Commit 3500218e authored by Yunus Sevinchan's avatar Yunus Sevinchan
Browse files

Merge branch '375-upgrade-ci-to-ubuntu-24-04-lts' into 'master' 

Resolve "Upgrade CI test image to Ubuntu 24.04 LTS"

Closes #375

See merge request utopia-project/utopia!312
parents 2a5aea8a b275284b

.gitlab-ci.yml

+37 −35
Original line number Diff line number Diff line
@@ -14,24 +14,23 @@ variables: 
  # Need to clone submodules as well

  GIT_SUBMODULE_STRATEGY: recursive



  #

  # Variables needed for docker image deployment

  # The different segments of the resulting test image tag

  BASE_IMAGE_UBUNTU_VERSION: jammy  # NOTE Adjust upon new Ubuntu Release

  BASE_IMAGE_VERSION: "2.1"         # NOTE Increment when changing dockerfile

  BASE_IMAGE_NAME: ccees/utopia-base

  BASE_IMAGE: "${BASE_IMAGE_NAME}:${BASE_IMAGE_UBUNTU_VERSION}-v${BASE_IMAGE_VERSION}"

  # NOTE Do not forget to increment the BASE_IMAGE_VERSION when changes to the

  #      docker file are introduced.



  # Variables controlling the deployed Utopia image and its development

  # counterpart (deployed from the ci_test stage for testing)

  UTOPIA_IMAGE_NAME: ccees/utopia

  UTOPIA_IMAGE_REMOTE_URL: https://gitlab.com/utopia-project/utopia.git

  UTOPIA_IMAGE_BRANCH: master

  #

  # The default values are set in docker/Makefile, but can be overwritten here

  # via environment variables. (Commented-out: use defaults)

  #



  # Utopia virtual environment shortcuts

  RUN_IN_UTOPIA_ENV: $CI_PROJECT_DIR/build/run-in-utopia-env

  ENTER_UTOPIA_ENV: source $CI_PROJECT_DIR/build/activate

  # UTOPIA_BASE_IMAGE_NAME: ccees/utopia-base

  # UTOPIA_BASE_IMAGE_UBUNTU_VERSION: jammy

  # UTOPIA_BASE_IMAGE_VERSION: "2.1"

  # UTOPIA_BASE_IMAGE_BUILD_OPTIONS:



  # UTOPIA_IMAGE_NAME: ccees/utopia

  # UTOPIA_IMAGE_REMOTE_URL: https://gitlab.com/utopia-project/utopia.git

  # UTOPIA_IMAGE_BRANCH: master

  # UTOPIA_IMAGE_BUILD_PROCNUM: 1

  # UTOPIA_IMAGE_BUILD_OPTIONS:



  # Docker Hub login command

  DOCKER_HUB_LOGIN: docker login -u $DOCKER_HUB_USER -p $DOCKER_HUB_PW
@@ -42,8 +41,16 @@ variables: 
  # The GitLab Pages where artifacts can be shown

  PAGES_URL: https://utopia-project.gitlab.io/-/utopia



  #

  # Utopia virtual environment shortcuts

  #

  RUN_IN_UTOPIA_ENV: $CI_PROJECT_DIR/build/run-in-utopia-env

  ENTER_UTOPIA_ENV: source $CI_PROJECT_DIR/build/activate



  #

  # Variables that control whether certain jobs are executed.

  # These can be overwritten via the GitLab CI/CD interface.

  #

  UPDATE_UTOPIA_BASE_IMAGE: "false"

  DEPLOY_DOCKER_IMAGE: "false"

  DEPLOY_DOCS: "false"
@@ -68,8 +75,11 @@ workflow: 
    - if: $CI_COMMIT_BRANCH == $CI_DEFAULT_BRANCH





# As base image for the jobs, use the Utopia image created in the setup stage

image: ${BASE_IMAGE}

# As default image for jobs, use the Utopia base image (created in setup stage)

#

# By choosing the :latest tag, the default values from docker/Makefile will be

# used (once there was a successful build and push).

image: ccees/utopia-base:latest





# .. YAML Templates ...........................................................
@@ -115,17 +125,21 @@ image: ${BASE_IMAGE} 


# Use the Docker-in-Docker executor and services, log into Docker Hub

.dind:

  image: docker:stable

  image: docker:dind  # based on alpine linux

  extends:

    - .use_multicore_runner

  services:

    - docker:dind

  variables:

    DOCKER_DRIVER: overlay2

    UTOPIA_IMAGE_BUILD_PROCNUM: $CPUS_DIND

  before_script:

    - docker info

    - $DOCKER_HUB_LOGIN



    # need some build tools

    - apk add build-base make
@@ -143,13 +157,7 @@ setup:utopia-base: 
      when: always

    - when: never

  script:

    - docker build -f docker/utopia-base.dockerfile

                   -t ${BASE_IMAGE}

                   -t ${BASE_IMAGE_NAME}:latest

                   --build-arg UBUNTU_VERSION=${BASE_IMAGE_UBUNTU_VERSION}

                   .

