build(docker): upgrade to Ubuntu 24.04 and Python 3.12 (#458)

Closes reanahub/reana#808
reanahub · Aug 6, 2024 · f65641a · f65641a
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diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -10,7 +10,7 @@ on: [push, pull_request]
 
 jobs:
   lint-commitlint:
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-24.04
     steps:
       - name: Checkout
         uses: actions/checkout@v4
@@ -36,7 +36,7 @@ jobs:
           ./run-tests.sh --check-commitlint ${{ github.event.pull_request.head.sha }}~${{ github.event.pull_request.commits }} ${{ github.event.pull_request.head.sha }} ${{ github.event.pull_request.number }}
 
   lint-shellcheck:
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-24.04
     steps:
       - name: Checkout
         uses: actions/checkout@v4
@@ -47,15 +47,15 @@ jobs:
           ./run-tests.sh --check-shellcheck
 
   lint-black:
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-24.04
     steps:
       - name: Checkout
         uses: actions/checkout@v4
 
       - name: Setup Python
         uses: actions/setup-python@v5
         with:
-          python-version: "3.8"
+          python-version: "3.12"
 
       - name: Check Python code formatting
         run: |
@@ -64,15 +64,15 @@ jobs:
           ./run-tests.sh --check-black
 
   lint-flake8:
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-24.04
     steps:
       - name: Checkout
         uses: actions/checkout@v4
 
       - name: Setup Python
         uses: actions/setup-python@v5
         with:
-          python-version: "3.8"
+          python-version: "3.12"
 
       - name: Check compliance with pep8, pyflakes and circular complexity
         run: |
@@ -81,15 +81,15 @@ jobs:
           ./run-tests.sh --check-flake8
 
   lint-pydocstyle:
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-24.04
     steps:
       - name: Checkout
         uses: actions/checkout@v4
 
       - name: Setup Python
         uses: actions/setup-python@v5
         with:
-          python-version: "3.8"
+          python-version: "3.12"
 
       - name: Check compliance with Python docstring conventions
         run: |
@@ -98,15 +98,15 @@ jobs:
           ./run-tests.sh --check-pydocstyle
 
   lint-check-manifest:
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-24.04
     steps:
       - name: Checkout
         uses: actions/checkout@v4
 
       - name: Setup Python
         uses: actions/setup-python@v5
         with:
-          python-version: "3.8"
+          python-version: "3.12"
 
       - name: Check Python manifest completeness
         run: |
@@ -115,15 +115,15 @@ jobs:
           ./run-tests.sh --check-manifest
 
   docs-sphinx:
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-24.04
     steps:
       - name: Checkout
         uses: actions/checkout@v4
 
       - name: Setup Python
         uses: actions/setup-python@v5
         with:
-          python-version: "3.8"
+          python-version: "3.12"
 
       - name: Install system dependencies
         run: |
@@ -142,7 +142,7 @@ jobs:
         run: ./run-tests.sh --check-sphinx
 
   python-tests:
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-24.04
     steps:
       - name: Checkout
         uses: actions/checkout@v4
@@ -155,7 +155,7 @@ jobs:
       - name: Setup Python
         uses: actions/setup-python@v5
         with:
-          python-version: "3.8"
+          python-version: "3.12"
 
       - name: Install Python dependencies
         run: |
@@ -177,7 +177,7 @@ jobs:
           files: coverage.xml
 
   lint-dockerfile:
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-24.04
     steps:
       - name: Checkout
         uses: actions/checkout@v4
@@ -186,7 +186,7 @@ jobs:
         run: ./run-tests.sh --check-dockerfile
 
   docker-build:
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-24.04
     steps:
       - name: Checkout
         uses: actions/checkout@v4
@@ -195,7 +195,7 @@ jobs:
         run: ./run-tests.sh --check-docker-build
 
   release-docker:
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-24.04
     if: >
       vars.RELEASE_DOCKER == 'true' &&
       github.event_name == 'push' &&

diff --git a/.readthedocs.yaml b/.readthedocs.yaml
@@ -7,9 +7,9 @@
 version: 2
 
 build:
-  os: ubuntu-22.04
+  os: ubuntu-24.04
   tools:
-    python: "3.8"
+    python: "3.12"
 
 sphinx:
   configuration: docs/conf.py

diff --git a/Dockerfile b/Dockerfile
@@ -1,22 +1,20 @@
 # This file is part of REANA.
-# Copyright (C) 2017, 2018, 2019, 2020, 2021, 2022, 2023 CERN.
+# Copyright (C) 2017, 2018, 2019, 2020, 2021, 2022, 2023, 2024 CERN.
 #
 # REANA is free software; you can redistribute it and/or modify it
 # under the terms of the MIT License; see LICENSE file for more details.
 
