Help with building a python package

Help
1

Hi! I’m trying to install the python package pymc. It has a nix package available but when installing it, it tries to download 8Gb of data and install 15Gb of data while dropping my pc to its knees (I don’t have a very beefy pc but I have installed this library in much smaller computers). Problem is the derivation tries to install additional dependencies like dm-haiku which is a ML library which I don’t need. To solve this I want to install a custom derivation to see if I can tinker the dependencies to the minimum. Here’s what I’ve got:

      devShells = forEachSupportedSystem ({ pkgs }:
        let

          concatMajorMinor = v:
            pkgs.lib.pipe v [
              pkgs.lib.versions.splitVersion
              (pkgs.lib.sublist 0 2)
              pkgs.lib.concatStrings
            ];

          python = pkgs."python${concatMajorMinor version}";
          pymcLocal = ps: ps.callPackage ./pymc.nix {};
          myPython = python.withPackages(ps: with ps; [
            (pymcLocal ps)
          ]);

          sysPkgs = with pkgs; [
            go
            pkg-config
            pyright
            gotools
            gopls
            pgadmin4
            golangci-lint
          ];

          pythonPkgs = with myPython.pkgs; [
            venvShellHook
            pip
            numpy
            pandas
            seaborn
            psycopg2
            cvxpy
            pymcLocal
          ];
          in
            {

            default = pkgs.mkShell {
              venvDir = ".venv";
              postShellHook = ''
                # UV_PYTHON_DOWNLOADS=never
                echo "INIT PYENV..."
                echo $(which python)
                source ./venv/bin/activate
            '';

              packages = sysPkgs ++ pythonPkgs;
            };
      });

I have a flake.nix which builds the shell and tries to install the pymc package, I’m following the wiki here but I don’t know if I’m doing it correctly
Here’s pymc.nix which is only a copy paste from the nixpkgs repo:


{
  lib,
  buildPythonPackage,
  fetchFromGitHub,

  # build-system
  setuptools,
  versioneer,

  # dependencies
  arviz,
  cachetools,
  cloudpickle,
  numpy,
  pandas,
  pytensor,
  rich,
  scipy,
  threadpoolctl,
  typing-extensions,
}:

buildPythonPackage rec {
  pname = "pymc";
  version = "5.25.1";
  pyproject = true;

  src = fetchFromGitHub {
    owner = "pymc-devs";
    repo = "pymc";
    tag = "v${version}";
    hash = "sha256-zh6FsCEviuyqapguTrUDsWKq70ef0IKRhnn2dkgQ/KA=";
  };

  build-system = [
    setuptools
    versioneer
  ];

  pythonRelaxDeps = [
    "pytensor"
  ];

  dependencies = [
    arviz
    cachetools
    cloudpickle
    numpy
    pandas
    pytensor
    rich
    scipy
    threadpoolctl
    typing-extensions
  ];

  # The test suite is computationally intensive and test failures are not
  # indicative for package usability hence tests are disabled by default.
  doCheck = false;

  pythonImportsCheck = [ "pymc" ];

  meta = {
    description = "Bayesian estimation, particularly using Markov chain Monte Carlo (MCMC)";
    homepage = "https://github.com/pymc-devs/pymc";
    changelog = "https://github.com/pymc-devs/pymc/releases/tag/v${version}";
    license = lib.licenses.asl20;
    maintainers = with lib.maintainers; [
      nidabdella
      ferrine
    ];
  };
}

This errors out with:

error:
       … while calling the 'derivationStrict' builtin
         at <nix/derivation-internal.nix>:37:12:
           36|
           37|   strict = derivationStrict drvAttrs;
             |            ^
           38|

       … while evaluating derivation 'nix-shell'
         whose name attribute is located at /nix/store/3abvz230bn897gbja4y653jx152m9fqw-source/pkgs/stdenv/generic/make-derivation.nix:482:13

       … while evaluating attribute 'nativeBuildInputs' of derivation 'nix-shell'
         at /nix/store/3abvz230bn897gbja4y653jx152m9fqw-source/pkgs/stdenv/generic/make-derivation.nix:534:13:
          533|             depsBuildBuild = elemAt (elemAt dependencies 0) 0;
          534|             nativeBuildInputs = elemAt (elemAt dependencies 0) 1;
             |             ^
          535|             depsBuildTarget = elemAt (elemAt dependencies 0) 2;

       (stack trace truncated; use '--show-trace' to show the full, detailed trace)

       error: Dependency is not of a valid type: element 15 of nativeBuildInputs for nix-shell

Running --show-trace provides no useful extra info,
Any help is appreciated!

2

Your dev-shell is extremely unreadable, but the issue is that in pythonPkgs you use pymcLocal by itself, which you declared to be a function.

3

Yes! Thanks for the info, I wasn’t aware of typing since I’m not good at nix. Problem is how do I reference pymcLocal in the pythonPkgs list? Isn’t already using the myPython.pkgs namespace?

4

Just don’t use that pythonPkgs list, use the withPackages list and put myPython in your dev shell.