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Update docs to reflect change to Miniforge
Revised deployment instructions to use Miniforge-pypy3 following the deprecation of Mambaforge in July 2024. Updated activation commands from `conda` to `mamba` throughout for consistency. Adjusted relevant links and clarified environment setup details.
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docs/deployment/arbutus_cloud.rst

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@@ -778,9 +778,10 @@ Fetch and merge changes from the `FVCOM41 repo on GitLab`_ and do a clean build:
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Python Packages
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===============
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Install the `Miniconda`_ environment and package manager:
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Install the `Miniforge-pypy3`_ environment and package manager:
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.. _Miniforge-pypy3: https://github.com/conda-forge/miniforge
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.. _Miniconda: https://docs.conda.io/en/latest/miniconda.html
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.. code-block:: bash
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docs/deployment/skookum.rst

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.. note::
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In Mar-2022 the Python environment and package management tool used for the system
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was changed from Miniconda3 to `Mambaforge-pypy3`_.
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was changed from Miniconda3 to Mambaforge-pypy3.
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In Oct-2024 it was changed again to `Miniforge-pypy3`_ to reflect the merge of
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Mambaforge into Miniforge and the deprecation of mambaforge in Jul-2024.
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.. _Mambaforge-pypy3: https://github.com/conda-forge/miniforge
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.. _Miniforge-pypy3: https://github.com/conda-forge/miniforge
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For the ``SalishSeaCast`` automation system:
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$ mamba env create \
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--prefix /SalishSeaCast/salishsea-site-env \
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-f salishsea-site/envs/environment-prod.yaml
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$ conda activate /SalishSeaCast/salishsea-site-env
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$ mamba activate /SalishSeaCast/salishsea-site-env
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(/SalishSeaCast/salishsea-site-env) $ python3 -m pip install --editable salishsea-site/
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The :file:`/SalishSeaCast/sarracenia-env` environment variables are included in the
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:file:`SalishSeaNowcast/envs/environment-sarracenia.yaml` file so that they are managed by
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:command:`conda` to automatically :command:`export` the environment variables required by the
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:command:`mamba` to automatically :command:`export` the environment variables required by the
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sarracenia client when the environment is activated and :command:`unset` them when the
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environment is deactivated.
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To see the variables and their values:
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$ cd /SalishSeaCast/sarracenia-env
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$ source activate /SalishSeaCast/salishsea-site-env
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(/SalishSeaCast/salishsea-site-env) $ conda env config vars list
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(/SalishSeaCast/salishsea-site-env) $ mamba env config vars list
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:file:`/SalishSeaCast/salishsea-site-env`
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.. code-block:: bash
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$ conda activate /SalishSeaCast/nowcast-env
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$ mamba activate /SalishSeaCast/nowcast-env
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(/SalishSeaCast/nowcast-env)$ dask scheduler --port 4386 --dashboard-address :4387
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Use :kbd:`Control-b ,` to rename the :program:`tmux` terminal to ``dask-scheduler``.
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.. code-block:: bash
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$ conda activate /SalishSeaCast/nowcast-env
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$ mamba activate /SalishSeaCast/nowcast-env
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(/SalishSeaCast/nowcast-env)$ dask worker --nworkers=4 --nthreads=1 --memory-limit 64G \
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--local-directory /tmp/SalishSeaCast \
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--lifetime 3600 --lifetime-stagger 60 --lifetime-restart \

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