Specifying expat version to avoid incompatibility with later version

9c06bafb · Martin Genet · c9f69a14 · 9c06bafb
Commit 9c06bafb authored 4 months ago by Martin Genet
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -2,7 +2,7 @@ stages:
  - test
  - deploy

-# tests-on-ubuntu-20.04-with-apt: # MG2023068: This leads to seg fault while manipulating vtk objects inside cpp fenics expressions…
+# tests-on-ubuntu-20.04-with-apt: # MG2023068: This leads to seg fault while manipulating vtk objects inside cpp fenics expressions… # MG20241020: I think the mesh reader fails…
 #   stage: test
 #   only:
 #     - devel
@@ -15,15 +15,14 @@ stages:
 #     - apt update; DEBIAN_FRONTEND=noninteractive TZ=Europe/Paris apt upgrade -y
 #     - apt update; DEBIAN_FRONTEND=noninteractive TZ=Europe/Paris apt install -y build-essential git gnuplot python3-matplotlib python3-numpy python3-pandas python3-pip python-is-python3 # MG20220814: environment variables are needed to prevent tzdata installation hanging while waiting timezone info, cf. https://anonoz.github.io/tech/2020/04/24/docker-build-stuck-tzdata.html
 #     - apt update; DEBIAN_FRONTEND=noninteractive TZ=Europe/Paris apt install -y software-properties-common; add-apt-repository -y ppa:fenics-packages/fenics; apt update; apt install -y fenics; export DISPLAY=0:0
-# #     - apt update; apt install -y libopenblas-base; export OMP_NUM_THREADS="1" # MG20221201: This seems to fail in ubuntu 20.04
+# #     - apt update; apt install -y libopenblas-base; export OMP_NUM_THREADS="1" # MG20221201: This seems to fail in Ubuntu 20.04
 #     - apt update; apt install -y libvtk7-dev python3-vtk7; export CPATH="/usr/include/vtk-7.1":$CPATH
 #     - apt update; apt install -y libgl1-mesa-dev libglu1-mesa-dev libxcursor-dev libxft-dev libxinerama1 gcc-multilib xvfb gmsh; pip install gmsh
-#     - apt update; apt install -y python3-h5py; pip install meshio; pip install --upgrade numpy # MG20220814: meshio needs latest numpy apparently
-#     - pip install numpy==1.23.5 # MG20230103: apparently numpy >= 1.24 does not work anymore with the old version of pandas (and probably other stuff) present in Ubuntu 20.04 apt repo, cf. https://stackoverflow.com/a/74975994
+#     - apt update; apt install -y python3-h5py; pip install meshio; pip install numpy==1.23.5 # MG20220814: meshio needs updated numpy apparently # MG20230103: apparently numpy >= 1.24 does not work anymore with the old version of pandas (and probably other stuff) present in Ubuntu 20.04 apt repo, cf. https://stackoverflow.com/a/74975994
 #     - pip install git+https://gitlab.inria.fr/mgenet/myPythonLibrary.git git+https://gitlab.inria.fr/mgenet/myVTKPythonLibrary.git git+https://gitlab.inria.fr/mgenet/vtkpython_cbl.git git+https://gitlab.inria.fr/mgenet/dolfin_mech.git
 #     - cd Tests; ln -s ../dolfin_warp; make

-# tests-on-ubuntu-22.04-with-apt: # MG2023068: This leads to seg fault while manipulating vtk objects inside cpp fenics expressions…
+# tests-on-ubuntu-22.04-with-apt: # MG2023068: This leads to seg fault while manipulating vtk objects inside cpp fenics expressions… # MG20241020: I think the image reader fails…
 #   stage: test
 #   only:
 #     - devel
@@ -39,10 +38,30 @@ stages:
