build(docker): upgrade base image to ubuntu 24.04 (#99)

reanahub · Aug 2, 2024 · b265591 · b265591
1 parent 2dd079e
commit b265591
Show file tree

Hide file tree

Showing 6 changed files with 75 additions and 71 deletions.
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.base.sha }} ${{ 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: |
@@ -134,35 +134,35 @@ jobs:
       - name: Install system dependencies
         run: |
           sudo apt-get update -y
-          sudo apt-get install python3-dev graphviz libgraphviz-dev pkg-config
+          sudo apt-get install python3.12-dev graphviz libgraphviz-dev pkg-config uuid-dev
 
       - name: Install Python dependencies
         run: |
-          pip install --upgrade pip 'setuptools<65.6' py wheel
+          pip install --upgrade pip 'setuptools' py wheel
           pip install -e .[all]
 
       - name: Run Sphinx documentation with doctests
         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 system dependencies
         run: |
           sudo apt-get update -y
-          sudo apt-get install python3-dev graphviz libgraphviz-dev pkg-config
+          sudo apt-get install python3.12-dev graphviz libgraphviz-dev pkg-config uuid-dev
 
       - name: Install Python dependencies
         run: |
-          pip install --upgrade pip 'setuptools<65.6' py
+          pip install --upgrade pip 'setuptools' py
           pip install twine wheel
           pip install -e .[all]
 
@@ -176,7 +176,7 @@ jobs:
           files: coverage.xml
 
   lint-dockerfile:
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-24.04
     steps:
       - name: Checkout
         uses: actions/checkout@v4
@@ -185,7 +185,7 @@ 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
@@ -194,7 +194,7 @@ 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/AUTHORS.md b/AUTHORS.md
@@ -9,5 +9,6 @@ The list of contributors in alphabetical order:
 - [Marco Donadoni](https://orcid.org/0000-0003-2922-5505)
 - [Marco Vidal](https://orcid.org/0000-0002-9363-4971)
 - [Sinclert Perez](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)
diff --git a/Dockerfile b/Dockerfile
@@ -5,18 +5,16 @@
 # 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/
@@ -35,14 +33,14 @@ RUN apt-get update -y && \
         imagemagick \
         krb5-config \
         krb5-user \
-        libauthen-krb5-perl \
+        libauthen-krb5-simple-perl \
         libkrb5-dev \
         libssl-dev \
         make \
         pkg-config \
-        python3-dev \
+        python3.12-dev \
         python3-pip \
-        python3.8 \
+        python3.12 \
         uuid-dev \
         vim-tiny && \
     # Install xrootd
@@ -60,7 +58,7 @@ RUN apt-get update -y && \
           libxrootd-client-dev \
           xrootd-client) \
     fi && \
-    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 \
         cmake \
@@ -70,7 +68,7 @@ RUN apt-get update -y && \
         libssl-dev \
         make \
         pkg-config \
-        python3-dev \
+        python3.12-dev \
         uuid-dev && \
     apt-get autoremove -y && \
     apt-get clean && \
@@ -82,7 +80,7 @@ COPY . /code
 
 # Add magick wrapper command to simulate ImageMagick v7 that is necessary by Snakemake
 # to produce thumbnails in generated reports. The wrapper simply passes conversion
-# requests to ImageMagick v6 available on Ubuntu 20.04.
+# requests to ImageMagick v6 available on Ubuntu 24.04.
 COPY scripts/magick-wrapper.sh /usr/local/bin/magick
 RUN chmod +x /usr/local/bin/magick
 

