We present preliminary results for the contributions to the neutron EDM arising from the QCD $\theta$-term, the Weinberg three-gluon and the quark chromo-EDM operators from our ongoing lattice calculations using clover valence quarks on the MILC HISQ lattices. We use the gradient-flow technique to smooth the lattices and renormalize the gluonic operators, and use the Schwinger source method to incorporate the quark chromo-EDM interactions in the quark propagator. For the QCD $\theta$-term and the Weinberg three-gluon operator, we report results in the gradient-flow scheme from 8 ensembles at four lattice spacings and three pion masses, including 2 physical pion mass ensembles. For the quark chromo-EDM, unrenormalized results are presented at two lattice spacings, $a=0.12$ and $0.09$ fm, and two pion masses, $M_\pi = 310$ MeV and $220$ MeV.