`--no-pre-install-wheels --requirements-pex .. --layout packed` gives `[Errno 21] Is a directory: '.../.deps/....whl'` errors

[huonw]

It seems pex emits "Is a directory" errors referring to wheels for invocations that use all three of --requirements-pex ... --no-pre-install-wheels --layout packed.

For instance:

curl -OLs https://github.com/pex-tool/pex/releases/download/v2.2.2/pex
chmod +x ./pex

./pex cowsay==6.1 -o reqs.pex
./pex --layout packed --no-pre-install-wheels --requirements-pex reqs.pex -o output.pex

Output:

[Errno 21] Is a directory: '/private/var/folders/sv/vd266m4d4lvctgs2wpnhjs9w0000gn/T/tmp4032w10a/.deps/cowsay-6.1-py3-none-any.whl'

Output with PEX_VERBOSE=1 on second invocation

pex: Laying out PEX zipfile /Users/huon/tmp/pex-loose-no-pre-install/pex: 0.1ms
pex: Executing installed PEX for /Users/huon/tmp/pex-loose-no-pre-install/./pex at /Users/huon/.pex/unzipped_pexes/ad5d02c39f095829e9578f565f825d0835bfcd73
pex:   Testing /Users/huon/.pyenv/versions/3.10.4/bin/python3.10 can resolve PEX at /Users/huon/.pex/unzipped_pexes/ad5d02c39f095829e9578f565f825d0835bfcd73: 2.8ms
pex: Using the current interpreter /Users/huon/.pyenv/versions/3.10.4/bin/python since it matches constraints and PYTHONPATH is not set.
pex: Discarding site packages path: /Users/huon/.pyenv/versions/3.10.4/lib/python3.10/site-packages
pex: Tainted path element: /Users/huon/.pyenv/versions/3.10.4/lib/python3.10/site-packages
pex: Scrubbing from user site: /Users/huon/.local/lib/python3.10/site-packages
pex: Scrubbing from site-packages: /Users/huon/.pyenv/versions/3.10.4/lib/python3.10/site-packages
pex: New sys.path: ['/Users/huon/.pex/unzipped_pexes/ad5d02c39f095829e9578f565f825d0835bfcd73/.bootstrap/pex/vendor/_vendored/attrs', '/Users/huon/.pex/unzipped_pexes/ad5d02c39f095829e9578f565f825d0835bfcd73/.bootstrap', '/Users/huon/.pex/unzipped_pexes/ad5d02c39f095829e9578f565f825d0835bfcd73', '/Users/huon/.pyenv/versions/3.10.4/lib/python310.zip', '/Users/huon/.pyenv/versions/3.10.4/lib/python3.10', '/Users/huon/.pyenv/versions/3.10.4/lib/python3.10/lib-dynload']
pex: Activating PEX virtual environment from /Users/huon/.pex/unzipped_pexes/ad5d02c39f095829e9578f565f825d0835bfcd73: 0.2ms
pex: Bootstrap complete, performing final sys.path modifications...
pex: PYTHONPATH contains:
pex:     /Users/huon/.pex/unzipped_pexes/ad5d02c39f095829e9578f565f825d0835bfcd73
pex:   * /Users/huon/.pyenv/versions/3.10.4/lib/python310.zip
pex:     /Users/huon/.pyenv/versions/3.10.4/lib/python3.10
pex:     /Users/huon/.pyenv/versions/3.10.4/lib/python3.10/lib-dynload
pex:     /Users/huon/.pex/installed_wheels/5f30587359f5364bfbab6d6f902d7418fc7ef9e81e0d6329781a775d3a189b97/pex-2.2.2-py2.py3-none-any.whl
pex:     /Users/huon/.pex/unzipped_pexes/ad5d02c39f095829e9578f565f825d0835bfcd73/.bootstrap
pex:   * - paths that do not exist or will be imported via zipimport
pex: Building pex: 3.4ms                         
pex:   Adding distributions from pexes: reqs.pex: 2.5ms
pex:     Laying out PEX zipfile reqs.pex: 0.1ms
pex:   Resolving distributions for requirements: : 0.1ms
pex:     Resolving requirements.: 0.1ms
pex:   Configuring PEX dependencies: 0.2ms
Previous binary unexpectedly exists, cleaning: output.pex
pex: Zipping PEX .bootstrap/ code.: 0.0ms
Traceback (most recent call last):
  File "/Users/huon/.pex/installed_wheels/5f30587359f5364bfbab6d6f902d7418fc7ef9e81e0d6329781a775d3a189b97/pex-2.2.2-py2.py3-none-any.whl/pex/common.py", line 111, in safe_copy
    os.link(source, dest)
PermissionError: [Errno 1] Operation not permitted: '/private/var/folders/sv/vd266m4d4lvctgs2wpnhjs9w0000gn/T/tmp970ao6ze/.deps/cowsay-6.1-py3-none-any.whl' -> 'output.pex~/.deps/cowsay-6.1-py3-none-any.whl'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/Users/huon/.pex/installed_wheels/5f30587359f5364bfbab6d6f902d7418fc7ef9e81e0d6329781a775d3a189b97/pex-2.2.2-py2.py3-none-any.whl/pex/result.py", line 105, in catch
    return func(*args, **kwargs)
  File "/Users/huon/.pex/installed_wheels/5f30587359f5364bfbab6d6f902d7418fc7ef9e81e0d6329781a775d3a189b97/pex-2.2.2-py2.py3-none-any.whl/pex/bin/pex.py", line 1072, in do_main
    pex_builder.build(
  File "/Users/huon/.pex/installed_wheels/5f30587359f5364bfbab6d6f902d7418fc7ef9e81e0d6329781a775d3a189b97/pex-2.2.2-py2.py3-none-any.whl/pex/pex_builder.py", line 739, in build
    self._build_packedapp(
  File "/Users/huon/.pex/installed_wheels/5f30587359f5364bfbab6d6f902d7418fc7ef9e81e0d6329781a775d3a189b97/pex-2.2.2-py2.py3-none-any.whl/pex/pex_builder.py", line 844, in _build_packedapp
    safe_copy(os.path.join(self._chroot.chroot, path), dest)
  File "/Users/huon/.pex/installed_wheels/5f30587359f5364bfbab6d6f902d7418fc7ef9e81e0d6329781a775d3a189b97/pex-2.2.2-py2.py3-none-any.whl/pex/common.py", line 129, in safe_copy
    do_copy()
  File "/Users/huon/.pex/installed_wheels/5f30587359f5364bfbab6d6f902d7418fc7ef9e81e0d6329781a775d3a189b97/pex-2.2.2-py2.py3-none-any.whl/pex/common.py", line 104, in do_copy
    shutil.copy(source, temp_dest)
  File "/Users/huon/.pyenv/versions/3.10.4/lib/python3.10/shutil.py", line 417, in copy
    copyfile(src, dst, follow_symlinks=follow_symlinks)
  File "/Users/huon/.pyenv/versions/3.10.4/lib/python3.10/shutil.py", line 254, in copyfile
    with open(src, 'rb') as fsrc:
IsADirectoryError: [Errno 21] Is a directory: '/private/var/folders/sv/vd266m4d4lvctgs2wpnhjs9w0000gn/T/tmp970ao6ze/.deps/cowsay-6.1-py3-none-any.whl'
[Errno 21] Is a directory: '/private/var/folders/sv/vd266m4d4lvctgs2wpnhjs9w0000gn/T/tmp970ao6ze/.deps/cowsay-6.1-py3-none-any.whl'

