Recently, saga algorithm disappeared from the processing panel. However, they are still listed under processing->options.
How to make them available again?
According to this link, from QGIS 2.18.10, only SAGA 2.3 is supported in QGIS.
However, in the OSGeo4W installer, the standard saga version is 2.1.2.2, whereas the LTR version is 2.3.
By installing the LTR version instead of the normal one, the tools are back in the processing panel and usable both within QGIS and with python script.