SalishSeaCast · douglatornell · Jan 14, 2026 · Jan 14, 2026 · Jan 14, 2026 · Jan 14, 2026
diff --git a/code-notes/salishsea-nemo/repos-maint/nemo-3.6.rst b/code-notes/salishsea-nemo/repos-maint/nemo-3.6.rst
@@ -4,6 +4,15 @@
 NEMO-3.6 Code Repo Maintenance
 ******************************
 
+.. warning::
+
+   This section is completely out of date because NEMO now uses Git for version control rather than SVN,
+   and we now use Git and GitHub for our Salish Sea NEMO code repository rather than Mercurial and Bitbucket.
+
+   This section is retained to provide guidance for development of a future maintenance workflow
+   when we move to a newer version of NEMO.
+
+
 .. _NEMO-3.6MaintSetup:
 
 Set-up
@@ -69,7 +78,9 @@ The workflow sections below explain how these 4 repo clones are used to pull cha
 Workflow to Pull Changes from NEMO-3.6 :command:`svn` Repo
 ==========================================================
 
-The workflow to pull changes from the master NEMO :command:`svn` repo and commit them to our :file:`NEMO-3.6-hg-mirror` repo is somewhat automated by the :ref:`Marlin`.
+The workflow to pull changes from the master NEMO :command:`svn` repo and commit them to our :file:`NEMO-3.6-hg-mirror` repo was somewhat automated by the
+(now deprecated)
+``Marlin`` tool that we developed.
 
 #. Review the upstream changes in the source browser at ``http://forge.ipsl.jussieu.fr/nemo/svn/branches/2015/nemo_v3_6_STABLE`` to select a range of changes to be pulled into our :file:`NEMO-3.6-hg-mirror` repo.
 

diff --git a/code-notes/salishsea-nemo/repos-maint/xios-2.rst b/code-notes/salishsea-nemo/repos-maint/xios-2.rst
@@ -4,6 +4,14 @@
 XIOS-2 Code Repo Maintenance
 ****************************
 
+.. warning::
+
+   This section is completely out of date we now use Git and GitHub for our XIOS-2 code repository rather than Mercurial and Bitbucket.
+
+   This section is retained to provide guidance for development of a future maintenance workflow
+   when we move to a newer version of XIOS-2.
+
+
 .. _XIOS-2MaintSetup:
 
 Set-up
@@ -113,7 +121,9 @@ The workflow sections below explain how these 4 repo clones are used to pull cha
 Workflow to Pull Changes from XIOS-2 :command:`svn` Repo
 ========================================================
 
-The workflow to pull changes from the master XIOS :command:`svn` repo and commit them to our :file:`XIOS-2-hg-mirror` repo is somewhat automated by the :ref:`Marlin`.
+The workflow to pull changes from the master XIOS :command:`svn` repo and commit them to our :file:`XIOS-2-hg-mirror` repo was somewhat automated by the
+(now deprecated)
+``Marlin`` tool that we developed.
 
 #. Review the upstream changes in the source browser at https://forge.ipsl.fr/ioserver/log/
 to select a range of changes to be pulled into our :file:`XIOS-2-hg-mirror` repo.

diff --git a/conf.py b/conf.py
@@ -66,6 +66,8 @@
     linkcheck_ignore.extend(
         [
             r"https://alliancecan.ca/.*",
+            r"https://www.alliancecan.ca/.*",
+            r"https://www.emacswiki.org/.*",
         ]
     )
 linkcheck_anchors_ignore_for_url = [

diff --git a/repos_organization.rst b/repos_organization.rst
@@ -24,7 +24,7 @@ General
 * Docs from public repos will be rendered as HTML on `readthedocs.org`_.
   readthedocs also provides PDF rendering.
 
-  .. _readthedocs.org: https://readthedocs.org/profiles/salishsea/
+  .. _readthedocs.org: https://app.readthedocs.org/profiles/salishsea/
 
 * There is no provision for rendering docs from private repos.
 

diff --git a/tidalcurrents/onc_adcp.rst b/tidalcurrents/onc_adcp.rst
@@ -276,7 +276,7 @@ If you will be running the processing in a new directory for the first time ther
 
 * 1. In :file:`compare_daily.m` change the path to be where you want everything to be saved. Many extra files will appear in this directory every time you run the scripts.
 
