Update deployment docs (#334)

* Update deployment docs

Updated deployment instructions to replace `conda` with `mamba` for
environment activation and creation. Replaced `python3` with `python`
for pip installations and switched to Miniforge instead of Miniconda.
Fixed outdated supervisor URLs for a more accurate reference.

* 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.

Author: douglatornell

docs/deployment/arbutus_cloud.rst

@@ -778,41 +778,41 @@ Fetch and merge changes from the `FVCOM41 repo on GitLab`_ and do a clean build:
 Python Packages
 ===============
 
-Install the `Miniconda`_ environment and package manager:
+Install the `Miniforge-pypy3`_ environment and package manager:
+
+.. _Miniforge-pypy3: https://github.com/conda-forge/miniforge
 
-.. _Miniconda: https://docs.conda.io/en/latest/miniconda.html
 
 .. code-block:: bash
 
     $ cd /nemoShare/MEOPAR/nowcast-sys/
-    $ curl -LO https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh
-    $ bash Miniconda3-latest-Linux-x86_64.sh
+    $ curl -LO https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge-pypy3-Linux-x86_64.sh
+    $ bash Miniforge-pypy3-Linux-x86_64.sh
 
-Answer :file:`/nemoShare/MEOPAR/nowcast-sys/miniconda3` when the installer asks for an installation location.
+Answer :file:`/nemoShare/MEOPAR/nowcast-sys/miniforge-pypy3` when the installer asks for an installation location.
 
-Answer no when the install asks :guilabel:`Do you wish the installer to initialize Miniconda3 by running conda init? [yes|no]`.
+Answer ``yes`` when the install asks :guilabel:`Do you wish to update your shell profile to automatically initialize conda? ... [yes|no]`.
 
 The Python packages that the system depends on are installed in a conda environment with:
 
 .. code-block:: bash
 
     $ cd /nemoShare/MEOPAR/nowcast-sys/
-    $ conda update -n base -c defaults conda
-    $ conda env create \
+    $ mamba env create \
         --prefix /nemoShare/MEOPAR/nowcast-sys/nowcast-env \
         -f SalishSeaNowcast/envs/environment-prod.yaml
-    $ source /nemoShare/MEOPAR/nowcast-sys/miniconda3/bin/activate /nemoShare/MEOPAR/nowcast-sys/nowcast-env/
-    (/nemoShare/MEOPAR/nowcast-sys/nowcast-env)$ python3 -m pip install --editable NEMO_Nowcast/
-    (/nemoShare/MEOPAR/nowcast-sys/nowcast-env)$ python3 -m pip install --editable moad_tools/
-    (/nemoShare/MEOPAR/nowcast-sys/nowcast-env)$ python3 -m pip install --editable tools/SalishSeaTools/
+    $ mamba activate /nemoShare/MEOPAR/nowcast-sys/nowcast-env/
+    (/nemoShare/MEOPAR/nowcast-sys/nowcast-env)$ python -m pip install --editable NEMO_Nowcast/
+    (/nemoShare/MEOPAR/nowcast-sys/nowcast-env)$ python -m pip install --editable moad_tools/
+    (/nemoShare/MEOPAR/nowcast-sys/nowcast-env)$ python -m pip install --editable tools/SalishSeaTools/
     (/nemoShare/MEOPAR/nowcast-sys/nowcast-env)$ cd OPPTools/
     (/nemoShare/MEOPAR/nowcast-sys/nowcast-env)$ git switch SalishSeaCast-prod
     (/nemoShare/MEOPAR/nowcast-sys/nowcast-env)$ cd /nemoShare/MEOPAR/nowcast-sys/
-    (/nemoShare/MEOPAR/nowcast-sys/nowcast-env)$ python3 -m pip install --editable OPPTools/
-    (/nemoShare/MEOPAR/nowcast-sys/nowcast-env)$ python3 -m pip install --editable NEMO-Cmd/
-    (/nemoShare/MEOPAR/nowcast-sys/nowcast-env)$ python3 -m pip install --editable SalishSeaCmd/
-    (/nemoShare/MEOPAR/nowcast-sys/nowcast-env)$ python3 -m pip install --editable FVCOM-Cmd/
-    (/nemoShare/MEOPAR/nowcast-sys/nowcast-env)$ python3 -m pip install --editable SalishSeaNowcast/
+    (/nemoShare/MEOPAR/nowcast-sys/nowcast-env)$ python -m pip install --editable OPPTools/
+    (/nemoShare/MEOPAR/nowcast-sys/nowcast-env)$ python -m pip install --editable NEMO-Cmd/
+    (/nemoShare/MEOPAR/nowcast-sys/nowcast-env)$ python -m pip install --editable SalishSeaCmd/
+    (/nemoShare/MEOPAR/nowcast-sys/nowcast-env)$ python -m pip install --editable FVCOM-Cmd/
+    (/nemoShare/MEOPAR/nowcast-sys/nowcast-env)$ python -m pip install --editable SalishSeaNowcast/
 