 #     - apt update; apt install -y libopenblas-base; export OMP_NUM_THREADS="1"
 #     - apt update; apt install -y libvtk9-dev python3-vtk9; export CPATH="/usr/include/vtk-9.1":$CPATH
 #     - apt update; apt install -y libgl1-mesa-dev libglu1-mesa-dev libxcursor-dev libxft-dev libxinerama1 gcc-multilib xvfb gmsh; pip install gmsh
-#     - apt update; apt install -y python3-h5py; pip install meshio; pip install --upgrade numpy # MG20220814: meshio needs latest numpy apparently
+#     - apt update; apt install -y python3-h5py; pip install meshio; pip install numpy==1.24.4 # MG20220814: meshio needs updated numpy apparently # MG20230103: apparently numpy >= 1.25 does not work with FEniCS
 #     - pip install git+https://gitlab.inria.fr/mgenet/myPythonLibrary.git git+https://gitlab.inria.fr/mgenet/myVTKPythonLibrary.git git+https://gitlab.inria.fr/mgenet/vtkpython_cbl.git git+https://gitlab.inria.fr/mgenet/dolfin_mech.git
 #     - cd Tests; ln -s ../dolfin_warp; make

+# tests-on-ubuntu-24.04-with-apt: # MG 20241017: apt python version is 3.12, which seems incompatible with numpy 1.24…
+#   stage: test
+#   only:
+#     - devel
+#     - /^devel-.*/
+#   tags:
+#     - ci.inria.fr
+#     - large
+#   image: ubuntu:24.04
+#   script:
+#     - apt update; DEBIAN_FRONTEND=noninteractive TZ=Europe/Paris apt upgrade -y
+#     - apt update; DEBIAN_FRONTEND=noninteractive TZ=Europe/Paris apt install -y build-essential git gnuplot python3-matplotlib python3-numpy python3-pandas python3-pip python-is-python3 # MG20220814: environment variables are needed to prevent tzdata installation hanging while waiting timezone info, cf. https://anonoz.github.io/tech/2020/04/24/docker-build-stuck-tzdata.html
+#     - apt update; apt install -y software-properties-common; add-apt-repository -y ppa:fenics-packages/fenics; apt update; apt install -y fenics; export DISPLAY=0:0
+#     # - apt update; apt install -y libopenblas-base; export OMP_NUM_THREADS="1" # MG20241017: Not present in Ubuntu 24.04
+#     - apt update; apt install -y libvtk9-dev python3-vtk9; export CPATH="/usr/include/vtk-9.1":$CPATH
+#     - apt update; apt install -y libgl1-mesa-dev libglu1-mesa-dev libxcursor-dev libxft-dev libxinerama1 gcc-multilib xvfb gmsh; pip install --break-system-packages gmsh
+#     - apt update; apt install -y python3-h5py; pip install --break-system-packages meshio; pip install --break-system-packages numpy==1.24.4 # MG20220814: meshio needs latest numpy apparently # MG20230103: apparently numpy >= 1.25 does not work with FEniCS
+#     - pip install --break-system-packages git+https://gitlab.inria.fr/mgenet/myPythonLibrary.git git+https://gitlab.inria.fr/mgenet/myVTKPythonLibrary.git git+https://gitlab.inria.fr/mgenet/vtkpython_cbl.git git+https://gitlab.inria.fr/mgenet/dolfin_mech.git
+#     - cd Tests; ln -s ../dolfin_warp; make
+
 tests-on-ubuntu-20.04:
  stage: test
  only:
@@ -55,15 +74,12 @@ tests-on-ubuntu-20.04:
  script:
    - apt update; DEBIAN_FRONTEND=noninteractive TZ=Europe/Paris apt upgrade -y
    - apt update; DEBIAN_FRONTEND=noninteractive TZ=Europe/Paris apt install -y build-essential gcc-multilib git gnuplot libgl1-mesa-dev libglu1-mesa-dev libxcursor-dev libxinerama1 libxft-dev wget xvfb
-    # - apt update; DEBIAN_FRONTEND=noninteractive TZ=Europe/Paris apt install -y libopenblas-base; export OMP_NUM_THREADS="1" # MG20221201: This seems to fail in ubuntu 20.04
-    - wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh
