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Poetry2nix

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26 Jan 2022
@akiiino:matrix.orgakiiinoNope, Intel, and never had any problems with python before16:18:35
@k900:0upti.meK900It's possible you manually upgraded pip then16:19:35
@k900:0upti.meK900Either way try building your environment with 3.9 or even 3.1016:19:51
@k900:0upti.meK900It might work 16:19:54
@akiiino:matrix.orgakiiinoNope, similar error. I think it's trying to install a wheel for the wrong OS version (i.e. 10.9, while I'm on 11.6)16:22:06
@k900:0upti.meK900 I believe 10.9 is the minimum version 16:22:37
29 Jan 2022
@rolandco:matrix.orgRoland Coeurjoly joined the room.15:00:01
@rolandco:matrix.orgRoland CoeurjolyHi beautiful people! I'm trying get a shell with graphtage and wildq. No problem with the latter, but graphtage fails. >>> from graphtage import json Traceback (most recent call last): File “<stdin>”, line 1, in <module> File “/nix/store/x99l21wg669djr6a77sjzwga06s9zxmk-python3-3.9.9-env/lib/python3.9/site-packages/graphtage/__init__.py”, line 1, in <module> from . import graphtage File “/nix/store/x99l21wg669djr6a77sjzwga06s9zxmk-python3-3.9.9-env/lib/python3.9/site-packages/graphtage/graphtage.py”, line 11, in <module> from .multiset import MultiSetEdit File “/nix/store/x99l21wg669djr6a77sjzwga06s9zxmk-python3-3.9.9-env/lib/python3.9/site-packages/graphtage/multiset.py”, line 12, in <module> from .matching import WeightedBipartiteMatcher File “/nix/store/x99l21wg669djr6a77sjzwga06s9zxmk-python3-3.9.9-env/lib/python3.9/site-packages/graphtage/matching.py”, line 44, in <module> from scipy.optimize import linear_sum_assignment File “/nix/store/x99l21wg669djr6a77sjzwga06s9zxmk-python3-3.9.9-env/lib/python3.9/site-packages/scipy/optimize/__init__.py”, line 413, in <module> from ._linprog import linprog, linprog_verbose_callback File “/nix/store/x99l21wg669djr6a77sjzwga06s9zxmk-python3-3.9.9-env/lib/python3.9/site-packages/scipy/optimize/_linprog.py”, line 23, in <module> from ._linprog_ip import _linprog_ip File “/nix/store/x99l21wg669djr6a77sjzwga06s9zxmk-python3-3.9.9-env/lib/python3.9/site-packages/scipy/optimize/_linprog_ip.py”, line 27, in <module> from ._linprog_util import _postsolve File “/nix/store/x99l21wg669djr6a77sjzwga06s9zxmk-python3-3.9.9-env/lib/python3.9/site-packages/scipy/optimize/_linprog_util.py”, line 9, in <module> from scipy.optimize._remove_redundancy import ( File “/nix/store/x99l21wg669djr6a77sjzwga06s9zxmk-python3-3.9.9-env/lib/python3.9/site-packages/scipy/optimize/_remove_redundancy.py”, line 9, in <module> from scipy.linalg.interpolative import interp_decomp File “/nix/store/x99l21wg669djr6a77sjzwga06s9zxmk-python3-3.9.9-env/lib/python3.9/site-packages/scipy/linalg/interpolative.py”, line 385, in <module> import scipy.linalg._interpolative_backend as backend File “/nix/store/x99l21wg669djr6a77sjzwga06s9zxmk-python3-3.9.9-env/lib/python3.9/site-packages/scipy/linalg/_interpolative_backend.py”, line 34, in <module> import scipy.linalg._interpolative as _id ImportError: /nix/store/x99l21wg669djr6a77sjzwga06s9zxmk-python3-3.9.9-env/lib/python3.9/site-packages/scipy/linalg/_interpolative.cpython-39-x86_64-linux-gnu.so: undefined symbol: _ZGVbN2v_cos It seems to be a problem with scipy. Looking around it seems to be solved by compiling with -lmvec, with provides support for mathematical vectors in libc16:23:47
@rolandco:matrix.orgRoland CoeurjolyI have tried putting an override for scipy with lmvec, to no avail16:24:40
@mou_bugtracker:matrix.orgmoumaybe you could provide you expression? it will be much easier if there will be ability to experiment and run localy16:26:55
@mou_bugtracker:matrix.orgmou * maybe you could provide your expression? it will be much easier if there will be ability to experiment and run localy16:28:57
@rolandco:matrix.orgRoland Coeurjoly
In reply to @mou_bugtracker:matrix.org
maybe you could provide your expression? it will be much easier if there will be ability to experiment and run localy