 
 Environment Variables

docs/deployment/operations.rst

@@ -39,7 +39,7 @@ and the manager,
 are managed by the `supervisor`_ process manager tool.
 So is the `sarracenia client`_ that maintains mirrors of the HRDPS forecast files and rivers hydrometric files from the `ECCC MSC datamart service`_.
 
-.. _supervisor: http://supervisord.org/
+.. _supervisor: https://supervisord.org/
 .. _sarracenia client: https://github.com/MetPX/sarracenia/blob/v2_dev/doc/sr_subscribe.1.rst
 .. _ECCC MSC datamart service: https://dd.weather.gc.ca/
 
@@ -73,7 +73,7 @@ Start it with:
     $ source activate /results/nowcast-sys/nowcast-env
     (/results/nowcast-sys/nowcast-env)$ supervisorctl --configuration $NOWCAST_CONFIG/supervisord.ini
 
-.. _supervisorctl: http://supervisord.org/running.html#running-supervisorctl
+.. _supervisorctl: https://supervisord.org/running.html#running-supervisorctl
 
 See the `supervisorctl`_ docs,
 or use the ``help`` command within :command:`supervisorctl` to get information on the available commands.

docs/deployment/skookum.rst

@@ -56,9 +56,11 @@ The Python packages that the system depends on are installed in conda environmen
 
 .. note::
    In Mar-2022 the Python environment and package management tool used for the system
-   was changed from Miniconda3 to `Mambaforge-pypy3`_.
+   was changed from Miniconda3 to Mambaforge-pypy3.
+   In Oct-2024 it was changed again to `Miniforge-pypy3`_ to reflect the merge of
+   Mambaforge into Miniforge and the deprecation of mambaforge in Jul-2024.
 
-   .. _Mambaforge-pypy3: https://github.com/conda-forge/miniforge
+   .. _Miniforge-pypy3: https://github.com/conda-forge/miniforge
 
 For the ``SalishSeaCast`` automation system:
 
@@ -68,18 +70,18 @@ For the ``SalishSeaCast`` automation system:
     $ mamba env create \
         --prefix /SalishSeaCast/nowcast-env \
         -f SalishSeaNowcast/envs/environment-prod.yaml
-    $ conda activate /SalishSeaCast/nowcast-env
-    (/SalishSeaCast/nowcast-env)$ python3 -m pip install --editable NEMO_Nowcast/
-    (/SalishSeaCast/nowcast-env)$ python3 -m pip install --editable moad_tools/
-    (/SalishSeaCast/nowcast-env)$ python3 -m pip install --editable Reshapr/
-    (/SalishSeaCast/nowcast-env)$ python3 -m pip install --editable tools/SalishSeaTools/
+    $ mamba activate /SalishSeaCast/nowcast-env
+    (/SalishSeaCast/nowcast-env)$ python -m pip install --editable NEMO_Nowcast/
+    (/SalishSeaCast/nowcast-env)$ python -m pip install --editable moad_tools/
+    (/SalishSeaCast/nowcast-env)$ python -m pip install --editable Reshapr/
+    (/SalishSeaCast/nowcast-env)$ python -m pip install --editable tools/SalishSeaTools/
     (/SalishSeaCast/nowcast-env)$ cd OPPTools/
     (/SalishSeaCast/nowcast-env)$ git switch SalishSeaCast-prod
     (/SalishSeaCast/nowcast-env)$ cd /SalishSeaCast/
-    (/SalishSeaCast/nowcast-env)$ python3 -m pip install --editable OPPTools/
-    (/SalishSeaCast/nowcast-env)$ python3 -m pip install --editable NEMO-Cmd/
-    (/SalishSeaCast/nowcast-env)$ python3 -m pip install --editable SalishSeaCmd/
-    (/SalishSeaCast/nowcast-env)$ python3 -m pip install --editable SalishSeaNowcast/
+    (/SalishSeaCast/nowcast-env)$ python -m pip install --editable OPPTools/
+    (/SalishSeaCast/nowcast-env)$ python -m pip install --editable NEMO-Cmd/
+    (/SalishSeaCast/nowcast-env)$ python -m pip install --editable SalishSeaCmd/
+    (/SalishSeaCast/nowcast-env)$ python -m pip install --editable SalishSeaNowcast/
 
