update conda setup

.github/actions/initialize_conda_env/action.yaml

@@ -5,17 +5,16 @@ inputs:
     description: Python version to install
     required: true
     type: string
-    default: "3.10"
+    default: "3.12"
 
 runs:
   using: composite
   steps:
     # cache ref https://github.com/conda-incubator/setup-miniconda#caching-packages
 
     - name: Setup conda-forge
-      uses: conda-incubator/setup-miniconda@v2
+      uses: conda-incubator/setup-miniconda@v3
       with:
-          miniforge-variant: Mambaforge
           miniforge-version: latest
           activate-environment: sscp-env
           python-version: ${{ inputs.python-version }}

environment.yml

@@ -5,28 +5,31 @@ channels:
   - minrk
 
 dependencies:
-
-
-#   # scientific packages
-  - fenics=2019.1.0
-  - mshr=2019.1.0
-  - sympy
+  # scientific packages
+  - fenics-dolfinx=0.9.0
+  # need 2019.2.0.dev to use ufl_legacy
+  # to avoid conflict with dolfinx
+  - conda-forge/label/fenics-dev::fenics=2019.2.0.dev20240219
+  # - mshr=2019.1.0
+  - sympy<1.14
   - neuron
   # lfpy/pytorch seem to have conflicts
   # - lfpy=2.2.5
   - lfpy
   - python-neo
   - browndye
+  - brian2
 
   # packaged in this repo:
-  - "minrk::opencarp=12"
-  # TODO:
-  # - carputils?
+  - "minrk::opencarp=18"
+  - "minrk::carputils=18"
 
   # basic Python
-  - python=3.10
+  - python=3.12
+  - pip
   - black
   - isort
+  - ruff
   - matplotlib-base
   - cython
   - scipy
@@ -41,12 +44,11 @@ dependencies:
   - wurlitzer
 
   # IPython/Jupyter
-  # - nodejs=14
-  - jupyterlab
-  - jupyterhub-base=4.0.0
+  - jupyterlab=4.*
+  - jupyter-resource-usage
+  - jupyterhub-base=5.3.0
   - jupyterlab_code_formatter
   - jupyterlab-git
-  - nbclassic
   - nbdime
   - notebook
   - ipykernel
@@ -57,4 +59,4 @@ dependencies:
   - jupyter-book
 
   # Progress-bars
-  - tqdm
+  - tqdm