-    - bash Miniconda3-latest-Linux-x86_64.sh -b -p /root/miniconda
-    - eval "$(/root/miniconda/bin/conda shell.bash hook)"
-    - conda init
-    - conda install conda-libmamba-solver; conda config --set solver libmamba
-    - conda create -y -c conda-forge -n dolfin_warp fenics=2019.1.0 meshio=5.3 mpi4py=3.1.3 pip python=3.8 vtk=9.1; conda activate dolfin_warp # MG20230608: need to install meshio via conda because pip install has h5py dependency issues # MG20230608: need to install vtk9 because vtk7 from conda seems to require python2
+    # - apt update; DEBIAN_FRONTEND=noninteractive TZ=Europe/Paris apt install -y libopenblas-base; export OMP_NUM_THREADS="1" # MG20221201: This seems to fail in Ubuntu 20.04
+    - wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh; bash Miniconda3-latest-Linux-x86_64.sh -b -p /root/miniconda; eval "$(/root/miniconda/bin/conda shell.bash hook)"; conda init
+    # - conda install conda-libmamba-solver; conda config --set solver libmamba # MG20241017: This is now the default solver, cf. https://conda.org/blog/2023-11-06-conda-23-10-0-release
+    - conda create -y -c conda-forge -n dolfin_warp expat=2.5 fenics=2019.1.0 matplotlib=3.5 meshio=5.3 mpi4py=3.1.3 numpy=1.23.5 pandas=1.3 pip python=3.10 scipy=1.8 vtk=9.1; conda activate dolfin_warp # MG20230608: need to install meshio via conda because pip install has h5py dependency issues # MG20230608: need to install vtk9 because vtk7 seems to require python2 # MG20241020: expat > 2.5 seems to break vtkXMLDataParser, cf. https://gitlab.kitware.com/vtk/vtk/-/issues/19258
    - conda activate dolfin_warp; conda env config vars set CPATH=$CONDA_PREFIX/include/vtk-9.1; conda deactivate; conda activate dolfin_warp
-    - pip install gmsh matplotlib numpy pandas scipy git+https://gitlab.inria.fr/mgenet/myPythonLibrary.git git+https://gitlab.inria.fr/mgenet/myVTKPythonLibrary.git git+https://gitlab.inria.fr/mgenet/vtkpython_cbl.git git+https://gitlab.inria.fr/mgenet/dolfin_mech.git # MG20230608: Need to install numpy, scipy, etc via pip, not apt, otherwise it is not accessible to python from conda
+    - pip install gmsh git+https://gitlab.inria.fr/mgenet/myPythonLibrary.git git+https://gitlab.inria.fr/mgenet/myVTKPythonLibrary.git git+https://gitlab.inria.fr/mgenet/vtkpython_cbl.git git+https://gitlab.inria.fr/mgenet/dolfin_mech.git
    - cd Tests; ln -s ../dolfin_warp; make

 tests-on-ubuntu-22.04:
@@ -79,61 +95,32 @@ tests-on-ubuntu-22.04:
    - apt update; DEBIAN_FRONTEND=noninteractive TZ=Europe/Paris apt upgrade -y
    - apt update; DEBIAN_FRONTEND=noninteractive TZ=Europe/Paris apt install -y build-essential gcc-multilib git gnuplot libgl1-mesa-dev libglu1-mesa-dev libxcursor-dev libxinerama1 libxft-dev wget xvfb
    - apt update; DEBIAN_FRONTEND=noninteractive TZ=Europe/Paris apt install -y libopenblas-base; export OMP_NUM_THREADS="1"
-    - wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh
-    - bash Miniconda3-latest-Linux-x86_64.sh -b -p /root/miniconda
-    - eval "$(/root/miniconda/bin/conda shell.bash hook)"
-    - conda init
-    - conda install conda-libmamba-solver; conda config --set solver libmamba
-    - conda create -y -c conda-forge -n dolfin_warp fenics=2019.1.0 meshio=5.3 mpi4py=3.1.3 pip python=3.10 vtk=9.1; conda activate dolfin_warp # MG20230608: need to install meshio via conda because pip install has h5py dependency issues
