change base to ubuntu & update packages

cyvcf2 could not compile properly on alpine so changing base to slim

Author: blankdots

Dockerfile

@@ -1,33 +1,33 @@
-FROM python:3.10.12-alpine3.18 as BUILD
+FROM python:3.10.12-slim as BUILD
 
-RUN apk add --update \
-    && apk add --no-cache build-base curl-dev linux-headers bash git musl-dev\
-    && apk add --no-cache openssl-dev libffi-dev autoconf bzip2-dev xz-dev\
-    && apk add --no-cache python3-dev rust cargo \
-    && rm -rf /var/cache/apk/*
+RUN apt-get update \
+    && apt-get install -y build-essential bash git gcc \
+    && apt-get install -y zlib1g-dev liblzma-dev libcurl4-gnutls-dev libssl-dev libffi-dev autoconf libbz2-dev xz-utils \
+    && apt-get install -y python3-dev libdeflate-dev libncurses5-dev libncursesw5-dev libreadline-dev
 
 COPY requirements.txt /root/beacon/requirements.txt
 
 ENV CYTHONIZE=1
+# the following related to https://github.com/brentp/cyvcf2/issues/240#issuecomment-1534257675
+ENV LIBDEFLATE=1
 
-RUN pip install --upgrade pip && \
-    pip install Cython==0.29.26 && \
-    pip install -r /root/beacon/requirements.txt
+RUN pip install --upgrade pip \
+    && pip install -r /root/beacon/requirements.txt
 
 COPY setup.py /root/beacon/setup.py
 COPY beacon_api /root/beacon/beacon_api
 RUN pip install /root/beacon
 
-FROM python:3.10.12-alpine3.18
+FROM python:3.10.12-slim
 
-RUN apk add --no-cache --update bash
+RUN apt-get install -y bash
 
 LABEL maintainer "CSC Developers"
 LABEL org.label-schema.schema-version="1.0"
 LABEL org.label-schema.vcs-url="https://github.com/CSCFI/beacon-python"
 
-RUN apk add --update \
-    && apk add --no-cache curl bzip2 xz
+RUN apt-get update \
+    && apt-get install -y curl bzip2 xz-utils
 
 COPY --from=BUILD usr/local/lib/python3.10/ usr/local/lib/python3.10/
 

requirements.txt

@@ -1,11 +1,11 @@
 aiohttp==3.8.4
 aiohttp-cors==0.7.0
-asyncpg==0.27.0
-jsonschema==4.17.3
-Cython==0.29.35
-cyvcf2==0.30.18
+asyncpg==0.28.0
+jsonschema==4.18.3
+Cython==3.0.0
+cyvcf2==0.30.22
 uvloop==0.17.0
 aiocache==0.11.1
 ujson==5.8.0
 Authlib==1.2.0
-gunicorn==20.1.0
+gunicorn==21.0.1

setup.py

@@ -36,22 +36,22 @@
         "Programming Language :: Python :: 3.10",
     ],
     install_requires=[
-        "asyncpg==0.27.0",
+        "asyncpg==0.28.0",
         "aiohttp==3.8.4",
         "Authlib==1.2.0",
         "aiohttp-cors==0.7.0",
-        "jsonschema==4.17.3",
-        "gunicorn==20.1.0",
+        "jsonschema==4.18.3",
+        "gunicorn==21.0.1",
         "uvloop==0.17.0",
-        "cyvcf2==0.30.18",
+        "cyvcf2==0.30.22",
         "aiocache==0.11.1",
         "ujson==5.8.0",
     ],
     extras_require={
         "vcf": [
-            "numpy==1.25.0",
-            "cyvcf2==0.30.18",
-            "Cython==0.29.35",
+            "numpy==1.25.1",
+            "cyvcf2==0.30.22",
+            "Cython==3.0.0",
         ],
         "test": [
             "coverage==7.2.7",
@@ -62,7 +62,7 @@
             "flake8==6.0.0",
             "flake8-docstrings==1.7.0",
             "aioresponses==0.7.4",
-            "black==23.3.0",
+            "black==23.7.0",
         ],
         "docs": ["sphinx >= 1.4", "sphinx_rtd_theme==1.2.2"],
     },