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python3packages.stytra: init at 0.8.26 #72353

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merged 6 commits into from
Dec 16, 2019
Merged

python3packages.stytra: init at 0.8.26 #72353

merged 6 commits into from
Dec 16, 2019
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tbenst
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@tbenst tbenst commented Oct 31, 2019 •
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WIP - wanted to get feedback on help as this is my first time packing using wheel.

It seems like propogatedBuildInputs is not behaving the same way--if I only have a package here I get failures like:

ERROR: Could not find a version that satisfies the requirement pyqtgraph>=0.10.0 (from stytra==0.8.26) (from versions: none)
ERROR: No matching distribution found for pyqtgraph>=0.10.0 (from stytra==0.8.26)
builder for '/nix/store/brscmbwx2nzr56f8wdh3n8vnjq2ih58p-python3.7-stytra-0.8.26.drv' failed with exit code 1

As a result, I'm including in both buildInputs, and propogatedBuildInputs, which feels wrong. It does build, but when I try open a shell the following happens:

> python
>>> import stytra
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/nix/store/prr2jha833ix3qa30w0cbfgcr1zxh75s-python3-3.7.5-env/lib/python3.7/site-packages/stytra/__init__.py", line 3, in <module>
    from stytra.experiments import VisualExperiment
  File "/nix/store/prr2jha833ix3qa30w0cbfgcr1zxh75s-python3-3.7.5-env/lib/python3.7/site-packages/stytra/experiments/__init__.py", line 5, in <module>
    import numpy as np
ModuleNotFoundError: No module named 'numpy'
>>> import numpy
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
ModuleNotFoundError: No module named 'numpy'

This seems very odd, as in any other derivation I test, I can import from propogatedBuildInputs in python shell. To debug, I switched back to using the tar.gz file, and found an unexpected error:

these derivations will be built:
  /nix/store/25sy04zv5h91a02nkbdxy5lkf73ibn33-python3-3.7.5-env.drv
building '/nix/store/25sy04zv5h91a02nkbdxy5lkf73ibn33-python3-3.7.5-env.drv'...
collision between `/nix/store/10b0xgqaqacaxiwlvcklp9nbl20y5wcx-python3.7-sip-4.19.18/bin/sip' and `/nix/store/nqa4rbzhi6aj0ry54dwc82r2900zlnmr-python3.7-PyQt5.sip-4.19.18/bin/sip'
builder for '/nix/store/25sy04zv5h91a02nkbdxy5lkf73ibn33-python3-3.7.5-env.drv' failed with exit code 255
error: build of '/nix/store/25sy04zv5h91a02nkbdxy5lkf73ibn33-python3-3.7.5-env.drv' failed

Any thoughts or tips? Thanks!

Motivation for this change

Add module for closed-loop experiments for larval zebrafish.

Things done
  • Tested using sandboxing (nix.useSandbox on NixOS, or option sandbox in nix.conf on non-NixOS linux)
  • Built on platform(s)
    • NixOS
    • macOS
    • other Linux distributions
  • Tested via one or more NixOS test(s) if existing and applicable for the change (look inside nixos/tests)
  • Tested compilation of all pkgs that depend on this change using nix-shell -p nix-review --run "nix-review wip"
  • Tested execution of all binary files (usually in ./result/bin/)
  • Determined the impact on package closure size (by running nix path-info -S before and after)
  • Ensured that relevant documentation is up to date
  • Fits CONTRIBUTING.md.

Sorry, something went wrong.

@tbenst tbenst changed the title <!-- Nixpkgs has a lot of new incoming Pull Requests, but not enough people to review this constant stream. Even if you aren't a committer, we would appreciate reviews of other PRs, especially simple ones like package updates. Just testing the relevant package/service and leaving a comment saying what you tested, how you tested it and whether it worked would be great. List of open PRs: <https://github.com/NixOS/nixpkgs/pulls>, for more about reviewing contributions: <https://hydra.nixos.org/job/nixpkgs/trunk/manual/latest/download/1/nixpkgs/manual.html#chap-reviewing-contributions>. Reviewing isn't mandatory, but it would help out a lot and reduce the average time-to-merge for all of us. Thanks a lot if you do! --> ###### Motivation for this change python3packages.stytra: init at 0.8.26 Oct 31, 2019
jonringer
jonringer reviewed Oct 31, 2019
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I don't see you declaring the pyqtgraph package in the propagated build inputs....

python packages should go into propagatedBuildInputs

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tbenst commented Oct 31, 2019 •
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I don't see you declaring the pyqtgraph package in the propagated build inputs....
python packages should go into propagatedBuildInputs

It's there (via commonInputs). If pyqtgraph is only in propogatedBuildInputs, I get the error above. It goes away if I add to buildInputs, too, as is currently done in the code

Edit: for posterity, if I use format = "wheel" all hell breaks loose, but easy enough with setuptools

@tbenst tbenst force-pushed the stytra branch 2 times, most recently from 78d383d to 8d1a549 Compare October 31, 2019 21:01
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tbenst commented Oct 31, 2019 •
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This is blocked until #72378 is merged, but reviews in the meantime are welcome!

Edit: forgot to mention that the package is running according to my tests locally:

> nix-shell -I nixpkgs=. -p 'python3.buildEnv.override { extraLibs = [ python3Packages.stytra ]; ignoreCollisions = true; }'
$ python -m stytra.examples.looming_exp
[success!]

@ofborg ofborg bot added the 11.by: package-maintainer This PR was created by the maintainer of the package it changes label Nov 1, 2019
jonringer
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please remove all instances of pulling down wheels when a source distribution is available, the only way a wheel should be allowed is if there no way to pull down source through pypi or the repo

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tbenst commented Dec 12, 2019

Thanks @jonringer. This is ready for final review

jonringer
jonringer suggested changes Dec 15, 2019
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please squash the fixup to adhere to contributing guidelines

git reset HEAD^
git add pkgs/
git commit --amend --no-edit
git push <fork> <branch> --force

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tbenst commented Dec 15, 2019

@jonringer done

jonringer
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diff LGTM
commits LGTM

https://github.com/NixOS/nixpkgs/pull/72353
12 package were built:
python27Packages.colorspacious python27Packages.flammkuchen python37Packages.arrayqueues python37Packages.colorspacious python37Packages.flammkuchen python37Packages.lightparam python37Packages.qimage2ndarray python37Packages.stytra python38Packages.arrayqueues python38Packages.colorspacious python38Packages.lightparam python38Packages.qimage2ndarray

@jonringer jonringer merged commit 60829ec into NixOS:master Dec 16, 2019
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6.topic: python 8.has: package (new) This PR adds a new package 10.rebuild-darwin: 11-100 10.rebuild-linux: 11-100 11.by: package-maintainer This PR was created by the maintainer of the package it changes
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