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Switch doc examples to use nbsphinx #3105

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Jul 13, 2019
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Switch doc examples to use nbsphinx #3105

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baa0ec5
switching out examples to use nbsphinx
rabernat Jul 13, 2019
e3651a1
added jupyter_client to doc env
rabernat Jul 13, 2019
163a0a6
added ipykernel to doc env
rabernat Jul 13, 2019
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19 changes: 12 additions & 7 deletions doc/conf.py
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Original file line number Diff line number Diff line change
Expand Up @@ -69,18 +69,23 @@
'numpydoc',
'IPython.sphinxext.ipython_directive',
'IPython.sphinxext.ipython_console_highlighting',
'sphinx_gallery.gen_gallery',
'nbsphinx'
]

extlinks = {'issue': ('https://github.com/pydata/xarray/issues/%s', 'GH'),
'pull': ('https://github.com/pydata/xarray/pull/%s', 'PR'),
}

sphinx_gallery_conf = {'examples_dirs': 'gallery',
'gallery_dirs': 'auto_gallery',
'backreferences_dir': False,
'expected_failing_examples': list(allowed_failures)
}
nbsphinx_timeout = 600
nbsphinx_execute = "always"
nbsphinx_prolog = """
{% set docname = env.doc2path(env.docname, base=None) %}

You can run this notebook in a `live session <https://mybinder.org/v2/gh/pydata/xarray/doc/examples/master?urlpath=lab/tree/doc/{{ docname }}>`_ |Binder| or view it `on Github <https://github.com/pydata/xarray/blob/master/doc/{{ docname }}>`_.

.. |Binder| image:: https://mybinder.org/badge.svg
:target: https://mybinder.org/v2/gh/pydata/xarray/master?urlpath=lab/tree/doc/{{ docname }}
"""

autosummary_generate = True

Expand Down Expand Up @@ -124,7 +129,7 @@

# List of patterns, relative to source directory, that match files and
# directories to ignore when looking for source files.
exclude_patterns = ['_build']
exclude_patterns = ['_build', '**.ipynb_checkpoints']

