fix: requirements.txt to reduce vulnerabilities

The following vulnerabilities are fixed by pinning transitive dependencies:
- https://snyk.io/vuln/SNYK-PYTHON-CERTIFI-3164749
- https://snyk.io/vuln/SNYK-PYTHON-CERTIFI-5805047
- https://snyk.io/vuln/SNYK-PYTHON-JOBLIB-3027033
- https://snyk.io/vuln/SNYK-PYTHON-NUMPY-2321964
- https://snyk.io/vuln/SNYK-PYTHON-NUMPY-2321966
- https://snyk.io/vuln/SNYK-PYTHON-NUMPY-2321969
- https://snyk.io/vuln/SNYK-PYTHON-NUMPY-2321970
- https://snyk.io/vuln/SNYK-PYTHON-REQUESTS-5595532
- https://snyk.io/vuln/SNYK-PYTHON-SCIKITLEARN-1079100
- https://snyk.io/vuln/SNYK-PYTHON-SCIKITLEARN-3186293
- https://snyk.io/vuln/SNYK-PYTHON-SCIPY-5756497
- https://snyk.io/vuln/SNYK-PYTHON-SCIPY-5759266
- https://snyk.io/vuln/SNYK-PYTHON-SETUPTOOLS-3180412

requirements.txt

@@ -4,7 +4,7 @@ intervaltree
 luigi
 more-itertools
 # for tf 2.6.0
-numpy==1.19.2
+numpy==1.22.2
 pandas
 pre-commit
 pynvml
@@ -25,3 +25,8 @@ tqdm
 numba==0.48
 #numba>=0.49.0 # not directly required, pinned by Snyk to avoid a vulnerability
 scikit-learn>=0.24.2 # not directly required, pinned by Snyk to avoid a vulnerability
+certifi>=2023.7.22 # not directly required, pinned by Snyk to avoid a vulnerability
+joblib>=1.1.1 # not directly required, pinned by Snyk to avoid a vulnerability
+requests>=2.31.0 # not directly required, pinned by Snyk to avoid a vulnerability
+scipy>=1.10.0rc1 # not directly required, pinned by Snyk to avoid a vulnerability
+setuptools>=65.5.1 # not directly required, pinned by Snyk to avoid a vulnerability