 # Use Ubuntu LTS base image
-FROM docker.io/library/ubuntu:20.04
+FROM docker.io/library/ubuntu:24.04
 
 # Recognise target architecture
 ARG TARGETARCH
 
 # Use default answers in installation commands
 ENV DEBIAN_FRONTEND=noninteractive
 
-# Use distutils provided by the standard Python library instead of the vendored one in
-# setuptools, so that editable installations are stored in the right directory.
-# See https://github.com/pypa/setuptools/issues/3301
-ENV SETUPTOOLS_USE_DISTUTILS=stdlib
+# Allow pip to install packages in the system site-packages dir
+ENV PIP_BREAK_SYSTEM_PACKAGES=true
 
 # Prepare list of Python dependencies
 COPY requirements.txt /code/
@@ -28,15 +26,16 @@ RUN apt-get update -y && \
       gcc \
       krb5-config \
       krb5-user \
-      libauthen-krb5-perl \
+      libauthen-krb5-simple-perl \
       libkrb5-dev \
       openssh-client \
-      python3-gssapi \
+      # matches version in setup.py/requirements.in
+      python3-gssapi=1.8.2-1ubuntu1 \
       python3-pip \
-      python3.8 \
-      python3.8-dev \
+      python3.12 \
+      python3.12-dev \
       vim-tiny && \
-    pip install --no-cache-dir --upgrade pip 'setuptools<71' && \
+    pip install --no-cache-dir --upgrade setuptools && \
     pip install --no-cache-dir -r /code/requirements.txt && \
     apt-get remove -y \
       gcc && \
@@ -52,17 +51,12 @@ ARG COMPUTE_BACKENDS=kubernetes
 RUN if echo "$COMPUTE_BACKENDS" | grep -q "htcondorcern"; then \
       set -e; \
       apt-get update -y; \
-      apt-get install --no-install-recommends -y wget alien gnupg2 rand; \
-      wget -q -O ngbauth-submit.rpm https://linuxsoft.cern.ch/internal/repos/batch8s-stable/x86_64/os/Packages/n/ngbauth-submit-0.26-2.el8s.noarch.rpm; \
-      wget -q -O myschedd.rpm https://linuxsoft.cern.ch/internal/repos/batch8s-stable/x86_64/os/Packages/m/myschedd-1.9-2.el8s.x86_64.rpm; \
+      apt-get install --no-install-recommends -y wget alien gnupg2 condor; \
+      wget -q -O ngbauth-submit.rpm https://linuxsoft.cern.ch/internal/repos/batch9al-stable/x86_64/os/Packages/n/ngbauth-submit-0.31-1.al9.cern.noarch.rpm; \
+      wget -q -O myschedd.rpm https://linuxsoft.cern.ch/internal/repos/batch9al-stable/x86_64/os/Packages/m/myschedd-1.9-2.al9.cern.x86_64.rpm; \
       yes | alien -i myschedd.rpm; \
       yes | alien -i ngbauth-submit.rpm; \
       rm -rf myschedd.rpm ngbauth-submit.rpm; \
-      wget -qO - https://research.cs.wisc.edu/htcondor/repo/keys/HTCondor-9.0-Key | apt-key add -; \
-      echo "deb https://research.cs.wisc.edu/htcondor/repo/ubuntu/9.0 focal main" >> /etc/apt/sources.list; \
-      echo "deb-src https://research.cs.wisc.edu/htcondor/repo/ubuntu/9.0 focal main" >> /etc/apt/sources.list; \
-      apt-get update -y; \
-      apt-get install --no-install-recommends -y condor; \
       apt-get remove -y gnupg2 wget alien; \
       apt-get autoremove -y; \
       apt-get clean; \
@@ -131,6 +125,10 @@ ENV COMPUTE_BACKENDS=$COMPUTE_BACKENDS \
     FLASK_APP=reana_job_controller/app.py \
     TERM=xterm
 
