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Fixed outdated supervisor URLs for a more accurate reference.

Author: douglatornell

docs/deployment/arbutus_cloud.rst

@@ -785,34 +785,33 @@ Install the `Miniconda`_ environment and package manager:
 .. 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

@@ -68,18 +68,18 @@ 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 +93,7 @@ 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/: