updated requirements for numpy 2.0

requirements.txt

@@ -1,18 +1,18 @@
-numpy>=1.24.0,<2
-matplotlib>=3.9.0
+numpy>=2.0.0,<3
+matplotlib>=3.9.2
 seaborn>=0.13.2
 statsmodels>=0.14.0
 scikit-learn>=1.4.0
 grid_strategy>=0.0.1
 pyyaml>=6.0
-UpSetPlot>=0.8.0
-matplotlib-venn>=0.11.9
-scipy>=1.13.0
+UpSetPlot>=0.9.0
+matplotlib-venn>=1.1.1
+scipy>=1.14.0
 scikit-learn-extra>=0.3.0
 pairwisedist>=1.3.1
 requests>=2.24.0
 graphviz>=0.20.1
-joblib>=1.2.0
+joblib>=1.4.2
 tqdm>=4.65
 appdirs>=1.4.0
 typing_extensions>=4.5
@@ -27,5 +27,5 @@ tenacity>=8.2.3
 mslex>=1.1.0
 nest-asyncio>=1.6.0
 fastcluster>=1.2.6
-polars[async,numpy,pyarrow,matplotlib,pandas]>=0.20.31
+polars[async,numpy,pyarrow,matplotlib,pandas]>=1.5.0
 pandas[performance,parquet]

requirements_extra.txt

@@ -3,10 +3,10 @@
 #
 # package[version_required]: tag1, tag2, ...
 
-hdbscan>=0.8.33:    hdbscan
-xlmhglite>=1.1.0:   single-set
-numba>=0.57.0:      randomization
-cutadapt>=4.4:      fastq
+hdbscan>=0.8.38:    hdbscan
+xlmhglite>=1.1.1:   single-set
+numba>=0.60.0:      randomization
+cutadapt>=4.9:      fastq
 pyvis>=0.3.2:       reports
 networkx>=3.0.0:    reports
 install-jdk>=1.1.0: picardtools