Merge pull request #23 from bdevans/oracular

Oracular

.github/workflows/docker-image.yml

@@ -31,6 +31,8 @@ jobs:
           type=semver,pattern={{version}}
           type=semver,pattern={{major}}.{{minor}}
           type=semver,pattern={{major}}
+          # Update the following line to match the base ubuntu image
+          type=raw,value=oracular
           type=sha
         labels: |
           org.opencontainers.image.title=Chaste Base Image

Dockerfile

@@ -4,7 +4,7 @@
 # docker build --target base -t chaste/base .  # Alternative: build base image
 # docker run -it --rm -v chaste_data:/home/chaste chaste
 
-ARG BASE=jammy
+ARG BASE=oracular
 FROM ubuntu:${BASE} AS base
 LABEL maintainer="Ben Evans <[email protected]>" \
     author.orcid="https://orcid.org/0000-0002-1734-6070" \
@@ -32,41 +32,33 @@ RUN apt-get update && \
     sudo \
     wget
 
-# Add signing key to install GitHub CLI
-# https://github.com/cli/cli/blob/trunk/docs/install_linux.md
+# Add signing key to install GitHub CLI: https://github.com/cli/cli/blob/trunk/docs/install_linux.md
 RUN wget -O /etc/apt/keyrings/github-cli.gpg https://cli.github.com/packages/githubcli-archive-keyring.gpg \
     && echo "deb [arch=$(dpkg --print-architecture) signed-by=/etc/apt/keyrings/github-cli.gpg] https://cli.github.com/packages stable main" >> /etc/apt/sources.list.d/github-cli.list
 
-# Declare BASE in this build stage (the value is inherited from the global stage)
-# https://github.com/moby/moby/issues/34482
+# Declare BASE in this build stage (the value is inherited from the global stage): https://github.com/moby/moby/issues/34482
 ARG BASE
-# Install the Chaste repo list and key
-# https://chaste.github.io/docs/installguides/ubuntu-package/
+# Install the Chaste repo list and key: https://chaste.github.io/docs/installguides/ubuntu-package/
 RUN wget -O /usr/share/keyrings/chaste.asc https://chaste.github.io/chaste.asc \
     && echo "deb [signed-by=/usr/share/keyrings/chaste.asc] https://chaste.github.io/ubuntu ${BASE}/" >> /etc/apt/sources.list.d/chaste.list
 
 # https://github.com/Chaste/dependency-modules/wiki
+# https://github.com/Chaste/infrastructure-scripts/blob/main/debian-package/debian/control
+# https://github.com/Chaste/ubuntu/tree/main/debs
 # Package: chaste-dependencies
-# Version: 2022.04.11
+# Version: 2024.10.28
 # Architecture: all
-# Depends: cmake | scons, g++, libopenmpi-dev, petsc-dev, libhdf5-openmpi-dev, xsdcxx, libboost-serialization-dev, libboost-filesystem-dev, libboost-program-options-dev, libparmetis-dev, libmetis-dev, libxerces-c-dev, libsundials-dev, libvtk7-dev | libvtk6-dev, python3, python3-venv
-# Recommends: git, valgrind, libpetsc-real3.15-dbg | libpetsc-real3.14-dbg | libpetsc-real3.12-dbg, libfltk1.1, hdf5-tools, cmake-curses-gui
-# Suggests: libgoogle-perftools-dev, doxygen, graphviz, subversion, git-svn, gnuplot, paraview
-# DEPRECATED: scons will be removed in the next release
+# Depends: cmake, g++, git, libopenmpi-dev, petsc-dev, libhdf5-openmpi-dev, xsdcxx, libboost-serialization-dev, libboost-filesystem-dev, libboost-program-options-dev, libparmetis-dev, libmetis-dev, libxerces-c-dev, libsundials-dev, libvtk9-dev (>= 9.3.0), python3, python3-venv
+# Recommends: valgrind, libpetsc-real3.20-dbg|libpetsc-real3.19t64-dbg|libpetsc-real3.18-dbg|libpetsc-real3.15-dbg, hdf5-tools, cmake-curses-gui, doxygen, graphviz, gnuplot, paraview
 
-# Install dependencies with recommended, applicable suggested and other useful packages
+# Install dependencies with applicable recommended and other useful packages
 RUN apt-get update && \
     apt-get install -y --no-install-recommends \
     chaste-dependencies \
-    cmake \
     clang \
     lldb \
     gdb \
-    # libvtk7-dev \  # Dependency of chaste-dependencies (check 7 not 6 is installed)
-    python3-dev \
-    python3-pip \
     gh \
-    git \
     valgrind \
     "libpetsc-real*-dbg" \
     hdf5-tools \
@@ -75,17 +67,11 @@ RUN apt-get update && \
     graphviz && \
     rm -rf /var/lib/apt/lists/*
 
