Build docs

docs/source/api.rst

@@ -38,7 +38,7 @@ Toolbox
    genBasinMasks
 
 Plotting tools
-~~~~~~~~
+~~~~~~~~~~~~~~~~
 
 .. autosummary::
    xyplot

docs/source/examples/forcing.ipynb

@@ -4,7 +4,11 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "<h1><center>Analysis of Forcing Fields</center></h1>\n",
+    "# Analysis of Forcing Fields\n",
+    "\n",
+    "`mom6_tools.MOM6grid` returns an object with MOM6 grid data.\n",
+    "\n",
+    "`mom6_tools.latlon_analysis` has a collection of tools used to perform spatial analysis  (e.g., time averages and spatial mean).\n",
     "\n",
     "The goal of this notebook is the following:\n",
     "\n",
@@ -21,23 +25,13 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 1,
+   "execution_count": 2,
    "metadata": {},
-   "outputs": [
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
-      "Basemap module not found. Some regional plots may not function properly\n"
-     ]
-    }
-   ],
+   "outputs": [],
    "source": [
     "%matplotlib inline\n",
-    "import sys\n",
-    "sys.path.append(\"/glade/u/home/gmarques/libs/CESM_MOM6_analysis/mom6_tools\")\n",
-    "from MOM6grid import MOM6grid\n",
-    "from latlon_analysis import time_mean_latlon\n",
+    "from mom6_tools.MOM6grid import MOM6grid\n",
+    "from mom6_tools.latlon_analysis import time_mean_latlon\n",
     "import matplotlib.pyplot as plt"
    ]
   },
@@ -408,9 +402,9 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "Pangeo (Python 3.6)",
+   "display_name": "Python [conda env:analysis]",
    "language": "python",
-   "name": "pangeo-3.6"
+   "name": "conda-env-analysis-py"
   },
   "language_info": {
    "codemirror_mode": {
@@ -422,7 +416,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.6.7"
+   "version": "3.7.3"
   }
  },
  "nbformat": 4,

docs/source/examples/globally_averaged_ocean_properties.ipynb

@@ -4,7 +4,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "<h1><center>Globally Averaged Ocean Temperature and Salinity</center></h1>"
+    "# Globally Averaged Ocean Temperature and Salinity"
    ]
   },
   {

docs/source/examples/meridional_overturning.ipynb

@@ -4,7 +4,9 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "<h1><center>Meridional Overturning</center></h1>\n",
+    "# Meridional Overturning\n",
+    "\n",
+    "`mom6_tools.moc` functions for computing and plotting meridional overturning. \n",
     "\n",
     "The goal of this notebook is the following:\n",
     "\n",
@@ -17,25 +19,23 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 1,
+   "execution_count": 3,
    "metadata": {},
    "outputs": [],
    "source": [
     "%matplotlib inline\n",
-    "import sys\n",
-    "sys.path.append(\"/glade/u/home/gmarques/libs/CESM_MOM6_analysis/mom6_tools\")\n",
-    "from meridional_overturning import  *\n",
-    "from latlon_analysis import check_time_interval\n",
-    "from m6toolbox import genBasinMasks\n",
-    "import matplotlib.pyplot as plt\n",
     "import matplotlib\n",
     "import numpy as np\n",
-    "import xarray as xr"
+    "import xarray as xr\n",
+    "# mom6_tools\n",
+    "from mom6_tools.moc import  *\n",
+    "from mom6_tools.m6toolbox import check_time_interval, genBasinMasks \n",
+    "import matplotlib.pyplot as plt\n"
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": 14,
+   "execution_count": 4,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -67,7 +67,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 15,
+   "execution_count": 5,
    "metadata": {},
    "outputs": [
     {
@@ -78,6 +78,14 @@
       "\n",
       "11.16428 64.78855 [391, 434]\n"
      ]
+    },
+    {
+     "name": "stderr",
+     "output_type": "stream",
+     "text": [
+      "/glade/u/home/gmarques/miniconda3/envs/analysis/lib/python3.7/site-packages/dask/array/numpy_compat.py:28: RuntimeWarning: invalid value encountered in true_divide\n",
+      "  x = np.divide(x1, x2, out)\n"
+     ]
     }
    ],
    "source": [