+# Delete default `ubuntu` user, as its UID (1000) clashes with REANA's default one
+# See https://bugs.launchpad.net/cloud-images/+bug/2005129
+RUN userdel -r ubuntu
+
 # Expose ports to clients
 EXPOSE 5000
 

diff --git a/requirements.in b/requirements.in
@@ -5,4 +5,4 @@
 # under the terms of the MIT License; see LICENSE file for more details.
 
 paramiko[gssapi]==3.0.0
-gssapi==1.6.1
+gssapi==1.8.2 # matches version in Dockerfile
diff --git a/requirements.txt b/requirements.txt
@@ -1,82 +1,86 @@
 #
-# This file is autogenerated by pip-compile with Python 3.8
+# This file is autogenerated by pip-compile with Python 3.12
 # by the following command:
 #
 #    pip-compile --annotation-style=line --output-file=requirements.txt requirements.in setup.py
 #
-alembic==1.13.1           # via reana-db
+alembic==1.13.2           # via reana-db
 amqp==5.2.0               # via kombu
 apispec[yaml]==3.3.2      # via apispec-webframeworks, reana-job-controller (setup.py)
 apispec-webframeworks==0.5.2  # via reana-job-controller (setup.py)
 appdirs==1.4.4            # via fs
-attrs==23.2.0             # via jsonschema
-backports-zoneinfo[tzdata]==0.2.1  # via backports-zoneinfo, kombu
-bcrypt==4.1.2             # via paramiko
+arrow==1.3.0              # via isoduration
+attrs==23.2.0             # via jsonschema, referencing
+bcrypt==4.2.0             # via paramiko
 bracex==2.4               # via wcmatch
 bravado==10.3.2           # via reana-commons
 bravado-core==6.1.0       # via bravado, reana-commons
-cachetools==5.3.3         # via google-auth
-certifi==2024.2.2         # via kubernetes, requests
+cachetools==5.4.0         # via google-auth
+certifi==2024.7.4         # via kubernetes, requests
 cffi==1.16.0              # via cryptography, pynacl
 charset-normalizer==3.3.2  # via requests
 checksumdir==1.1.9        # via reana-commons
 click==8.1.7              # via flask, reana-commons
-cryptography==42.0.5      # via paramiko, sqlalchemy-utils
+cryptography==43.0.0      # via paramiko, sqlalchemy-utils
 decorator==5.1.1          # via gssapi
-flask==2.1.3              # via reana-job-controller (setup.py)
+flask==2.2.5              # via reana-job-controller (setup.py)
+fqdn==1.5.1               # via jsonschema
 fs==2.4.16                # via reana-commons, reana-job-controller (setup.py)
-google-auth==2.28.1       # via kubernetes
-gssapi==1.6.1             # via -r requirements.in, paramiko
-idna==3.6                 # via jsonschema, requests
-importlib-metadata==7.0.1  # via alembic, flask
-importlib-resources==6.1.2  # via alembic
-itsdangerous==2.1.2       # via flask
+google-auth==2.32.0       # via kubernetes
+greenlet==3.0.3           # via sqlalchemy
+gssapi==1.8.2             # via -r requirements.in, paramiko
+idna==3.7                 # via jsonschema, requests
+importlib-resources==6.4.0  # via swagger-spec-validator
+isoduration==20.11.0      # via jsonschema
+itsdangerous==2.2.0       # via flask
 jinja2==3.0.3             # via flask, reana-job-controller (setup.py)
-jsonpointer==2.4          # via jsonschema
+jsonpointer==3.0.0        # via jsonschema
 jsonref==1.1.0            # via bravado-core
-jsonschema[format]==3.2.0  # via bravado-core, reana-commons, swagger-spec-validator
-kombu==5.3.5              # via reana-commons
+jsonschema[format]==4.23.0  # via bravado-core, reana-commons, swagger-spec-validator
+jsonschema-specifications==2023.12.1  # via jsonschema
+kombu==5.3.7              # via reana-commons
 kubernetes==22.6.0        # via reana-commons
-mako==1.3.2               # via alembic
+mako==1.3.5               # via alembic
 markupsafe==2.1.5         # via jinja2, mako, werkzeug
-marshmallow==2.20.1       # via reana-job-controller (setup.py)
