From 96d3cc964d4d6e2d723fdf3d27f94ac2ae0e5497 Mon Sep 17 00:00:00 2001 From: Chris Rosenthal Date: Wed, 7 Aug 2024 12:03:50 -0700 Subject: [PATCH] Updating and upgrading deps --- Dockerfile | 4 ++-- requirements.txt | 23 ++++++++++++----------- 2 files changed, 14 insertions(+), 13 deletions(-) diff --git a/Dockerfile b/Dockerfile index 7b3e03a..0d4f9a9 100644 --- a/Dockerfile +++ b/Dockerfile @@ -1,4 +1,4 @@ -FROM python:3.11-slim-bookworm +FROM python:3.12-slim-bookworm LABEL org.opencontainers.image.authors="sminot@fredhutch.org,nhoffman@uw.edu,crosenth@uw.edu" # 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/* && \ diff --git a/requirements.txt b/requirements.txt index 11a1c89..de3fead 100644 --- a/requirements.txt +++ b/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