-# Fix libexpat1 version for jammy: https://github.com/Chaste/Chaste/issues/249
-RUN apt-get update && \
-    apt-get install -y --allow-downgrades libexpat1=2.4.7-1 libexpat1-dev=2.4.7-1 && \
-    apt-mark hold libexpat1 libexpat1-dev && \
-    rm -rf /var/lib/apt/lists/*
-
 # Update system to use Python3 by default
-RUN update-alternatives --install /usr/bin/python python /usr/bin/python3 1 && \
-    update-alternatives --install /usr/bin/pip pip /usr/bin/pip3 1
+RUN update-alternatives --install /usr/bin/python python /usr/bin/python3 1
+    # update-alternatives --install /usr/bin/pip pip /usr/bin/pip3 1
 # Fix CMake warnings: https://github.com/autowarefoundation/autoware/issues/795 TODO: Check if this is still necessary with VTK9
-RUN update-alternatives --install /usr/bin/vtk vtk /usr/bin/vtk7 7
+# RUN update-alternatives --install /usr/bin/vtk vtk /usr/bin/vtk9 1
 
 # Set environment variables with args to allow for changes at build time
 ARG USER="chaste"
@@ -104,9 +90,10 @@ ENV USER=${USER} \
     CHASTE_SOURCE_DIR="${CHASTE_DIR}/src" \
     CHASTE_BUILD_DIR="${CHASTE_DIR}/build" \
     CHASTE_TEST_OUTPUT="${CHASTE_DIR}/output" \
-    PATH="${CHASTE_DIR}/scripts:${PATH}" \
-    TEXTTEST_HOME=/usr/local/bin/texttest
+    PATH="${CHASTE_DIR}/scripts:${PATH}"
+    # TEXTTEST_HOME=/usr/local/bin/texttest
 ENV CHASTE_PROJECTS_DIR="${CHASTE_SOURCE_DIR}/projects" \
+    TEXTTEST_HOME="${CHASTE_BUILD_DIR}/texttest_venv" \
     PYTHONPATH="${CHASTE_BUILD_DIR}/python"
 
 # Create user and working directory for Chaste files
@@ -119,18 +106,22 @@ COPY --chown=${USER}:${GROUP} scripts "${CHASTE_DIR}/scripts"
 
 USER ${USER}
 WORKDIR ${CHASTE_DIR}
+# SHELL [ "/bin/bash", "-exo", "pipefail", "-c" ]
 
 # Install TextTest for regression testing (requires pygtk)
 # NOTE: chaste-codegen is installed by CMake
-RUN python -m pip install --no-cache-dir --upgrade pip && \
+RUN python -m venv --upgrade-deps "${CHASTE_BUILD_DIR}/texttest_venv" && \
+    # source "${CHASTE_BUILD_DIR}/texttest_venv/bin/activate" && \
+    . "${CHASTE_BUILD_DIR}/texttest_venv/bin/activate" && \
+    # PATH=".local:${PATH}" && \
     python -m pip install --no-cache-dir texttest
 
 # Create Chaste src, build, output and projects folders
 RUN mkdir -p "${CHASTE_SOURCE_DIR}" "${CHASTE_BUILD_DIR}" "${CHASTE_TEST_OUTPUT}" && \
     ln -s "${CHASTE_PROJECTS_DIR}" projects
 # DEPRECATED: Transitionary symlinks for build and output directories
-RUN ln -s "${CHASTE_BUILD_DIR}" lib && \
-    ln -s "${CHASTE_TEST_OUTPUT}" testoutput
+# RUN ln -s "${CHASTE_BUILD_DIR}" lib && \
+#     ln -s "${CHASTE_TEST_OUTPUT}" testoutput
 
 # Fix git permissions issue CVE-2022-24765
 RUN git config --global --add safe.directory "${CHASTE_SOURCE_DIR}"

Makefile

@@ -5,20 +5,22 @@ help:
 	@echo "Perform a dry run with:"
 	@echo "  make [TARGET] -n"
 
-BASE ?= jammy
-GIT_TAG ?= 2024.1
+
+BASE ?= oracular
+GIT_TAG ?= 2024.2
 TEST_SUITE ?= -
 CHASTE_IMAGE ?= chaste/release
 CHASTE_DIR ?= "/home/chaste"
 CHASTE_DATA_VOLUME ?= chaste_data
-FRESH ?=
 OUT ?= auto
+FRESH ?=
 EXTRA_BUILD_FLAGS ?=
 
