diff --git a/.github/actions/initialize_conda_env/action.yaml b/.github/actions/initialize_conda_env/action.yaml index a4b401c..63cf7d8 100644 --- a/.github/actions/initialize_conda_env/action.yaml +++ b/.github/actions/initialize_conda_env/action.yaml @@ -5,7 +5,7 @@ inputs: description: Python version to install required: true type: string - default: "3.10" + default: "3.12" runs: using: composite @@ -13,9 +13,8 @@ runs: # 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 }} diff --git a/environment.yml b/environment.yml index 5b0bffd..e66131e 100644 --- a/environment.yml +++ b/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 \ No newline at end of file + - tqdm