024-09-24 at 17:01

learned some Lua to contribute to @joss. Now learning Haskell to contribute upstream to @pandoc 🙃

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Written by Charles Tapley Hoyt on 2024-09-17 at 10:09

@egonw @wikipathways it seems like https://new.wikipathways.org/academy/ is down, is there a new link for the tutorial?

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Written by Charles Tapley Hoyt on 2024-09-13 at 17:24

@dr_greg_landrum how would you feel about a PR to https://github.com/greglandrum/rdkit-blog that applies ruff to format all the Python code in the notebooks?

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Written by Charles Tapley Hoyt on 2024-09-11 at 10:05

@typst I am super excited to use you, but there is a total deluge of ugly templates. It would be great if you provided some high quality ones for us to get started with.

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Written by Charles Tapley Hoyt on 2024-09-04 at 21:19

The @ResearchOrgs integration I mentioned I was writing for @joss in https://scholar.social/@cthoyt/113028131169285000 is now merged!

You can now add a ror key in the affiliations list 🦁

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