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EasyBuild - building software with ease
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Cannot install easybuild-easyconfigs using pip if setuptools>61 #790

Closed ktaletsk closed 2 years ago

ktaletsk commented 2 years ago

Hi, I'm using easybuild in my Docker image, which uses miniconda environment for Python. Recently, after some updates I could not build my image anymore because pip install easybuild has failed with a large number of errors similar to package init file 'easybuild/__init__.py' not found (or not a regular file).

Full log ```javascript 19:19:53 Step 7/7 : RUN pip install --ignore-installed easybuild==4.5.1 19:19:53 ---> Running in c8da42b3c8a2 19:19:54 Collecting easybuild==4.5.1 19:19:54 Downloading easybuild-4.5.1.tar.gz (10 kB) 19:19:54 Preparing metadata (setup.py): started 19:19:55 Preparing metadata (setup.py): finished with status 'done' 19:19:55 Collecting easybuild-framework==4.5.1 19:19:55 Downloading easybuild-framework-4.5.1.tar.gz (2.0 MB) 19:19:55 ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 2.0/2.0 MB 40.4 MB/s eta 0:00:00 19:19:55 Preparing metadata (setup.py): started 19:19:57 Preparing metadata (setup.py): finished with status 'done' 19:19:57 Collecting easybuild-easyblocks==4.5.1 19:19:57 Downloading easybuild-easyblocks-4.5.1.tar.gz (512 kB) 19:19:57 ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 512.9/512.9 KB 50.6 MB/s eta 0:00:00 19:19:57 Preparing metadata (setup.py): started 19:19:58 Preparing metadata (setup.py): finished with status 'done' 19:19:58 Collecting easybuild-easyconfigs==4.5.1 19:19:58 Downloading easybuild-easyconfigs-4.5.1.tar.gz (7.1 MB) 19:19:58 ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 7.1/7.1 MB 87.0 MB/s eta 0:00:00 19:20:03 Preparing metadata (setup.py): started 19:20:05 Preparing metadata (setup.py): finished with status 'done' 19:20:05 Building wheels for collected packages: easybuild, easybuild-easyblocks, easybuild-easyconfigs, easybuild-framework 19:20:05 Building wheel for easybuild (setup.py): started 19:20:06 Building wheel for easybuild (setup.py): finished with status 'done' 19:20:06 Created wheel for easybuild: filename=easybuild-4.5.1-py3-none-any.whl size=10225 sha256=90c543a8f52f5748e7f39ce70c82c13ba856cd8598c47d967640644d04626eaa 19:20:06 Stored in directory: /home/jovyan/.cache/pip/wheels/e5/4d/03/71de5ed71b80ef1a238622c21c1d654cee06f80b32ba89681c 19:20:06 Building wheel for easybuild-easyblocks (setup.py): started 19:20:08 Building wheel for easybuild-easyblocks (setup.py): finished with status 'done' 19:20:08 Created wheel for easybuild-easyblocks: filename=easybuild_easyblocks-4.5.1-py3-none-any.whl size=784121 sha256=beecf56724cea8c7b4ed8cd061f440ab7d4d40cef3bcabab2c98af424cfba377 19:20:08 Stored in directory: /home/jovyan/.cache/pip/wheels/33/d1/f1/333e64b6bcbfa8c7735fd1065d429b1af23f87d45db763ef1c 19:20:08 Building wheel for easybuild-easyconfigs (setup.py): started 19:20:09 Building wheel for easybuild-easyconfigs (setup.py): finished with status 'error' 19:20:09  error: subprocess-exited-with-error 19:20:09 19:20:09 × python setup.py bdist_wheel did not run successfully. 