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uv 0.2.6

when installing pyyaml==5.4.1 I get:

Resolved 126 packages in 1.66s
error: Failed to download distributions
  Caused by: Failed to fetch wheel: pyyaml==5.4.1
  Caused by: Failed to build: `pyyaml==5.4.1`
  Caused by: Build backend failed to build wheel through `build_wheel()` with exit status: 1
--- stdout:

--- stderr:
usage: -c [global_opts] cmd1 [cmd1_opts] [cmd2 [cmd2_opts] ...]
   or: -c --help [cmd1 cmd2 ...]
   or: -c --help-commands
   or: -c cmd --help

error: invalid command 'bdist_wheel'
---
  Caused by: This error likely indicates that you need to `uv pip install wheel` into the build environment for pyyaml==5.4.1

If it knows what its missing, why doesn't it install that package?

Ah, it's package's job to declare its build dependencies. The "Caused by" at the end is us trying to provide a helpful hint for how to fix it, but we can't know that that's actually the problem, and it would be spec incompliant for us to make assumptions about it.

Related https://github.com/astral-sh/uv/issues/2252#issuecomment-1985287074

You could resolve this by using --no-build-isolation and installing the requisite build dependencies.

@konstin did you forget to make sure this special case message was only raised under --no-build-isolation? There's not a pull request linked in https://github.com/astral-sh/uv/issues/2342. I think the message is not helpful outside that context because installing wheel won't help.

I think it's helpful, but perhaps should be rephrased? It's way more helpful to know that the wheel package is missing than that bdist_wheel is an invalid command.

We indeed attach the context uncoditionally and lack the build isolation check. This shouldn't be the problem here, pyyaml 5.4.1 correctly declares a dependency on wheel (https://inspector.pypi.io/project/pyyaml/5.4.1/packages/a0/a4/d63f2d7597e1a4b55aa3b4d6c5b029991d3b824b5bd331af8d4ab1ed687d/PyYAML-5.4.1.tar.gz/PyYAML-5.4.1/pyproject.toml).

Can you share the commands to reproduce the error? It installs successfully for me on older python and on newer pythons i get a different error (windows and ubuntu):

