Use composeExtensions to preserve existing Python package overrides

[mcwitt]

Resolves #183

This PR addresses the scenario where the qchem overlay is applied after another overlay that overrides Python packages. Currently, the previously-applied overrides will be lost due to Python overrides not composing by default (NixOS/nixpkgs#44426).

The following is a minimal reproduction:

let
  qchemOverlay = import ./overlay.nix;

  myOverlay = _: prev: {
    python3 = prev.python3.override {
      packageOverrides = (_: _: { foo = 42; });
    };
  };

  pkgs = import <nixpkgs> {
    overlays = [
      myOverlay
      qchemOverlay
    ];
  };
in
pkgs.qchem.python3.pkgs.foo

Currently, this expression fails to evaluate:

$ nix eval -f test.nix
error: attribute 'foo' missing

This PR modifies the qchem overlay to preserve existing overrides, using the variant of override that accepts a function from old to new overrides and lib.composeExtensions. This is similar to the approach used in tweag/jupyterWith.

[markuskowa]

Currently, this expression fails to evaluate:

$ nix eval -f test.nix
error: attribute 'foo' missing

nix-build test.nix works with this (e.g. use a real package):

let
  qchemOverlay = import ./overlay.nix;

  myOverlay = _: prev: {
    python3 = prev.python3.override {
      packageOverrides = (_: p: { foo = p.numpy; });
    };
  };

  pkgs = import <nixpkgs> {
    overlays = [
      myOverlay
      qchemOverlay
    ];
  };
in
pkgs.qchem.python3.pkgs.foo

[mcwitt]

nix-build test.nix works with this (e.g. use a real package):

@markuskowa ah, that's a more realistic reproduction!

Just to clarify, I assume you mean this works only on the PR branch? (Before the patch, this also fails for me, as expected)

[markuskowa]

Yes, it works on the PR branch, and now also on master.
Thanks for submitting this patch!