Docs maintenance (#106)

* Update ReadTheDocs build config Upgraded the OS to Ubuntu 24.04 and updated the Python toolchain to mambaforge-23.11 in the .readthedocs.yaml file. This ensures compatibility with the latest environment settings available on readthedocs. * Update Sphinx & optional dependencies version pins Updated Sphinx and optional dependencies packages pinned versions in `environment-rtd.yaml` and `SalishSeaTools/environment.yaml` in preparation for Python 3.13 environment. * Drop Sphinx source_suffix config The deprecated list of strings appears to have been removed in Sphinx=8. The default `source_suffix = {'.rst': 'restructuredtext'}` is appropriate for this project. * Update cross-reference link in Marlin commands docs Changed the reference link from `PullChangesFromNEMOsvn` to `PullChangesFromNEMO-3.6svn` in the Marlin commands documentation. This directs users to the correct details for using the `marlin` command. * Refactor docstrings in geo_tools.get_ij_coordinates() Simplified and standardized the format of the docstrings for `geo_tools.get_ij_coordinates` function to improve readability. Changed the type annotations to inline format for better consistency with other parts of the code and to resolve warnings from Sphinx autodoc extension. * Fix many broken links
SalishSeaCast · Nov 14, 2024 · caf8a71 · caf8a71
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diff --git a/.readthedocs.yaml b/.readthedocs.yaml
@@ -1,9 +1,9 @@
 version: 2
 
 build:
-  os: ubuntu-22.04
+  os: ubuntu-24.04
   tools:
-    python: "mambaforge-22.9"
+    python: "mambaforge-23.11"
 
 conda:
   environment: environment-rtd.yaml

diff --git a/I_ForcingFiles/Atmos/CheckAltitude.ipynb b/I_ForcingFiles/Atmos/CheckAltitude.ipynb
@@ -132,9 +132,7 @@
     {
      "cell_type": "markdown",
      "metadata": {},
-     "source": [
-      "Monhtly average altitude files in 2003 have been computed using the tools/I_ForcingFiles/Atmos/altitude.py script. Now, use those files to come up with an annual average of the altitude if the CGRF grid points. "
-     ]
+     "source": "Monhtly average altitude files in 2003 have been computed using the tools/I_ForcingFiles/Atmos/altitude.py script. Now, use those files to come up with an annual average of the altitude if the CGRF grid points."
     },
     {
      "cell_type": "code",
@@ -145,12 +143,12 @@
       "Alt = np.zeros([12,alt.shape[0],alt.shape[1]])\n",
       "\n",
       "for month in range(1,13):\n",
-      "    m = \"%02d\" % (month,); \n",
+      "    m = \"%02d\" % (month,);\n",
       "    file_str='altitude_y'+str(y)+'m'+ str(m)+'.nc'\n",
-      "    \n",
+      "\n",
       "    f= nc.Dataset(file_str)\n",
       "    Alt[month-1,:,:]=f.variables['alt']\n",
-      "    \n",
+      "\n",
       "alt_avg=np.mean(Alt,0)"
      ],
      "language": "python",
@@ -209,9 +207,9 @@
       "alt_file = nc.Dataset(alt_str, 'w', zlib=True)\n",
       "# dataset attributes\n",
       "nc_tools.init_dataset_attrs(\n",
-      "    alt_file, \n",
-      "    title='Annual average altitude - ' +str(y), \n",
-      "    notebook_name='CheckAltitude.ipynb', \n",
+      "    alt_file,\n",
+      "    title='Annual average altitude - ' +str(y),\n",
+      "    notebook_name='CheckAltitude.ipynb',\n",
       "    nc_filepath='../tools/I_ForcingFiles/Atmos/' + alt_str,\n",
       "    comment='Average altitude at each CGRF grid cell')\n",
       "#dimensions\n",
@@ -299,7 +297,7 @@
       "press_corr=np.zeros(press.shape)\n",
       "for k in range(press.shape[0]):\n",
       "    press_corr[k,:,:] = slp(alt_avg,press[k,:,:],temp[k,:,:])\n",
-      "    \n",
+      "\n",
       "print time\n",
       "print lat"
      ],
@@ -342,7 +340,7 @@
      "cell_type": "code",
      "collapsed": false,
      "input": [
-      "vmin=95000;vmax=103000; \n",
+      "vmin=95000;vmax=103000;\n",
       "i=0\n",
       "fig,axs=plt.subplots(1,2,figsize=(10,5))\n",
       "ax=axs[0]\n",
@@ -389,7 +387,7 @@
      "source": [
       "It looks like the open ocean uncorrected pressure is about 1kPa higher than the corrected version. But I dont think we need to worry about that.\n",
       "\n",
-      "Save as a netcdf. "
+      "Save as a netcdf."
