Merge pull request #4719 from Xarthisius/issue_4718

ENH: fix notebook links
yt-project · Nov 2, 2023 · b3cfbf9 · b3cfbf9
2 parents bdd96bc + 098d22a
commit b3cfbf9
Show file tree

Hide file tree

Showing 44 changed files with 415 additions and 258 deletions.
diff --git a/doc/source/analyzing/Particle_Trajectories.ipynb b/doc/source/analyzing/Particle_Trajectories.ipynb
@@ -1,5 +1,12 @@
 {
  "cells": [
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "# Particle Trajectories"
+   ]
+  },
   {
    "cell_type": "markdown",
    "metadata": {},
@@ -11,7 +18,10 @@
    "cell_type": "code",
    "execution_count": null,
    "metadata": {
-    "collapsed": false
+    "collapsed": false,
+    "jupyter": {
+     "outputs_hidden": false
+    }
    },
    "outputs": [],
    "source": [
@@ -37,7 +47,10 @@
    "cell_type": "code",
    "execution_count": null,
    "metadata": {
-    "collapsed": false
+    "collapsed": false,
+    "jupyter": {
+     "outputs_hidden": false
+    }
    },
    "outputs": [],
    "source": [
@@ -56,7 +69,10 @@
    "cell_type": "code",
    "execution_count": null,
    "metadata": {
-    "collapsed": false
+    "collapsed": false,
+    "jupyter": {
+     "outputs_hidden": false
+    }
    },
    "outputs": [],
    "source": [
@@ -74,7 +90,10 @@
    "cell_type": "code",
    "execution_count": null,
    "metadata": {
-    "collapsed": false
+    "collapsed": false,
+    "jupyter": {
+     "outputs_hidden": false
+    }
    },
    "outputs": [],
    "source": [
@@ -95,7 +114,10 @@
    "cell_type": "code",
    "execution_count": null,
    "metadata": {
-    "collapsed": false
+    "collapsed": false,
+    "jupyter": {
+     "outputs_hidden": false
+    }
    },
    "outputs": [],
    "source": [
@@ -115,7 +137,10 @@
    "cell_type": "code",
    "execution_count": null,
    "metadata": {
-    "collapsed": false
+    "collapsed": false,
+    "jupyter": {
+     "outputs_hidden": false
+    }
    },
    "outputs": [],
    "source": [
@@ -134,7 +159,10 @@
    "cell_type": "code",
    "execution_count": null,
    "metadata": {
-    "collapsed": false
+    "collapsed": false,
+    "jupyter": {
+     "outputs_hidden": false
+    }
    },
    "outputs": [],
    "source": [
@@ -154,7 +182,10 @@
    "cell_type": "code",
    "execution_count": null,
    "metadata": {
-    "collapsed": false
+    "collapsed": false,
+    "jupyter": {
+     "outputs_hidden": false
+    }
    },
    "outputs": [],
    "source": [
@@ -174,7 +205,10 @@
    "cell_type": "code",
    "execution_count": null,
    "metadata": {
-    "collapsed": false
+    "collapsed": false,
+    "jupyter": {
+     "outputs_hidden": false
+    }
    },
    "outputs": [],
    "source": [
@@ -194,7 +228,10 @@
    "cell_type": "code",
    "execution_count": null,
    "metadata": {
-    "collapsed": false
+    "collapsed": false,
+    "jupyter": {
+     "outputs_hidden": false
+    }
    },
    "outputs": [],
    "source": [
@@ -215,7 +252,10 @@
    "cell_type": "code",
    "execution_count": null,
    "metadata": {
-    "collapsed": false
+    "collapsed": false,
+    "jupyter": {
+     "outputs_hidden": false
+    }
    },
    "outputs": [],
    "source": [
@@ -241,7 +281,10 @@
    "cell_type": "code",
    "execution_count": null,
    "metadata": {
-    "collapsed": false
+    "collapsed": false,
+    "jupyter": {
+     "outputs_hidden": false
+    }
    },
    "outputs": [],
    "source": [
@@ -260,7 +303,10 @@
    "cell_type": "code",
    "execution_count": null,
    "metadata": {
-    "collapsed": false
+    "collapsed": false,
+    "jupyter": {
+     "outputs_hidden": false
+    }
    },
    "outputs": [],
    "source": [
@@ -281,7 +327,10 @@
    "cell_type": "code",
    "execution_count": null,
    "metadata": {
-    "collapsed": false
+    "collapsed": false,
+    "jupyter": {
+     "outputs_hidden": false
+    }
    },
    "outputs": [],
    "source": [
@@ -315,7 +364,10 @@
    "cell_type": "code",
    "execution_count": null,
    "metadata": {
-    "collapsed": false
+    "collapsed": false,
+    "jupyter": {
+     "outputs_hidden": false
+    }
    },
    "outputs": [],
    "source": [
@@ -336,7 +388,10 @@
    "cell_type": "code",
    "execution_count": null,
    "metadata": {
-    "collapsed": false
+    "collapsed": false,
+    "jupyter": {
+     "outputs_hidden": false
+    }
    },
    "outputs": [],
    "source": [
@@ -354,7 +409,10 @@
    "cell_type": "code",
    "execution_count": null,
    "metadata": {
-    "collapsed": false
+    "collapsed": false,
+    "jupyter": {
+     "outputs_hidden": false
+    }
    },
    "outputs": [],
    "source": [
@@ -376,7 +434,10 @@
    "cell_type": "code",
    "execution_count": null,
    "metadata": {
-    "collapsed": false
+    "collapsed": false,
+    "jupyter": {
+     "outputs_hidden": false
+    }
    },
    "outputs": [],
    "source": [
@@ -392,7 +453,7 @@
  "metadata": {
   "anaconda-cloud": {},
   "kernelspec": {
-   "display_name": "Python [default]",
+   "display_name": "Python 3 (ipykernel)",
    "language": "python",
    "name": "python3"
   },
@@ -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
 }
diff --git a/doc/source/analyzing/astropy_integrations.rst b/doc/source/analyzing/astropy_integrations.rst
@@ -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
 ----------------------------------------------------------------