# The reST default role (used for this markup: `text`) to use for all
# documents.
Expand Down
3 changes: 3 additions & 0 deletions doc/environment.yml
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Expand Up @@ -24,4 +24,7 @@ dependencies:
- pillow=5.4.1
- sphinx_rtd_theme=0.4.2
- mock=2.0.0
- nbsphinx=0.4.2
- jupyter_client=5.3.1
- ipykernel=5.1.1
- pip
325 changes: 325 additions & 0 deletions doc/examples/monthly-means.ipynb
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@@ -0,0 +1,325 @@
{
"cells": [
{
"cell_type": "markdown",
"metadata": {},
"source": [
"Calculating Seasonal Averages from Timeseries of Monthly Means \n",
"=====\n",
"\n",
"Author: [Joe Hamman](https://github.com/jhamman/)\n",
"\n",
"The data used for this example can be found in the [xarray-data](https://github.com/pydata/xarray-data) repository. You may need to change the path to `rasm.nc` below.\n",
"\n",
"Suppose we have a netCDF or `xarray.Dataset` of monthly mean data and we want to calculate the seasonal average. To do this properly, we need to calculate the weighted average considering that each month has a different number of days."
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {
"ExecuteTime": {
"end_time": "2018-11-28T20:51:35.958210Z",
"start_time": "2018-11-28T20:51:35.936966Z"
}
},
"outputs": [],
"source": [
"%matplotlib inline\n",
"import numpy as np\n",
"import pandas as pd\n",
"import xarray as xr\n",
"from netCDF4 import num2date\n",
"import matplotlib.pyplot as plt "
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"#### Some calendar information so we can support any netCDF calendar. "
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {
"ExecuteTime": {
"end_time": "2018-11-28T20:51:35.991620Z",
"start_time": "2018-11-28T20:51:35.960336Z"
}
},
"outputs": [],
"source": [
"dpm = {'noleap': [0, 31, 28, 31, 30, 31, 30, 31, 31, 30, 31, 30, 31],\n",
" '365_day': [0, 31, 28, 31, 30, 31, 30, 31, 31, 30, 31, 30, 31],\n",
" 'standard': [0, 31, 28, 31, 30, 31, 30, 31, 31, 30, 31, 30, 31],\n",
" 'gregorian': [0, 31, 28, 31, 30, 31, 30, 31, 31, 30, 31, 30, 31],\n",
" 'proleptic_gregorian': [0, 31, 28, 31, 30, 31, 30, 31, 31, 30, 31, 30, 31],\n",
" 'all_leap': [0, 31, 29, 31, 30, 31, 30, 31, 31, 30, 31, 30, 31],\n",
" '366_day': [0, 31, 29, 31, 30, 31, 30, 31, 31, 30, 31, 30, 31],\n",
" '360_day': [0, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30]} "
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"#### A few calendar functions to determine the number of days in each month\n",
"If you were just using the standard calendar, it would be easy to use the `calendar.month_range` function."
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {
"ExecuteTime": {
"end_time": "2018-11-28T20:51:36.015151Z",
"start_time": "2018-11-28T20:51:35.994079Z"
}
},
"outputs": [],
"source": [
"def leap_year(year, calendar='standard'):\n",
" \"\"\"Determine if year is a leap year\"\"\"\n",
" leap = False\n",
" if ((calendar in ['standard', 'gregorian',\n",
" 'proleptic_gregorian', 'julian']) and\n",
" (year % 4 == 0)):\n",
" leap = True\n",
" if ((calendar == 'proleptic_gregorian') and\n",
" (year % 100 == 0) and\n",
" (year % 400 != 0)):\n",
" leap = False\n",
" elif ((calendar in ['standard', 'gregorian']) and\n",
" (year % 100 == 0) and (year % 400 != 0) and\n",
" (year < 1583)):\n",
" leap = False\n",
" return leap\n",
"\n",
"def get_dpm(time, calendar='standard'):\n",
" \"\"\"\n",
" return a array of days per month corresponding to the months provided in `months`\n",
" \"\"\"\n",
" month_length = np.zeros(len(time), dtype=np.int)\n",
" \n",
" cal_days = dpm[calendar]\n",
" \n",
" for i, (month, year) in enumerate(zip(time.month, time.year)):\n",
" month_length[i] = cal_days[month]\n",
" if leap_year(year, calendar=calendar):\n",
" month_length[i] += 1\n",
" return month_length"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"#### Open the `Dataset`"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {
"ExecuteTime": {
"end_time": "2018-11-28T20:51:36.072316Z",
"start_time": "2018-11-28T20:51:36.016594Z"
}
},
"outputs": [],
"source": [
"ds = xr.tutorial.open_dataset('rasm').load()\n",
"print(ds)"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"#### Now for the heavy lifting:\n",
"We first have to come up with the weights,\n",
"- calculate the month lengths for each monthly data record\n",
"- calculate weights using `groupby('time.season')`\n",
"\n",
"Finally, we just need to multiply our weights by the `Dataset` and sum allong the time dimension. "
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {
"ExecuteTime": {
"end_time": "2018-11-28T20:51:36.132413Z",
