build(docker): upgrade to Ubuntu 24.04 and Python 3.12 (#283)

Author: wirespecter

.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: |
@@ -140,15 +140,15 @@ 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
 
       - name: Setup Python
         uses: actions/setup-python@v5
         with:
-          python-version: "3.8"
+          python-version: "3.12"
 
       - name: Install Python dependencies
         run: |
@@ -166,7 +166,7 @@ jobs:
           files: coverage.xml
 
   lint-dockerfile:
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-24.04
     steps:
       - name: Checkout
         uses: actions/checkout@v4
@@ -175,7 +175,7 @@ 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
@@ -184,7 +184,7 @@ 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' &&

.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

AUTHORS.md

@@ -19,5 +19,6 @@ The list of contributors in alphabetical order:
 - [Parth Shandilya](https://github.com/ParthS007)
 - [Rokas Maciulaitis](https://orcid.org/0000-0003-1064-6967)
 - [Sinclert Pérez](https://www.linkedin.com/in/sinclert)
+- [Stavros Moiras](https://orcid.org/0009-0005-4331-096X)
 - [Tibor Simko](https://orcid.org/0000-0001-7202-5803)
 - [Vladyslav Moisieienkov](https://orcid.org/0000-0001-9717-0775)

Dockerfile

@@ -1,19 +1,17 @@
 # This file is part of REANA.
-# Copyright (C) 2018, 2019, 2020, 2021, 2022, 2023 CERN.
+# Copyright (C) 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
 
 # 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/
@@ -24,15 +22,15 @@ RUN apt-get update -y && \
     apt-get install --no-install-recommends -y \
       gcc \
       nodejs \
-      python3.8 \
-      python3-dev \
+      python3.12 \
+      python3.12-dev \
       python3-pip \
       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 \
-      python3-dev && \
+      python3.12-dev && \
     apt-get autoremove -y && \
     apt-get clean && \
     rm -rf /var/lib/apt/lists/*

reana_workflow_engine_cwl/cwl_reana.py

@@ -488,7 +488,7 @@ def is_done(self, operation):
         if operation["status"] in terminal_states:
             log.info(
                 f"[job {self.name}] FINAL JOB STATE: "
-                f"{ operation['status']} ------------------"
+                f"{operation['status']} ------------------"
             )
             if operation["status"] == "finished":
                 self.rcode = 0