{ description = “graphtage”;

inputs.nixpkgs.url = “github:NixOS/nixpkgs/d9e21f284317f85b3476c0043f4efea87a226c3a”;

outputs = { self, nixpkgs }: let pkgs = nixpkgs.legacyPackages.x86_64-linux; myPoetryEnv = pkgs.poetry2nix.mkPoetryEnv { pyproject = ./pyproject.toml; poetrylock = ./poetry.lock; }; in { devShell.x86_64-linux = myPoetryEnv; }; }

This is the full content of the flake

16:50:05
@rolandco:matrix.orgRoland CoeurjolyTo reproduce, nix develop; graphtage --help16:50:34
@mou_bugtracker:matrix.orgmouSome wierd quotes (16:51:46
@mou_bugtracker:matrix.orgmou
In reply to @rolandco:matrix.org
To reproduce, nix develop; graphtage --help
pyproject.toml and poetry.lock needed too
16:54:24
@mou_bugtracker:matrix.orgmouor just pyproject.toml16:54:59
@rolandco:matrix.orgRoland Coeurjoly
In reply to @mou_bugtracker:matrix.org
or just pyproject.toml

[tool.poetry] name = “graphtage-tool” version = “0.1.0” description = “” authors = [“Roland Coeurjoly rolandcoeurjoly@gmail.com”]

[tool.poetry.dependencies] python = “>=3.9,<3.11” graphtage = “^0.2.5” wildq = “^1.1.10”

[tool.poetry.dev-dependencies]

[build-system] requires = [“poetry-core>=1.0.0”] build-backend = “poetry.core.masonry.api”

17:00:06
@rolandco:matrix.orgRoland CoeurjolySorry17:00:34
@rolandco:matrix.orgRoland CoeurjolyHow can you reproduce without poetry.lock? Nix complaints without it17:01:26
@rolandco:matrix.orgRoland Coeurjolyhttps://github.com/RCoeurjoly/nix_graphtage17:11:45
@rolandco:matrix.orgRoland Coeurjoly mou: you can find the repo above 17:12:17
@mou_bugtracker:matrix.orgmouthanks17:12:36
@mou_bugtracker:matrix.orgmouit take time to build17:12:44
@rolandco:matrix.orgRoland CoeurjolyThe package graphtage is in nixpkgs, and I can create a shell with it easily18:52:16
@rolandco:matrix.orgRoland CoeurjolyBut wildq is not in nixpkgs18:52:29
@rolandco:matrix.orgRoland CoeurjolyIs there a way to create a shell with python modules from nixpkgs and also some installed with poetry?18:54:10
@mou_bugtracker:matrix.orgmouunfortunately my time is over for today. I was not able to figure out cause of problem. But i think cause lies in missing native build dependencies like gfortran and similar. Here is definition for scypi in nixpkgs https://github.com/NixOS/nixpkgs/blob/master/pkgs/development/python-modules/scipy/default.nix And 19:36:21
@mou_bugtracker:matrix.orgmouConsider use poetry2nix not from nixpkgs, but latest version from git. because it has pretty haevy override for scipy https://github.com/nix-community/poetry2nix/blob/master/overrides/default.nix#L167119:39:18
@mou_bugtracker:matrix.orgmou

i take standard template for poetry2nix and tried to build. ended up with cythonization fail ((