$ uv venv -p 3.12
$ uv pip install pyyaml==5.4.1
Resolved 1 package in 280ms
error: Failed to download distributions
  Caused by: Failed to fetch wheel: pyyaml==5.4.1
  Caused by: Failed to build: `pyyaml==5.4.1`
  Caused by: Build backend failed to determine extra requires with `build_wheel()` with exit code: 1
--- stdout:
running egg_info
writing lib3\PyYAML.egg-info\PKG-INFO
writing dependency_links to lib3\PyYAML.egg-info\dependency_links.txt
writing top-level names to lib3\PyYAML.egg-info\top_level.txt
--- stderr:
Traceback (most recent call last):
  File "<string>", line 14, in <module>
  File "C:\Users\Konstantin\AppData\Local\uv\cache\.tmpTnVWP3\.venv\Lib\site-packages\setuptools\build_meta.py", line 325, in get_requires_for_build_wheel
    return self._get_build_requires(config_settings, requirements=['wheel'])
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "C:\Users\Konstantin\AppData\Local\uv\cache\.tmpTnVWP3\.venv\Lib\site-packages\setuptools\build_meta.py", line 295, in _get_build_requires
    self.run_setup()
  File "C:\Users\Konstantin\AppData\Local\uv\cache\.tmpTnVWP3\.venv\Lib\site-packages\setuptools\build_meta.py", line 311, in run_setup
    exec(code, locals())
  File "<string>", line 271, in <module>
  File "C:\Users\Konstantin\AppData\Local\uv\cache\.tmpTnVWP3\.venv\Lib\site-packages\setuptools\__init__.py", line 103, in setup
    return distutils.core.setup(**attrs)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "C:\Users\Konstantin\AppData\Local\uv\cache\.tmpTnVWP3\.venv\Lib\site-packages\setuptools\_distutils\core.py", line 184, in setup
    return run_commands(dist)
           ^^^^^^^^^^^^^^^^^^
  File "C:\Users\Konstantin\AppData\Local\uv\cache\.tmpTnVWP3\.venv\Lib\site-packages\setuptools\_distutils\core.py", line 200, in run_commands
    dist.run_commands()
  File "C:\Users\Konstantin\AppData\Local\uv\cache\.tmpTnVWP3\.venv\Lib\site-packages\setuptools\_distutils\dist.py", line 969, in run_commands
    self.run_command(cmd)
  File "C:\Users\Konstantin\AppData\Local\uv\cache\.tmpTnVWP3\.venv\Lib\site-packages\setuptools\dist.py", line 968, in run_command
    super().run_command(command)
  File "C:\Users\Konstantin\AppData\Local\uv\cache\.tmpTnVWP3\.venv\Lib\site-packages\setuptools\_distutils\dist.py", line 988, in run_command
    cmd_obj.run()
  File "C:\Users\Konstantin\AppData\Local\uv\cache\.tmpTnVWP3\.venv\Lib\site-packages\setuptools\command\egg_info.py", line 321, in run
    self.find_sources()
  File "C:\Users\Konstantin\AppData\Local\uv\cache\.tmpTnVWP3\.venv\Lib\site-packages\setuptools\command\egg_info.py", line 329, in find_sources
    mm.run()
  File "C:\Users\Konstantin\AppData\Local\uv\cache\.tmpTnVWP3\.venv\Lib\site-packages\setuptools\command\egg_info.py", line 550, in run
    self.add_defaults()
  File "C:\Users\Konstantin\AppData\Local\uv\cache\.tmpTnVWP3\.venv\Lib\site-packages\setuptools\command\egg_info.py", line 588, in add_defaults
    sdist.add_defaults(self)
  File "C:\Users\Konstantin\AppData\Local\uv\cache\.tmpTnVWP3\.venv\Lib\site-packages\setuptools\command\sdist.py", line 102, in add_defaults
    super().add_defaults()
  File "C:\Users\Konstantin\AppData\Local\uv\cache\.tmpTnVWP3\.venv\Lib\site-packages\setuptools\_distutils\command\sdist.py", line 250, in add_defaults
    self._add_defaults_ext()
  File "C:\Users\Konstantin\AppData\Local\uv\cache\.tmpTnVWP3\.venv\Lib\site-packages\setuptools\_distutils\command\sdist.py", line 335, in _add_defaults_ext
    self.filelist.extend(build_ext.get_source_files())
                         ^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "<string>", line 201, in get_source_files
  File "C:\Users\Konstantin\AppData\Local\uv\cache\.tmpTnVWP3\.venv\Lib\site-packages\setuptools\_distutils\cmd.py", line 107, in __getattr__
    raise AttributeError(attr)
AttributeError: cython_sources
---

well, I'm just using nixos which makes 0 assumtions about the things that are installed. its absolute barebones python, no global packages. the only binary I got is python3.10

then I just do uv pip install pyyaml==5.4.1

Yeah, it's the fault of the package at that specific version. It looks like you need to use PyYAML 6.0.1 in order to have a working install.

There is effectively nothing that uv can do here. That version of the package does not declare the correct build dependencies. So you either need to install them yourself out-of-band (uv pip install wheel, then uv pip install --no-build-isolation pyyaml==5.4.1) or update to a newer version.

(Adding to the existing ticket because I think it's the same issue; if it's actually a different issue I'm happy to file a new ticket.)

