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Pin Python 3.13 in the conda environment - #209
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Python 3.14.8 (#205) cannot be installed on a machine without a C compiler: hdmf-zarr==0.13.0 requires numcodecs<0.16, numcodecs 0.15.1 ships no Python 3.14 wheel, so pip compiles it from source, and that source does not build with a current GCC either (its bundled c-blosc defines `bool` via typedef, which C23 rejects). CI only passes because GitHub-hosted runners have an older gcc. Pin the newest Python 3.13 instead (3.13.16 on conda-forge for linux-64, osx-arm64, osx-64 and win-64); every dependency has wheels for it. Python 3.14 can come back together with hdmf-zarr 0.14 / zarr 3, which allow numcodecs 0.17 and its 3.14 wheels. Co-Authored-By: Claude Fable 5.1 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01ToiYPiSdU8NM9h1UmLgsq8
CodyCBakerPhD
marked this pull request as ready for review
October 7, 2026 18:01
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@rly Yeah IDK I'm then having problems with 3.14 and latest HDMF-Zarr + numcodecs maybe we can agree on this (3.13)? |
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I forgot about the numcodecs issue. Yes let's do 3.13 |
rly
approved these changes
Oct 7, 2026
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|
Thanks for investigating! |
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Problem
Since #205 the environment file pins
python=3.14.8together withhdmf-zarr==0.13.0. hdmf-zarr 0.13.0 requiresnumcodecs<0.16, and numcodecs 0.15.1 ships no Python 3.14 wheel, soconda env createmakes pip compile it from source. On a machine without a C compiler that fails:With a current GCC it fails too: the bundled c-blosc in numcodecs 0.15.1 declares
typedef _Bool bool;, which C23 (GCC 15+ default) rejects, so it only builds with-std=gnu17. CI here passes only because GitHub-hosted runners carry an older gcc.This surfaced on the first self-hosted benchmark runner (CodyCBakerPhD/nwb-benchmarks-runner, run 37646509500).
Change
python=3.14.8→python=3.13.16, the newest 3.13 on conda-forge for linux-64, osx-arm64, osx-64 and win-64. Every dependency has wheels for 3.13, so no compiler is needed anywhere.pyproject.tomlkeepsrequires-python = ">=3.10,<3.15".Python 3.14 can come back together with hdmf-zarr 0.14 (zarr 3), which allows numcodecs 0.17 and its 3.14 wheels.
🤖 Generated with Claude Code
https://claude.ai/code/session_01ToiYPiSdU8NM9h1UmLgsq8
Generated by Claude Code