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[Bug]: Python kernel with matplotlib fails to nix evaluate #395

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MMesch opened this issue Dec 19, 2022 · 2 comments
Closed

[Bug]: Python kernel with matplotlib fails to nix evaluate #395

MMesch opened this issue Dec 19, 2022 · 2 comments
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@djacu
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bug Something isn't working

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@MMesch
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MMesch commented Dec 19, 2022 •
edited
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Current Behavior

jupyterWith fails to build the Python kernel when matplotlib is added as extraPackage.

Expected Behavior

Should work since this is one of the most common Python packages out there.

Steps To Reproduce

Copy the template:

nix flake init -t github:tweag/jupyterWith

Then change the python kernel to:

{
  name,
  availableKernels,
  extraArgs,
}:
availableKernels.python {
  name = "custom-${name}";
  inherit (extraArgs) system;
  displayName = "Custom ${name}";
  extraPackages = ps: [ ps.matplotlib ];
}

On my machine this produces:

warning: Using saved setting for 'extra-substituters = https://tweag-jupyter.cachix.org' from ~/.local/share/nix/trusted-settings.json.
warning: Using saved setting for 'extra-trusted-public-keys = tweag-jupyter.cachix.org-1:UtNH4Zs6hVUFpFBTLaA4ejYavPo5EFFqgd7G7FxGW9g=' from ~/.local/share/nix/trusted-settings.json.
error: attribute 'format' missing

       at /nix/store/4myxpy1b0lipw5mcrvvghj99n1b89a49-source/overrides/default.nix:1499:40:

         1498|             ++ lib.optionals (self.isPyPy) [ tk xorg.libX11 ];
         1499|           preConfigure = lib.optional (old.format != "wheel") preConfigure;
             |                                        ^
         1500|         }
(use '--show-trace' to show detailed location information)