docs/source/examples/poleward_heat_transport.ipynb

@@ -4,7 +4,9 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "<h1><center>Poleward Heat Transport</center></h1>\n",
+    "# Poleward Heat Transport\n",
+    "\n",
+    "`mom6_tools.polar_heat_transport` collection of functions for computing and plotting poleward heat transport.\n",
     "\n",
     "The goal of this notebook is the following:\n",
     "\n",
@@ -22,11 +24,8 @@
    "outputs": [],
    "source": [
     "%matplotlib inline\n",
-    "import sys\n",
-    "sys.path.append(\"/glade/u/home/gmarques/libs/CESM_MOM6_analysis/mom6_tools\")\n",
-    "from poleward_heat_transport import  *\n",
-    "from latlon_analysis import check_time_interval\n",
-    "from m6toolbox import genBasinMasks\n",
+    "from mom6_tools.poleward_heat_transport import  *\n",
+    "from mom6_tools.m6toolbox import check_time_interval, genBasinMasks\n",
     "import matplotlib.pyplot as plt\n",
     "import matplotlib\n",
     "import numpy as np\n",

docs/source/examples/section_transports.ipynb

@@ -4,7 +4,9 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "<h1><center>Transport across sections</center></h1>\n",
+    "# Transport across sections\n",
+    "\n",
+    "`mom6_tools.section_transports` collection of functions for computing and plotting time-series of transports across vertical sections.\n",
     "\n",
     "The goal of this notebook is the following:\n",
     "\n",
@@ -17,14 +19,12 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 7,
+   "execution_count": 1,
    "metadata": {},
    "outputs": [],
    "source": [
     "%matplotlib inline\n",
-    "import sys\n",
-    "sys.path.append(\"/glade/u/home/gmarques/libs/CESM_MOM6_analysis/mom6_tools\")\n",
-    "from section_transports import Transport, options\n",
+    "from mom6_tools.section_transports import Transport, options\n",
     "import matplotlib.pyplot as plt"
    ]
   },

docs/source/examples/surface.ipynb

@@ -4,7 +4,11 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "<h1><center>Analysis of Surface Fields </center></h1>\n",
+    "# Analysis of Forcing Fields\n",
+    "\n",
+    "`mom6_tools.MOM6grid` returns an object with MOM6 grid data.\n",
+    "\n",
+    "`mom6_tools.latlon_analysis` has a collection of tools used to perform spatial analysis  (e.g., time averages and spatial mean).\n",
     "\n",
     "The goal of this notebook is the following:\n",
     "\n",
@@ -23,21 +27,11 @@
    "cell_type": "code",
    "execution_count": 1,
    "metadata": {},
-   "outputs": [
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
-      "Basemap module not found. Some regional plots may not function properly\n"
-     ]
-    }
-   ],
+   "outputs": [],
    "source": [
     "%matplotlib inline\n",
-    "import sys\n",
-    "sys.path.append(\"/glade/u/home/gmarques/libs/CESM_MOM6_analysis/mom6_tools\")\n",
-    "from MOM6grid import MOM6grid\n",
-    "from latlon_analysis import time_mean_latlon\n",
+    "from mom6_tools.MOM6grid import MOM6grid\n",
+    "from mom6_tools.latlon_analysis import time_mean_latlon\n",
     "import matplotlib.pyplot as plt"
    ]
   },
@@ -208,9 +202,9 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "Pangeo (Python 3.6)",
+   "display_name": "Python [conda env:analysis]",
    "language": "python",
-   "name": "pangeo-3.6"
+   "name": "conda-env-analysis-py"
   },
   "language_info": {
    "codemirror_mode": {
@@ -222,7 +216,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.6.7"
+   "version": "3.7.3"
   }
  },
  "nbformat": 4,

mom6_tools/__init__.py

@@ -9,10 +9,10 @@
 
 from pkg_resources import DistributionNotFound, get_distribution
 
-from .MOM6grid import *
-from .section_transports import *
-from .latlon_analysis import *
-from .poleward_heat_transport import *
+#from MOM6grid import *
+#from section_transports import *
+#from latlon_analysis import *
+#from poleward_heat_transport import *
 
