  We introduce an open-source and unified framework for transition analysis for
laminar boundary layer natural transition at transonic conditions and over
complex geometries, where surface irregularities may be present. Different
computational tools are integrated in the framework, and therefore overcomes
the difficulties of two separate and usually quite disparate processes when
using $e^N$ method for transition analysis. To generate a baseflow with desired
pressure distribution, appropriate pressure compatible inflow boundary
condition needs to be developed and enforced. We first derive the system for 1D
numerical stability analysis for boundary conditions, and construct three types
of pressure compatible inflow. We demonstrate that the entropy-pressure
compatible inflow is stable unlike other choices. Compared with the steady
baseflow computation, the unsteady simulation for the disturbance field is more
challenging for compressible flows because of complex wave reflections, which
can easily contaminate the results. We therefore introduce the two main sources
of wave decontamination and corresponding methods to obtain clean signal. The
workflow within the framework is then verified by computing the disturbance
development in 2D flat plate boundary layer flows at Mach $0.8$. The
$N$-factors over a clean flat plate and a flat plate with a forward-facing step
are generated, and agree well with the results from the reference. Following
the verified workflow, We then analyze the disturbance growth on a wing section
of the CRM-NLF model. The N-factor on a 2D simulation is generated and studied.