 # Optional mounts
 # PROJECTS ?= "${HOME}/projects"
 # TEST_OUTPUT ?= "${HOME}/output"
 
+
 # https://github.com/pytorch/pytorch/blob/main/docker.Makefile
 MULTI_ARCH_BUILD ?= true
 ifeq ("$(MULTI_ARCH_BUILD)", "true")
@@ -67,14 +69,14 @@ develop main release: BUILD_ARGS += --build-arg GIT_TAG=$(GIT_TAG) \
 		--build-arg TEST_SUITE=$(TEST_SUITE)
 
 develop main: CMAKE_BUILD_TYPE="Debug"
-develop main: Chaste_ERROR_ON_WARNING="ON"
+develop main: Chaste_ERROR_ON_WARNING ?= "ON"
 develop main: Chaste_UPDATE_PROVENANCE="OFF"
 develop main: GIT_TAG=$@
 
 release: CMAKE_BUILD_TYPE="Release"
-release: Chaste_ERROR_ON_WARNING="OFF"
+release: Chaste_ERROR_ON_WARNING ?= "OFF"
 release: Chaste_UPDATE_PROVENANCE="ON"
-release: TEST_SUITE="Continuous"
+# release: TEST_SUITE = "Continuous"
 
 base develop main release: CHASTE_IMAGE = chaste/$@
 base develop main release: DOCKER_TAGS = -t $(CHASTE_IMAGE)

README.md

@@ -68,7 +68,7 @@ Install [Docker](https://www.docker.com/products/docker-desktop/) and configure
     ```
     docker run --init -it --rm -v chaste_data:/home/chaste chaste/release
     ```
-    If needed, you can also specify an [available tag](https://hub.docker.com/r/chaste/release/tags) in the image name in the form `chaste/release:<tag>` to pull a particular release (e.g. `chaste/release:2024.1`) rather than defaulting to the latest version. 
+    If needed, you can also specify an [available tag](https://hub.docker.com/r/chaste/release/tags) in the image name in the form `chaste/release:<tag>` to pull a particular release (e.g. `chaste/release:2024.2`) rather than defaulting to the latest version. 
 2. Alternatively, if you want to use the latest development code from the `develop` branch, use this command to pull and run the latest `chaste/develop` image instead:
     ```
     docker run --init -it --rm -v chaste_data:/home/chaste chaste/develop
@@ -147,7 +147,7 @@ For further details and illustrations of the Docker mount options see the [stora
 
 ### Bind mounts
 
-Any host directory (specified with an absolute path e.g. `/path/to/output`) may be mounted in the container e.g. the `output` directory. Alternatively, navigate to the folder on the host which contains these directories e.g. `C:\Users\$USERNAME\chaste` (Windows) or `~/chaste` (Linux/macOS) and use `$(pwd)/output` instead as shown below. In the following examples, the image name (final argument) is assumed to be `chaste/release` rather than e.g. `chaste/develop` or `chaste/release:2024.1` for simplicity. 
+Any host directory (specified with an absolute path e.g. `/path/to/output`) may be mounted in the container e.g. the `output` directory. Alternatively, navigate to the folder on the host which contains these directories e.g. `C:\Users\$USERNAME\chaste` (Windows) or `~/chaste` (Linux/macOS) and use `$(pwd)/output` instead as shown below. In the following examples, the image name (final argument) is assumed to be `chaste/release` rather than e.g. `chaste/develop` or `chaste/release:2024.2` for simplicity. 
 ```
 docker run -it --init --rm -v chaste_data:/home/chaste -v "${PWD}"/output:/home/chaste/output chaste/release
 ```
@@ -222,7 +222,7 @@ If you're a more advanced developer and want to build your own image with a part
         ```
     2. Alternatively a specific branch or tag may be specified through the argument `--build-arg GIT_TAG=<branch|tag>` (with the same tag appended onto the docker image name for clarity) e.g.:
         ```
-        docker build -t chaste:custom --build-arg GIT_TAG=2024.1 https://github.com/chaste/chaste-docker.git
+        docker build -t chaste:custom --build-arg GIT_TAG=2024.2 https://github.com/chaste/chaste-docker.git
         ```
     3. Finally, if you want a bare container ready for you to clone and compile your own Chaste code, pull a `base` image with `docker pull chaste/base` (specifying an [available Ubuntu distribution](https://hub.docker.com/repository/docker/chaste/base/tags) if desired e.g. `chaste/base:focal`) Alternatively, build a fresh image by running the following command (omitting the `--build-arg GIT_TAG=<branch|tag>` argument above, or explicitly passing `--build-arg GIT_TAG=-`, which will skip compiling Chaste within the image):
         ```