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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
Edited by Utkarsh Ayachit

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