    - docker push ${BASE_IMAGE}

    - docker push ${BASE_IMAGE_NAME}:latest

    - cd docker && make build_and_push_base_image
@@ -520,7 +528,8 @@ docs:build: 
    - cd build

    - cmake ..



    # Install dependencies and show installation result

    # Enter utopia-env and install dependencies

    - source activate

    - pip install -r ../doc/requirements.txt

    - pip freeze

  script:
@@ -654,14 +663,7 @@ deploy:dockerhub: 
      when: always

    - when: never

  script:

    - docker build -f docker/utopia.dockerfile

                   --build-arg BASE_IMAGE=$BASE_IMAGE

                   --build-arg PROCNUM=$CPUS_DIND

                   --build-arg GIT_CHECKOUT=$UTOPIA_IMAGE_BRANCH

                   --build-arg GIT_REMOTE_URL=$UTOPIA_IMAGE_REMOTE_URL

                   -t $UTOPIA_IMAGE_NAME:latest

                   ./

    - docker push $UTOPIA_IMAGE_NAME:latest

    - cd docker && make build_and_push_utopia_image

  environment:

    name: production/docker-latest

    url: https://hub.docker.com/r/$UTOPIA_IMAGE_NAME

README.md

+4 −4
Original line number Diff line number Diff line
@@ -67,7 +67,7 @@ These instructions are intended for 'clean' __macOS__ (both Intel and Apple Sili 
Since __Windows__ supports the installation of Ubuntu via [Windows Subsystem for Linux](https://en.wikipedia.org/wiki/Windows_Subsystem_for_Linux), Utopia can also be used on Windows.

Follow the [WSL Installation Guide](https://docs.microsoft.com/en-us/windows/wsl/install-win10) to install Ubuntu, then follow the instructions for Ubuntu in this README.



**Note:** Utopia is always tested against a recent Ubuntu release, currently [Ubuntu 22.04](https://releases.ubuntu.com/22.04/).

**Note:** Utopia is always tested against a recent Ubuntu release, currently [Ubuntu 24.04 (LTS)](https://releases.ubuntu.com/24.04/).

However, you can use Utopia with any earlier release, as long as the [dependencies](#dependencies) can be fulfilled.



⚠️ If you encounter difficulties, have a look at the [**troubleshooting section**](#troubleshooting).
@@ -98,7 +98,7 @@ Install the third-party dependencies using a package manager. 
However, notice that there might be issues during [the configuration step](#3-configure-and-build).

Have a look at the [troubleshooting](#troubleshooting) section to see how to address them.