diff --git a/requirements.txt b/requirements.txt
@@ -1,77 +1,82 @@
 #
-# 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
 #
 amqp==5.2.0               # via kombu
 appdirs==1.4.4            # via fs, snakemake
-attrs==23.2.0             # via jsonschema
-backports-zoneinfo[tzdata]==0.2.1  # via backports-zoneinfo, kombu
+arrow==1.3.0              # via isoduration
+attrs==23.2.0             # via jsonschema, referencing
 bracex==2.4               # via wcmatch
 bravado==10.3.2           # via reana-commons
 bravado-core==6.1.0       # via bravado, reana-commons
-certifi==2024.2.2         # via requests
+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
 configargparse==1.7       # via snakemake
 connection-pool==0.0.3    # via snakemake
 datrie==0.8.2             # via snakemake
-docutils==0.20.1          # via snakemake
-dpath==2.1.6              # via yte
-fastjsonschema==2.19.1    # via nbformat
+docutils==0.21.2          # via snakemake
+dpath==2.2.0              # via yte
+fastjsonschema==2.20.0    # via nbformat
+fqdn==1.5.1               # via jsonschema
 fs==2.4.16                # via reana-commons
 gitdb==4.0.11             # via gitpython
-gitpython==3.1.42         # via snakemake
+gitpython==3.1.43         # via snakemake
 humanfriendly==10.0       # via snakemake
-idna==3.6                 # via jsonschema, requests
-jinja2==3.1.3             # via snakemake
-jsonpointer==2.4          # via jsonschema
+idna==3.7                 # via jsonschema, requests
+importlib-resources==6.4.0  # via swagger-spec-validator
+isoduration==20.11.0      # via jsonschema
+jinja2==3.1.4             # via snakemake
+jsonpointer==3.0.0        # via jsonschema
 jsonref==1.1.0            # via bravado-core
-jsonschema[format]==3.2.0  # via bravado-core, nbformat, reana-commons, snakemake, swagger-spec-validator
-jupyter-core==5.7.1       # via nbformat
-kombu==5.3.5              # via reana-commons
+jsonschema[format]==4.23.0  # via bravado-core, nbformat, reana-commons, snakemake, swagger-spec-validator
+jsonschema-specifications==2023.12.1  # via jsonschema
+jupyter-core==5.7.2       # via nbformat
+kombu==5.3.7              # via reana-commons
 markupsafe==2.1.5         # via jinja2, werkzeug
 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
-nbformat==5.9.2           # via snakemake
-packaging==23.2           # via snakemake
+nbformat==5.10.4          # via snakemake
+packaging==24.1           # via snakemake
 plac==1.4.3               # via yte
-platformdirs==4.2.0       # via jupyter-core
-psutil==5.9.8             # via snakemake
+platformdirs==4.2.2       # via jupyter-core
+psutil==6.0.0             # via snakemake
 pulp==2.7.0               # via reana-commons, snakemake
-pygments==2.17.2          # via snakemake
-pygraphviz==1.7           # via reana-commons
-pyrsistent==0.20.0        # via jsonschema
-python-dateutil==2.9.0    # via bravado, bravado-core
+pygments==2.18.0          # via snakemake
+python-dateutil==2.9.0.post0  # via arrow, bravado, bravado-core
 pytz==2024.1              # via bravado-core
 pyyaml==6.0.1             # via bravado, bravado-core, reana-commons, snakemake, swagger-spec-validator, yte
-reana-commons[snakemake-reports]==0.95.0a2	# via reana-workflow-engine-snakemake (setup.py)
-requests==2.31.0          # via bravado, bravado-core, snakemake
+reana-commons[snakemake-reports]==0.95.0a3  # via reana-workflow-engine-snakemake (setup.py)
+referencing==0.35.1       # via jsonschema, jsonschema-specifications
+requests==2.32.3          # via bravado, bravado-core, snakemake
 reretry==0.11.8           # via snakemake
+rfc3339-validator==0.1.4  # via jsonschema
 rfc3987==1.3.8            # via jsonschema
+rpds-py==0.19.0           # via jsonschema, referencing
 simplejson==3.19.2        # via bravado, bravado-core
-six==1.16.0               # via bravado, bravado-core, fs, jsonschema, mock, python-dateutil
-smart-open==7.0.1         # via snakemake
+six==1.16.0               # via bravado, bravado-core, fs, mock, python-dateutil, rfc3339-validator
+smart-open==7.0.4         # via snakemake
 smmap==5.0.1              # via gitdb
 snakemake[reports]==7.32.4  # via reana-commons
 stopit==1.1.2             # via snakemake
-strict-rfc3339==0.7       # via jsonschema
-swagger-spec-validator==3.0.3  # via bravado-core
-tabulate==0.8.10          # via reana-commons, snakemake
+swagger-spec-validator==3.0.4  # via bravado-core
+tabulate==0.9.0           # via snakemake
 throttler==1.2.2          # via snakemake
 toposort==1.10            # via snakemake
-traitlets==5.14.1         # via jupyter-core, nbformat
-typing-extensions==4.10.0  # via bravado, kombu, swagger-spec-validator
-tzdata==2024.1            # via backports-zoneinfo
-urllib3==2.2.1            # via requests
+traitlets==5.14.3         # via jupyter-core, nbformat
+types-python-dateutil==2.9.0.20240316  # via arrow
+typing-extensions==4.12.2  # via bravado, 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
+webcolors==24.6.0         # via jsonschema
+werkzeug==3.0.3           # via reana-commons
 wrapt==1.16.0             # via smart-open, snakemake
 xrootd==5.6.0             # via -r requirements.in
 yte==1.5.4                # via snakemake

diff --git a/setup.py b/setup.py
@@ -85,7 +85,7 @@
         "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",