OS

nixos build with flakes

Version

flake.lock is attached below

Additional Context

{
  "nodes": {
    "flake-compat": {
      "flake": false,
      "locked": {
        "lastModified": 1668681692,
        "narHash": "sha256-Ht91NGdewz8IQLtWZ9LCeNXMSXHUss+9COoqu6JLmXU=",
        "owner": "edolstra",
        "repo": "flake-compat",
        "rev": "009399224d5e398d03b22badca40a37ac85412a1",
        "type": "github"
      },
      "original": {
        "owner": "edolstra",
        "repo": "flake-compat",
        "type": "github"
      }
    },
    "flake-compat_2": {
      "flake": false,
      "locked": {
        "lastModified": 1668681692,
        "narHash": "sha256-Ht91NGdewz8IQLtWZ9LCeNXMSXHUss+9COoqu6JLmXU=",
        "owner": "edolstra",
        "repo": "flake-compat",
        "rev": "009399224d5e398d03b22badca40a37ac85412a1",
        "type": "github"
      },
      "original": {
        "owner": "edolstra",
        "repo": "flake-compat",
        "type": "github"
      }
    },
    "flake-compat_3": {
      "flake": false,
      "locked": {
        "lastModified": 1627913399,
        "narHash": "sha256-hY8g6H2KFL8ownSiFeMOjwPC8P0ueXpCVEbxgda3pko=",
        "owner": "edolstra",
        "repo": "flake-compat",
        "rev": "12c64ca55c1014cdc1b16ed5a804aa8576601ff2",
        "type": "github"
      },
      "original": {
        "owner": "edolstra",
        "repo": "flake-compat",
        "type": "github"
      }
    },
    "flake-compat_4": {
      "flake": false,
      "locked": {
        "lastModified": 1668681692,
        "narHash": "sha256-Ht91NGdewz8IQLtWZ9LCeNXMSXHUss+9COoqu6JLmXU=",
        "owner": "edolstra",
        "repo": "flake-compat",
        "rev": "009399224d5e398d03b22badca40a37ac85412a1",
        "type": "github"
      },
      "original": {
        "owner": "edolstra",
        "repo": "flake-compat",
        "type": "github"
      }
    },
    "flake-utils": {
      "locked": {
        "lastModified": 1667395993,
        "narHash": "sha256-nuEHfE/LcWyuSWnS8t12N1wc105Qtau+/OdUAjtQ0rA=",
        "owner": "numtide",
        "repo": "flake-utils",
        "rev": "5aed5285a952e0b949eb3ba02c12fa4fcfef535f",
        "type": "github"
      },
      "original": {
        "owner": "numtide",
        "repo": "flake-utils",
        "type": "github"
      }
    },
    "flake-utils_2": {
      "locked": {
        "lastModified": 1667395993,
        "narHash": "sha256-nuEHfE/LcWyuSWnS8t12N1wc105Qtau+/OdUAjtQ0rA=",
        "owner": "numtide",
        "repo": "flake-utils",
        "rev": "5aed5285a952e0b949eb3ba02c12fa4fcfef535f",
        "type": "github"
      },
      "original": {
        "owner": "numtide",
        "repo": "flake-utils",
        "type": "github"
      }
    },
    "flake-utils_3": {
      "locked": {
        "lastModified": 1629481132,
        "narHash": "sha256-JHgasjPR0/J1J3DRm4KxM4zTyAj4IOJY8vIl75v/kPI=",
        "owner": "numtide",
        "repo": "flake-utils",
        "rev": "997f7efcb746a9c140ce1f13c72263189225f482",
        "type": "github"
      },
      "original": {
        "owner": "numtide",
        "repo": "flake-utils",
        "type": "github"
      }
    },
    "gitignore": {
      "flake": false,
      "locked": {
        "lastModified": 1611672876,
        "narHash": "sha256-qHu3uZ/o9jBHiA3MEKHJ06k7w4heOhA+4HCSIvflRxo=",
        "owner": "hercules-ci",
        "repo": "gitignore.nix",
        "rev": "211907489e9f198594c0eb0ca9256a1949c9d412",
        "type": "github"
      },
      "original": {
        "owner": "hercules-ci",
        "repo": "gitignore.nix",
        "type": "github"
      }
    },
    "gitignore_2": {
      "inputs": {
        "nixpkgs": [
          "jupyterWith",
          "pre-commit-hooks",
          "nixpkgs"
        ]
      },
      "locked": {
        "lastModified": 1660459072,
        "narHash": "sha256-8DFJjXG8zqoONA1vXtgeKXy68KdJL5UaXR8NtVMUbx8=",
