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ENH: fix notebook links #4719

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Nov 2, 2023
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ENH: fix notebook links #4719

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103 changes: 82 additions & 21 deletions doc/source/analyzing/Particle_Trajectories.ipynb
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Original file line number Diff line number Diff line change
@@ -1,5 +1,12 @@
{
"cells": [
{
"cell_type": "markdown",
"metadata": {},
"source": [
"# Particle Trajectories"
]
},
{
"cell_type": "markdown",
"metadata": {},
Expand All @@ -11,7 +18,10 @@
"cell_type": "code",
"execution_count": null,
"metadata": {
"collapsed": false
"collapsed": false,
"jupyter": {
"outputs_hidden": false
}
},
"outputs": [],
"source": [
Expand All @@ -37,7 +47,10 @@
"cell_type": "code",
"execution_count": null,
"metadata": {
"collapsed": false
"collapsed": false,
"jupyter": {
"outputs_hidden": false
}
},
"outputs": [],
"source": [
Expand All @@ -56,7 +69,10 @@
"cell_type": "code",
"execution_count": null,
"metadata": {
"collapsed": false
"collapsed": false,
"jupyter": {
"outputs_hidden": false
}
},
"outputs": [],
"source": [
Expand All @@ -74,7 +90,10 @@
"cell_type": "code",
"execution_count": null,
"metadata": {
"collapsed": false
"collapsed": false,
"jupyter": {
"outputs_hidden": false
}
},
"outputs": [],
"source": [
Expand All @@ -95,7 +114,10 @@
"cell_type": "code",
"execution_count": null,
"metadata": {
"collapsed": false
"collapsed": false,
"jupyter": {
"outputs_hidden": false
}
},
"outputs": [],
"source": [
Expand All @@ -115,7 +137,10 @@
"cell_type": "code",
"execution_count": null,
"metadata": {
"collapsed": false
"collapsed": false,
"jupyter": {
"outputs_hidden": false
}
},
"outputs": [],
"source": [
Expand All @@ -134,7 +159,10 @@
"cell_type": "code",
"execution_count": null,
"metadata": {
"collapsed": false
"collapsed": false,
"jupyter": {
"outputs_hidden": false
}
},
"outputs": [],
"source": [
Expand All @@ -154,7 +182,10 @@
"cell_type": "code",
"execution_count": null,
"metadata": {
"collapsed": false
"collapsed": false,
"jupyter": {
"outputs_hidden": false
}
},
"outputs": [],
"source": [
Expand All @@ -174,7 +205,10 @@
"cell_type": "code",
"execution_count": null,
"metadata": {
"collapsed": false
"collapsed": false,
"jupyter": {
"outputs_hidden": false
}
},
"outputs": [],
"source": [
Expand All @@ -194,7 +228,10 @@
"cell_type": "code",
"execution_count": null,
"metadata": {
"collapsed": false
"collapsed": false,
"jupyter": {
"outputs_hidden": false
}
},
"outputs": [],
"source": [
Expand All @@ -215,7 +252,10 @@
"cell_type": "code",
"execution_count": null,
"metadata": {
"collapsed": false
"collapsed": false,
"jupyter": {
"outputs_hidden": false
}
},
"outputs": [],
"source": [
Expand All @@ -241,7 +281,10 @@
"cell_type": "code",
"execution_count": null,
"metadata": {
"collapsed": false
"collapsed": false,
"jupyter": {
"outputs_hidden": false
}
},
"outputs": [],
"source": [
Expand All @@ -260,7 +303,10 @@
"cell_type": "code",
"execution_count": null,
"metadata": {
"collapsed": false
"collapsed": false,
"jupyter": {
"outputs_hidden": false
}
},
"outputs": [],
"source": [
Expand All @@ -281,7 +327,10 @@
"cell_type": "code",
"execution_count": null,
"metadata": {
"collapsed": false
"collapsed": false,
"jupyter": {
"outputs_hidden": false
}
},
"outputs": [],
"source": [
Expand Down Expand Up @@ -315,7 +364,10 @@
"cell_type": "code",
"execution_count": null,
"metadata": {
"collapsed": false
"collapsed": false,
"jupyter": {
"outputs_hidden": false
}
},
"outputs": [],
"source": [
Expand All @@ -336,7 +388,10 @@
"cell_type": "code",
"execution_count": null,
"metadata": {
"collapsed": false
"collapsed": false,
"jupyter": {
"outputs_hidden": false
}
},
"outputs": [],
"source": [
Expand All @@ -354,7 +409,10 @@
"cell_type": "code",
"execution_count": null,
"metadata": {
"collapsed": false
"collapsed": false,
"jupyter": {
"outputs_hidden": false
}
},
"outputs": [],
"source": [
Expand All @@ -376,7 +434,10 @@
"cell_type": "code",
"execution_count": null,
"metadata": {
"collapsed": false
"collapsed": false,
"jupyter": {
"outputs_hidden": false
}
},
"outputs": [],
"source": [
Expand All @@ -392,7 +453,7 @@
"metadata": {
"anaconda-cloud": {},
"kernelspec": {
"display_name": "Python [default]",
"display_name": "Python 3 (ipykernel)",
"language": "python",
"name": "python3"
},
Expand All @@ -406,9 +467,9 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.5.2"
"version": "3.10.12"
}
},
"nbformat": 4,
"nbformat_minor": 0
"nbformat_minor": 4
}
4 changes: 2 additions & 2 deletions doc/source/analyzing/astropy_integrations.rst
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Original file line number Diff line number Diff line change
Expand Up @@ -33,8 +33,8 @@ Fixed-resolution two-dimensional images generated from datasets using yt (such a
slices or projections) and fixed-resolution three-dimensional grids can be written
to FITS files using yt's :class:`~yt.visualization.fits_image.FITSImageData` class
and its subclasses. Multiple images can be combined into a single file, operations
can be performed on the images and their coordinates, etc. See :ref:`writing_fits_images`
for more information.
can be performed on the images and their coordinates, etc. See
:doc:`../visualizing/FITSImageData` for more information.