19:20:09 │ exit code: 1 19:20:09 ╰─> [35 lines of output] 19:20:09 Installing version 4.5.1 (required versions: API >= 4, easyblocks >= 4.5) 19:20:09 running bdist_wheel 19:20:09 running build 19:20:09 running build_py 19:20:09 package init file 'easybuild/__init__.py' not found (or not a regular file) 19:20:09 package init file 'easybuild/easyconfigs/__init__.py' not found (or not a regular file) 19:20:09 package init file 'easybuild/easyconfigs/x/__init__.py' not found (or not a regular file) 19:20:09 package init file 'easybuild/easyconfigs/i/__init__.py' not found (or not a regular file) 19:20:09 package init file 'easybuild/easyconfigs/e/__init__.py' not found (or not a regular file) 19:20:09 package init file 'easybuild/easyconfigs/r/__init__.py' not found (or not a regular file) 19:20:09 package init file 'easybuild/easyconfigs/a/__init__.py' not found (or not a regular file) 19:20:09 package init file 'easybuild/easyconfigs/w/__init__.py' not found (or not a regular file) 19:20:09 package init file 'easybuild/easyconfigs/c/__init__.py' not found (or not a regular file) 19:20:09 package init file 'easybuild/easyconfigs/j/__init__.py' not found (or not a regular file) 19:20:09 package init file 'easybuild/easyconfigs/y/__init__.py' not found (or not a regular file) 19:20:09 package init file 'easybuild/easyconfigs/t/__init__.py' not found (or not a regular file) 19:20:09 package init file 'easybuild/easyconfigs/m/__init__.py' not found (or not a regular file) 19:20:09 package init file 'easybuild/easyconfigs/q/__init__.py' not found (or not a regular file) 19:20:09 package init file 'easybuild/easyconfigs/s/__init__.py' not found (or not a regular file) 19:20:09 package init file 'easybuild/easyconfigs/z/__init__.py' not found (or not a regular file) 19:20:09 package init file 'easybuild/easyconfigs/g/__init__.py' not found (or not a regular file) 19:20:09 package init file 'easybuild/easyconfigs/v/__init__.py' not found (or not a regular file) 19:20:09 package init file 'easybuild/easyconfigs/o/__init__.py' not found (or not a regular file) 19:20:09 package init file 'easybuild/easyconfigs/d/__init__.py' not found (or not a regular file) 19:20:09 package init file 'easybuild/easyconfigs/u/__init__.py' not found (or not a regular file) 19:20:09 package init file 'easybuild/easyconfigs/k/__init__.py' not found (or not a regular file) 19:20:09 package init file 'easybuild/easyconfigs/b/__init__.py' not found (or not a regular file) 19:20:09 package init file 'easybuild/easyconfigs/l/__init__.py' not found (or not a regular file) 19:20:09 package init file 'easybuild/easyconfigs/p/__init__.py' not found (or not a regular file) 19:20:09 creating build 19:20:09 creating build/lib 19:20:09 creating build/lib/easybuild 19:20:09 creating build/lib/easybuild/easyconfigs 19:20:09 creating build/lib/easybuild/easyconfigs/p 19:20:09 error: can't copy 'easybuild/easyconfigs/p/plotly.py': doesn't exist or not a regular file 19:20:09 [end of output] 19:20:09 19:20:09 note: This error originates from a subprocess, and is likely not a problem with pip. 19:20:09  ERROR: Failed building wheel for easybuild-easyconfigs 19:20:09  Running setup.py clean for easybuild-easyconfigs 19:20:10 Building wheel for easybuild-framework (setup.py): started 19:20:13 Building wheel for easybuild-framework (setup.py): finished with status 'done' 19:20:13 Created wheel for easybuild-framework: filename=easybuild_framework-4.5.1-py3-none-any.whl size=3595163 sha256=23a751e990d25a9acebe225168d382f08eecaee45a3556d753c21fd30d5510bf 19:20:13 Stored in directory: /home/jovyan/.cache/pip/wheels/b4/f8/e1/4b87f276053032e2ddc1459b9270850d010f0875972bde7340 19:20:13 Successfully built easybuild easybuild-easyblocks easybuild-framework 19:20:13 Failed to build easybuild-easyconfigs 19:20:14 Installing collected packages: easybuild-framework, easybuild-easyconfigs, easybuild-easyblocks, easybuild 19:20:15 Running setup.py install for easybuild-easyconfigs: started 19:20:16 Running setup.py install for easybuild-easyconfigs: finished with status 'error' 19:20:16  error: subprocess-exited-with-error 19:20:16 19:20:16 × Running setup.py install for easybuild-easyconfigs did not run successfully. 