+marshmallow==2.21.0       # via reana-job-controller (setup.py)
 mock==3.0.5               # via reana-commons
 monotonic==1.6            # via bravado
-msgpack==1.0.7            # via bravado-core
+msgpack==1.0.8            # via bravado-core
 msgpack-python==0.5.6     # via bravado
 oauthlib==3.2.2           # via requests-oauthlib
 paramiko[gssapi]==3.0.0   # via -r requirements.in
 psycopg2-binary==2.9.9    # via reana-db
-pyasn1==0.5.1             # via paramiko, pyasn1-modules, rsa
-pyasn1-modules==0.3.0     # via google-auth
-pycparser==2.21           # via cffi
+pyasn1==0.6.0             # via paramiko, pyasn1-modules, rsa
+pyasn1-modules==0.4.0     # via google-auth
+pycparser==2.22           # via cffi
 pynacl==1.5.0             # via paramiko
-pyrsistent==0.20.0        # via jsonschema
-python-dateutil==2.9.0    # via bravado, bravado-core, kubernetes
+python-dateutil==2.9.0.post0  # via arrow, bravado, bravado-core, kubernetes
 pytz==2024.1              # via bravado-core
 pyyaml==6.0.1             # via apispec, bravado, bravado-core, kubernetes, reana-commons, swagger-spec-validator
-reana-commons[kubernetes]==0.95.0a2	# via reana-db, reana-job-controller (setup.py)
-reana-db==0.95.0a2	# via reana-job-controller (setup.py)
-requests==2.31.0          # via bravado, bravado-core, kubernetes, requests-oauthlib
-requests-oauthlib==1.3.1  # via kubernetes
+reana-commons[kubernetes]==0.95.0a3  # via reana-db, reana-job-controller (setup.py)
+reana-db==0.95.0a3        # via reana-job-controller (setup.py)
+referencing==0.35.1       # via jsonschema, jsonschema-specifications
+requests==2.32.3          # via bravado, bravado-core, kubernetes, requests-oauthlib
+requests-oauthlib==2.0.0  # via kubernetes
 retrying==1.3.4           # via reana-job-controller (setup.py)
+rfc3339-validator==0.1.4  # via jsonschema
 rfc3987==1.3.8            # via jsonschema
+rpds-py==0.19.0           # via jsonschema, referencing
 rsa==4.9                  # via google-auth
 simplejson==3.19.2        # via bravado, bravado-core
-six==1.16.0               # via bravado, bravado-core, fs, gssapi, jsonschema, kubernetes, mock, python-dateutil, retrying
-sqlalchemy==1.3.24        # via alembic, reana-db, sqlalchemy-utils
-sqlalchemy-utils[encrypted]==0.41.1  # via reana-db, sqlalchemy-utils
-strict-rfc3339==0.7       # via jsonschema
-swagger-spec-validator==3.0.3  # via bravado-core
-typing-extensions==4.10.0  # via alembic, bravado, kombu, swagger-spec-validator
-tzdata==2024.1            # via backports-zoneinfo
-urllib3==2.2.1            # via kubernetes, requests
+six==1.16.0               # via bravado, bravado-core, fs, kubernetes, mock, python-dateutil, retrying, rfc3339-validator
+sqlalchemy==1.4.52        # via alembic, reana-db, sqlalchemy-utils
+sqlalchemy-utils[encrypted]==0.41.2  # via reana-db, sqlalchemy-utils
+swagger-spec-validator==3.0.4  # via bravado-core
+types-python-dateutil==2.9.0.20240316  # via arrow
+typing-extensions==4.12.2  # via alembic, bravado, swagger-spec-validator
+uri-template==1.3.0       # via jsonschema
+urllib3==2.2.2            # via kubernetes, requests
 vine==5.1.0               # via amqp, kombu
 wcmatch==8.4.1            # via reana-commons
-webcolors==1.13           # via jsonschema
-websocket-client==1.7.0   # via kubernetes
-werkzeug==2.3.8           # via flask, reana-commons, reana-job-controller (setup.py)
-zipp==3.17.0              # via importlib-metadata, importlib-resources
+webcolors==24.6.0         # via jsonschema
+websocket-client==1.8.0   # via kubernetes
+werkzeug==2.2.3           # via flask, reana-commons, reana-job-controller (setup.py)
 
 # The following packages are considered to be unsafe in a requirements file:
 # setuptools