I did a macOS 14.7 Sonoma clean install on an external SSD and pyenv-virtualenv is behaving normally, without any delays.

At least on my platform, macOS Sequoia has a huge issue with some shell programs.

I recommend to postpone the Sequoia upgrade until this is fixed on macOS side.

I encountered this same problem yesterday on my Intel Mac running macOS 14.7 (Sonoma) when I updated from Xcode 15.3 to Xcode 16. I presume that your fresh install of macOS 15 (Sequoia) had Xcode 16, and I'd be curious to see whether downgrading only Xcode without downgrading the OS would solve the problem. I'm also curious about whether this is a problem only on Intel Macs or if it's a problem on Apple Silicon as well.

I noticed a variety of pyenv and pyenv-virtualenv commands being much slower, and I was able to figure out that the command pyenv sh-activate --quiet command run in the shell hook was taking most of the time when I hit "Enter" on a blank line. I ran the following command to help test out the problem:

time env -i bash -cx 'export PYENV_DEBUG=1; command pyenv sh-activate --quiet'

With Xcode 16, the command takes over 10 s to execute, while with Xcode 15.3, the command takes ~0.3 s to execute.

I can help with debugging the problem because I can't delay upgrading Xcode indefinitely. However, I have no clue how to profile shell scripts. If anyone has tooling recommendations, I can hopefully figure out exactly where the regression is happening.

However, I have no clue how to profile shell scripts.

#259 (comment):

Try localizing the issue by timing the code that runs at prompt with:

export PS4='+($(date "+%s.%N")) (${BASH_SOURCE:-}:${LINENO}): ${FUNCNAME[0]:+${FUNCNAME[0]}(): }'
set -x
<reproduce the problem>
set +x

Also add the same date invocation to PS4 assignments throughout Pyenv and Pyenv-Virtualenv and set PYENV_DEBUG=1

I forgot to mention this, but I switched to an Apple silicon laptop a week or two after encountering this issue, and I had no problems using Xcode 16 on it. I think this regression is purely for Intel Mac users.

Someone else is obviously free to debug this, but I'm not going to spend the time debugging it myself.