        "owner": "hercules-ci",
        "repo": "gitignore.nix",
        "rev": "a20de23b925fd8264fd7fad6454652e142fd7f73",
        "type": "github"
      },
      "original": {
        "owner": "hercules-ci",
        "repo": "gitignore.nix",
        "type": "github"
      }
    },
    "hls": {
      "inputs": {
        "flake-compat": "flake-compat_3",
        "flake-utils": "flake-utils_3",
        "gitignore": "gitignore",
        "nixpkgs": "nixpkgs",
        "pre-commit-hooks": "pre-commit-hooks"
      },
      "locked": {
        "lastModified": 1637213318,
        "narHash": "sha256-ZgxPwV7t4DyGYP7aXoetq+JHtd73XlOV2fYSflQmOXw=",
        "owner": "haskell",
        "repo": "haskell-language-server",
        "rev": "311107eabbf0537e0c192b2c377d282505b4eff1",
        "type": "github"
      },
      "original": {
        "owner": "haskell",
        "repo": "haskell-language-server",
        "type": "github"
      }
    },
    "ihaskell": {
      "inputs": {
        "flake-compat": [
          "jupyterWith",
          "flake-compat"
        ],
        "flake-utils": [
          "jupyterWith",
          "flake-utils"
        ],
        "hls": "hls",
        "nixpkgs": [
          "jupyterWith",
          "nixpkgs"
        ]
      },
      "locked": {
        "lastModified": 1668371230,
        "narHash": "sha256-yGqXQj+swFEgOFa2CJn9oW/syFuMzZF9pyDQfxOYgT4=",
        "owner": "ihaskell",
        "repo": "ihaskell",
        "rev": "465fded2f705cedbc791d210508ca9febc04a208",
        "type": "github"
      },
      "original": {
        "owner": "ihaskell",
        "repo": "ihaskell",
        "type": "github"
      }
    },
    "jupyterWith": {
      "inputs": {
        "flake-compat": "flake-compat_2",
        "flake-utils": "flake-utils_2",
        "ihaskell": "ihaskell",
        "nixpkgs": "nixpkgs_2",
        "nixpkgs-stable": "nixpkgs-stable",
        "npmlock2nix": "npmlock2nix",
        "opam-nix": "opam-nix",
        "poetry2nix": "poetry2nix",
        "pre-commit-hooks": "pre-commit-hooks_2",
        "rust-overlay": "rust-overlay"
      },
      "locked": {
        "lastModified": 1670546271,
        "narHash": "sha256-h+qEvQS+elTt7xfPjktjfbuTcQiBh1M0P5F3+osxpFs=",
        "owner": "tweag",
        "repo": "jupyterWith",
        "rev": "778ec10b5ed23153b4552418e85fdba9321d59cc",
        "type": "github"
      },
      "original": {
        "owner": "tweag",
        "repo": "jupyterWith",
        "type": "github"
      }
    },
    "mirage-opam-overlays": {
      "flake": false,
      "locked": {
        "lastModified": 1661959605,
        "narHash": "sha256-CPTuhYML3F4J58flfp3ZbMNhkRkVFKmBEYBZY5tnQwA=",
        "owner": "dune-universe",
        "repo": "mirage-opam-overlays",
        "rev": "05f1c1823d891ce4d8adab91f5db3ac51d86dc0b",
        "type": "github"
      },
      "original": {
        "owner": "dune-universe",
        "repo": "mirage-opam-overlays",
        "type": "github"
      }
    },
    "nixpkgs": {
      "locked": {
        "lastModified": 1630887066,
        "narHash": "sha256-0ecIlrLsNIIa+zrNmzXXmbMBLZlmHU/aWFsa4bq99Hk=",
        "owner": "NixOS",
        "repo": "nixpkgs",
        "rev": "5e47a07e9f2d7ed999f2c7943b0896f5f7321ca3",
        "type": "github"
      },
      "original": {
        "owner": "NixOS",
        "ref": "nixpkgs-unstable",
        "repo": "nixpkgs",
        "type": "github"
      }
    },
    "nixpkgs-stable": {
      "locked": {
        "lastModified": 1669546925,
        "narHash": "sha256-Gvtk9agz88tBgqmCdHl5U7gYttTkiuEd8/Rq1Im0pTg=",
        "owner": "nixos",
        "repo": "nixpkgs",
        "rev": "fecf05d4861f3985e8dee73f08bc82668ef75125",
        "type": "github"
      },
      "original": {
        "owner": "nixos",
        "ref": "nixos-22.05",
        "repo": "nixpkgs",
        "type": "github"
      }
    },
    "nixpkgs-stable_2": {
      "locked": {
