Automatic reconfiguration of optical filters is the key to novel flexible RF photonic receivers and Software Defined Radios (SDRs). Although silicon photonics (SiP) is a promising technology platform to realize such receivers, process variations and lack of in-situ tuning capability limits the adoption of SiP filters in widely-tunable RF photonic receivers. To address this issue, this work presents a first 'in-situ' automatic reconfiguration algorithm and demonstrates a software configurable integrated optical filter that can be reconfigured on-the-fly based on user specifications. The presented reconfiguration scheme avoids the use of expensive and bulky equipment such as Optical Vector Network Analyzer (OVNA), does not use simulation data for reconfiguration, reduces the total number of thermo-optic tuning elements required and eliminates several time consuming configuration steps as in the prior art. This makes this filter ideal in a real world scenario where user specifies the filter center frequency, bandwidth, required rejection & filter type (Butterworth, Chebyshev, etc.) and the filter is automatically configured regardless of process, voltage & temperature (PVT) variations. We fabricated our design in AIM Photonics' Active SiP process and have demonstrated our reconfiguration algorithm for a second-order filter with 3dB bandwidth of 3 GHz, 2.2 dB insertion loss and >30 dB out-of-band rejection using only two reference laser wavelength settings. Since the filter photonic integrated circuit (PIC) is fabricated using a CMOS-compatible SiP foundry, the design is manufacturable with repeatable and scalable performance suited for its integration with electronics to realize complex chip-scale RF photonic systems.