requirements.txt

@@ -1,72 +1,75 @@
 #
-# 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 setup.py
 #
 amqp==5.2.0               # via kombu
 appdirs==1.4.4            # via fs
-argcomplete==3.2.2        # via cwltool
-attrs==23.2.0             # via jsonschema
-backports-zoneinfo[tzdata]==0.2.1  # via backports-zoneinfo, kombu
+argcomplete==3.4.0        # via cwltool
+arrow==1.3.0              # via isoduration
+attrs==23.2.0             # via jsonschema, referencing
 bagit==1.8.1              # via cwltool
 bracex==2.4               # via wcmatch
 bravado==10.3.2           # via reana-commons
 bravado-core==6.1.0       # via bravado, reana-commons
-cachecontrol[filecache]==0.13.1  # via cachecontrol, schema-salad
-certifi==2024.2.2         # via requests
+cachecontrol[filecache]==0.14.0  # via cachecontrol, schema-salad
+certifi==2024.7.4         # via requests
 charset-normalizer==3.3.2  # via requests
 checksumdir==1.1.9        # via reana-commons
 click==8.1.7              # via reana-commons
 coloredlogs==15.0.1       # via cwltool
 cwltool==3.1.20210628163208  # via reana-commons
-filelock==3.13.1          # via cachecontrol
+filelock==3.15.4          # via cachecontrol
+fqdn==1.5.1               # via jsonschema
 fs==2.4.16                # via reana-commons
 humanfriendly==10.0       # via coloredlogs
-idna==3.6                 # via jsonschema, requests
-importlib-resources==6.1.2  # via schema-salad
+idna==3.7                 # via jsonschema, requests
+importlib-resources==6.4.0  # via swagger-spec-validator
 isodate==0.6.1            # via rdflib
-jsonpointer==2.4          # via jsonschema
+isoduration==20.11.0      # 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
-lxml==5.1.0               # via prov
+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
+lxml==5.2.2               # via prov
 markupsafe==2.1.5         # via werkzeug
-mistune==2.0.5            # via schema-salad
+mistune==3.0.2            # via schema-salad
 mock==3.0.5               # via reana-commons
 monotonic==1.6            # via bravado
-msgpack==1.0.7            # via bravado-core, cachecontrol
+msgpack==1.0.8            # via bravado-core, cachecontrol
 msgpack-python==0.5.6     # via bravado
 mypy-extensions==1.0.0    # via cwltool, schema-salad
-networkx==3.1             # via prov
+networkx==3.3             # via prov
 prov==1.5.1               # via cwltool
-psutil==5.9.8             # via cwltool
-pydot==2.0.0              # via cwltool
-pyparsing==3.1.1          # via pydot, rdflib
-pyrsistent==0.20.0        # via jsonschema
-python-dateutil==2.9.0    # via bravado, bravado-core, prov
+psutil==6.0.0             # via cwltool
+pydot==3.0.1              # via cwltool
+pyparsing==3.1.2          # via pydot, rdflib
+python-dateutil==2.9.0.post0  # via arrow, bravado, bravado-core, prov
 pytz==2024.1              # via bravado-core
 pyyaml==6.0.1             # via bravado, bravado-core, reana-commons, swagger-spec-validator
 rdflib==5.0.0             # via cwltool, prov, schema-salad
-reana-commons[cwl]==0.95.0a2	# via reana-workflow-engine-cwl (setup.py)
-requests==2.31.0          # via bravado, bravado-core, cachecontrol, cwltool, schema-salad
+reana-commons[cwl]==0.95.0a3  # via reana-workflow-engine-cwl (setup.py)
+referencing==0.35.1       # via jsonschema, jsonschema-specifications
+requests==2.32.3          # via bravado, bravado-core, cachecontrol, cwltool, schema-salad
+rfc3339-validator==0.1.4  # via jsonschema
 rfc3987==1.3.8            # via jsonschema
+rpds-py==0.19.0           # via jsonschema, referencing
 ruamel-yaml==0.17.10      # via cwltool, schema-salad
-ruamel-yaml-clib==0.2.8   # via ruamel-yaml
-schema-salad==8.5.20240102191335  # via cwltool
+schema-salad==8.7.20240718183047  # via cwltool
 shellescape==3.8.1        # via cwltool
 simplejson==3.19.2        # via bravado, bravado-core
-six==1.16.0               # via bravado, bravado-core, fs, isodate, jsonschema, mock, prov, python-dateutil, rdflib
-strict-rfc3339==0.7       # via jsonschema
-swagger-spec-validator==3.0.3  # via bravado-core
-typing-extensions==4.10.0  # via bravado, cwltool, kombu, swagger-spec-validator
-tzdata==2024.1            # via backports-zoneinfo
-urllib3==2.2.1            # via requests
+six==1.16.0               # via bravado, bravado-core, fs, isodate, mock, prov, python-dateutil, rdflib, rfc3339-validator
+swagger-spec-validator==3.0.4  # via bravado-core
+types-python-dateutil==2.9.0.20240316  # via arrow
+typing-extensions==4.12.2  # via bravado, cwltool, swagger-spec-validator
+uri-template==1.3.0       # via jsonschema
+urllib3==2.2.2            # via requests
 vine==5.1.0               # via amqp, kombu
 wcmatch==8.4.1            # via reana-commons
-webcolors==1.13           # via jsonschema
-werkzeug==3.0.1           # via reana-commons
-zipp==3.17.0              # via importlib-resources
+webcolors==24.6.0         # via jsonschema
+werkzeug==3.0.3           # via reana-commons
 
 # The following packages are considered to be unsafe in a requirements file:
 # setuptools

setup.py

@@ -75,7 +75,7 @@
         "License :: OSI Approved :: MIT License",
         "Operating System :: OS Independent",
         "Programming Language :: Python :: 3",
-        "Programming Language :: Python :: 3.8",
+        "Programming Language :: Python :: 3.12",
         "Programming Language :: Python :: Implementation :: CPython",
         "Programming Language :: Python",
         "Topic :: Internet :: WWW/HTTP :: Dynamic Content",