I switched a project from pip to uv. It worked for a little while, but then this problem broke the build:

root@27436ccb1f5b:/srv# pip install --upgrade pip setuptools uv wheel
root@27436ccb1f5b:/srv# uv pip install --no-cache --reinstall --system --verbose biopython==1.77
DEBUG uv 0.2.13
DEBUG Searching for Python interpreter in search path
DEBUG Found cpython 3.10.12 at `/usr/local/bin/python3` (search path)
DEBUG Using Python 3.10.12 environment at /usr/local/bin/python3
DEBUG Acquired lock for `/usr/local`
DEBUG Using request timeout of 30s
DEBUG Solving with installed Python version: 3.10.12
DEBUG Adding direct dependency: biopython==1.77
DEBUG No cache entry for: https://pypi.org/simple/biopython/
DEBUG Searching for a compatible version of biopython (==1.77)
DEBUG Selecting: biopython==1.77 (biopython-1.77.tar.gz)
DEBUG No cache entry for: https://files.pythonhosted.org/packages/4f/47/323e23c427b3246cc092a767f1868396a47ae05a7a135ce828600e7fe177/biopython-1.77-cp36-cp36m-macosx_10_9_x86_64.whl.metadata
DEBUG Adding transitive dependency for biopython==1.77: numpy*
DEBUG No cache entry for: https://pypi.org/simple/numpy/
DEBUG Searching for a compatible version of numpy (*)
DEBUG Selecting: numpy==2.0.0 (numpy-2.0.0-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl)
DEBUG No cache entry for: https://files.pythonhosted.org/packages/d6/a8/6a2419c40c7b6f7cb4ef52c532c88e55490c4fa92885964757d507adddce/numpy-2.0.0-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata
DEBUG Tried 2 versions: biopython 1, numpy 1
Resolved 2 packages in 479ms
DEBUG Identified uncached requirement: biopython==1.77
DEBUG Identified uncached requirement: numpy==2.0.0
[...]
DEBUG Solving with installed Python version: 3.10.12
DEBUG Adding direct dependency: setuptools>=40.8.0
DEBUG No cache entry for: https://pypi.org/simple/setuptools/
DEBUG Searching for a compatible version of setuptools (>=40.8.0)
DEBUG Selecting: setuptools==70.1.0 (setuptools-70.1.0-py3-none-any.whl)
DEBUG No cache entry for: https://files.pythonhosted.org/packages/55/b3/b3a3415d2debd837106ed417f8681d8af63037fed367fa1b85dbfef081f1/setuptools-70.1.0-py3-none-any.whl.metadata
DEBUG Tried 1 versions: setuptools 1
DEBUG Installing in setuptools==70.1.0 in /root/.cache/uv/environments-v0/.tmp4GN5pP
DEBUG Identified uncached requirement: setuptools==70.1.0
DEBUG Downloading and building requirement for build: setuptools==70.1.0
DEBUG No cache entry for: https://files.pythonhosted.org/packages/55/b3/b3a3415d2debd837106ed417f8681d8af63037fed367fa1b85dbfef081f1/setuptools-70.1.0-py3-none-any.whl
DEBUG Installing build requirement: setuptools==70.1.0
DEBUG Calling `setuptools.build_meta:__legacy__.get_requires_for_build_wheel()`
DEBUG Calling `setuptools.build_meta:__legacy__.build_wheel("/root/.cache/uv/built-wheels-v3/pypi/biopython/1.77/s1czoIEwLOoCMojvWuoZF/.tmpCPVxEH", {}, None)`
error: Failed to download distributions
  Caused by: Failed to fetch wheel: biopython==1.77
  Caused by: Failed to build: `biopython==1.77`
  Caused by: Build backend failed to build wheel through `build_wheel()` with exit status: 1
--- stdout:

--- stderr:
We need both setuptools AND wheel packages installed for bdist_wheel to work. Try running: pip install wheel
---

This is in a container based on Debian 11 Bullseye. Please let me know if you're like a Dockerfile+docker-compose.yaml that reproduce the issue.

