Set numpy and scipy as direct dependencies

These are currently installed as dependencies of dependencies. Since
they are directly imported in this codebase, they should be direct
dependencies with pinned versions.

Note: The latest version of scipy is 1.10.0, but 1.7.3 is the last
version compatible with Python 3.7 which is still supported by Augur.

setup.py

@@ -57,10 +57,12 @@
         "isodate ==0.6.*",
         "jsonschema >=3.0.0, ==3.*",
         "networkx >= 2.5, ==2.*",
+        "numpy ==1.*",
         "packaging >=19.2",
         "pandas >=1.0.0, ==1.*",
         "phylo-treetime >=0.9.3, ==0.9.*",
         "pyfastx >=0.8.4, ==0.8.*",
+        "scipy ==1.7.*",
         "xopen[zstd] >=1.7.0, ==1.*"
     ],
     extras_require = {