diff --git a/doc/source/analyzing/domain_analysis/XrayEmissionFields.ipynb b/doc/source/analyzing/domain_analysis/XrayEmissionFields.ipynb
@@ -1,5 +1,12 @@
 {
  "cells": [
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "# X-ray Emission Fields"
+   ]
+  },
   {
    "cell_type": "markdown",
    "metadata": {},
@@ -34,9 +41,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {
-    "scrolled": false
-   },
+   "metadata": {},
    "outputs": [],
    "source": [
     "import yt\n",
@@ -103,9 +108,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {
-    "scrolled": false
-   },
+   "metadata": {},
    "outputs": [],
    "source": [
     "slc = yt.SlicePlot(\n",
@@ -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",
@@ -178,9 +179,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {
-    "scrolled": false
-   },
+   "metadata": {},
    "outputs": [],
    "source": [
     "prj = yt.ProjectionPlot(\n",
@@ -228,9 +227,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {
-    "scrolled": false
-   },
+   "metadata": {},
    "outputs": [],
    "source": [
     "prj = yt.ProjectionPlot(\n",
@@ -248,7 +245,7 @@
  "metadata": {
   "anaconda-cloud": {},
   "kernelspec": {
-   "display_name": "Python 3",
+   "display_name": "Python 3 (ipykernel)",
    "language": "python",
    "name": "python3"
   },
@@ -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
 }
diff --git a/doc/source/analyzing/domain_analysis/index.rst b/doc/source/analyzing/domain_analysis/index.rst
@@ -24,7 +24,7 @@ These modules exist within yt itself.
 
    cosmology_calculator
    clump_finding
-   xray_emission_fields
+   XrayEmissionFields
    xray_data_README
 
 External Analysis Modules

diff --git a/doc/source/analyzing/domain_analysis/xray_emission_fields.rst b/doc/source/analyzing/domain_analysis/xray_emission_fields.rst
diff --git a/doc/source/analyzing/filtering.rst b/doc/source/analyzing/filtering.rst
@@ -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
@@ -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:
 

diff --git a/doc/source/analyzing/index.rst b/doc/source/analyzing/index.rst
@@ -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