From 6cf18683aa49436ecfa11ba2902f683a86b8b0b7 Mon Sep 17 00:00:00 2001 From: Gertjan van den Burg Date: Fri, 25 Jul 2025 10:33:43 +0100 Subject: [PATCH 1/4] Bump python, ubuntu, and workflow versions --- .github/workflows/build.yml | 10 +++++----- Dockerfile | 2 +- 2 files changed, 6 insertions(+), 6 deletions(-) diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml index 119b6f70b79..341fbe4c14f 100644 --- a/.github/workflows/build.yml +++ b/.github/workflows/build.yml @@ -20,10 +20,10 @@ jobs: run: sudo apt-get update && sudo apt-get install build-essential latexmk texlive-latex-extra shell: bash - - name: Install Python 3.8 - uses: actions/setup-python@v2 + - name: Install Python 3.12 + uses: actions/setup-python@v5 with: - python-version: '3.8' + python-version: '3.12' - name: Install R uses: r-lib/actions/setup-r@v2-branch @@ -36,7 +36,7 @@ jobs: shell: Rscript {0} - name: Checkout code - uses: actions/checkout@v2 + uses: actions/checkout@v4 with: submodules: true @@ -73,7 +73,7 @@ jobs: runs-on: ubuntu-latest steps: - name: Checkout - uses: actions/checkout@v2 + uses: actions/checkout@v4 - name: TCPDBench docker check run: ./.github/scripts/test_docker.sh diff --git a/Dockerfile b/Dockerfile index 5ff106f796c..d0bd8872f0c 100644 --- a/Dockerfile +++ b/Dockerfile @@ -1,4 +1,4 @@ -FROM ubuntu:20.04 +FROM ubuntu:24.04 RUN apt-get update && \ DEBIAN_FRONTEND=noninteractive apt-get install -y tzdata && \ From 3f1ad3d97f7604a0cb787ede43bd52f3d93401f4 Mon Sep 17 00:00:00 2001 From: Gertjan van den Burg Date: Mon, 28 Jul 2025 16:15:04 +0100 Subject: [PATCH 2/4] Reset python version --- .github/workflows/build.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml index 341fbe4c14f..616f31c82c8 100644 --- a/.github/workflows/build.yml +++ b/.github/workflows/build.yml @@ -20,10 +20,10 @@ jobs: run: sudo apt-get update && sudo apt-get install build-essential latexmk texlive-latex-extra shell: bash - - name: Install Python 3.12 + - name: Install Python 3.8 uses: actions/setup-python@v5 with: - python-version: '3.12' + python-version: '3.8' - name: Install R uses: r-lib/actions/setup-r@v2-branch From ed6d3bac742a86a73d1fb9172d59b3d21948bacf Mon Sep 17 00:00:00 2001 From: Gertjan van den Burg Date: Mon, 28 Jul 2025 16:33:47 +0100 Subject: [PATCH 3/4] bump python version to 3.9 --- .github/workflows/build.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml index 616f31c82c8..41d84d83073 100644 --- a/.github/workflows/build.yml +++ b/.github/workflows/build.yml @@ -20,10 +20,10 @@ jobs: run: sudo apt-get update && sudo apt-get install build-essential latexmk texlive-latex-extra shell: bash - - name: Install Python 3.8 + - name: Install Python 3.9 uses: actions/setup-python@v5 with: - python-version: '3.8' + python-version: '3.9' - name: Install R uses: r-lib/actions/setup-r@v2-branch From 0f00a4c88d81d4f04491269527d7f1e3d07645cb Mon Sep 17 00:00:00 2001 From: Gertjan van den Burg Date: Thu, 31 Jul 2025 19:17:37 +0100 Subject: [PATCH 4/4] attempt to fix docker build --- Dockerfile | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/Dockerfile b/Dockerfile index d0bd8872f0c..efabcf451cd 100644 --- a/Dockerfile +++ b/Dockerfile @@ -35,12 +35,12 @@ RUN apt-get install -y --no-install-recommends \ python3-tk \ python3-venv \ python3-pip && \ - pip3 install --no-cache-dir --upgrade setuptools && \ + pip3 install --break-system-packages --no-cache-dir --upgrade setuptools && \ echo "alias python='python3'" >> /root/.bash_aliases && \ echo "alias pip='pip3'" >> /root/.bash_aliases && \ cd /usr/local/bin && ln -s /usr/bin/python3 python && \ cd /usr/local/bin && ln -s /usr/bin/pip3 pip && \ - pip install virtualenv abed wheel + pip install --break-system-packages virtualenv abed wheel # Set the default shell to bash RUN mv /bin/sh /bin/sh.old && cp /bin/bash /bin/sh @@ -58,7 +58,7 @@ RUN git clone --recurse-submodules https://github.com/alan-turing-institute/TCPD RUN mkdir -p /TCPDBench/datasets && cp TCPD/export/*.json /TCPDBench/datasets/ # Install Python dependencies -RUN pip install -r /TCPDBench/analysis/requirements.txt +RUN pip install --break-system-packages -r /TCPDBench/analysis/requirements.txt # Install R dependencies RUN Rscript -e "install.packages(c('argparse', 'exactRankTests'))"