update various dependencies

bzip2 -> 1.0.8
hdf5 -> 1.12.0
python3 -> 3.9.0
freetype -> 2.10.2
libxml2 -> 2.9.10
nlohmannjson -> 3.9.1
numpy -> 1.19.2
scipy -> 1.5.2

held back:

matplotlib -> 3.3.2