##### On Ubuntu (22.04)

##### On Ubuntu (24.04 LTS)

```bash

apt update

apt install cmake gcc g++ gfortran git libarmadillo-dev libboost-all-dev \
@@ -489,8 +489,8 @@ cmake -DCMAKE_EXPORT_PACKAGE_REGISTRY=On .. 
| [Python3](https://www.python.org/downloads/)   | >= 3.6           | 3.10.4          | |



Utopia aims to allow rapid development, and is thus being tested only against the more recent releases of its dependencies.

Currently, Utopia is tested against the packages provided by [**Ubuntu 22.04**][Ubuntu-packages].

However the above version _requirements_ (i.e., those _enforced_ by the build system) can be fulfilled also with Ubuntu 19.10.

Currently, Utopia is tested against the packages provided by [**Ubuntu 24.04**][Ubuntu-packages].

However the above version _requirements_ (i.e., those _enforced_ by the build system) can be fulfilled also with Ubuntu 19.10; we just don't test against them any more.



To get Utopia running on a system with an earlier Ubuntu version, the above dependencies still need to be fulfilled.

You can use the [Ubuntu Package Search][Ubuntu-packages] to find the versions available on your system.

doc/conf.py.in

+8 −8
Original line number Diff line number Diff line
@@ -409,13 +409,14 @@ for line in open(f"{doc_dir}/.nitpick-ignore"): 
        nitpick_ignore.append((reftype, target.strip()))









# -----------------------------------------------------------------------------

# Link-checking

# -- Link-checking ------------------------------------------------------------

# -----------------------------------------------------------------------------

# Docs:

#   https://www.sphinx-doc.org/en/master/usage/configuration.html#options-for-the-linkcheck-builder



linkcheck_retries = 2



# Link patterns to ignore

linkcheck_ignore = [

    # With linkcheck failing to check relative links to the doxygen output,
@@ -431,15 +432,14 @@ linkcheck_ignore = [ 
    # And the IUP homepage, which has some weird certificate settings

    r".*(www\.)?iup\.uni-heidelberg\.de/.*",

    #

    # Sites that do not allow the sphinx linkcheck client (403 client error)

    # Sites that do not allow the sphinx linkcheck user agent, or forward to

    # such sites (typically shows a 403 client error) ... even if a custom

    # user agent is set, these sites are not happy.

    r".*(www\.)?intel\.com/.*",

    r".*doi\.org/10\.1103/[Pp]hys[Rr]ev[Ll]ett.*",

]





linkcheck_retries = 2

doc/dev/workflow.rst

+1 −1
Original line number Diff line number Diff line
@@ -72,7 +72,7 @@ The first line of your output should confirm that you are now on your new branch 


Well done! You have now created your own development branch. Utopia comes with a host of pre-implemented models for you to use and experiment with. And in the :ref:`impl_step_by_step` on how to build a model you can learn how to use these as a starting point, meaning you do not have to start from scratch when developing new models.



Now that you have created a new branch, you are ready to code and upload your changes using git. There are a lot of guides and tutorials online where you can learn how to use git. A quick start would be `this one <https://git-scm.com/book/en/v2/Getting-Started-Git-Basics>`_; a longer one can be found on `git-tower <https://www.git-tower.com/learn/git/ebook>`_. Also, the `git documentation <https://git-scm.com/doc>`_ is quite comprehensive and well-written.

Now that you have created a new branch, you are ready to code and upload your changes using git. There are a lot of guides and tutorials online where you can learn how to use git. A quick start would be `this one <https://git-scm.com/book/en/v2>`_; a longer one can be found on `git-tower <https://www.git-tower.com/learn/git/ebook>`_. Also, the `git documentation <https://git-scm.com/doc>`_ is quite comprehensive and well-written.



Here, we provide only a small selection of commands that you will use a lot during your code development and address some frequent issues encountered when starting to use git. If you have questions or run into problems, it is always worth consulting the ``git <command> --help`` or checking out the guides linked above. Also, searching the internet for what you want to do is usually quite effective when it comes to questions with git.

doc/doxygen/CMakeLists.txt

+11 −0
Original line number Diff line number Diff line
@@ -5,10 +5,16 @@ if (DOXYGEN_FOUND) 
    # configure doxygen

    set(DOXYGEN_QUIET YES)

    set(DOXYGEN_EXTRACT_ALL YES)

    set(DOXYGEN_EXTRACT_PACKAGE YES)

    set(DOXYGEN_EXTRACT_PRIVATE YES)

    set(DOXYGEN_EXTRACT_PRIV_VIRTUAL YES)

    set(DOXYGEN_EXTRACT_STATIC YES)

    set(DOXYGEN_EXTRACT_LOCAL_CLASSES YES)

    set(DOXYGEN_EXTRACT_LOCAL_METHODS YES)

    set(DOXYGEN_GENERATE_HTML YES)

    set(DOXYGEN_GENERATE_XML YES)

    set(DOXYGEN_INLINE_SOURCES YES)

    set(DOXYGEN_FULL_PATH_NAMES YES)

    set(DOXYGEN_WARN_LOGFILE ${CMAKE_CURRENT_BINARY_DIR}/doxygen_warnings.log)



    # For persistent HTML page names, explicitly set file names to be generated
@@ -19,6 +25,11 @@ if (DOXYGEN_FOUND) 
    # Use MathJax for nicer formulas

    set(DOXYGEN_USE_MATHJAX YES)



    # Increase verbosity

    set(DOXYGEN_WARN_NO_PARAMDOC YES)

    set(DOXYGEN_WARN_UNDOC_ENUM_VAL YES)

    set(DOXYGEN_WARN_AS_ERROR NO)  # TODO ... worth considering though!



    # register the target

    doxygen_add_docs(doxygen_utopia

        ${doxygen_dirs}