 try:
     __version__ = get_distribution(__name__).version

mom6_tools/latlon_analysis.py

@@ -9,8 +9,8 @@
 import warnings
 import os
 
-import .m6plot
-from .MOM6grid import MOM6grid
+from mom6_tools import m6plot
+from mom6_tools.MOM6grid import MOM6grid
 
 class MyError(Exception):
   """
@@ -118,14 +118,6 @@ def plot_area_ave_stats(ds, var, args, aspect=[16,9], resolution=576, debug=Fals
 
   return
 
-def check_time_interval(ti,tf,nc):
- ''' Checks if year_start and year_end are within the time interval of the dataset'''
- if ti < nc.time.min() or tf > nc.time.max():
-    #raise NameError('Selected start/end years outside the range of the dataset. Please fix that and run again.')
-    raise SyntaxError('Selected start/end years outside the range of the dataset. Please fix that and run again.')
-
- return
-
 # -- time-average 2D latlon fields and call plotting function
 def time_mean_latlon(args, grd, variables=[]):
   xr_mfopen_args = {'decode_times':False,

mom6_tools/m6plot.py

@@ -13,8 +13,7 @@
 from matplotlib.ticker import MaxNLocator
 import math
 import numpy, numpy.matlib
-import .m6toolbox
-import .VerticalSplitScale
+from mom6_tools import m6toolbox
 
 try: from mpl_toolkits.basemap import Basemap
 except: print('Basemap module not found. Some regional plots may not function properly')

mom6_tools/m6toolbox.py

@@ -6,6 +6,15 @@
 from scipy.io import netcdf
 import xarray as xr
 
+
+def check_time_interval(ti,tf,nc):
+ ''' Checks if year_start and year_end are within the time interval of the dataset'''
+ if ti < nc.time.min() or tf > nc.time.max():
+    #raise NameError('Selected start/end years outside the range of the dataset. Please fix that and run again.')
+    raise SyntaxError('Selected start/end years outside the range of the dataset. Please fix that and run again.')
+
+ return
+
 def section2quadmesh(x, z, q, representation='pcm'):
   """
   Creates the appropriate quadmesh coordinates to plot a scalar q(1:nk,1:ni) at

mom6_tools/meridional_overturning.py → mom6_tools/moc.py

@@ -2,15 +2,14 @@
 
 import io
 import numpy
-import m6plot
-import m6toolbox
 import matplotlib.pyplot as plt
 import os
 import sys
 import xarray as xr
 
-from .latlon_analysis import check_time_interval
-from .MOM6grid import MOM6grid
+from mom6_tools import m6plot
+from mom6_tools import m6toolbox
+from mom6_tools.MOM6grid import MOM6grid
 
 def options():
   try: import argparse
@@ -51,7 +50,7 @@ def main(stream=False):
   ti = args.year_start
   tf = args.year_end
   # check if data includes years between ti and tf
-  check_time_interval(ti,tf,ds)
+  m6toolbox.check_time_interval(ti,tf,ds)
 
   # create a ndarray subclass
   class C(numpy.ndarray): pass

mom6_tools/poleward_heat_transport.py

@@ -9,10 +9,9 @@
 import warnings
 import xarray as xr
 
-import .m6plot
-import .m6toolbox
-from .latlon_analysis import check_time_interval
-from .MOM6grid import MOM6grid
+from mom6_tools import m6plot
+from mom6_tools  import m6toolbox
+from mom6_tools.MOM6grid import MOM6grid
 
 def options():
   try: import argparse
@@ -47,7 +46,7 @@ def main(stream=False):
   ti = args.year_start
   tf = args.year_end
   # check if data includes years between ti and tf
-  check_time_interval(ti,tf,ds)
+  m6toolbox.check_time_interval(ti,tf,ds)
 
   # create a ndarray subclass
   class C(numpy.ndarray): pass

mom6_tools/section_transports.py

@@ -6,7 +6,7 @@
 import numpy
 import matplotlib.pyplot as plt
 import os
-from .latlon_analysis  import check_time_interval
+from mom6_tools.m6toolbox import check_time_interval
 
 try: import argparse
 except: raise Exception('This version of python is not new enough. python 2.7 or newer is required.')