        "lastModified": 1668984258,
        "narHash": "sha256-0gDMJ2T3qf58xgcSbYoXiRGUkPWmKyr5C3vcathWhKs=",
        "owner": "NixOS",
        "repo": "nixpkgs",
        "rev": "cf63ade6f74bbc9d2a017290f1b2e33e8fbfa70a",
        "type": "github"
      },
      "original": {
        "owner": "NixOS",
        "ref": "nixos-22.05",
        "repo": "nixpkgs",
        "type": "github"
      }
    },
    "nixpkgs_2": {
      "locked": {
        "lastModified": 1669542132,
        "narHash": "sha256-DRlg++NJAwPh8io3ExBJdNW7Djs3plVI5jgYQ+iXAZQ=",
        "owner": "nixos",
        "repo": "nixpkgs",
        "rev": "a115bb9bd56831941be3776c8a94005867f316a7",
        "type": "github"
      },
      "original": {
        "owner": "nixos",
        "ref": "nixos-unstable",
        "repo": "nixpkgs",
        "type": "github"
      }
    },
    "nixpkgs_3": {
      "locked": {
        "lastModified": 1671359686,
        "narHash": "sha256-3MpC6yZo+Xn9cPordGz2/ii6IJpP2n8LE8e/ebUXLrs=",
        "owner": "nixos",
        "repo": "nixpkgs",
        "rev": "04f574a1c0fde90b51bf68198e2297ca4e7cccf4",
        "type": "github"
      },
      "original": {
        "owner": "nixos",
        "ref": "nixos-unstable",
        "repo": "nixpkgs",
        "type": "github"
      }
    },
    "npmlock2nix": {
      "flake": false,
      "locked": {
        "lastModified": 1668989938,
        "narHash": "sha256-/IxdS0AiqSN0/VEOLnnfHyi4nP17yPrkhGf6KlXVwrc=",
        "owner": "nix-community",
        "repo": "npmlock2nix",
        "rev": "0ba0746d62974403daf717cded3f24c617622bc7",
        "type": "github"
      },
      "original": {
        "owner": "nix-community",
        "repo": "npmlock2nix",
        "type": "github"
      }
    },
    "opam-nix": {
      "inputs": {
        "flake-compat": [
          "jupyterWith",
          "flake-compat"
        ],
        "flake-utils": [
          "jupyterWith",
          "flake-utils"
        ],
        "mirage-opam-overlays": "mirage-opam-overlays",
        "nixpkgs": [
          "jupyterWith",
          "nixpkgs"
        ],
        "opam-overlays": "opam-overlays",
        "opam-repository": "opam-repository",
        "opam2json": "opam2json"
      },
      "locked": {
        "lastModified": 1669980144,
        "narHash": "sha256-1z9Lza41Ii30/Ljdeozoz7okm0+X+QyHilGjChzrZHo=",
        "owner": "tweag",
        "repo": "opam-nix",
        "rev": "a89f779c5b248c06136143e139848acae5d0ea49",
        "type": "github"
      },
      "original": {
        "owner": "tweag",
        "ref": "fix-list-repo-func",
        "repo": "opam-nix",
        "type": "github"
      }
    },
    "opam-overlays": {
      "flake": false,
      "locked": {
        "lastModified": 1654162756,
        "narHash": "sha256-RV68fUK+O3zTx61iiHIoS0LvIk0E4voMp+0SwRg6G6c=",
        "owner": "dune-universe",
        "repo": "opam-overlays",
        "rev": "c8f6ef0fc5272f254df4a971a47de7848cc1c8a4",
        "type": "github"
      },
      "original": {
        "owner": "dune-universe",
        "repo": "opam-overlays",
        "type": "github"
      }
    },
    "opam-repository": {
      "flake": false,
      "locked": {
        "lastModified": 1661161626,
        "narHash": "sha256-J3P+mXLwE2oEKTlMnx8sYRxwD/uNGSKM0AkAB7BNTxA=",
        "owner": "ocaml",
        "repo": "opam-repository",
        "rev": "54e69ff0949a3aaec0d5e3d67898bb7f279ab09f",
        "type": "github"
      },
      "original": {
        "owner": "ocaml",
        "repo": "opam-repository",
        "type": "github"
      }
    },
    "opam2json": {
      "inputs": {
        "nixpkgs": [
          "jupyterWith",
          "opam-nix",
          "nixpkgs"
        ]
      },
      "locked": {
        "lastModified": 1665671715,
        "narHash": "sha256-7f75C6fIkiLzfkwLpJxlQIKf+YORGsXGV8Dr2LDDi+A=",
        "owner": "tweag",
        "repo": "opam2json",
        "rev": "32fa2dcd993a27f9e75ee46fb8b78a7cd5d05113",