      ]
     },
     {
@@ -401,9 +399,9 @@
       "slp_file = nc.Dataset(slp_str, 'w', zlib=True)\n",
       "# dataset attributes\n",
       "nc_tools.init_dataset_attrs(\n",
-      "    slp_file, \n",
-      "    title='CGRF pressure corrected to sea level - ' +str(y)+'/'+str(m)+'/'+str(d), \n",
-      "    notebook_name='CheckAltitude.ipynb', \n",
+      "    slp_file,\n",
+      "    title='CGRF pressure corrected to sea level - ' +str(y)+'/'+str(m)+'/'+str(d),\n",
+      "    notebook_name='CheckAltitude.ipynb',\n",
       "    nc_filepath='../tools/I_ForcingFiles/Atmos/' + alt_str,\n",
       "    comment='Corrected sea level pressure -CGRF')\n",
       "#dimensions\n",
@@ -467,9 +465,9 @@
      "cell_type": "markdown",
      "metadata": {},
      "source": [
-      "Next, these procedures will be written into a script to process the CGRF data for storm surges. \n",
+      "Next, these procedures will be written into a script to process the CGRF data for storm surges.\n",
       "\n",
-      "The I will work on adding to the get_CGRF routine. "
+      "The I will work on adding to the get_CGRF routine."
      ]
     },
     {
@@ -519,9 +517,9 @@
       "\n",
       "would produce a file called slp_corr_y2006m02d04.nc\n",
       "\n",
-      "Also, we need to add this to the get_CGRF command. I think I might be able to do that, but it might not be pythonic. \n",
+      "Also, we need to add this to the get_CGRF command. I think I might be able to do that, but it might not be pythonic.\n",
       "\n",
-      "For now, I will write a script to correct pressure files and put them in a local directory for myself. "
+      "For now, I will write a script to correct pressure files and put them in a local directory for myself."
      ]
     },
     {
@@ -564,7 +562,7 @@
      "cell_type": "code",
      "collapsed": false,
      "input": [
-      "vmin=95000;vmax=103000; \n",
+      "vmin=95000;vmax=103000;\n",
       "i=0\n",
       "fig,axs=plt.subplots(1,2,figsize=(10,5))\n",
       "ax=axs[0]\n",
@@ -663,7 +661,7 @@
       "        'PatriciaBay': 11007\n",
       "    }\n",
       "    wind_spd, pressure = [], []\n",
-      "    url = 'http://climate.weather.gc.ca/climateData/bulkdata_e.html'\n",
+      "    url = 'https://climate.weather.gc.ca/climateData/bulkdata_e.html'\n",
       "    query = {\n",
       "        'timeframe': 1,\n",
       "        'stationID': station_ids[station],\n",
@@ -700,7 +698,7 @@
       "                    pressure.append(0)\n",
       "    wind_spd= np.array(wind_spd) * 1000 / 3600\n",
       "    pressure = np.array(pressure)\n",
-      "    \n",
+      "\n",
       "    return wind_spd, pressure"
      ],
      "language": "python",
@@ -712,7 +710,7 @@
      "cell_type": "code",
      "collapsed": false,
      "input": [
-      "[wind,press_o] = get_pressure_obs('YVR', 19, 19,9,2002) \n",
+      "[wind,press_o] = get_pressure_obs('YVR', 19, 19,9,2002)\n",
       "\n",
       "# CGRF Point close to YVR\n",
       "point =[463, 526]\n",
@@ -755,9 +753,7 @@
     {
      "cell_type": "markdown",
      "metadata": {},
-     "source": [
-      "Corrected pressure is still a little lower than observations (500-1400 hPa). But I think this will give us better ssh, especially in the inlets. It is still better than the original CGRF. "
-     ]
+     "source": "Corrected pressure is still a little lower than observations (500-1400 hPa). But I think this will give us better ssh, especially in the inlets. It is still better than the original CGRF."