Converting Field Container and 1D Profile Data to AstroPy Tables
----------------------------------------------------------------
Expand Down
33 changes: 15 additions & 18 deletions doc/source/analyzing/domain_analysis/XrayEmissionFields.ipynb
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Original file line number Diff line number Diff line change
@@ -1,5 +1,12 @@
{
"cells": [
{
"cell_type": "markdown",
"metadata": {},
"source": [
"# X-ray Emission Fields"
]
},
{
"cell_type": "markdown",
"metadata": {},
Expand Down Expand Up @@ -34,9 +41,7 @@
{
"cell_type": "code",
"execution_count": null,
"metadata": {
"scrolled": false
},
"metadata": {},
"outputs": [],
"source": [
"import yt\n",
Expand Down Expand Up @@ -103,9 +108,7 @@
{
"cell_type": "code",
"execution_count": null,
"metadata": {
"scrolled": false
},
"metadata": {},
"outputs": [],
"source": [
"slc = yt.SlicePlot(\n",
Expand All @@ -132,9 +135,7 @@
{
"cell_type": "code",
"execution_count": null,
"metadata": {
"scrolled": false
},
"metadata": {},
"outputs": [],
"source": [
"ds2 = yt.load(\"D9p_500/10MpcBox_HartGal_csf_a0.500.d\", default_species_fields=\"ionized\")\n",
Expand Down Expand Up @@ -178,9 +179,7 @@
{
"cell_type": "code",
"execution_count": null,
"metadata": {
"scrolled": false
},
"metadata": {},
"outputs": [],
"source": [
"prj = yt.ProjectionPlot(\n",
Expand Down Expand Up @@ -228,9 +227,7 @@
{
"cell_type": "code",
"execution_count": null,
"metadata": {
"scrolled": false
},
"metadata": {},
"outputs": [],
"source": [
"prj = yt.ProjectionPlot(\n",
Expand All @@ -248,7 +245,7 @@
"metadata": {
"anaconda-cloud": {},
"kernelspec": {
"display_name": "Python 3",
"display_name": "Python 3 (ipykernel)",
"language": "python",
"name": "python3"
},
Expand All @@ -262,9 +259,9 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.7.1"
"version": "3.10.12"
}
},
"nbformat": 4,
"nbformat_minor": 2
"nbformat_minor": 4
}
2 changes: 1 addition & 1 deletion doc/source/analyzing/domain_analysis/index.rst
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Expand Up @@ -24,7 +24,7 @@ These modules exist within yt itself.

cosmology_calculator
clump_finding
xray_emission_fields
XrayEmissionFields
xray_data_README

External Analysis Modules
Expand Down
6 changes: 0 additions & 6 deletions doc/source/analyzing/domain_analysis/xray_emission_fields.rst
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This file was deleted.

6 changes: 2 additions & 4 deletions doc/source/analyzing/filtering.rst
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Expand Up @@ -96,9 +96,7 @@ Cut Regions

Cut regions are a more general solution to filtering mesh fields. The output
of a cut region is an entirely new data object, which can be treated like any
other data object to generate images, examine its values, etc.

.. notebook:: mesh_filter.ipynb
other data object to generate images, examine its values, etc. See `this <mesh_filter>`_.

In addition to inputting string parameters into cut_region to specify filters,
wrapper functions exist that allow the user to use a simplified syntax for
Expand Down Expand Up @@ -252,7 +250,7 @@ to the dataset, it will also add ``stars`` filter to the dataset.
ds.add_particle_filter("young_stars")
.. notebook:: particle_filter.ipynb
Additional example of particle filters can be found in the `notebook <particle_filter>`_.

.. _particle-unions:

Expand Down
2 changes: 1 addition & 1 deletion doc/source/analyzing/index.rst
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Expand Up @@ -22,6 +22,6 @@ multiple processors to accomplish tasks faster.
generating_processed_data
saving_data
time_series_analysis
particle_trajectories
Particle_Trajectories
parallel_computation
astropy_integrations
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