19:20:16 │ exit code: 1 19:20:16 ╰─> [37 lines of output] 19:20:16 Installing version 4.5.1 (required versions: API >= 4, easyblocks >= 4.5) 19:20:16 running install 19:20:16 /opt/conda/lib/python3.9/site-packages/setuptools/command/install.py:34: SetuptoolsDeprecationWarning: setup.py install is deprecated. Use build and pip and other standards-based tools. 19:20:16 warnings.warn( 19:20:16 running build 19:20:16 running build_py 19:20:16 package init file 'easybuild/__init__.py' not found (or not a regular file) 19:20:16 package init file 'easybuild/easyconfigs/__init__.py' not found (or not a regular file) 19:20:16 package init file 'easybuild/easyconfigs/x/__init__.py' not found (or not a regular file) 19:20:16 package init file 'easybuild/easyconfigs/i/__init__.py' not found (or not a regular file) 19:20:16 package init file 'easybuild/easyconfigs/e/__init__.py' not found (or not a regular file) 19:20:16 package init file 'easybuild/easyconfigs/r/__init__.py' not found (or not a regular file) 19:20:16 package init file 'easybuild/easyconfigs/a/__init__.py' not found (or not a regular file) 19:20:16 package init file 'easybuild/easyconfigs/w/__init__.py' not found (or not a regular file) 19:20:16 package init file 'easybuild/easyconfigs/c/__init__.py' not found (or not a regular file) 19:20:16 package init file 'easybuild/easyconfigs/j/__init__.py' not found (or not a regular file) 19:20:16 package init file 'easybuild/easyconfigs/y/__init__.py' not found (or not a regular file) 19:20:16 package init file 'easybuild/easyconfigs/t/__init__.py' not found (or not a regular file) 19:20:16 package init file 'easybuild/easyconfigs/m/__init__.py' not found (or not a regular file) 19:20:16 package init file 'easybuild/easyconfigs/q/__init__.py' not found (or not a regular file) 19:20:16 package init file 'easybuild/easyconfigs/s/__init__.py' not found (or not a regular file) 19:20:16 package init file 'easybuild/easyconfigs/z/__init__.py' not found (or not a regular file) 19:20:16 package init file 'easybuild/easyconfigs/g/__init__.py' not found (or not a regular file) 19:20:16 package init file 'easybuild/easyconfigs/v/__init__.py' not found (or not a regular file) 19:20:16 package init file 'easybuild/easyconfigs/o/__init__.py' not found (or not a regular file) 19:20:16 package init file 'easybuild/easyconfigs/d/__init__.py' not found (or not a regular file) 19:20:16 package init file 'easybuild/easyconfigs/u/__init__.py' not found (or not a regular file) 19:20:16 package init file 'easybuild/easyconfigs/k/__init__.py' not found (or not a regular file) 19:20:16 package init file 'easybuild/easyconfigs/b/__init__.py' not found (or not a regular file) 19:20:16 package init file 'easybuild/easyconfigs/l/__init__.py' not found (or not a regular file) 19:20:16 package init file 'easybuild/easyconfigs/p/__init__.py' not found (or not a regular file) 19:20:16 creating build 19:20:16 creating build/lib 19:20:16 creating build/lib/easybuild 19:20:16 creating build/lib/easybuild/easyconfigs 19:20:16 creating build/lib/easybuild/easyconfigs/p 19:20:16 error: can't copy 'easybuild/easyconfigs/p/plotly.py': doesn't exist or not a regular file 19:20:16 [end of output] 19:20:16 19:20:16 note: This error originates from a subprocess, and is likely not a problem with pip. 19:20:16 error: legacy-install-failure 19:20:16 19:20:16 × Encountered error while trying to install package. 19:20:16 ╰─> easybuild-easyconfigs 19:20:16 19:20:16 note: This is an issue with the package mentioned above, not pip. 19:20:16 hint: See above for output from the failure. 19:20:17 The command '/bin/sh -c pip install --ignore-installed easybuild==4.5.1' returned a non-zero code: 1 ```
For a context, here are versions that I have in my container version
python 3.9.12
conda 4.10.3
pip 22.0.4
setuptools 61.2.0