-* 2. Make an account on https://data.oceannetworks.ca/home to get userId. In :file:`getSoGAdcpDataMay15_mod.m` insert your email and userId at lines 173 and 174 of the script. You will receive an email every time you load raw data from the website.
+* 2. Make an account on https://data.oceannetworks.ca/ to get userId. In :file:`getSoGAdcpDataMay15_mod.m` insert your email and userId at lines 173 and 174 of the script. You will receive an email every time you load raw data from the website.
 
 * 3. In :file:`GET_DATA_fun` change the firstdate variable to be at least 3 days before the lastdate. This is because the filter length in :file:`LTIM_fun` needs at least that much data for the processing.
 

diff --git a/tidalcurrents/tidal_current_tools.rst b/tidalcurrents/tidal_current_tools.rst
@@ -21,7 +21,7 @@ Observations
 * The ONC data is then processed by Dr. Rich Pawlowicz.
 * Phase and amplitude information can be reported in papers, we use values reported in Foreman et al. (2004).
 
-.. _Ocean Networks Canada (ONC) website: https://data.oceannetworks.ca/home
+.. _Ocean Networks Canada (ONC) website: https://data.oceannetworks.ca/
 
 
 Tidal Ellipses

diff --git a/tides/tides_data_acquisition.rst b/tides/tides_data_acquisition.rst
@@ -80,7 +80,7 @@ Four months of current observations in Johnstone Strait
 TPXO7.1 modelled tidal predictions
 ----------------------------------------------
 
-`TPXO7.1 <https://www.esr.org/research/polar-tide-models/tmd-software/>`_ is an online tidal prediction tool funded by NASA. The predictions are based on the model by Egbert and Erofeeva (2002) at Oregon State University. The model is a 1/4 degree x 1/4 degree global inverse tide model. Predictions can be calculated using a Matlab based GUI called TMD (the Tide Model Driver).
+`TPXO7.1 <https://www.esr.org/data-products/polar-tide-models/>`_ is an online tidal prediction tool funded by NASA. The predictions are based on the model by Egbert and Erofeeva (2002) at Oregon State University. The model is a 1/4 degree x 1/4 degree global inverse tide model. Predictions can be calculated using a Matlab based GUI called TMD (the Tide Model Driver).
 
 TPXO7.1 was used for the boundary conditions of the model by :ref:`sutherlandetal11`... but resolution is coarse in Juan de Fuca Strait and the Strait of Georgia is an inland sea... Sutherland et al. (2011) used the tidal predictions for a straight boundary along 127 degrees W. The TPXO7.1 predictions are probably only useful when boundaries are offshore from the coast.
 

diff --git a/work_env/emacs_config.rst b/work_env/emacs_config.rst
@@ -265,24 +265,3 @@ Configure :program:`emacs` to enable :kbd:`python-outline` mode:
     ;; add Python-outline mode
     (require 'python-outline)
     (setq auto-mode-alist (append '(("\\.py" . python-outline)) auto-mode-alist))
-
-
-Mercurial Mode
---------------
-
-Allows you to work with Mercurial from within :program:`emacs`.
-
-Download :file:`mercurial.el` from http://hg.intevation.org/mercurial/file/tip/contrib/mercurial.el into your :file:`$HOME/elisp/` directory:
-
-.. code-block:: bash
-
-    cd $HOME/elisp/
-    wget http://hg.intevation.org/mercurial/file/tip/contrib/mercurial.el
-
-Configure :program:`emacs` to always load Mercurial mode:
-
-.. code-block:: scheme
-
-    ;; always load mercurial support
-    ;; http://hg.intevation.org/mercurial/file/tip/contrib/mercurial.el
-    (load-file "~/elisp/mercurial.elc")
diff --git a/work_env/index.rst b/work_env/index.rst
@@ -43,7 +43,7 @@ Other machines that you may need working environments on later include:
   Those machines are used for longer research runs of the model.
   The cluster that we use most often is ``nibi.alliancecan.ca`` at the University of Waterloo.
 
-  .. _Digital Research Alliance of Canada: https://alliancecan.ca/en
+  .. _Digital Research Alliance of Canada: https://www.alliancecan.ca/en
 
 When you are ready to run on those machines,
 please see the :ref:`QuickStartGuide` for instructions on setting working environments on them.