 For the `sarracenia client`_ that maintains mirrors of the HRDPS forecast files and
 rivers hydrometric files from the `ECCC MSC datamart service`_:
@@ -93,7 +95,7 @@ rivers hydrometric files from the `ECCC MSC datamart service`_:
     $ mamba env create \
         --prefix /SalishSeaCast/sarracenia-env \
         -f SalishSeaNowcast/envs/environment-sarracenia.yaml
-    $ conda activate /SalishSeaCast/sarracenia-env
+    $ mamba activate /SalishSeaCast/sarracenia-env
     (/SalishSeaCast/sarracenia-env)$ sr_subscribe edit credentials.conf  # initialize datamart credentials
 
 For the `salishsea-site web app`_ that is mounted at https://salishsea.eos.ubc.ca/:
@@ -106,7 +108,7 @@ For the `salishsea-site web app`_ that is mounted at https://salishsea.eos.ubc.c
     $ mamba env create \
         --prefix /SalishSeaCast/salishsea-site-env \
         -f salishsea-site/envs/environment-prod.yaml
-    $ conda activate /SalishSeaCast/salishsea-site-env
+    $ mamba activate /SalishSeaCast/salishsea-site-env
     (/SalishSeaCast/salishsea-site-env) $ python3 -m pip install --editable salishsea-site/
 
 
@@ -163,7 +165,7 @@ and :command:`unset` them when it is deactivated.
 
 The :file:`/SalishSeaCast/sarracenia-env` environment variables are included in the
 :file:`SalishSeaNowcast/envs/environment-sarracenia.yaml` file so that they are managed by
-:command:`conda` to automatically :command:`export` the environment variables required by the
+:command:`mamba` to automatically :command:`export` the environment variables required by the
 sarracenia client when the environment is activated and :command:`unset` them when the
 environment is deactivated.
 To see the variables and their values:
@@ -172,7 +174,7 @@ To see the variables and their values:
 
     $ cd /SalishSeaCast/sarracenia-env
     $ source activate /SalishSeaCast/salishsea-site-env
-    (/SalishSeaCast/salishsea-site-env) $ conda env config vars list
+    (/SalishSeaCast/salishsea-site-env) $ mamba env config vars list
 
 
 :file:`/SalishSeaCast/salishsea-site-env`
@@ -353,7 +355,7 @@ and its dashboard port on 4387:
 
 .. code-block:: bash
 
-    $ conda activate /SalishSeaCast/nowcast-env
+    $ mamba activate /SalishSeaCast/nowcast-env
     (/SalishSeaCast/nowcast-env)$ dask scheduler --port 4386 --dashboard-address :4387
 
 Use :kbd:`Control-b ,` to rename the :program:`tmux` terminal to ``dask-scheduler``.
@@ -370,7 +372,7 @@ and launch the 4 :command:`dask worker` processes with these properties:
 
 .. code-block:: bash
 
-    $ conda activate /SalishSeaCast/nowcast-env
+    $ mamba activate /SalishSeaCast/nowcast-env
     (/SalishSeaCast/nowcast-env)$ dask worker --nworkers=4 --nthreads=1 --memory-limit 64G \
       --local-directory /tmp/SalishSeaCast \
       --lifetime 3600 --lifetime-stagger 60 --lifetime-restart \