I noticed on Stackoverflow someone recently had the same issue recently https://stackoverflow.com/questions/71648527/how-to-solve-easybuild-installation-problems

The issue seem to be isolated specifically in building a Python wheel for easybuild-easyconfigs package. I tried to isolate any issues related to my container by running popular public containers. Below are the results of my testing:

  1. Python Docker image, docker run --rm -it python pip install easybuild-easyconfigs. Success.
version
python 3.10.4
conda N/A
pip 22.0.4
setuptools 58.1.0
Full log ```bash Collecting easybuild-easyconfigs Downloading easybuild-easyconfigs-4.5.3.tar.gz (7.3 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 7.3/7.3 MB 15.9 MB/s eta 0:00:00 Preparing metadata (setup.py) ... done Building wheels for collected packages: easybuild-easyconfigs Building wheel for easybuild-easyconfigs (setup.py) ... done Created wheel for easybuild-easyconfigs: filename=easybuild_easyconfigs-4.5.3-py3-none-any.whl size=22498617 sha256=c11bf548aea702685b75c08847304b62ea4702501d3e755cc7419dad60de945e Stored in directory: /root/.cache/pip/wheels/38/81/59/0001c055d5ca749b81d1f0149dce8cd71d803e370ee4b3be4f Successfully built easybuild-easyconfigs Installing collected packages: easybuild-easyconfigs Successfully installed easybuild-easyconfigs-4.5.3 WARNING: Running pip as the 'root' user can result in broken permissions and conflicting behaviour with the system package manager. It is recommended to use a virtual environment instead: https://pip.pypa.io/warnings/venv ```
  1. Jupyter Minimal Notebook Docker image from March 21, docker run --rm -it jupyter/minimal-notebook:2022-03-21 pip install easybuild-easyconfigs==4.5.3. Success.
version
python 3.9.10
conda 4.11.0
pip 22.0.3
setuptools 60.9.3
Full log ```bash Collecting easybuild-easyconfigs==4.5.3 Downloading easybuild-easyconfigs-4.5.3.tar.gz (7.3 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 7.3/7.3 MB 16.8 MB/s eta 0:00:00 Preparing metadata (setup.py) ... done Building wheels for collected packages: easybuild-easyconfigs Building wheel for easybuild-easyconfigs (setup.py) ... done Created wheel for easybuild-easyconfigs: filename=easybuild_easyconfigs-4.5.3-py3-none-any.whl size=22498617 sha256=32a9aa13ca84779bd2a59f3c4ebd00995626c0a4b4fcaf830dd15b27d9dd5759 Stored in directory: /home/jovyan/.cache/pip/wheels/71/e6/f0/d353f5e1b8aff637cadf674d069ebf1e0a34e653f3ccded3ee Successfully built easybuild-easyconfigs Installing collected packages: easybuild-easyconfigs Successfully installed easybuild-easyconfigs-4.5.3 ```
  1. Jupyter Minimal Notebook Docker image from March 28, docker run --rm -it jupyter/minimal-notebook:2022-03-28 pip install easybuild-easyconfigs==4.5.3. Failure.
version
python 3.9.10
conda 4.12.0
pip 22.0.4
setuptools 61.1.1
Full log ```bash Collecting easybuild-easyconfigs==4.5.3 Downloading easybuild-easyconfigs-4.5.3.tar.gz (7.3 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 7.3/7.3 MB 13.0 MB/s eta 0:00:00 Preparing metadata (setup.py) ... done Building wheels for collected packages: easybuild-easyconfigs Building wheel for easybuild-easyconfigs (setup.py) ... error error: subprocess-exited-with-error × python setup.py bdist_wheel did not run successfully. │ exit code: 1 ╰─> [20 lines of output] Installing version 4.5.3 (required versions: API >= 4, easyblocks >= 4.5) running bdist_wheel running build running build_py package init file 'easybuild/__init__.py' not found (or not a regular file) package init file 'easybuild/easyconfigs/__init__.py' not found (or not a regular file) package init file 'easybuild/easyconfigs/v/__init__.py' not found (or not a regular file) package init file 'easybuild/easyconfigs/a/__init__.py' not found (or not a regular file) package init file 'easybuild/easyconfigs/g/__init__.py' not found (or not a regular file) package init file 'easybuild/easyconfigs/k/__init__.py' not found (or not a regular file) package init file 'easybuild/easyconfigs/z/__init__.py' not found (or not a regular file) package init file 'easybuild/easyconfigs/i/__init__.py' not found (or not a regular file) package init file 'easybuild/easyconfigs/__archive__/__init__.py' not found (or not a regular file) package init file 'easybuild/easyconfigs/p/__init__.py' not found (or not a regular file) creating build creating build/lib creating build/lib/easybuild creating build/lib/easybuild/easyconfigs creating build/lib/easybuild/easyconfigs/p error: can't copy 'easybuild/easyconfigs/p/path.py': doesn't exist or not a regular file [end of output] note: This error originates from a subprocess, and is likely not a problem with pip. ERROR: Failed building wheel for easybuild-easyconfigs Running setup.py clean for easybuild-easyconfigs Failed to build easybuild-easyconfigs Installing collected packages: easybuild-easyconfigs Running setup.py install for easybuild-easyconfigs ... error error: subprocess-exited-with-error × Running setup.py install for easybuild-easyconfigs did not run successfully. │ exit code: 1 ╰─> [22 lines of output] Installing version 4.5.3 (required versions: API >= 4, easyblocks >= 4.5) running install /opt/conda/lib/python3.9/site-packages/setuptools/command/install.py:34: SetuptoolsDeprecationWarning: setup.py install is deprecated. Use build and pip and other standards-based tools. warnings.warn( running build running build_py package init file 'easybuild/__init__.py' not found (or not a regular file) package init file 'easybuild/easyconfigs/__init__.py' not found (or not a regular file) package init file 'easybuild/easyconfigs/v/__init__.py' not found (or not a regular file) package init file 'easybuild/easyconfigs/a/__init__.py' not found (or not a regular file) package init file 'easybuild/easyconfigs/g/__init__.py' not found (or not a regular file) package init file 'easybuild/easyconfigs/k/__init__.py' not found (or not a regular file) package init file 'easybuild/easyconfigs/z/__init__.py' not found (or not a regular file) package init file 'easybuild/easyconfigs/i/__init__.py' not found (or not a regular file) package init file 'easybuild/easyconfigs/__archive__/__init__.py' not found (or not a regular file) package init file 'easybuild/easyconfigs/p/__init__.py' not found (or not a regular file) creating build creating build/lib creating build/lib/easybuild creating build/lib/easybuild/easyconfigs creating build/lib/easybuild/easyconfigs/p error: can't copy 'easybuild/easyconfigs/p/path.py': doesn't exist or not a regular file [end of output] note: This error originates from a subprocess, and is likely not a problem with pip. error: legacy-install-failure × Encountered error while trying to install package. ╰─> easybuild-easyconfigs note: This is an issue with the package mentioned above, not pip. hint: See above for output from the failure. ```