+    - wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh; bash Miniconda3-latest-Linux-x86_64.sh -b -p /root/miniconda; eval "$(/root/miniconda/bin/conda shell.bash hook)"; conda init
+    # - conda install conda-libmamba-solver; conda config --set solver libmamba # MG20241017: This is now the default solver, cf. https://conda.org/blog/2023-11-06-conda-23-10-0-release
+    - conda create -y -c conda-forge -n dolfin_warp expat=2.5 fenics=2019.1.0 matplotlib=3.5 meshio=5.3 mpi4py=3.1.3 numpy=1.23.5 pandas=1.3 pip python=3.10 scipy=1.8 vtk=9.1; conda activate dolfin_warp # MG20230608: need to install meshio via conda because pip install has h5py dependency issues
    - conda activate dolfin_warp; conda env config vars set CPATH=$CONDA_PREFIX/include/vtk-9.1; conda deactivate; conda activate dolfin_warp
-    - pip install gmsh matplotlib numpy pandas scipy git+https://gitlab.inria.fr/mgenet/myPythonLibrary.git git+https://gitlab.inria.fr/mgenet/myVTKPythonLibrary.git git+https://gitlab.inria.fr/mgenet/vtkpython_cbl.git git+https://gitlab.inria.fr/mgenet/dolfin_mech.git # MG20230608: Need to install numpy, scipy, etc via pip, not apt, otherwise it is not accessible to python from conda
+    - pip install gmsh git+https://gitlab.inria.fr/mgenet/myPythonLibrary.git git+https://gitlab.inria.fr/mgenet/myVTKPythonLibrary.git git+https://gitlab.inria.fr/mgenet/vtkpython_cbl.git git+https://gitlab.inria.fr/mgenet/dolfin_mech.git
    - cd Tests; ln -s ../dolfin_warp; make

-# tests-on-ubuntu-20.04-with-full-conda:
-#   stage: test
-#   only:
-#     - devel
-#     - /^devel-.*/
-#   tags:
-#     - ci.inria.fr
-#     - large
-#   image: ubuntu:20.04
-#   script:
-#     - apt update; DEBIAN_FRONTEND=noninteractive TZ=Europe/Paris apt upgrade -y
-#     - apt update; DEBIAN_FRONTEND=noninteractive TZ=Europe/Paris apt install -y build-essential gcc-multilib git gnuplot libgl1-mesa-dev libglu1-mesa-dev libxcursor-dev libxinerama1 libxft-dev wget xvfb
-#     # - apt update; DEBIAN_FRONTEND=noninteractive TZ=Europe/Paris apt install -y libopenblas-base; export OMP_NUM_THREADS="1" # MG20221201: This seems to fail in ubuntu 20.04
-#     - wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh
-#     - bash Miniconda3-latest-Linux-x86_64.sh -b -p /root/miniconda
-#     - eval "$(/root/miniconda/bin/conda shell.bash hook)"
-#     - conda init
-#     - conda install conda-libmamba-solver; conda config --set solver libmamba
-#     - conda create -y -c conda-forge -n dolfin_warp fenics=2019.1.0 matplotlib=3.1 meshio=5.3 mpi4py=3.1.3 numpy=1.17 pandas=0.25 pip python=3.8 scipy=1.3 vtk=9.1; conda activate dolfin_warp # MG20230608: need to install meshio via conda because pip install has h5py dependency issues # MG20230608: need to install vtk9 because vtk7 seems to require python2
-#     - conda activate dolfin_warp; conda env config vars set CPATH=$CONDA_PREFIX/include/vtk-9.1; conda deactivate; conda activate dolfin_warp
-#     - pip install gmsh git+https://gitlab.inria.fr/mgenet/myPythonLibrary.git git+https://gitlab.inria.fr/mgenet/myVTKPythonLibrary.git git+https://gitlab.inria.fr/mgenet/vtkpython_cbl.git git+https://gitlab.inria.fr/mgenet/dolfin_mech.git
-#     - cd Tests; ln -s ../dolfin_warp; make
-
-# tests-on-ubuntu-22.04-with-full-conda:
-#   stage: test
-#   only:
-#     - devel