     },
     {
      "cell_type": "heading",
@@ -791,7 +787,7 @@
      "cell_type": "code",
      "collapsed": false,
      "input": [
-      "vmin=95000;vmax=103000; \n",
+      "vmin=95000;vmax=103000;\n",
       "i=0\n",
       "fig,axs=plt.subplots(1,2,figsize=(10,5))\n",
       "ax=axs[0]\n",
@@ -862,7 +858,7 @@
      "cell_type": "code",
      "collapsed": false,
      "input": [
-      "[wind,press_o] = get_pressure_obs('YVR', 4, 4,2,2006) \n",
+      "[wind,press_o] = get_pressure_obs('YVR', 4, 4,2,2006)\n",
       "\n",
       "# CGRF Point close to YVR\n",
       "point =[463, 526]\n",
@@ -922,9 +918,7 @@
     {
      "cell_type": "markdown",
      "metadata": {},
-     "source": [
-      "Look at Fred's correction and calculate the grid cell heights based on Fred's pressure correction. \n"
-     ]
+     "source": "Look at Fred's correction and calculate the grid cell heights based on Fred's pressure correction.\n"
     },
     {
      "cell_type": "code",
@@ -1022,7 +1016,7 @@
      "collapsed": false,
      "input": [
       "#Load Data\n",
-      "[wind,press_o] = get_pressure_obs('YVR', 4, 4,2,2006) \n",
+      "[wind,press_o] = get_pressure_obs('YVR', 4, 4,2,2006)\n",
       "f=nc.Dataset('/ocean/dlatorne/MEOPAR/CGRF/NEMO-atmos/slp_y2006m02d04.nc')\n",
       "press=f.variables['atmpres']\n",
       "f=nc.Dataset('/ocean/dlatorne/MEOPAR/CGRF/NEMO-atmos/t2_y2006m02d04.nc')\n",
@@ -1039,7 +1033,7 @@
       "# CGRF Point close to YVR\n",
       "point =[463, 526]\n",
       "\n",
-      "#Calculate corrected pressure with our algorithm but Fred's Altitude \n",
+      "#Calculate corrected pressure with our algorithm but Fred's Altitude\n",
       "p_Zfred = slp_correct(Zcorr[:],press[:],T[:])\n",
       "\n",
       "#plot\n",
@@ -1089,7 +1083,7 @@
      "collapsed": false,
      "input": [
       "#Load Data\n",
-      "[wind,press_o] = get_pressure_obs('YVR', 15, 15,9,2002) \n",
+      "[wind,press_o] = get_pressure_obs('YVR', 15, 15,9,2002)\n",
       "f=nc.Dataset('/ocean/dlatorne/MEOPAR/CGRF/NEMO-atmos/slp_y2002m09d15.nc')\n",
       "press=f.variables['atmpres']\n",
       "f=nc.Dataset('/ocean/dlatorne/MEOPAR/CGRF/NEMO-atmos/t2_y2002m09d15.nc')\n",
@@ -1103,7 +1097,7 @@
       "# CGRF Point close to YVR\n",
       "point =[463, 526]\n",
       "\n",
-      "#Calculate corrected pressure with our algorithm but Fred's Altitude \n",
+      "#Calculate corrected pressure with our algorithm but Fred's Altitude\n",
       "p_Zfred = slp_correct(Zcorr[:],press[:],T[:])\n",
       "\n",
       "#plot\n",
@@ -1155,9 +1149,9 @@
       "alt_file = nc.Dataset(alt_str, 'w', zlib=True)\n",
       "# dataset attributes\n",
       "nc_tools.init_dataset_attrs(\n",
-      "    alt_file, \n",
-      "    title='Altitude of CGRF grid cell', \n",
-      "    notebook_name='CheckAltitude.ipynb', \n",
+      "    alt_file,\n",
+      "    title='Altitude of CGRF grid cell',\n",
+      "    notebook_name='CheckAltitude.ipynb',\n",
       "    nc_filepath='../tools/I_ForcingFiles/Atmos/' + alt_str,\n",
       "    comment='Based on pressure correction provided by Frederic Dupont')\n",
       "#dimensions\n",