Japan was under heavy rain last week and some towns in the provinces of Hiroshima and Okayama, west of Kyoto and Osaka, were severely affected. However, Kyoto and Osaka are fine, and Tokyo, east of Kyoto, is also fine. Since all transportation in Kyoto, Osaka, Tokyo are fully operational, you do not need to worry about the climate and floods when you come to Kyoto. If you were planning to visit Hiroshima or Okayama for your excursion, I do not advice you to go there this time.
Currently, rain stopped in Kyoto and sunny days will start from tomorrow. So, please be advised to prepare for a hot summer.