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• ran brew update and can still reproduce the problem?
• ran brew doctor, fixed all issues and can still reproduce the problem?
• ran brew gist-logs <formula> (where <formula> is the name of the formula that failed) and included the output link?
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To help us debug your issue please explain:

• What you were trying to do (and why)
• What happened (include command output)
• What you expected to happen
• Step-by-step reproduction instructions (by running brew install commands)

Here's a script which reproduces my problem:

#!/usr/bin/env bash
set -euxo pipefail

brew install python

rm -rf venv bin

BREW_PYTHON="/usr/local/bin/python3"
VENV="${PWD}/venv"
EXE="${VENV}/bin/python"

: make a virtualenv to have a separate python executable that acts normal
curl --silent https://asottile.github.io/get-virtualenv.py |
    "${BREW_PYTHON}" - "${VENV}" >& /dev/null

: write a small script which just prints what executable it ran from
mkdir bin
echo -e '#!'"${EXE}\nimport sys;print(sys.executable)" > bin/t
chmod +x bin/t

export PATH="${PWD}/bin:${PATH}"

: normal invocation of 't' works
test "$(t)" = "${EXE}"

: running t from a python subprocess is different though?
test "$(/usr/local/opt/python/libexec/bin/python -c 'import subprocess; subprocess.call(("t",))')" = "${EXE}"

Despite my script bin/t having a full shebang (here's what it ends up looking like):

#!/tmp/t/venv/bin/python
import sys;print(sys.executable)

When run as a subprocess from brew's python it is reporting an executable which is entirely different from the one being used.

I suspect this is due to this

Here's the output on my machine (script returns 1)

$ bash test.sh
+ brew install python
Updating Homebrew...
==> Auto-updated Homebrew!
Updated 1 tap (homebrew/cask).
No changes to formulae.

Warning: python 3.7.0 is already installed and up-to-date
To reinstall 3.7.0, run `brew reinstall python`
+ rm -rf venv bin
+ BREW_PYTHON=/usr/local/bin/python3
+ VENV=/tmp/t/venv
+ EXE=/tmp/t/venv/bin/python
+ : make a virtualenv to have a separate python executable that acts normal
+ curl --silent https://asottile.github.io/get-virtualenv.py
+ /usr/local/bin/python3 - /tmp/t/venv
+ : write a small script which just prints what executable it ran from
+ mkdir bin
+ echo -e '#!/tmp/t/venv/bin/python\nimport sys;print(sys.executable)'
+ chmod +x bin/t
+ export 'PATH=/tmp/t/bin:/Users/asottile/.cargo/bin:/Users/asottile/bin:/usr/local/opt/findutils/libexec/gnubin:/usr/local/opt/coreutils/libexec/gnubin:/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/Applications/VMware Fusion.app/Contents/Public'
+ PATH='/tmp/t/bin:/Users/asottile/.cargo/bin:/Users/asottile/bin:/usr/local/opt/findutils/libexec/gnubin:/usr/local/opt/coreutils/libexec/gnubin:/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/Applications/VMware Fusion.app/Contents/Public'
+ : normal invocation of t works
++ t
+ test /tmp/t/venv/bin/python = /tmp/t/venv/bin/python
+ : running t from a python subprocess is different 'though?'
++ /usr/local/opt/python/libexec/bin/python -c 'import subprocess; subprocess.call(("t",))'
+ test /usr/local/Cellar/python/3.7.0/libexec/bin/python = /tmp/t/venv/bin/python