Updating and upgrading deps

Dockerfile

@@ -1,4 +1,4 @@
-FROM python:3.11-slim-bookworm
+FROM python:3.12-slim-bookworm
 LABEL org.opencontainers.image.authors="[email protected],[email protected],[email protected]"
 
 # Install prerequisites
@@ -18,7 +18,7 @@ RUN cd /usr/local/share/deenurp/ && \
     PYTHON=/usr/local/bin/python3 \
     DEENURP=/usr/local/share/deenurp/ \
     bin/bootstrap.sh /usr/local/ \
-    pip install --upgrade --requirement requirements.txt
+    pip install --requirement requirements.txt --root-user-action=ignore
 
 # clean up sources apt packages
 RUN rm -rf /var/lib/apt/lists/* && \

requirements.txt

@@ -1,31 +1,32 @@
-biopython==1.83
-Cython==0.29.37
+biopython==1.84
+Cython==3.0.11
 decorator==5.1.1
-deenurp @ file:///mnt/home/crosenth/src/ya16sdb/src/deenurp
 DendroPy==5.0.1
 fastalite==0.4.1
 greenlet==3.0.3
-hdbscan==0.8.37
+hdbscan==0.8.38.post1
 Jinja2==3.1.4
 joblib==1.4.2
 MarkupSafe==2.1.5
-numpy==1.26.4
+numpy==2.0.1
 packaging==24.1
 pandas==2.2.2
-psycopg==3.1.19
-psycopg-binary==3.1.19
+psycopg==3.2.1
+psycopg-binary==3.2.1
 psycopg2-binary==2.9.9
 pygtrie==2.5.0
 python-dateutil==2.9.0.post0
 pytz==2024.1
-PyYAML==6.0.1
-scikit-learn==1.5.0
+PyYAML==6.0.2
+scikit-learn==1.5.1
 scipy==1.14.0
 seqmagick==0.8.6
+setuptools==72.1.0
 six==1.16.0
-SQLAlchemy==2.0.31
-sqlparse==0.5.0
+SQLAlchemy==2.0.32
+sqlparse==0.5.1
 taxtastic==0.10.0
 threadpoolctl==3.5.0
 typing_extensions==4.12.2
 tzdata==2024.1
+wheel==0.44.0