Details of the full 3×3 grid of requirements/outputs layouts

As part of my investigation, I wondered whether the layout of the --requirements-pex mattered. It doesn't seem to, but here's what I did. Script that does all of them:

cd $(mktemp -d)

curl -OL https://github.com/pex-tool/pex/releases/download/v2.2.2/pex
chmod +x ./pex

for reqs in loose packed zipapp; do
    rm -rf reqs.pex
    ./pex --layout $reqs cowsay==6.1 -o reqs-$reqs.pex
    for output in loose packed zipapp; do
        echo
        echo "*** requirements=$reqs, output=$output"
        rm -rf target.pex
        ./pex --layout $output --no-pre-install-wheels --requirements-pex reqs-$reqs.pex -o output-$reqs-$output.pex
    done
done

requirements \ output	loose	packed	zipapp
loose	✅	❌	✅
packed	✅	❌	✅
zipapp	✅	❌	✅

[jsirois]

You won't like the answer here - although a bug, the fix will be merely to make the error message a controlled one. This is the ~same case as here, which I did catch when adding this feature: https://github.com/pex-tool/pex/blob/27c2db2bf26039bef41323c964bc4e0317a7b4f5/pex/environment.py#L284-L289

Fixing this (and the code above) will only be possible with the completion of #2299. I have #2299 all but done, but I've been side-tracked working on the lock update support Pants needs; so won't be circling back to that until #2373 ships.

[huonw]

You won't like the answer here

Perfectly happy with "unsupported, but we can make the error message better".

[jsirois]

The OP is not solved since it relies on functionality forthcoming in #2299; so I'll leave this issue open but stop progress / un-assign for now.