For the theist, spirit is exogenous. God is spirit. The Word becomes flesh. There is an incarnation of spirit into a holistic body-spirit being, a human being.
For the atheist, spirit is endogenous. The physical generates and hosts the metaphysical in a prevenient philosophy. For both interpretations, human being is both body and spirit. The result appears the same, but is arrived at from opposite syntheses.
In the atheist interpretation, spirituality is authentically human, and not a divine implant. The same applies to atheist ethics, which are essentially human and not divine dictat. We are good because we choose the good, rather than because we are commanded to be good. Theist ethics deny human agency and render us moral robots.
Reductionist versions of atheism insist on total physicalism. But physicalism does not deny intellect and emotion, and so does not necessarily deny spirituality. Physicalism has no account for metaphysical intellect, emotion and spirit, but their existence is evident. The building becomes a home, the sound notes become a symphony. Meaning is a metaphysical interpretation.
Secular society has migrated to a more physical focus. This is however a very partial shift, in which intellect and emotion have been preserved, but spirituality less so. The result is the pervasive rationalist-materialist consumer society. This is an unsatisfying and unsatisfactory state. There is an urgent need to rediscover and redefine a human spirituality. Otherwise we live an unexamined life whose value is compromised.
Recent writing on the meaning of life compares theistic, objective natural, and subjective natural accounts, the majority of authors favouring an objective natural understanding. Human spirituality is by definition natural, and need not fear a subjective reference.
What is the substance of a human spirituality? For some writers, it is mysticism. But this forces spirituality to oppose rational Enlightenment, and is accessible to few initiated people on very limited occasions. It is essentially gnostic. A more general accessible spirituality is needed. A contender for the definition of human spirituality is virtue.