gistfile1.txt

I am defining the overlay (for pkgs, python2Packages, python3Packages and nodePackages) like this:
https://github.com/betaboon/nixcfg/blob/wip-restructure/packages/overlay.nix

I am using it in a basic system-configuration like this:
https://github.com/betaboon/nixcfg/blob/wip-restructure/config/base-small.nix#L12

which is used a system or container configuration as an import, like this:
https://github.com/betaboon/nixcfg/blob/wip-restructure/machines/vps/containers/taiga.nix#L46

The service that is supposed to use a python-package with python3:
https://github.com/betaboon/nixcfg/blob/wip-restructure/options/services/web-apps/taiga.nix#L29

And the python-package:
https://github.com/betaboon/nixcfg/blob/wip-restructure/packages/development/python-modules/taiga-back/default.nix

nixos-rebuild runs into:

building Nix...
building the system configuration...
these derivations will be built:
  /nix/store/y069dx3fnh0mz875swfmjdqpry4gflx5-python3.5-django-sampledatahelper-0.4.1.drv
  /nix/store/k5d0b6pnml3zgf9vy9yrbfak8q8vi10k-taiga-back-3.1.0.drv
  /nix/store/aas2rm3jidr85m2f648cbvryw507cd92-taiga-back-config-package.drv
  /nix/store/cdg7xfan24hw6nciy2sd2iq2jr5yk90a-unit-script.drv
  /nix/store/q75gjmh30r6sfjsg76lvii12g78wwxrv-python3-3.5.3-env.drv
  /nix/store/znvm2yr0gxx2bak26y065glhz27xj1qd-unit-taiga-back.service.drv
  /nix/store/brwwdxy8s1i2h9nj3vj68xq4v95g0jbp-system-units.drv
  /nix/store/qj0nz3vkmrp386gv789b8152sr4x30l5-etc.drv
  /nix/store/1z232rkkvr7mm7vyjwmlql980i9mpmrs-nixos-system-taiga-17.03.1665.055e5c3578.drv
  /nix/store/i1khldnx5lxldvkjw14p55la06dgzac3-etc-taiga.conf.drv
  /nix/store/j2m357f9yc8q34ak8ggxj7il6r4g7wyj-unit-container-taiga.service.drv
  /nix/store/jl410n2aqz0cljvkja9lmdisyha65qh5-system-units.drv
  /nix/store/903dfd5c82nah0yckqcq9skms65s90m4-etc.drv
  /nix/store/5z8v4f18h5922sph6y156b9gzclnn1sd-nixos-system-gargantua1-17.03.1665.055e5c3578.drv
building path(s) ‘/nix/store/abi9m2spsz98qpa8zzh5lanlj3f0fvg6-python3.5-django-sampledatahelper-0.4.1’
unpacking sources
unpacking source archive /nix/store/yyvb288andh9q9fh6gq67966ivy57ipb-django-sampledatahelper-0.4.1.tar.gz
source root is django-sampledatahelper-0.4.1
setting SOURCE_DATE_EPOCH to timestamp 1480575706 of file django-sampledatahelper-0.4.1/setup.cfg
patching sources
configuring
building

Installed /tmp/nix-build-python3.5-django-sampledatahelper-0.4.1.drv-0/django-sampledatahelper-0.4.1/.eggs/versiontools-1.9.1-py3.5.egg
/nix/store/c7kxm7wdkbkgx5spw92j5kvnwhfbd2hb-python2.7-setuptools-30.2.0/lib/python2.7/site-packages/setuptools-30.2.0-py2.7.egg/setuptools/dist.py:340: UserWarning: The version specified (':versiontools:versiontools') is an invalid version, this may not work as expected with newer versions of setuptools, pip, and PyPI. Please see PEP 440 for more details.
usage: nix_run_setup.py [global_opts] cmd1 [cmd1_opts] [cmd2 [cmd2_opts] ...]
   or: nix_run_setup.py --help [cmd1 cmd2 ...]
   or: nix_run_setup.py --help-commands
   or: nix_run_setup.py cmd --help

error: invalid command 'bdist_wheel'
builder for ‘/nix/store/y069dx3fnh0mz875swfmjdqpry4gflx5-python3.5-django-sampledatahelper-0.4.1.drv’ failed with exit code 1
cannot build derivation ‘/nix/store/k5d0b6pnml3zgf9vy9yrbfak8q8vi10k-taiga-back-3.1.0.drv’: 1 dependencies couldn't be built
cannot build derivation ‘/nix/store/aas2rm3jidr85m2f648cbvryw507cd92-taiga-back-config-package.drv’: 1 dependencies couldn't be built
cannot build derivation ‘/nix/store/cdg7xfan24hw6nciy2sd2iq2jr5yk90a-unit-script.drv’: 1 dependencies couldn't be built
cannot build derivation ‘/nix/store/q75gjmh30r6sfjsg76lvii12g78wwxrv-python3-3.5.3-env.drv’: 3 dependencies couldn't be built
cannot build derivation ‘/nix/store/znvm2yr0gxx2bak26y065glhz27xj1qd-unit-taiga-back.service.drv’: 3 dependencies couldn't be built
cannot build derivation ‘/nix/store/brwwdxy8s1i2h9nj3vj68xq4v95g0jbp-system-units.drv’: 1 dependencies couldn't be built
cannot build derivation ‘/nix/store/qj0nz3vkmrp386gv789b8152sr4x30l5-etc.drv’: 1 dependencies couldn't be built
cannot build derivation ‘/nix/store/1z232rkkvr7mm7vyjwmlql980i9mpmrs-nixos-system-taiga-17.03.1665.055e5c3578.drv’: 1 dependencies couldn't be built
cannot build derivation ‘/nix/store/i1khldnx5lxldvkjw14p55la06dgzac3-etc-taiga.conf.drv’: 1 dependencies couldn't be built
cannot build derivation ‘/nix/store/j2m357f9yc8q34ak8ggxj7il6r4g7wyj-unit-container-taiga.service.drv’: 1 dependencies couldn't be built
cannot build derivation ‘/nix/store/jl410n2aqz0cljvkja9lmdisyha65qh5-system-units.drv’: 1 dependencies couldn't be built
cannot build derivation ‘/nix/store/903dfd5c82nah0yckqcq9skms65s90m4-etc.drv’: 2 dependencies couldn't be built
cannot build derivation ‘/nix/store/5z8v4f18h5922sph6y156b9gzclnn1sd-nixos-system-gargantua1-17.03.1665.055e5c3578.drv’: 1 dependencies couldn't be built
error: build of ‘/nix/store/5z8v4f18h5922sph6y156b9gzclnn1sd-nixos-system-gargantua1-17.03.1665.055e5c3578.drv’ failed

Why are you importing the top-level sets? These are the ones from Nixpkgs, right?
https://github.com/betaboon/nixcfg/blob/wip-restructure/packages/overlay.nix#L6
https://github.com/betaboon/nixcfg/blob/wip-restructure/packages/overlay.nix#L10
No need to touch those.

Instead of considering individual Python packages you may need to put them in an environment (e.g. python.WithPackages) if they need to be able to import modules from each other.
https://github.com/betaboon/nixcfg/blob/wip-restructure/options/services/web-apps/taiga.nix#L29