        "type": "github"
      },
      "original": {
        "owner": "tweag",
        "repo": "opam2json",
        "type": "github"
      }
    },
    "poetry2nix": {
      "inputs": {
        "flake-utils": [
          "jupyterWith",
          "flake-utils"
        ],
        "nixpkgs": [
          "jupyterWith",
          "nixpkgs"
        ]
      },
      "locked": {
        "lastModified": 1669635649,
        "narHash": "sha256-jGu5WoQrFLQBqT1BrwUtFsktzGkNoq9r6w6jwJdCpB8=",
        "owner": "nix-community",
        "repo": "poetry2nix",
        "rev": "ce8425ccc2884c1065927a38d1700024f431cf0f",
        "type": "github"
      },
      "original": {
        "owner": "nix-community",
        "repo": "poetry2nix",
        "type": "github"
      }
    },
    "pre-commit-hooks": {
      "inputs": {
        "flake-utils": [
          "jupyterWith",
          "ihaskell",
          "hls",
          "flake-utils"
        ],
        "nixpkgs": [
          "jupyterWith",
          "ihaskell",
          "hls",
          "nixpkgs"
        ]
      },
      "locked": {
        "lastModified": 1624971177,
        "narHash": "sha256-Amf/nBj1E77RmbSSmV+hg6YOpR+rddCbbVgo5C7BS0I=",
        "owner": "cachix",
        "repo": "pre-commit-hooks.nix",
        "rev": "397f0713d007250a2c7a745e555fa16c5dc8cadb",
        "type": "github"
      },
      "original": {
        "owner": "cachix",
        "repo": "pre-commit-hooks.nix",
        "type": "github"
      }
    },
    "pre-commit-hooks_2": {
      "inputs": {
        "flake-compat": "flake-compat_4",
        "flake-utils": [
          "jupyterWith",
          "flake-utils"
        ],
        "gitignore": "gitignore_2",
        "nixpkgs": [
          "jupyterWith",
          "nixpkgs"
        ],
        "nixpkgs-stable": "nixpkgs-stable_2"
      },
      "locked": {
        "lastModified": 1669152228,
        "narHash": "sha256-FEDReoTLWJHXcNso7aaAlAUU7uOqIR6Hc/C/nqlfooE=",
        "owner": "cachix",
        "repo": "pre-commit-hooks.nix",
        "rev": "078b0dee35e2da01334af682ec347463b70a9986",
        "type": "github"
      },
      "original": {
        "owner": "cachix",
        "repo": "pre-commit-hooks.nix",
        "type": "github"
      }
    },
    "root": {
      "inputs": {
        "flake-compat": "flake-compat",
        "flake-utils": "flake-utils",
        "jupyterWith": "jupyterWith",
        "nixpkgs": "nixpkgs_3"
      }
    },
    "rust-overlay": {
      "inputs": {
        "flake-utils": [
          "jupyterWith",
          "flake-utils"
        ],
        "nixpkgs": [
          "jupyterWith",
          "nixpkgs"
        ]
      },
      "locked": {
        "lastModified": 1669602829,
        "narHash": "sha256-I3LBvBiVui4Rf0iQvTqUIgBovaLDzpOzsoNEzCsDowg=",
        "owner": "oxalica",
        "repo": "rust-overlay",
        "rev": "b9da8e68a08707115be750c0cf7ade33f49d8ec4",
        "type": "github"
      },
      "original": {
        "owner": "oxalica",
        "repo": "rust-overlay",
        "type": "github"
      }
    }
  },
  "root": "root",
  "version": 7
}

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@MMesch MMesch added the bug Something isn't working label Dec 19, 2022
@GTrunSec
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GTrunSec commented Dec 23, 2022 •
edited
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It can be determined that the problem is caused by poetry. #361

@michelav michelav mentioned this issue Jan 10, 2023
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@djacu
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djacu commented Jan 20, 2023

This should be fixed with #415.
A new example kernel was added to the CI that pulls in numpy, scipy, and matplotlib via extraPackages. All seems to be working now.

@djacu djacu closed this as completed Jan 20, 2023
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