diff --git a/code-notes/salishsea-nemo/repos-maint/nemo-3.6.rst b/code-notes/salishsea-nemo/repos-maint/nemo-3.6.rst index 42e8581..266e305 100644 --- 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 warning:: + + This section is completely out of date because NEMO now uses Git for version control rather than SVN, + and we now use Git and GitHub for our Salish Sea NEMO code repository rather than Mercurial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 index f1141a4..f11644c 100644 --- 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 warning:: + + This section is completely out of date we now use Git and GitHub for our XIOS-2 code repository rather than Mercurial and Bitbucket.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 index 8119b2d..dfcb5de 100644 --- 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 index 2eee7a0..4bf1bdb 100644 --- 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 index e5fcf8a..ca8cb77 100644 --- 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 index e74bd96..074364d 100644 --- 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 index 489494a..c00e10f 100644 --- 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 `_ 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 `_ 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 index 82d48d3..e1ef5dc 100644 --- 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 index 6d6d2c0..8188d06 100644 --- 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.