Processing scipy/optimize/_group_columns.pyx
  Processing scipy/interpolate/interpnd.pyx
  Processing scipy/optimize/_highs/cython/src/_highs_wrapper.pyx
  Processing scipy/optimize/_highs/cython/src/_highs_constants.pyx
  Traceback (most recent call last):
    File "/build/scipy-1.7.3/tools/cythonize.py", line 324, in <module>
      main()
    File "/build/scipy-1.7.3/tools/cythonize.py", line 320, in main
      find_process_files(root_dir)
    File "/build/scipy-1.7.3/tools/cythonize.py", line 309, in find_process_files
  Processing scipy/optimize/_trlib/_trlib.pyx
      for result in pool.imap_unordered(lambda args: process(*args), jobs):
    File "/nix/store/i6vabb4div9iy6lsl642d86k1q8riasn-python3-3.9.9/lib/python3.9/multiprocessing/pool.py", line 870, in next
      raise value
    File "/nix/store/i6vabb4div9iy6lsl642d86k1q8riasn-python3-3.9.9/lib/python3.9/multiprocessing/pool.py", line 125, in worker
      result = (True, func(*args, **kwds))
    File "/build/scipy-1.7.3/tools/cythonize.py", line 309, in <lambda>
      for result in pool.imap_unordered(lambda args: process(*args), jobs):
    File "/build/scipy-1.7.3/tools/cythonize.py", line 243, in process
      processor_function(fromfile, tofile, cwd=path)
    File "/build/scipy-1.7.3/tools/cythonize.py", line 80, in process_pyx
      min_required_version, max_required_version = line.split(split_on)
  ValueError: too many values to unpack (expected 2)
  Processing scipy/optimize/cython_optimize/_zeros.pyx.in
  Cythonizing sources
19:54:23
@mou_bugtracker:matrix.orgmou *

i took standard template for poetry2nix and tried to build. ended up with cythonization fail ((

Processing scipy/optimize/_group_columns.pyx
  Processing scipy/interpolate/interpnd.pyx
  Processing scipy/optimize/_highs/cython/src/_highs_wrapper.pyx
  Processing scipy/optimize/_highs/cython/src/_highs_constants.pyx
  Traceback (most recent call last):
    File "/build/scipy-1.7.3/tools/cythonize.py", line 324, in <module>
      main()
    File "/build/scipy-1.7.3/tools/cythonize.py", line 320, in main
      find_process_files(root_dir)
    File "/build/scipy-1.7.3/tools/cythonize.py", line 309, in find_process_files
  Processing scipy/optimize/_trlib/_trlib.pyx
      for result in pool.imap_unordered(lambda args: process(*args), jobs):
    File "/nix/store/i6vabb4div9iy6lsl642d86k1q8riasn-python3-3.9.9/lib/python3.9/multiprocessing/pool.py", line 870, in next
      raise value
    File "/nix/store/i6vabb4div9iy6lsl642d86k1q8riasn-python3-3.9.9/lib/python3.9/multiprocessing/pool.py", line 125, in worker
      result = (True, func(*args, **kwds))
    File "/build/scipy-1.7.3/tools/cythonize.py", line 309, in <lambda>
      for result in pool.imap_unordered(lambda args: process(*args), jobs):
    File "/build/scipy-1.7.3/tools/cythonize.py", line 243, in process
      processor_function(fromfile, tofile, cwd=path)
    File "/build/scipy-1.7.3/tools/cythonize.py", line 80, in process_pyx
      min_required_version, max_required_version = line.split(split_on)
  ValueError: too many values to unpack (expected 2)
  Processing scipy/optimize/cython_optimize/_zeros.pyx.in
  Cythonizing sources
21:53:16

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