Updating environment

Author: mgenet

.gitlab-ci.yml

@@ -15,13 +15,12 @@ build_docker:
   tags:
     - ci.inria.fr
     - large
-  image: registry.gitlab.inria.fr/inria-ci/docker/ubuntu:20.04
-  # image: ubuntu:20.04
+  # image: registry.gitlab.inria.fr/inria-ci/docker/ubuntu:20.04
+  image: ubuntu:20.04
   script:
-    - apt update; apt install -y python3 python3-pip mercurial git ca-certificates curl gnupg lsb-release
+    - apt update; DEBIAN_FRONTEND=noninteractive apt install -y ca-certificates curl git gnupg lsb-release mercurial python3 python3-pip tzdata
     - curl -fsSL https://download.docker.com/linux/ubuntu/gpg | gpg --dearmor -o /usr/share/keyrings/docker-archive-keyring.gpg
     - echo "deb [arch=$(dpkg --print-architecture) signed-by=/usr/share/keyrings/docker-archive-keyring.gpg] https://download.docker.com/linux/ubuntu $(lsb_release -cs) stable" | tee /etc/apt/sources.list.d/docker.list > /dev/null
-    - DEBIAN_FRONTEND=noninteractive apt install -y tzdata
     - apt update; apt install -y docker-ce docker-ce-cli containerd.io
     - docker images
     - docker rmi -f $CI_REGISTRY_IMAGE || true

.repo2docker/environment.yml

@@ -15,42 +15,51 @@ channels:
 dependencies:
 # python
   - mpi4py=3.1.3 # MG20220906: To avoid mpi warnings in FEniCS, cf. https://fenicsproject.discourse.group/t/runtimewarning-mpi4py-mpi-file-size-changed-may-indicate-binary-incompatibility-expected-32-from-c-header-got-40-from-pyobject-def-compile-class-cpp-data-mpi-comm-mpi-comm-world/6496 # MG20220906: Note that 3.0.3 leads to a `RuntimeError: Error when importing mpi4py`, but 3.1.3 seems to work.
-  - numpy=1.21.5 # MG20221220: later numpy versions seem incompatible with itkwidgets 0.32
-  - python
-  - scipy
-  - sympy
+  - numpy=1.21.6 # MG20221220: later numpy versions seem incompatible with itkwidgets 0.32
+  - python=3.8
+  - scipy=1.9
+  - sympy=1.9
 
 # jupyter
-  - "ipywidgets<8" # MG20221226: cf. https://github.com/InsightSoftwareConsortium/itkwidgets/pull/590/files # MG20230601: Somehow this is still needed, despite the updated itkwidgets version…
-  - itkwidgets=0.32.6
-  - jupyter
-  - jupyter_contrib_nbextensions
-  - jupyter_nbextensions_configurator
-  - "jupyterlab<4" # MG20230602: This seems to be needed as well, otherwise jupyter does not start on binder
-  - "notebook<6.5" # MG20221226: cf. https://github.com/InsightSoftwareConsortium/itkwidgets/pull/590/files # MG20230601: Somehow this is still needed, despite the updated itkwidgets version…
+  - ipywidgets=7.6 # MG20221226: cf. https://github.com/InsightSoftwareConsortium/itkwidgets/pull/590/files # MG20230601: Somehow this is still needed, despite the updated itkwidgets version…
+  - itkwidgets=0.32
+  # MG20240123: Specified all these versions based on the 2023 build to get ipywidgets and itkwidgets to properly interact
+  - jupyter=1.0.0
+  - jupyter_client=7.4.8
+  - jupyter_console=6.4.4
+  - jupyter_contrib_core=0.4.0
+  - jupyter_contrib_nbextensions=0.5.1
+  - jupyter_core=5.1.3
+  - jupyter_highlight_selected_word=0.2.0
+  - jupyter_latex_envs=1.4.6
+  - jupyter_nbextensions_configurator=0.4.1
+  - jupyter_server=2.0.6
+  - jupyter_server_terminals=0.4.3
+  # MG20240123: Specified all these versions based on the 2023 build to get ipywidgets and itkwidgets to properly interact
+  - jupyterlab=3.5 # MG20230602: This seems to be needed as well, otherwise jupyter does not start on binder
+  - notebook=6.4 # MG20221226: cf. https://github.com/InsightSoftwareConsortium/itkwidgets/pull/590/files # MG20230601: Somehow this is still needed, despite the updated itkwidgets version…
 
 # coding stuff
-  - git
+  - git=2.39
 
 # computing stuff
+  - expat=2.5
   - fenics=2019.1.0
-  - gmsh
-  - meshio
   - vtk=9.0 # MG20201223: Need to correspond to the environment variable CPATH # MG20220628: Apparently there is some kind of conflict between vtk9.1 & libstdc++.so.6 in Ubuntu 20.04… # MG20221220: Apparently there is some kind of conflict between vtk9.1 & itkwidgets 0.32…
 
 # plotting stuff
-  - matplotlib
-  - gnuplot
+  - matplotlib=3.5
+  - gnuplot=5.4
 
   - pip
   - pip:
   # python
-    - numpy==1.21.5 # MG20240605: meshio seems to be installing a newer numpy…
+    - numpy==1.21.6 # MG20240605: meshio seems to be installing a newer numpy…
     - zstd
 
   # computing stuff
-    - gmsh
-    - meshio
+    - gmsh==4.9.0
+    - meshio==5.3.4
 
   # tracking stuff
     - dolfin_warp