Python Nix表达式构建报错[Errno 13] Permission denied如何解决

• 直接原因：Nix的/nix/store路径是全局只读的，你构建自定义markdown-it-py 1.1.0时，pip检测到构建环境中已经存在来自nixpkgs官方源的旧版本markdown-it-py 1.0.0，尝试卸载旧版本修改/nix/store内容，触发权限不足报错。
• 根本原因：你的配置存在依赖版本冲突：
  1. 你在jupyter-book的Nix表达式中单独定义了1.1.0版本的markdown-it-py，但jupytext的依赖声明中用的是python3Packages.markdown-it-py（即nixpkgs自带的1.0.0版本）
  2. 你自定义的markdown-it-py依赖python3Packages.mdit-py-plugins，而这个包本身依赖官方源的旧版本markdown-it-py 1.0.0，导致两个版本同时被引入构建环境。

推荐通过Nix overlay全局覆盖Python包版本，确保所有依赖都使用同一版本的相关包，避免冲突：

1. 修改flake.nix，新增overlay覆盖需要自定义版本的Python包：

{
  description = "Introduction to Computational Literary Analysis, a Textbook";

  outputs = { self, nixpkgs }: let
    system = "x86_64-linux";
    # 定义覆盖Python包的overlay
    pythonOverlay = final: prev: {
      python3Packages = prev.python3Packages.overrideScope (pyFinal: pyPrev: {
        attrs = pyPrev.buildPythonPackage rec {
          pname = "attrs";
          version = "20.3.0";
          src = pyPrev.fetchPypi {
            inherit pname version;
            sha256 = "007pchhxk2nh6m2rgflkkij9xjwysq3fl7xr72cy8i4pw76s6al3";
          };
          doCheck = false;
        };
        click = pyPrev.buildPythonPackage rec {
          pname = "click";
          version = "7.1";
          src = pyPrev.fetchPypi {
            inherit pname version;
            sha256 = "1qk0x1bh6pmn2al9kq6cbgvm7pchnzl6ahf4zzpbjljl5lpmabs8";
          };
        };
        markdown-it-py = pyPrev.buildPythonPackage rec {
          pname = "markdown-it-py";
          version = "1.1.0";
          src = pyPrev.fetchFromGitHub {
            owner = "executablebooks";
            repo = "markdown-it-py";
            rev = "1d27af1da41fd3b00da8307040e6e274925437b2";
            sha256 = "priZH3ZbJxLm4drYt5Br5BWe+OSf4ZM0tpU7zPKw+UA=";
          };
          propagatedBuildInputs = [
            pyFinal.attrs pyFinal.mdit-py-plugins
          ];
          doCheck = false;
        };
      });
    };
    # 导入nixpkgs时应用overlay
    pkgs = import nixpkgs { inherit system; overlays = [ pythonOverlay ]; };
  in {
    jupyterBook = pkgs.callPackage ./jupyter-book.nix {};

    myPython = (pkgs.python3.withPackages
      (ps: with ps; [
        jupyter
        jupyterlab
        self.jupyterBook
        pandas
        nltk
      ]));

    defaultPackage.${system} = self.myPython;
  };
}

2. 简化jupyter-book.nix，删除原本单独定义的attrs20、click、markdown-it-py等包，直接使用overlay覆盖后的python3Packages中的对应版本：

{ python3Packages, fetchFromGitHub }:

let
  inherit (python3Packages) buildPythonPackage fetchPypi;
  jupytext = buildPythonPackage rec {
    pname = "jupytext";
    version = "1.10.3";
    src = fetchPypi {
      inherit pname version;
      sha256 = "09f0ra3ndq4sxb0q3pjx713pfyc731y6fkzx93481mc7qm2cym5x";
    };
    propagatedBuildInputs = with python3Packages; [
      toml
      pyyaml
      markdown-it-py
    ];
  };
  sphinxExternalTOC = buildPythonPackage rec {
    pname = "sphinx-external-toc";
    version = "0.2.2";
    src = fetchPypi {
      pname = "sphinx_external_toc";
      inherit version;
      sha256 = "a72c5861f670f1c7a1b92f2159fc9c7c5370e079cad1e3a7be4b269fa8048e8a";
    };
    propagatedBuildInputs = with python3Packages; [
      sphinx
      attrs
      click
      pyyaml
    ];
  };
  sphinxComments = buildPythonPackage rec {
    pname = "sphinx-comments";
    version = "0.0.3";
    src = fetchPypi {
      inherit version pname;
      sha256 = "00170afff27019fad08e421da1ae49c681831fb2759786f07c826e89ac94cf21";
    };
    propagatedBuildInputs = with python3Packages; [
      sphinx
    ];
  };
in buildPythonPackage rec {
  pname = "jupyter-book";
  version = "0.11.2";
  src = fetchPypi {
    inherit version pname;
    sha256 = "e32298e03c19f514c745062891143693c5e001a098bae9d59d2e4434b2099c54";
  };
  propagatedBuildInputs = with python3Packages; [
    attrs
    linkify-it-py
    sphinx
    sphinxComments
    sphinxExternalTOC
    jupytext
  ];
}

这种方案会让所有Python包的依赖树都使用你指定版本的attrs、click、markdown-it-py，不会出现多版本冲突，pip也就不会尝试卸载只读路径下的旧版本包。

内容的提问来源于stack exchange，提问作者Jonathan