Trying older releases, this appears to be a regression: 0.1.17 is the newest release that works for me, while 0.1.18 is the oldest release that fails for me. https://github.com/astral-sh/uv/issues/2313 https://github.com/astral-sh/uv/pull/2341 caught my eye in the commit titles https://github.com/astral-sh/uv/compare/0.1.17...0.1.18

@charliermarsh I see at the time, your spider sense tingled https://github.com/astral-sh/uv/issues/2313#issuecomment-1986875178

The --no-build-isolation flag mentioned above and the --legacy-setup-py flag mentioned in #2341 both work around the issue:

root@bb2a87c16f30:/srv# uv pip install --no-build-isolation --no-cache --system --reinstall biopython==1.77
+ uv pip install --no-build-isolation --no-cache --system --reinstall biopython==1.77
Resolved 2 packages in 233ms
   Built biopython==1.77
Downloaded 2 packages in 8.43s
Uninstalled 2 packages in 17ms
Installed 2 packages in 15ms
 - biopython==1.77
 + biopython==1.77
 - numpy==2.0.0
 + numpy==2.0.0

root@bb2a87c16f30:/srv# uv pip install --no-cache --system --reinstall --legacy-setup-py biopython==1.77
+ uv pip install --no-cache --system --reinstall --legacy-setup-py biopython==1.77
Resolved 2 packages in 474ms
   Built biopython==1.77
Downloaded 2 packages in 6.83s
Uninstalled 2 packages in 32ms
Installed 2 packages in 13ms
 - biopython==1.77
 + biopython==1.77
 - numpy==2.0.0
 + numpy==2.0.0

The latest version of biopython git+https://github.com/biopython/biopython.git seems to behave the same as version 1.77.

I can reproduce the issue with pip 24.1 with the major difference that it works by default and only fails if --use-pep517 is explicitly chosen.

root@bb2a87c16f30:/srv# pip install --force-reinstall git+https://github.com/biopython/biopython.git
+ pip install --force-reinstall git+https://github.com/biopython/biopython.git
Collecting git+https://github.com/biopython/biopython.git
  Cloning https://github.com/biopython/biopython.git to /tmp/pip-req-build-str6jtfe
  Running command git clone --filter=blob:none --quiet https://github.com/biopython/biopython.git /tmp/pip-req-build-str6jtfe
  Resolved https://github.com/biopython/biopython.git to commit cca7983d2e054db56123295034f4eefc919cb7fa
  Preparing metadata (setup.py) ... done
Collecting numpy (from biopython==1.84.dev0)
  Using cached numpy-2.0.0-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (60 kB)
Using cached numpy-2.0.0-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (19.3 MB)
Building wheels for collected packages: biopython
  Building wheel for biopython (setup.py) ... done
  Created wheel for biopython: filename=biopython-1.84.dev0-cp310-cp310-linux_x86_64.whl size=3168711 sha256=a2589ad16cecf149ca311cbca2c0da225b06dd9951f736b4d8e75351603237ef
  Stored in directory: /tmp/pip-ephem-wheel-cache-w490jw9c/wheels/c0/e3/29/3b7bf898d7fe6d4de17fcab24cd454bc9e1deec60388309d51
Successfully built biopython
Installing collected packages: numpy, biopython
  Attempting uninstall: numpy
    Found existing installation: numpy 2.0.0
    Uninstalling numpy-2.0.0:
      Successfully uninstalled numpy-2.0.0
  Attempting uninstall: biopython
    Found existing installation: biopython 1.84.dev0
    Uninstalling biopython-1.84.dev0:
      Successfully uninstalled biopython-1.84.dev0
[...]
Successfully installed biopython-1.84.dev0 numpy-2.0.0

root@bb2a87c16f30:/srv# pip install --force-reinstall --use-pep517 --quiet git+https://github.com/biopython/biopython.git
+ pip install --force-reinstall --use-pep517 --quiet git+https://github.com/biopython/biopython.git
  error: subprocess-exited-with-error
  
  × Building wheel for biopython (pyproject.toml) did not run successfully.
  │ exit code: 1
  ╰─> [1 lines of output]
      We need both setuptools AND wheel packages installed for bdist_wheel to work. Try running: pip install wheel
      [end of output]
  
  note: This error originates from a subprocess, and is likely not a problem with pip.
  ERROR: Failed building wheel for biopython
ERROR: ERROR: Failed to build installable wheels for some pyproject.toml based projects (biopython)

Thanks for the write-up! I think this is expected since we use PEP 517 by default, and (as you noted) the package doesn't seem to install with --use-pep517. In that case, the package itself would need to be fixed to enable installing without build isolation.