"start_time": "2018-11-28T20:51:36.073708Z"
}
},
"outputs": [],
"source": [
"# Make a DataArray with the number of days in each month, size = len(time)\n",
"month_length = xr.DataArray(get_dpm(ds.time.to_index(), calendar='noleap'),\n",
" coords=[ds.time], name='month_length')\n",
"\n",
"# Calculate the weights by grouping by 'time.season'.\n",
"# Conversion to float type ('astype(float)') only necessary for Python 2.x\n",
"weights = month_length.groupby('time.season') / month_length.astype(float).groupby('time.season').sum()\n",
"\n",
"# Test that the sum of the weights for each season is 1.0\n",
"np.testing.assert_allclose(weights.groupby('time.season').sum().values, np.ones(4))\n",
"\n",
"# Calculate the weighted average\n",
"ds_weighted = (ds * weights).groupby('time.season').sum(dim='time')"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {
"ExecuteTime": {
"end_time": "2018-11-28T20:51:36.152913Z",
"start_time": "2018-11-28T20:51:36.133997Z"
}
},
"outputs": [],
"source": [
"print(ds_weighted)"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {
"ExecuteTime": {
"end_time": "2018-11-28T20:51:36.190765Z",
"start_time": "2018-11-28T20:51:36.154416Z"
}
},
"outputs": [],
"source": [
"# only used for comparisons\n",
"ds_unweighted = ds.groupby('time.season').mean('time')\n",
"ds_diff = ds_weighted - ds_unweighted"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {
"ExecuteTime": {
"end_time": "2018-11-28T20:51:40.264871Z",
"start_time": "2018-11-28T20:51:36.192467Z"
}
},
"outputs": [],
"source": [
"# Quick plot to show the results\n",
"notnull = pd.notnull(ds_unweighted['Tair'][0])\n",
"\n",
"fig, axes = plt.subplots(nrows=4, ncols=3, figsize=(14,12))\n",
"for i, season in enumerate(('DJF', 'MAM', 'JJA', 'SON')):\n",
" ds_weighted['Tair'].sel(season=season).where(notnull).plot.pcolormesh(\n",
" ax=axes[i, 0], vmin=-30, vmax=30, cmap='Spectral_r', \n",
" add_colorbar=True, extend='both')\n",
" \n",
" ds_unweighted['Tair'].sel(season=season).where(notnull).plot.pcolormesh(\n",
" ax=axes[i, 1], vmin=-30, vmax=30, cmap='Spectral_r', \n",
" add_colorbar=True, extend='both')\n",
"\n",
" ds_diff['Tair'].sel(season=season).where(notnull).plot.pcolormesh(\n",
" ax=axes[i, 2], vmin=-0.1, vmax=.1, cmap='RdBu_r',\n",
" add_colorbar=True, extend='both')\n",
"\n",
" axes[i, 0].set_ylabel(season)\n",
" axes[i, 1].set_ylabel('')\n",
" axes[i, 2].set_ylabel('')\n",
"\n",
"for ax in axes.flat:\n",
" ax.axes.get_xaxis().set_ticklabels([])\n",
" ax.axes.get_yaxis().set_ticklabels([])\n",
" ax.axes.axis('tight')\n",
" ax.set_xlabel('')\n",
" \n",
"axes[0, 0].set_title('Weighted by DPM')\n",
"axes[0, 1].set_title('Equal Weighting')\n",
"axes[0, 2].set_title('Difference')\n",
" \n",
"plt.tight_layout()\n",
"\n",
"fig.suptitle('Seasonal Surface Air Temperature', fontsize=16, y=1.02)"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {
"ExecuteTime": {
"end_time": "2018-11-28T20:51:40.284898Z",
"start_time": "2018-11-28T20:51:40.266406Z"
}
},
"outputs": [],
"source": [
"# Wrap it into a simple function\n",
"def season_mean(ds, calendar='standard'):\n",
" # Make a DataArray of season/year groups\n",
" year_season = xr.DataArray(ds.time.to_index().to_period(freq='Q-NOV').to_timestamp(how='E'),\n",
" coords=[ds.time], name='year_season')\n",
"\n",
" # Make a DataArray with the number of days in each month, size = len(time)\n",
" month_length = xr.DataArray(get_dpm(ds.time.to_index(), calendar=calendar),\n",
" coords=[ds.time], name='month_length')\n",
" # Calculate the weights by grouping by 'time.season'\n",
" weights = month_length.groupby('time.season') / month_length.groupby('time.season').sum()\n",
"\n",
" # Test that the sum of the weights for each season is 1.0\n",
" np.testing.assert_allclose(weights.groupby('time.season').sum().values, np.ones(4))\n",
"\n",
" # Calculate the weighted average\n",
" return (ds * weights).groupby('time.season').sum(dim='time')"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": []
}
],
"metadata": {
"anaconda-cloud": {},
"kernelspec": {
"display_name": "Python 3",
"language": "python",
"name": "python3"
},
"language_info": {
"codemirror_mode": {
"name": "ipython",
"version": 3
},
"file_extension": ".py",
"mimetype": "text/x-python",
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.6.8"
},
"toc": {
"base_numbering": 1,
"nav_menu": {},
"number_sections": true,
"sideBar": true,
"skip_h1_title": false,
"title_cell": "Table of Contents",
"title_sidebar": "Contents",
"toc_cell": true,
"toc_position": {},
"toc_section_display": true,
"toc_window_display": true
}
},
"nbformat": 4,
"nbformat_minor": 2
}
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