I am confused what's going on. There seem to be no clear correlation of the issue with versions of Python, Conda or pip.

UPD: Added setuptools versions to the scenarios and it seems like the version 61 is the one causing issues

ktaletsk commented 2 years ago

Workaround for anyone affected -- build a wheel easybuild-easyconfigs in an environment where it works and copy it to your main environment. If using Docker, you can utilize a multistage build to do that

# Add this pre-build stage
----------
FROM python:3.9
RUN pip wheel easybuild-easyconfigs==4.5.3
----------

# Your normal Dockerfile
FROM ...

# Add this COPY command
----------
COPY --from=0 /easybuild* .
----------

RUN pip install easybuild_easyconfigs-4.5.3-py3-none-any.whl easybuild==4.5.3

After applying this changes, build proceeds without issues

boegel commented 2 years ago

Any relation to a similar issue that was reported at https://github.com/easybuilders/easybuild-framework/issues/3984 ?

It seems like some kind of breaking change was introduced in a recent version of setuptools or pip that we're hitting?

boegel commented 2 years ago

@ktaletsk Can you update the issue description with the setuptools version that was used in each case?

ktaletsk commented 2 years ago

@boegel Added setuptools versions. Looks like easybuild-easyconfigs is incompatible with setuptools above version 61. As a check, downgrading setuptools to <61, and trying install again, works:


> docker run --rm -it jupyter/minimal-notebook:2022-03-28 bash
$ pip install easybuild-easyconfigs==4.5.3
# Same failure as above

# Downgrade setuptools
$ pip install --upgrade setuptools==60.9.3

# Try installing again
$ pip install easybuild-easyconfigs==4.5.3
Collecting easybuild-easyconfigs==4.5.3
  Using cached easybuild-easyconfigs-4.5.3.tar.gz (7.3 MB)
  Preparing metadata (setup.py) ... done
Building wheels for collected packages: easybuild-easyconfigs
  Building wheel for easybuild-easyconfigs (setup.py) ... done
  Created wheel for easybuild-easyconfigs: filename=easybuild_easyconfigs-4.5.3-py3-none-any.whl size=22498617 sha256=97de381848c130dc53ad275c43c0b4a6e18c12200388072af10f9cc8410e791d
  Stored in directory: /home/jovyan/.cache/pip/wheels/71/e6/f0/d353f5e1b8aff637cadf674d069ebf1e0a34e653f3ccded3ee
Successfully built easybuild-easyconfigs
Installing collected packages: easybuild-easyconfigs
Successfully installed easybuild-easyconfigs-4.5.3
boegel commented 2 years ago

Thanks a lot, that's helpful.

It looks like we're being hit by a breaking change in setuptools 61.0, see https://github.com/pypa/setuptools/blob/main/CHANGES.rst#v6100, probably related to https://github.com/pypa/setuptools/pull/2894...

The easyconfigs package is a special case, since we're only packaging up data files (easyconfigs + patch files, basically), rather than Python code.

It seems like we have some homework to do to ensure compatibility with future setuptools versions...

boegel commented 2 years ago

There's a trivial fix for this, see https://github.com/easybuilders/easybuild-easyconfigs/pull/15206, we'll make sure that's included for the next EasyBuild release (but we also want to try setting up a CI workflow that catches problems like this)