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build/install tools + the release of numpy==1.20 broke installing cvxpy on Linux and in Docker #1040

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1fish2 opened this issue Feb 12, 2021 · 3 comments
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build/install tools + the release of numpy==1.20 broke installing cvxpy on Linux and in Docker #1040

1fish2 opened this issue Feb 12, 2021 · 3 comments
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1fish2 commented Feb 12, 2021

See pypa/pip#9542

  • Our Docker builds are broken.
  • Our current virtualenvs on Sherlock and other Linux machines are OK with their previously-installed cvxpy, but installing cvxpy now would break them.
  • Test by running python -c "import cvxpy". It should not throw a RuntimeError or an ImportError.

See https://github.com/cvxgrp/cvxpy/issues/1229
See pypa/pip#9542

Workaround 1: Update to cvxpy==1.1.10 which uses a pyproject.toml feature called "oldest-supported-numpy" to workaround this problem (for how long?).
I'll do this soon and have updated virtualenv wcEcoli3-staging on Sherlock.

Workaround 2: Update the wcEcoli project to numpy=1.20.1 and reinstall cvxpy. This will work until the next numpy binary incompatibility. I'm planning to test numpy=1.20 soon but it has deprecations to deal with, maybe API changes to deal with, and lots of code cleanup (removing Python 2.7 relics) which suggests lots of testing.
@1fish2 1fish2 added the bug label Feb 12, 2021
@1fish2 1fish2 self-assigned this Feb 12, 2021
1fish2 added a commit that referenced this issue Feb 12, 2021
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get the workaround in cvxpy==1.1.10
5915b84 
for #1040
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1fish2 commented Feb 12, 2021

Workaround 3: install cvxpy with the --no-build-isolation switch.

Workaround 1 seems to work for the master branch.
Workaround 3 might work for the Python 2 release snapshot.

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1fish2 commented Feb 13, 2021

The wcm-runtime Docker Image in WholeCellEcoliRelease still builds and loads cvxpy!

Building that Python 2.7 environment on Sherlock failed to compile qdldl: error: ‘for’ loop initial declarations are only allowed in C99 mode. Maybe it needs different modules to get a suitable compiler.

1fish2 added a commit that referenced this issue Feb 17, 2021
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Docker: optionally install OpenBLAS, numpy, & scipy from source
e119f6c 
When building a `wcm-runtime` Docker Image, make the default be to install numpy & scipy from wheels with their embedded copies of OpenBLAS.

It's **much faster** and it's the usual approach so we're less likely to hit installer bugs like #1040.

The reason for compiling OpenBLAS from source was originally to get a bug fix and later to avoid the AVX2 problem building it in Docker-for-Mac.

This does change Parca outputs but that's all part of #931.
@1fish2 1fish2 mentioned this issue Feb 17, 2021
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1fish2 added a commit that referenced this issue Feb 19, 2021
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Fix 1040: the release of numpy==1.20 broke installing cvxpy on Linux …
537d109 
…and in Docker (#1045)

* get the workaround in cvxpy==1.1.10 for #1040
* Docker: optionally install OpenBLAS, numpy, & scipy from source
* diff_simouts: ignore `shell.log` files; just compare tables, each of which is a subdir
@1fish2 1fish2 mentioned this issue Mar 4, 2021
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1fish2 commented Jun 9, 2021

Fixed by #1045.

@1fish2 1fish2 closed this as completed Jun 9, 2021
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