-#     - /^devel-.*/
-#   tags:
-#     - ci.inria.fr
-#     - large
-#   image: ubuntu:22.04
-#   script:
-#     - apt update; DEBIAN_FRONTEND=noninteractive TZ=Europe/Paris apt upgrade -y
-#     - apt update; DEBIAN_FRONTEND=noninteractive TZ=Europe/Paris apt install -y build-essential gcc-multilib git gnuplot libgl1-mesa-dev libglu1-mesa-dev libxcursor-dev libxinerama1 libxft-dev wget xvfb
-#     - apt update; DEBIAN_FRONTEND=noninteractive TZ=Europe/Paris apt install -y libopenblas-base; export OMP_NUM_THREADS="1"
-#     - wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh
-#     - bash Miniconda3-latest-Linux-x86_64.sh -b -p /root/miniconda
-#     - eval "$(/root/miniconda/bin/conda shell.bash hook)"
-#     - conda init
-#     - conda install conda-libmamba-solver; conda config --set solver libmamba
-#     - conda create -y -c conda-forge -n dolfin_warp fenics=2019.1.0 matplotlib=3.5 meshio=5.3 mpi4py=3.1.3 numpy=1.21 pandas=1.3 pip python=3.10 scipy=1.8 vtk=9.1; conda activate dolfin_warp # MG20230608: need to install meshio via conda because pip install has h5py dependency issues # MG20230608: need to install vtk9 because vtk7 seems to require python2
-#     - conda activate dolfin_warp; conda env config vars set CPATH=$CONDA_PREFIX/include/vtk-9.1; conda deactivate; conda activate dolfin_warp
-#     - pip install gmsh git+https://gitlab.inria.fr/mgenet/myPythonLibrary.git git+https://gitlab.inria.fr/mgenet/myVTKPythonLibrary.git git+https://gitlab.inria.fr/mgenet/vtkpython_cbl.git git+https://gitlab.inria.fr/mgenet/dolfin_mech.git
-#     - cd Tests; ln -s ../dolfin_warp; make
+tests-on-ubuntu-24.04:
+  stage: test
+  only:
+    - devel
+    - /^devel-.*/
+  tags:
+    - ci.inria.fr
+    - large
+  image: ubuntu:24.04
+  script:
+    - apt update; DEBIAN_FRONTEND=noninteractive TZ=Europe/Paris apt upgrade -y
+    - apt update; DEBIAN_FRONTEND=noninteractive TZ=Europe/Paris apt install -y build-essential gcc-multilib git gnuplot libgl1-mesa-dev libglu1-mesa-dev libxcursor-dev libxinerama1 libxft-dev wget xvfb
+    # - apt update; DEBIAN_FRONTEND=noninteractive TZ=Europe/Paris apt install -y libopenblas-base; export OMP_NUM_THREADS="1" # MG20241017: Not present in Ubuntu 24.04
+    - wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh; bash Miniconda3-latest-Linux-x86_64.sh -b -p /root/miniconda;  eval "$(/root/miniconda/bin/conda shell.bash hook)"; conda init
+    # - conda install conda-libmamba-solver; conda config --set solver libmamba # MG20241017: This is now the default solver, cf. https://conda.org/blog/2023-11-06-conda-23-10-0-release
+    - conda create -y -c conda-forge -n dolfin_warp expat=2.5 fenics=2019.1.0 matplotlib=3.5 meshio=5.3 mpi4py=3.1.3 numpy=1.23.5 pandas=1.3 pip python=3.10 scipy=1.8 vtk=9.1; conda activate dolfin_warp # MG20230608: need to install meshio via conda because pip install has h5py dependency issues
+    - conda activate dolfin_warp; conda env config vars set CPATH=$CONDA_PREFIX/include/vtk-9.1; conda deactivate; conda activate dolfin_warp
+    - pip install gmsh git+https://gitlab.inria.fr/mgenet/myPythonLibrary.git git+https://gitlab.inria.fr/mgenet/myVTKPythonLibrary.git git+https://gitlab.inria.fr/mgenet/vtkpython_cbl.git git+https://gitlab.inria.fr/mgenet/dolfin_mech.git
+    - cd Tests; ln -s ../dolfin_warp; make

 # docker:
 #   stage: deploy